From 3fe37526703ddbe1e452de43437dc7c366ce5c9e Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Mon, 9 Jun 2025 14:45:18 +1000 Subject: [PATCH 01/12] add adir1 class for anopheles dirus data release --- adir1_explore.ipynb | 451 ++++++++++++++++++++++++++++++++++++ malariagen_data/__init__.py | 1 + malariagen_data/adir1.py | 208 +++++++++++++++++ 3 files changed, 660 insertions(+) create mode 100644 adir1_explore.ipynb create mode 100644 malariagen_data/adir1.py diff --git a/adir1_explore.ipynb b/adir1_explore.ipynb new file mode 100644 index 000000000..c42d93dd5 --- /dev/null +++ b/adir1_explore.ipynb @@ -0,0 +1,451 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import malariagen_data" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "application/javascript": [ + "'use strict';\n", + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " const force = true;\n", + "\n", + " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", + " root._bokeh_onload_callbacks = [];\n", + " root._bokeh_is_loading = undefined;\n", + " }\n", + "\n", + "const JS_MIME_TYPE = 'application/javascript';\n", + " const HTML_MIME_TYPE = 'text/html';\n", + " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", + " const CLASS_NAME = 'output_bokeh rendered_html';\n", + "\n", + " /**\n", + " * Render data to the DOM node\n", + " */\n", + " function render(props, node) {\n", + " const script = document.createElement(\"script\");\n", + " node.appendChild(script);\n", + " }\n", + "\n", + " /**\n", + " * Handle when an output is cleared or removed\n", + " */\n", + " function handleClearOutput(event, handle) {\n", + " function drop(id) {\n", + " const view = Bokeh.index.get_by_id(id)\n", + " if (view != null) {\n", + " view.model.document.clear()\n", + " Bokeh.index.delete(view)\n", + " }\n", + " }\n", + "\n", + " const cell = handle.cell;\n", + "\n", + " const id = cell.output_area._bokeh_element_id;\n", + " const server_id = cell.output_area._bokeh_server_id;\n", + "\n", + " // Clean up Bokeh references\n", + " if (id != null) {\n", + " drop(id)\n", + " }\n", + "\n", + " if (server_id !== undefined) {\n", + " // Clean up Bokeh references\n", + " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", + " cell.notebook.kernel.execute(cmd_clean, {\n", + " iopub: {\n", + " output: function(msg) {\n", + " const id = msg.content.text.trim()\n", + " drop(id)\n", + " }\n", + " }\n", + " });\n", + " // Destroy server and session\n", + " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", + " cell.notebook.kernel.execute(cmd_destroy);\n", + " }\n", + " }\n", + "\n", + " /**\n", + " * Handle when a new output is added\n", + " */\n", + " function handleAddOutput(event, handle) {\n", + " const output_area = handle.output_area;\n", + " const output = handle.output;\n", + "\n", + " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", + " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", + " return\n", + " }\n", + "\n", + " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", + "\n", + " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", + " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", + " // store reference to embed id on output_area\n", + " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", + " }\n", + " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", + " const bk_div = document.createElement(\"div\");\n", + " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", + " const script_attrs = bk_div.children[0].attributes;\n", + " for (let i = 0; i < script_attrs.length; i++) {\n", + " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", + " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", + " }\n", + " // store reference to server id on output_area\n", + " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", + " }\n", + " }\n", + "\n", + " function register_renderer(events, OutputArea) {\n", + "\n", + " function append_mime(data, metadata, element) {\n", + " // create a DOM node to render to\n", + " const toinsert = this.create_output_subarea(\n", + " metadata,\n", + " CLASS_NAME,\n", + " EXEC_MIME_TYPE\n", + " );\n", + " this.keyboard_manager.register_events(toinsert);\n", + " // Render to node\n", + " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", + " render(props, toinsert[toinsert.length - 1]);\n", + " element.append(toinsert);\n", + " return toinsert\n", + " }\n", + "\n", + " /* Handle when an output is cleared or removed */\n", + " events.on('clear_output.CodeCell', handleClearOutput);\n", + " events.on('delete.Cell', handleClearOutput);\n", + "\n", + " /* Handle when a new output is added */\n", + " events.on('output_added.OutputArea', handleAddOutput);\n", + "\n", + " /**\n", + " * Register the mime type and append_mime function with output_area\n", + " */\n", + " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", + " /* Is output safe? */\n", + " safe: true,\n", + " /* Index of renderer in `output_area.display_order` */\n", + " index: 0\n", + " });\n", + " }\n", + "\n", + " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", + " if (root.Jupyter !== undefined) {\n", + " const events = require('base/js/events');\n", + " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", + "\n", + " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", + " register_renderer(events, OutputArea);\n", + " }\n", + " }\n", + " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", + " root._bokeh_timeout = Date.now() + 5000;\n", + " root._bokeh_failed_load = false;\n", + " }\n", + "\n", + " const NB_LOAD_WARNING = {'data': {'text/html':\n", + " \"
\\n\"+\n", + " \"

\\n\"+\n", + " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", + " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", + " \"

\\n\"+\n", + " \"\\n\"+\n", + " \"\\n\"+\n", + " \"from bokeh.resources import INLINE\\n\"+\n", + " \"output_notebook(resources=INLINE)\\n\"+\n", + " \"\\n\"+\n", + " \"
\"}};\n", + "\n", + " function display_loaded(error = null) {\n", + " const el = document.getElementById(null);\n", + " if (el != null) {\n", + " const html = (() => {\n", + " if (typeof root.Bokeh === \"undefined\") {\n", + " if (error == null) {\n", + " return \"BokehJS is loading ...\";\n", + " } else {\n", + " return \"BokehJS failed to load.\";\n", + " }\n", + " } else {\n", + " const prefix = `BokehJS ${root.Bokeh.version}`;\n", + " if (error == null) {\n", + " return `${prefix} successfully loaded.`;\n", + " } else {\n", + " return `${prefix} encountered errors while loading and may not function as expected.`;\n", + " }\n", + " }\n", + " })();\n", + " el.innerHTML = html;\n", + "\n", + " if (error != null) {\n", + " const wrapper = document.createElement(\"div\");\n", + " wrapper.style.overflow = \"auto\";\n", + " wrapper.style.height = \"5em\";\n", + " wrapper.style.resize = \"vertical\";\n", + " const content = document.createElement(\"div\");\n", + " content.style.fontFamily = \"monospace\";\n", + " content.style.whiteSpace = \"pre-wrap\";\n", + " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", + " content.textContent = error.stack ?? error.toString();\n", + " wrapper.append(content);\n", + " el.append(wrapper);\n", + " }\n", + " } else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(() => display_loaded(error), 100);\n", + " }\n", + " }\n", + "\n", + " function run_callbacks() {\n", + " try {\n", + " root._bokeh_onload_callbacks.forEach(function(callback) {\n", + " if (callback != null)\n", + " callback();\n", + " });\n", + " } finally {\n", + " delete root._bokeh_onload_callbacks\n", + " }\n", + " console.debug(\"Bokeh: all callbacks have finished\");\n", + " }\n", + "\n", + " function load_libs(css_urls, js_urls, callback) {\n", + " if (css_urls == null) css_urls = [];\n", + " if (js_urls == null) js_urls = [];\n", + "\n", + " root._bokeh_onload_callbacks.push(callback);\n", + " if (root._bokeh_is_loading > 0) {\n", + " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", + " return null;\n", + " }\n", + " if (js_urls == null || js_urls.length === 0) {\n", + " run_callbacks();\n", + " return null;\n", + " }\n", + " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", + " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", + "\n", + " function on_load() {\n", + " root._bokeh_is_loading--;\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", + " run_callbacks()\n", + " }\n", + " }\n", + "\n", + " function on_error(url) {\n", + " console.error(\"failed to load \" + url);\n", + " }\n", + "\n", + " for (let i = 0; i < css_urls.length; i++) {\n", + " const url = css_urls[i];\n", + " const element = document.createElement(\"link\");\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.rel = \"stylesheet\";\n", + " element.type = \"text/css\";\n", + " element.href = url;\n", + " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " for (let i = 0; i < js_urls.length; i++) {\n", + " const url = js_urls[i];\n", + " const element = document.createElement('script');\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.async = false;\n", + " element.src = url;\n", + " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", + " document.head.appendChild(element);\n", + " }\n", + " };\n", + "\n", + " function inject_raw_css(css) {\n", + " const element = document.createElement(\"style\");\n", + " element.appendChild(document.createTextNode(css));\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", + " const css_urls = [];\n", + "\n", + " const inline_js = [ function(Bokeh) {\n", + " Bokeh.set_log_level(\"info\");\n", + " },\n", + "function(Bokeh) {\n", + " }\n", + " ];\n", + "\n", + " function run_inline_js() {\n", + " if (root.Bokeh !== undefined || force === true) {\n", + " try {\n", + " for (let i = 0; i < inline_js.length; i++) {\n", + " inline_js[i].call(root, root.Bokeh);\n", + " }\n", + "\n", + " } catch (error) {throw error;\n", + " }} else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(run_inline_js, 100);\n", + " } else if (!root._bokeh_failed_load) {\n", + " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", + " root._bokeh_failed_load = true;\n", + " } else if (force !== true) {\n", + " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", + " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", + " }\n", + " }\n", + "\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", + " run_inline_js();\n", + " } else {\n", + " load_libs(css_urls, js_urls, function() {\n", + " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", + " run_inline_js();\n", + " });\n", + " }\n", + "}(window));" + ], + "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# Init API\n", + "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "f171c3b7-30c2-4e9f-9133-22206985de07", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "'KB672868'" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Are the contigs here? \n", + "chroms = adir1.contigs[:5]\n", + "chroms[1]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "ename": "FileNotFoundError", + "evalue": "b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:426\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 425\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_sets\u001b[49m\u001b[43m[\u001b[49m\u001b[43mrelease\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n", + "\u001b[0;31mKeyError\u001b[0m: '1.x'", + "\nDuring handling of the above exception, another exception occurred:\n", + "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[7], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m snps \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msnp_calls\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868:1000000-2000000\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/snp_data.py:1007\u001b[0m, in \u001b[0;36mAnophelesSnpData.snp_calls\u001b[0;34m(self, region, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, inline_array, chunks, cohort_size, min_cohort_size, max_cohort_size, random_seed)\u001b[0m\n\u001b[1;32m 1001\u001b[0m base_params\u001b[38;5;241m.\u001b[39mvalidate_sample_selection_params(\n\u001b[1;32m 1002\u001b[0m sample_query\u001b[38;5;241m=\u001b[39msample_query, sample_indices\u001b[38;5;241m=\u001b[39msample_indices\n\u001b[1;32m 1003\u001b[0m )\n\u001b[1;32m 1005\u001b[0m \u001b[38;5;66;03m# Normalise parameters.\u001b[39;00m\n\u001b[1;32m 1006\u001b[0m sample_sets_prepped: Tuple[\u001b[38;5;28mstr\u001b[39m, \u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mtuple\u001b[39m(\n\u001b[0;32m-> 1007\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_sets_param\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1008\u001b[0m )\n\u001b[1;32m 1009\u001b[0m \u001b[38;5;28;01mdel\u001b[39;00m sample_sets\n\u001b[1;32m 1010\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_indices \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:524\u001b[0m, in \u001b[0;36mAnophelesBase._prep_sample_sets_param\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 517\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_prep_sample_sets_param\u001b[39m(\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets]\n\u001b[1;32m 519\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m List[\u001b[38;5;28mstr\u001b[39m]:\n\u001b[1;32m 520\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Common handling for the `sample_sets` parameter. For convenience, we\u001b[39;00m\n\u001b[1;32m 521\u001b[0m \u001b[38;5;124;03m allow this to be a single sample set, or a list of sample sets, or a\u001b[39;00m\n\u001b[1;32m 522\u001b[0m \u001b[38;5;124;03m release identifier, or a list of release identifiers.\"\"\"\u001b[39;00m\n\u001b[0;32m--> 524\u001b[0m all_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mto_list()\n\u001b[1;32m 526\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_sets \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 527\u001b[0m \u001b[38;5;66;03m# All available sample sets.\u001b[39;00m\n\u001b[1;32m 528\u001b[0m prepped_sample_sets \u001b[38;5;241m=\u001b[39m all_sample_sets\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets(release\u001b[38;5;241m=\u001b[39mr) \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36m\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrelease\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mr\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:430\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release]\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n\u001b[0;32m--> 430\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_read_sample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43msingle_release\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrelease\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 431\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release] \u001b[38;5;241m=\u001b[39m df\n\u001b[1;32m 433\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(release, Sequence):\n\u001b[1;32m 434\u001b[0m \u001b[38;5;66;03m# Ensure no duplicates.\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:376\u001b[0m, in \u001b[0;36mAnophelesBase._read_sample_sets\u001b[0;34m(self, single_release)\u001b[0m\n\u001b[1;32m 373\u001b[0m manifest_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mrelease_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/manifest.tsv\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 375\u001b[0m \u001b[38;5;66;03m# Read the manifest into a pandas dataframe.\u001b[39;00m\n\u001b[0;32m--> 376\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen_file\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmanifest_path\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m 377\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mread_csv(f, sep\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;130;01m\\t\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, na_values\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 379\u001b[0m \u001b[38;5;66;03m# Add a \"release\" column for convenience.\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:218\u001b[0m, in \u001b[0;36mAnophelesBase.open_file\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 215\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 216\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mopen_file\u001b[39m(\u001b[38;5;28mself\u001b[39m, path: \u001b[38;5;28mstr\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m IO:\n\u001b[1;32m 217\u001b[0m full_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_base_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m--> 218\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfull_path\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/spec.py:1154\u001b[0m, in \u001b[0;36mAbstractFileSystem.open\u001b[0;34m(self, path, mode, block_size, cache_options, compression, **kwargs)\u001b[0m\n\u001b[1;32m 1152\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 1153\u001b[0m ac \u001b[38;5;241m=\u001b[39m kwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mautocommit\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_intrans)\n\u001b[0;32m-> 1154\u001b[0m f \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_open\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1155\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1156\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1157\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1158\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mac\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1159\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1160\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1161\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1162\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m compression \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfsspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcompression\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m compr\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1309\u001b[0m, in \u001b[0;36mGCSFileSystem._open\u001b[0;34m(self, path, mode, block_size, cache_options, acl, consistency, metadata, autocommit, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1307\u001b[0m block_size \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_block_size\n\u001b[1;32m 1308\u001b[0m const \u001b[38;5;241m=\u001b[39m consistency \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconsistency\n\u001b[0;32m-> 1309\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mGCSFile\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1311\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1312\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1313\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1314\u001b[0m \u001b[43m 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\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1321\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1468\u001b[0m, in \u001b[0;36mGCSFile.__init__\u001b[0;34m(self, gcsfs, path, mode, block_size, autocommit, cache_type, cache_options, acl, consistency, metadata, content_type, timeout, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1466\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAttempt to open a bucket\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1467\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgeneration \u001b[38;5;241m=\u001b[39m _coalesce_generation(generation, path_generation)\n\u001b[0;32m-> 1468\u001b[0m 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1509\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m-> 1510\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdetails\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msize\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[1;32m 1511\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcache \u001b[38;5;241m=\u001b[39m caches[cache_type](\n\u001b[1;32m 1512\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mblocksize, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_fetch_range, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mcache_options\n\u001b[1;32m 1513\u001b[0m )\n\u001b[1;32m 1514\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1504\u001b[0m, in 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\u001b[49m\u001b[43mgeneration\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneration\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1505\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:115\u001b[0m, in \u001b[0;36msync_wrapper..wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 114\u001b[0m \u001b[38;5;28mself\u001b[39m \u001b[38;5;241m=\u001b[39m obj \u001b[38;5;129;01mor\u001b[39;00m args[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m--> 115\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43msync\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mloop\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfunc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:100\u001b[0m, in \u001b[0;36msync\u001b[0;34m(loop, func, timeout, *args, **kwargs)\u001b[0m\n\u001b[1;32m 98\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m FSTimeoutError \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mreturn_result\u001b[39;00m\n\u001b[1;32m 99\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(return_result, \u001b[38;5;167;01mBaseException\u001b[39;00m):\n\u001b[0;32m--> 100\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m return_result\n\u001b[1;32m 101\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 102\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m return_result\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:55\u001b[0m, in \u001b[0;36m_runner\u001b[0;34m(event, coro, result, timeout)\u001b[0m\n\u001b[1;32m 53\u001b[0m coro \u001b[38;5;241m=\u001b[39m asyncio\u001b[38;5;241m.\u001b[39mwait_for(coro, timeout\u001b[38;5;241m=\u001b[39mtimeout)\n\u001b[1;32m 54\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 55\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m coro\n\u001b[1;32m 56\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m ex:\n\u001b[1;32m 57\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m ex\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:797\u001b[0m, in \u001b[0;36mGCSFileSystem._info\u001b[0;34m(self, path, generation, **kwargs)\u001b[0m\n\u001b[1;32m 795\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 796\u001b[0m kwargs[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdetail\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m \u001b[38;5;66;03m# Force to true for info\u001b[39;00m\n\u001b[0;32m--> 797\u001b[0m out \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ls(path, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 798\u001b[0m out0 \u001b[38;5;241m=\u001b[39m [o \u001b[38;5;28;01mfor\u001b[39;00m o \u001b[38;5;129;01min\u001b[39;00m out \u001b[38;5;28;01mif\u001b[39;00m o[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mname\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mrstrip(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;241m==\u001b[39m path]\n\u001b[1;32m 799\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m out0:\n\u001b[1;32m 800\u001b[0m \u001b[38;5;66;03m# exact hit\u001b[39;00m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:834\u001b[0m, in \u001b[0;36mGCSFileSystem._ls\u001b[0;34m(self, path, detail, prefix, versions, **kwargs)\u001b[0m\n\u001b[1;32m 832\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 833\u001b[0m out \u001b[38;5;241m=\u001b[39m []\n\u001b[0;32m--> 834\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m entry \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_list_objects(\n\u001b[1;32m 835\u001b[0m path, prefix\u001b[38;5;241m=\u001b[39mprefix, versions\u001b[38;5;241m=\u001b[39mversions\n\u001b[1;32m 836\u001b[0m ):\n\u001b[1;32m 837\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m versions \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgeneration\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m entry:\n\u001b[1;32m 838\u001b[0m entry \u001b[38;5;241m=\u001b[39m entry\u001b[38;5;241m.\u001b[39mcopy()\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:549\u001b[0m, in \u001b[0;36mGCSFileSystem._list_objects\u001b[0;34m(self, path, prefix, versions)\u001b[0m\n\u001b[1;32m 547\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m (items \u001b[38;5;241m+\u001b[39m pseudodirs):\n\u001b[1;32m 548\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m key:\n\u001b[0;32m--> 549\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m [\u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_object(path)]\n\u001b[1;32m 550\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 551\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m []\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:491\u001b[0m, in \u001b[0;36mGCSFileSystem._get_object\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 488\u001b[0m \u001b[38;5;66;03m# Work around various permission settings. Prefer an object get (storage.objects.get), but\u001b[39;00m\n\u001b[1;32m 489\u001b[0m \u001b[38;5;66;03m# fall back to a bucket list + filter to object name (storage.objects.list).\u001b[39;00m\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 491\u001b[0m res \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_call(\n\u001b[1;32m 492\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGET\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mb/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m/o/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, bucket, key, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m, generation\u001b[38;5;241m=\u001b[39mgeneration\n\u001b[1;32m 493\u001b[0m )\n\u001b[1;32m 494\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 495\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mstr\u001b[39m(e)\u001b[38;5;241m.\u001b[39mstartswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mForbidden\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:418\u001b[0m, in \u001b[0;36mGCSFileSystem._call\u001b[0;34m(self, method, path, json_out, info_out, *args, **kwargs)\u001b[0m\n\u001b[1;32m 414\u001b[0m \u001b[38;5;28;01masync\u001b[39;00m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_call\u001b[39m(\n\u001b[1;32m 415\u001b[0m \u001b[38;5;28mself\u001b[39m, method, path, \u001b[38;5;241m*\u001b[39margs, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, info_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 416\u001b[0m ):\n\u001b[1;32m 417\u001b[0m logger\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mmethod\u001b[38;5;241m.\u001b[39mupper()\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00margs\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mheaders\u001b[39m\u001b[38;5;124m'\u001b[39m)\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 418\u001b[0m status, headers, info, contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_request(\n\u001b[1;32m 419\u001b[0m method, path, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 420\u001b[0m )\n\u001b[1;32m 421\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m json_out:\n\u001b[1;32m 422\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m json\u001b[38;5;241m.\u001b[39mloads(contents)\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/decorator.py:221\u001b[0m, in \u001b[0;36mdecorate..fun\u001b[0;34m(*args, **kw)\u001b[0m\n\u001b[1;32m 219\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m kwsyntax:\n\u001b[1;32m 220\u001b[0m args, kw \u001b[38;5;241m=\u001b[39m fix(args, kw, sig)\n\u001b[0;32m--> 221\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m caller(func, \u001b[38;5;241m*\u001b[39m(extras \u001b[38;5;241m+\u001b[39m args), \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkw)\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:114\u001b[0m, in \u001b[0;36mretry_request\u001b[0;34m(func, retries, *args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m retry \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m asyncio\u001b[38;5;241m.\u001b[39msleep(\u001b[38;5;28mmin\u001b[39m(random\u001b[38;5;241m.\u001b[39mrandom() \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m2\u001b[39m \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39m (retry \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m), \u001b[38;5;241m32\u001b[39m))\n\u001b[0;32m--> 114\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m func(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 115\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (\n\u001b[1;32m 116\u001b[0m HttpError,\n\u001b[1;32m 117\u001b[0m requests\u001b[38;5;241m.\u001b[39mexceptions\u001b[38;5;241m.\u001b[39mRequestException,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 120\u001b[0m aiohttp\u001b[38;5;241m.\u001b[39mclient_exceptions\u001b[38;5;241m.\u001b[39mClientError,\n\u001b[1;32m 121\u001b[0m ) \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 122\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\n\u001b[1;32m 123\u001b[0m \u001b[38;5;28misinstance\u001b[39m(e, HttpError)\n\u001b[1;32m 124\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m e\u001b[38;5;241m.\u001b[39mcode \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m400\u001b[39m\n\u001b[1;32m 125\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mrequester pays\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m e\u001b[38;5;241m.\u001b[39mmessage\n\u001b[1;32m 126\u001b[0m ):\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:411\u001b[0m, in \u001b[0;36mGCSFileSystem._request\u001b[0;34m(self, method, path, headers, json, data, *args, **kwargs)\u001b[0m\n\u001b[1;32m 408\u001b[0m info \u001b[38;5;241m=\u001b[39m r\u001b[38;5;241m.\u001b[39mrequest_info \u001b[38;5;66;03m# for debug only\u001b[39;00m\n\u001b[1;32m 409\u001b[0m contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m r\u001b[38;5;241m.\u001b[39mread()\n\u001b[0;32m--> 411\u001b[0m \u001b[43mvalidate_response\u001b[49m\u001b[43m(\u001b[49m\u001b[43mstatus\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcontents\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43margs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 412\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m status, headers, info, contents\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:83\u001b[0m, in \u001b[0;36mvalidate_response\u001b[0;34m(status, content, path, args)\u001b[0m\n\u001b[1;32m 81\u001b[0m path \u001b[38;5;241m=\u001b[39m path\u001b[38;5;241m.\u001b[39mformat(\u001b[38;5;241m*\u001b[39m[quote(p) \u001b[38;5;28;01mfor\u001b[39;00m p \u001b[38;5;129;01min\u001b[39;00m args])\n\u001b[1;32m 82\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m status \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m404\u001b[39m:\n\u001b[0;32m---> 83\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m(path)\n\u001b[1;32m 85\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 86\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(content, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdecode\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", + "\u001b[0;31mFileNotFoundError\u001b[0m: b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv" + ] + } + ], + "source": [ + "snps = adir1.snp_calls(region=\"KB672868:1000000-2000000\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/malariagen_data/__init__.py b/malariagen_data/__init__.py index dfa555aa7..6bc938825 100644 --- a/malariagen_data/__init__.py +++ b/malariagen_data/__init__.py @@ -1,5 +1,6 @@ # flake8: noqa from .af1 import Af1 +from .adir1 import Adir1 from .ag3 import Ag3 from .amin1 import Amin1 from .anopheles import AnophelesDataResource, Region diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py new file mode 100644 index 000000000..9b053ca62 --- /dev/null +++ b/malariagen_data/adir1.py @@ -0,0 +1,208 @@ +import sys + +import plotly.express as px # type: ignore + +import malariagen_data +from .anopheles import AnophelesDataResource + +MAJOR_VERSION_NUMBER = 1 +MAJOR_VERSION_PATH = "v1.x" +CONFIG_PATH = "v1.x-config.json" +GCS_DEFAULT_URL = "gs://vo_adir_production_us_central1/" +GCS_DEFAULT_PUBLIC_URL = "gs://vo_adir_production_us_central1/v1.x/staging" +GCS_REGION_URLS = { + "us-central1": "gs://vo_adir_production_us_central1", +} +# XPEHH_GWSS_CACHE_NAME = "adir1_xpehh_gwss_v1" +# IHS_GWSS_CACHE_NAME = "adir1_ihs_gwss_v1" + +TAXON_PALETTE = px.colors.qualitative.Plotly +TAXON_COLORS = { + "dirus": TAXON_PALETTE[0], +} + + +class Adir1(AnophelesDataResource): + """Provides access to data from Adir1.x releases. + + Parameters + ---------- + url : str, optional + Base path to data. Defaults to use Google Cloud Storage, or can + be a local path on your file system if data have been downloaded. + site_filters_analysis : str, optional + Site filters analysis version. + bokeh_output_notebook : bool, optional + If True (default), configure bokeh to output plots to the notebook. + results_cache : str, optional + Path to directory on local file system to save results. + log : str or stream, optional + File path or stream output for logging messages. + debug : bool, optional + Set to True to enable debug level logging. + show_progress : bool, optional + If True, show a progress bar during longer-running computations. The default can be overridden using an environmental variable named MGEN_SHOW_PROGRESS. + check_location : bool, optional + If True, use ipinfo to check the location of the client system. + **kwargs + Passed through to fsspec when setting up file system access. + + Examples + -------- + Access data from Google Cloud Storage (default): + + >>> import malariagen_data + >>> adir1 = malariagen_data.Adir1() + + Access data downloaded to a local file system: + + >>> adir1 = malariagen_data.Adir1("/local/path/to/vo_adir_release/") + + Access data from Google Cloud Storage, with caching on the local file system + in a directory named "gcs_cache": + + >>> adir1 = malariagen_data.Adir1( + ... "simplecache::gs://vo_adir_production_us_central1", + ... simplecache=dict(cache_storage="gcs_cache"), + ... ) + + Set up caching of some longer-running computations on the local file system, + in a directory named "results_cache": + + >>> adir1 = malariagen_data.Adir1(results_cache="results_cache") + + """ + + # _xpehh_gwss_cache_name = XPEHH_GWSS_CACHE_NAME + # _ihs_gwss_cache_name = IHS_GWSS_CACHE_NAME + + def __init__( + self, + url=None, + bokeh_output_notebook=True, + results_cache=None, + log=sys.stdout, + debug=False, + show_progress=None, + check_location=True, + cohorts_analysis=None, + site_filters_analysis=None, + discordant_read_calls_analysis=None, + pre=False, + tqdm_class=None, + **storage_options, # used by fsspec via init_filesystem() + ): + super().__init__( + url=url, + config_path=CONFIG_PATH, + cohorts_analysis=cohorts_analysis, + aim_analysis=None, + aim_metadata_dtype=None, + aim_ids=None, + aim_palettes=None, + site_filters_analysis=site_filters_analysis, + discordant_read_calls_analysis=discordant_read_calls_analysis, + default_site_mask="funestus", + default_phasing_analysis="funestus", + default_coverage_calls_analysis="funestus", + bokeh_output_notebook=bokeh_output_notebook, + results_cache=results_cache, + log=log, + debug=debug, + show_progress=show_progress, + check_location=check_location, + pre=pre, + gcs_default_url=GCS_DEFAULT_URL, + gcs_region_urls=GCS_REGION_URLS, + major_version_number=MAJOR_VERSION_NUMBER, + major_version_path=MAJOR_VERSION_PATH, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + storage_options=storage_options, # used by fsspec via init_filesystem() + tqdm_class=tqdm_class, + taxon_colors=TAXON_COLORS, + virtual_contigs=None, + gene_names=None, + inversion_tag_path=None, + ) + + def __repr__(self): + text = ( + f"\n" + f"Storage URL : {self._url}\n" + f"Data releases available : {', '.join(self.releases)}\n" + f"Results cache : {self._results_cache}\n" + # f"Cohorts analysis : {self._cohorts_analysis}\n" + f"Site filters analysis : {self._site_filters_analysis}\n" + f"Software version : malariagen_data {malariagen_data.__version__}\n" + f"Client location : {self.client_location}\n" + f"---\n" + f"Please note that data are subject to terms of use,\n" + f"for more information see https://www.malariagen.net/data\n" + f"or contact support@malariagen.net. For API documentation see \n" + f"https://malariagen.github.io/malariagen-data-python/v{malariagen_data.__version__}/Adir1.html" + ) + return text + + def _repr_html_(self): + html = f""" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
MalariaGEN Adir1 API client
+ Please note that data are subject to terms of use, + for more information see + the MalariaGEN website or contact support@malariagen.net. + See also the Adir1 API docs. +
+ Storage URL + {self._url}
+ Data releases available + {', '.join(self.releases)}
+ Results cache + {self._results_cache}
+ Cohorts analysis + {self._cohorts_analysis}
+ Site filters analysis + {self._site_filters_analysis}
+ Software version + malariagen_data {malariagen_data.__version__}
+ Client location + {self.client_location}
+ """ + return html From 921b9c4c942fb1d10fcbe7350103000ce83c5fc7 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 10 Jun 2025 15:03:15 +1000 Subject: [PATCH 02/12] add notebook exploring / troubleshooting adir1 --- notebooks/adir1_explore.ipynb | 483 ++++++++++++++++++++++++++++++++++ 1 file changed, 483 insertions(+) create mode 100644 notebooks/adir1_explore.ipynb diff --git a/notebooks/adir1_explore.ipynb b/notebooks/adir1_explore.ipynb new file mode 100644 index 000000000..1fa71882d --- /dev/null +++ b/notebooks/adir1_explore.ipynb @@ -0,0 +1,483 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import malariagen_data" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "application/javascript": [ + "'use strict';\n", + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " const force = true;\n", + "\n", + " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", + " root._bokeh_onload_callbacks = [];\n", + " root._bokeh_is_loading = undefined;\n", + " }\n", + "\n", + "const JS_MIME_TYPE = 'application/javascript';\n", + " const HTML_MIME_TYPE = 'text/html';\n", + " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", + " const CLASS_NAME = 'output_bokeh rendered_html';\n", + "\n", + " /**\n", + " * Render data to the DOM node\n", + " */\n", + " function render(props, node) {\n", + " const script = document.createElement(\"script\");\n", + " node.appendChild(script);\n", + " }\n", + "\n", + " /**\n", + " * Handle when an output is cleared or removed\n", + " */\n", + " function handleClearOutput(event, handle) {\n", + " function drop(id) {\n", + " const view = Bokeh.index.get_by_id(id)\n", + " if (view != null) {\n", + " view.model.document.clear()\n", + " Bokeh.index.delete(view)\n", + " }\n", + " }\n", + "\n", + " const cell = handle.cell;\n", + "\n", + " const id = cell.output_area._bokeh_element_id;\n", + " const server_id = cell.output_area._bokeh_server_id;\n", + "\n", + " // Clean up Bokeh references\n", + " if (id != null) {\n", + " drop(id)\n", + " }\n", + "\n", + " if (server_id !== undefined) {\n", + " // Clean up Bokeh references\n", + " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", + " cell.notebook.kernel.execute(cmd_clean, {\n", + " iopub: {\n", + " output: function(msg) {\n", + " const id = msg.content.text.trim()\n", + " drop(id)\n", + " }\n", + " }\n", + " });\n", + " // Destroy server and session\n", + " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", + " cell.notebook.kernel.execute(cmd_destroy);\n", + " }\n", + " }\n", + "\n", + " /**\n", + " * Handle when a new output is added\n", + " */\n", + " function handleAddOutput(event, handle) {\n", + " const output_area = handle.output_area;\n", + " const output = handle.output;\n", + "\n", + " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", + " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", + " return\n", + " }\n", + "\n", + " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", + "\n", + " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", + " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", + " // store reference to embed id on output_area\n", + " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", + " }\n", + " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", + " const bk_div = document.createElement(\"div\");\n", + " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", + " const script_attrs = bk_div.children[0].attributes;\n", + " for (let i = 0; i < script_attrs.length; i++) {\n", + " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", + " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", + " }\n", + " // store reference to server id on output_area\n", + " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", + " }\n", + " }\n", + "\n", + " function register_renderer(events, OutputArea) {\n", + "\n", + " function append_mime(data, metadata, element) {\n", + " // create a DOM node to render to\n", + " const toinsert = this.create_output_subarea(\n", + " metadata,\n", + " CLASS_NAME,\n", + " EXEC_MIME_TYPE\n", + " );\n", + " this.keyboard_manager.register_events(toinsert);\n", + " // Render to node\n", + " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", + " render(props, toinsert[toinsert.length - 1]);\n", + " element.append(toinsert);\n", + " return toinsert\n", + " }\n", + "\n", + " /* Handle when an output is cleared or removed */\n", + " events.on('clear_output.CodeCell', handleClearOutput);\n", + " events.on('delete.Cell', handleClearOutput);\n", + "\n", + " /* Handle when a new output is added */\n", + " events.on('output_added.OutputArea', handleAddOutput);\n", + "\n", + " /**\n", + " * Register the mime type and append_mime function with output_area\n", + " */\n", + " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", + " /* Is output safe? */\n", + " safe: true,\n", + " /* Index of renderer in `output_area.display_order` */\n", + " index: 0\n", + " });\n", + " }\n", + "\n", + " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", + " if (root.Jupyter !== undefined) {\n", + " const events = require('base/js/events');\n", + " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", + "\n", + " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", + " register_renderer(events, OutputArea);\n", + " }\n", + " }\n", + " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", + " root._bokeh_timeout = Date.now() + 5000;\n", + " root._bokeh_failed_load = false;\n", + " }\n", + "\n", + " const NB_LOAD_WARNING = {'data': {'text/html':\n", + " \"
\\n\"+\n", + " \"

\\n\"+\n", + " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", + " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", + " \"

\\n\"+\n", + " \"
    \\n\"+\n", + " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n", + " \"
  • use INLINE resources instead, as so:
  • \\n\"+\n", + " \"
\\n\"+\n", + " \"\\n\"+\n", + " \"from bokeh.resources import INLINE\\n\"+\n", + " \"output_notebook(resources=INLINE)\\n\"+\n", + " \"\\n\"+\n", + " \"
\"}};\n", + "\n", + " function display_loaded(error = null) {\n", + " const el = document.getElementById(null);\n", + " if (el != null) {\n", + " const html = (() => {\n", + " if (typeof root.Bokeh === \"undefined\") {\n", + " if (error == null) {\n", + " return \"BokehJS is loading ...\";\n", + " } else {\n", + " return \"BokehJS failed to load.\";\n", + " }\n", + " } else {\n", + " const prefix = `BokehJS ${root.Bokeh.version}`;\n", + " if (error == null) {\n", + " return `${prefix} successfully loaded.`;\n", + " } else {\n", + " return `${prefix} encountered errors while loading and may not function as expected.`;\n", + " }\n", + " }\n", + " })();\n", + " el.innerHTML = html;\n", + "\n", + " if (error != null) {\n", + " const wrapper = document.createElement(\"div\");\n", + " wrapper.style.overflow = \"auto\";\n", + " wrapper.style.height = \"5em\";\n", + " wrapper.style.resize = \"vertical\";\n", + " const content = document.createElement(\"div\");\n", + " content.style.fontFamily = \"monospace\";\n", + " content.style.whiteSpace = \"pre-wrap\";\n", + " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", + " content.textContent = error.stack ?? error.toString();\n", + " wrapper.append(content);\n", + " el.append(wrapper);\n", + " }\n", + " } else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(() => display_loaded(error), 100);\n", + " }\n", + " }\n", + "\n", + " function run_callbacks() {\n", + " try {\n", + " root._bokeh_onload_callbacks.forEach(function(callback) {\n", + " if (callback != null)\n", + " callback();\n", + " });\n", + " } finally {\n", + " delete root._bokeh_onload_callbacks\n", + " }\n", + " console.debug(\"Bokeh: all callbacks have finished\");\n", + " }\n", + "\n", + " function load_libs(css_urls, js_urls, callback) {\n", + " if (css_urls == null) css_urls = [];\n", + " if (js_urls == null) js_urls = [];\n", + "\n", + " root._bokeh_onload_callbacks.push(callback);\n", + " if (root._bokeh_is_loading > 0) {\n", + " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", + " return null;\n", + " }\n", + " if (js_urls == null || js_urls.length === 0) {\n", + " run_callbacks();\n", + " return null;\n", + " }\n", + " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", + " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", + "\n", + " function on_load() {\n", + " root._bokeh_is_loading--;\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", + " run_callbacks()\n", + " }\n", + " }\n", + "\n", + " function on_error(url) {\n", + " console.error(\"failed to load \" + url);\n", + " }\n", + "\n", + " for (let i = 0; i < css_urls.length; i++) {\n", + " const url = css_urls[i];\n", + " const element = document.createElement(\"link\");\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.rel = \"stylesheet\";\n", + " element.type = \"text/css\";\n", + " element.href = url;\n", + " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " for (let i = 0; i < js_urls.length; i++) {\n", + " const url = js_urls[i];\n", + " const element = document.createElement('script');\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.async = false;\n", + " element.src = url;\n", + " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", + " document.head.appendChild(element);\n", + " }\n", + " };\n", + "\n", + " function inject_raw_css(css) {\n", + " const element = document.createElement(\"style\");\n", + " element.appendChild(document.createTextNode(css));\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", + " const css_urls = [];\n", + "\n", + " const inline_js = [ function(Bokeh) {\n", + " Bokeh.set_log_level(\"info\");\n", + " },\n", + "function(Bokeh) {\n", + " }\n", + " ];\n", + "\n", + " function run_inline_js() {\n", + " if (root.Bokeh !== undefined || force === true) {\n", + " try {\n", + " for (let i = 0; i < inline_js.length; i++) {\n", + " inline_js[i].call(root, root.Bokeh);\n", + " }\n", + "\n", + " } catch (error) {throw error;\n", + " }} else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(run_inline_js, 100);\n", + " } else if (!root._bokeh_failed_load) {\n", + " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", + " root._bokeh_failed_load = true;\n", + " } else if (force !== true) {\n", + " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", + " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", + " }\n", + " }\n", + "\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", + " run_inline_js();\n", + " } else {\n", + " load_libs(css_urls, js_urls, function() {\n", + " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", + " run_inline_js();\n", + " });\n", + " }\n", + "}(window));" + ], + "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n \"
  • use INLINE resources instead, as so:
  • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
MalariaGEN Adir1 API client
\n", + " Please note that data are subject to terms of use,\n", + " for more information see \n", + " the MalariaGEN website or contact support@malariagen.net.\n", + " See also the Adir1 API docs.\n", + "
\n", + " Storage URL\n", + " gs://vo_adir_production_us_central1/
\n", + " Data releases available\n", + " 1.x
\n", + " Results cache\n", + " /Users/dennistpw/Projects/malariagen_results
\n", + " Cohorts analysis\n", + " noneyet
\n", + " Site filters analysis\n", + " sc_20250610
\n", + " Software version\n", + " malariagen_data 13.3.0.post33+90e72d5a
\n", + " Client location\n", + " Queensland, Australia
\n", + " " + ], + "text/plain": [ + "\n", + "Storage URL : gs://vo_adir_production_us_central1/\n", + "Data releases available : 1.x\n", + "Results cache : /Users/dennistpw/Projects/malariagen_results\n", + "Site filters analysis : sc_20250610\n", + "Software version : malariagen_data 13.3.0.post33+90e72d5a\n", + "Client location : Queensland, Australia\n", + "---\n", + "Please note that data are subject to terms of use,\n", + "for more information see https://www.malariagen.net/data\n", + "or contact support@malariagen.net. For API documentation see \n", + "https://malariagen.github.io/malariagen-data-python/v13.3.0.post33+90e72d5a/Adir1.html" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Init Adir1 API\n", + "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')\n", + "adir1" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " \r" + ] + } + ], + "source": [ + "snps = adir1.snp_calls(region=\"KB672868:1000000-1010000\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e0489eab-e347-492d-88ce-97d61a0c0aba", + "metadata": {}, + "outputs": [], + "source": [ + "adir1.pca(region = \"KB672868\", n_snps = 100_000, " + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From e3e45fe81d7a2856fa8f45533161d07ef1966804 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 10 Jun 2025 15:21:09 +1000 Subject: [PATCH 03/12] comment out TOU lookups for metadata --- adir1_explore.ipynb | 451 ----------------------- malariagen_data/anoph/sample_metadata.py | 13 +- notebooks/adir1_explore.ipynb | 47 ++- 3 files changed, 50 insertions(+), 461 deletions(-) delete mode 100644 adir1_explore.ipynb diff --git a/adir1_explore.ipynb b/adir1_explore.ipynb deleted file mode 100644 index c42d93dd5..000000000 --- a/adir1_explore.ipynb +++ /dev/null @@ -1,451 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import malariagen_data" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "application/javascript": [ - "'use strict';\n", - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " const force = true;\n", - "\n", - " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", - " root._bokeh_onload_callbacks = [];\n", - " root._bokeh_is_loading = undefined;\n", - " }\n", - "\n", - "const JS_MIME_TYPE = 'application/javascript';\n", - " const HTML_MIME_TYPE = 'text/html';\n", - " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", - " const CLASS_NAME = 'output_bokeh rendered_html';\n", - "\n", - " /**\n", - " * Render data to the DOM node\n", - " */\n", - " function render(props, node) {\n", - " const script = document.createElement(\"script\");\n", - " node.appendChild(script);\n", - " }\n", - "\n", - " /**\n", - " * Handle when an output is cleared or removed\n", - " */\n", - " function handleClearOutput(event, handle) {\n", - " function drop(id) {\n", - " const view = Bokeh.index.get_by_id(id)\n", - " if (view != null) {\n", - " view.model.document.clear()\n", - " Bokeh.index.delete(view)\n", - " }\n", - " }\n", - "\n", - " const cell = handle.cell;\n", - "\n", - " const id = cell.output_area._bokeh_element_id;\n", - " const server_id = cell.output_area._bokeh_server_id;\n", - "\n", - " // Clean up Bokeh references\n", - " if (id != null) {\n", - " drop(id)\n", - " }\n", - "\n", - " if (server_id !== undefined) {\n", - " // Clean up Bokeh references\n", - " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", - " cell.notebook.kernel.execute(cmd_clean, {\n", - " iopub: {\n", - " output: function(msg) {\n", - " const id = msg.content.text.trim()\n", - " drop(id)\n", - " }\n", - " }\n", - " });\n", - " // Destroy server and session\n", - " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", - " cell.notebook.kernel.execute(cmd_destroy);\n", - " }\n", - " }\n", - "\n", - " /**\n", - " * Handle when a new output is added\n", - " */\n", - " function handleAddOutput(event, handle) {\n", - " const output_area = handle.output_area;\n", - " const output = handle.output;\n", - "\n", - " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", - " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", - " return\n", - " }\n", - "\n", - " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", - "\n", - " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", - " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", - " // store reference to embed id on output_area\n", - " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", - " }\n", - " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", - " const bk_div = document.createElement(\"div\");\n", - " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", - " const script_attrs = bk_div.children[0].attributes;\n", - " for (let i = 0; i < script_attrs.length; i++) {\n", - " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", - " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", - " }\n", - " // store reference to server id on output_area\n", - " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", - " }\n", - " }\n", - "\n", - " function register_renderer(events, OutputArea) {\n", - "\n", - " function append_mime(data, metadata, element) {\n", - " // create a DOM node to render to\n", - " const toinsert = this.create_output_subarea(\n", - " metadata,\n", - " CLASS_NAME,\n", - " EXEC_MIME_TYPE\n", - " );\n", - " this.keyboard_manager.register_events(toinsert);\n", - " // Render to node\n", - " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", - " render(props, toinsert[toinsert.length - 1]);\n", - " element.append(toinsert);\n", - " return toinsert\n", - " }\n", - "\n", - " /* Handle when an output is cleared or removed */\n", - " events.on('clear_output.CodeCell', handleClearOutput);\n", - " events.on('delete.Cell', handleClearOutput);\n", - "\n", - " /* Handle when a new output is added */\n", - " events.on('output_added.OutputArea', handleAddOutput);\n", - "\n", - " /**\n", - " * Register the mime type and append_mime function with output_area\n", - " */\n", - " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", - " /* Is output safe? */\n", - " safe: true,\n", - " /* Index of renderer in `output_area.display_order` */\n", - " index: 0\n", - " });\n", - " }\n", - "\n", - " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", - " if (root.Jupyter !== undefined) {\n", - " const events = require('base/js/events');\n", - " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", - "\n", - " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", - " register_renderer(events, OutputArea);\n", - " }\n", - " }\n", - " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", - " root._bokeh_timeout = Date.now() + 5000;\n", - " root._bokeh_failed_load = false;\n", - " }\n", - "\n", - " const NB_LOAD_WARNING = {'data': {'text/html':\n", - " \"
\\n\"+\n", - " \"

\\n\"+\n", - " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", - " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", - " \"

\\n\"+\n", - " \"
    \\n\"+\n", - " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n", - " \"
  • use INLINE resources instead, as so:
  • \\n\"+\n", - " \"
\\n\"+\n", - " \"\\n\"+\n", - " \"from bokeh.resources import INLINE\\n\"+\n", - " \"output_notebook(resources=INLINE)\\n\"+\n", - " \"\\n\"+\n", - " \"
\"}};\n", - "\n", - " function display_loaded(error = null) {\n", - " const el = document.getElementById(null);\n", - " if (el != null) {\n", - " const html = (() => {\n", - " if (typeof root.Bokeh === \"undefined\") {\n", - " if (error == null) {\n", - " return \"BokehJS is loading ...\";\n", - " } else {\n", - " return \"BokehJS failed to load.\";\n", - " }\n", - " } else {\n", - " const prefix = `BokehJS ${root.Bokeh.version}`;\n", - " if (error == null) {\n", - " return `${prefix} successfully loaded.`;\n", - " } else {\n", - " return `${prefix} encountered errors while loading and may not function as expected.`;\n", - " }\n", - " }\n", - " })();\n", - " el.innerHTML = html;\n", - "\n", - " if (error != null) {\n", - " const wrapper = document.createElement(\"div\");\n", - " wrapper.style.overflow = \"auto\";\n", - " wrapper.style.height = \"5em\";\n", - " wrapper.style.resize = \"vertical\";\n", - " const content = document.createElement(\"div\");\n", - " content.style.fontFamily = \"monospace\";\n", - " content.style.whiteSpace = \"pre-wrap\";\n", - " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", - " content.textContent = error.stack ?? error.toString();\n", - " wrapper.append(content);\n", - " el.append(wrapper);\n", - " }\n", - " } else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(() => display_loaded(error), 100);\n", - " }\n", - " }\n", - "\n", - " function run_callbacks() {\n", - " try {\n", - " root._bokeh_onload_callbacks.forEach(function(callback) {\n", - " if (callback != null)\n", - " callback();\n", - " });\n", - " } finally {\n", - " delete root._bokeh_onload_callbacks\n", - " }\n", - " console.debug(\"Bokeh: all callbacks have finished\");\n", - " }\n", - "\n", - " function load_libs(css_urls, js_urls, callback) {\n", - " if (css_urls == null) css_urls = [];\n", - " if (js_urls == null) js_urls = [];\n", - "\n", - " root._bokeh_onload_callbacks.push(callback);\n", - " if (root._bokeh_is_loading > 0) {\n", - " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", - " return null;\n", - " }\n", - " if (js_urls == null || js_urls.length === 0) {\n", - " run_callbacks();\n", - " return null;\n", - " }\n", - " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", - " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", - "\n", - " function on_load() {\n", - " root._bokeh_is_loading--;\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", - " run_callbacks()\n", - " }\n", - " }\n", - "\n", - " function on_error(url) {\n", - " console.error(\"failed to load \" + url);\n", - " }\n", - "\n", - " for (let i = 0; i < css_urls.length; i++) {\n", - " const url = css_urls[i];\n", - " const element = document.createElement(\"link\");\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.rel = \"stylesheet\";\n", - " element.type = \"text/css\";\n", - " element.href = url;\n", - " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " for (let i = 0; i < js_urls.length; i++) {\n", - " const url = js_urls[i];\n", - " const element = document.createElement('script');\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.async = false;\n", - " element.src = url;\n", - " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", - " document.head.appendChild(element);\n", - " }\n", - " };\n", - "\n", - " function inject_raw_css(css) {\n", - " const element = document.createElement(\"style\");\n", - " element.appendChild(document.createTextNode(css));\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", - " const css_urls = [];\n", - "\n", - " const inline_js = [ function(Bokeh) {\n", - " Bokeh.set_log_level(\"info\");\n", - " },\n", - "function(Bokeh) {\n", - " }\n", - " ];\n", - "\n", - " function run_inline_js() {\n", - " if (root.Bokeh !== undefined || force === true) {\n", - " try {\n", - " for (let i = 0; i < inline_js.length; i++) {\n", - " inline_js[i].call(root, root.Bokeh);\n", - " }\n", - "\n", - " } catch (error) {throw error;\n", - " }} else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(run_inline_js, 100);\n", - " } else if (!root._bokeh_failed_load) {\n", - " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", - " root._bokeh_failed_load = true;\n", - " } else if (force !== true) {\n", - " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", - " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", - " }\n", - " }\n", - "\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", - " run_inline_js();\n", - " } else {\n", - " load_libs(css_urls, js_urls, function() {\n", - " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", - " run_inline_js();\n", - " });\n", - " }\n", - "}(window));" - ], - "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n \"
  • use INLINE resources instead, as so:
  • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "# Init API\n", - "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "f171c3b7-30c2-4e9f-9133-22206985de07", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "'KB672868'" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# Are the contigs here? \n", - "chroms = adir1.contigs[:5]\n", - "chroms[1]" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "ename": "FileNotFoundError", - "evalue": "b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:426\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 425\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_sets\u001b[49m\u001b[43m[\u001b[49m\u001b[43mrelease\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n", - "\u001b[0;31mKeyError\u001b[0m: '1.x'", - "\nDuring handling of the above exception, another exception occurred:\n", - "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[7], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m snps \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msnp_calls\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868:1000000-2000000\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/snp_data.py:1007\u001b[0m, in \u001b[0;36mAnophelesSnpData.snp_calls\u001b[0;34m(self, region, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, inline_array, chunks, cohort_size, min_cohort_size, max_cohort_size, random_seed)\u001b[0m\n\u001b[1;32m 1001\u001b[0m base_params\u001b[38;5;241m.\u001b[39mvalidate_sample_selection_params(\n\u001b[1;32m 1002\u001b[0m sample_query\u001b[38;5;241m=\u001b[39msample_query, sample_indices\u001b[38;5;241m=\u001b[39msample_indices\n\u001b[1;32m 1003\u001b[0m )\n\u001b[1;32m 1005\u001b[0m \u001b[38;5;66;03m# Normalise parameters.\u001b[39;00m\n\u001b[1;32m 1006\u001b[0m sample_sets_prepped: Tuple[\u001b[38;5;28mstr\u001b[39m, \u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mtuple\u001b[39m(\n\u001b[0;32m-> 1007\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_sets_param\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1008\u001b[0m )\n\u001b[1;32m 1009\u001b[0m \u001b[38;5;28;01mdel\u001b[39;00m sample_sets\n\u001b[1;32m 1010\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_indices \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:524\u001b[0m, in \u001b[0;36mAnophelesBase._prep_sample_sets_param\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 517\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_prep_sample_sets_param\u001b[39m(\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets]\n\u001b[1;32m 519\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m List[\u001b[38;5;28mstr\u001b[39m]:\n\u001b[1;32m 520\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Common handling for the `sample_sets` parameter. For convenience, we\u001b[39;00m\n\u001b[1;32m 521\u001b[0m \u001b[38;5;124;03m allow this to be a single sample set, or a list of sample sets, or a\u001b[39;00m\n\u001b[1;32m 522\u001b[0m \u001b[38;5;124;03m release identifier, or a list of release identifiers.\"\"\"\u001b[39;00m\n\u001b[0;32m--> 524\u001b[0m all_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mto_list()\n\u001b[1;32m 526\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_sets \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 527\u001b[0m \u001b[38;5;66;03m# All available sample sets.\u001b[39;00m\n\u001b[1;32m 528\u001b[0m prepped_sample_sets \u001b[38;5;241m=\u001b[39m all_sample_sets\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets(release\u001b[38;5;241m=\u001b[39mr) \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36m\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrelease\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mr\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:430\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release]\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n\u001b[0;32m--> 430\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_read_sample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43msingle_release\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrelease\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 431\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release] \u001b[38;5;241m=\u001b[39m df\n\u001b[1;32m 433\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(release, Sequence):\n\u001b[1;32m 434\u001b[0m \u001b[38;5;66;03m# Ensure no duplicates.\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:376\u001b[0m, in \u001b[0;36mAnophelesBase._read_sample_sets\u001b[0;34m(self, single_release)\u001b[0m\n\u001b[1;32m 373\u001b[0m manifest_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mrelease_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/manifest.tsv\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 375\u001b[0m \u001b[38;5;66;03m# Read the manifest into a pandas dataframe.\u001b[39;00m\n\u001b[0;32m--> 376\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen_file\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmanifest_path\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m 377\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mread_csv(f, sep\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;130;01m\\t\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, na_values\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 379\u001b[0m \u001b[38;5;66;03m# Add a \"release\" column for convenience.\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:218\u001b[0m, in \u001b[0;36mAnophelesBase.open_file\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 215\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 216\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mopen_file\u001b[39m(\u001b[38;5;28mself\u001b[39m, path: \u001b[38;5;28mstr\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m IO:\n\u001b[1;32m 217\u001b[0m full_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_base_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m--> 218\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfull_path\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/spec.py:1154\u001b[0m, in \u001b[0;36mAbstractFileSystem.open\u001b[0;34m(self, path, mode, block_size, cache_options, compression, **kwargs)\u001b[0m\n\u001b[1;32m 1152\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 1153\u001b[0m ac \u001b[38;5;241m=\u001b[39m kwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mautocommit\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_intrans)\n\u001b[0;32m-> 1154\u001b[0m f \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_open\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1155\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1156\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1157\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1158\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mac\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1159\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1160\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1161\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1162\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m compression \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfsspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcompression\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m compr\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1309\u001b[0m, in \u001b[0;36mGCSFileSystem._open\u001b[0;34m(self, path, mode, block_size, cache_options, acl, consistency, metadata, autocommit, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1307\u001b[0m block_size \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_block_size\n\u001b[1;32m 1308\u001b[0m const \u001b[38;5;241m=\u001b[39m consistency \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconsistency\n\u001b[0;32m-> 1309\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mGCSFile\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1311\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1312\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1313\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1314\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1315\u001b[0m \u001b[43m \u001b[49m\u001b[43mconsistency\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mconst\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1316\u001b[0m \u001b[43m \u001b[49m\u001b[43mmetadata\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmetadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1317\u001b[0m \u001b[43m \u001b[49m\u001b[43macl\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43macl\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1318\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mautocommit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1319\u001b[0m \u001b[43m \u001b[49m\u001b[43mfixed_key_metadata\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfixed_key_metadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1320\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1321\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1468\u001b[0m, in \u001b[0;36mGCSFile.__init__\u001b[0;34m(self, gcsfs, path, mode, block_size, autocommit, cache_type, cache_options, acl, consistency, metadata, content_type, timeout, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1466\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAttempt to open a bucket\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1467\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgeneration \u001b[38;5;241m=\u001b[39m _coalesce_generation(generation, path_generation)\n\u001b[0;32m-> 1468\u001b[0m \u001b[38;5;28;43msuper\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1469\u001b[0m \u001b[43m \u001b[49m\u001b[43mgcsfs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1470\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1471\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1472\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1473\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mautocommit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1474\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_type\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_type\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1475\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1476\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1477\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1478\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgcsfs \u001b[38;5;241m=\u001b[39m gcsfs\n\u001b[1;32m 1479\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mbucket \u001b[38;5;241m=\u001b[39m bucket\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/spec.py:1510\u001b[0m, in \u001b[0;36mAbstractBufferedFile.__init__\u001b[0;34m(self, fs, path, mode, block_size, autocommit, cache_type, cache_options, size, **kwargs)\u001b[0m\n\u001b[1;32m 1508\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize \u001b[38;5;241m=\u001b[39m size\n\u001b[1;32m 1509\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m-> 1510\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdetails\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msize\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[1;32m 1511\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcache \u001b[38;5;241m=\u001b[39m caches[cache_type](\n\u001b[1;32m 1512\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mblocksize, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_fetch_range, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mcache_options\n\u001b[1;32m 1513\u001b[0m )\n\u001b[1;32m 1514\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1504\u001b[0m, in \u001b[0;36mGCSFile.details\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1501\u001b[0m \u001b[38;5;129m@property\u001b[39m\n\u001b[1;32m 1502\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdetails\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[1;32m 1503\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m-> 1504\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43minfo\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mgeneration\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneration\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1505\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:115\u001b[0m, in \u001b[0;36msync_wrapper..wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 114\u001b[0m \u001b[38;5;28mself\u001b[39m \u001b[38;5;241m=\u001b[39m obj \u001b[38;5;129;01mor\u001b[39;00m args[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m--> 115\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43msync\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mloop\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfunc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:100\u001b[0m, in \u001b[0;36msync\u001b[0;34m(loop, func, timeout, *args, **kwargs)\u001b[0m\n\u001b[1;32m 98\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m FSTimeoutError \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mreturn_result\u001b[39;00m\n\u001b[1;32m 99\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(return_result, \u001b[38;5;167;01mBaseException\u001b[39;00m):\n\u001b[0;32m--> 100\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m return_result\n\u001b[1;32m 101\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 102\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m return_result\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:55\u001b[0m, in \u001b[0;36m_runner\u001b[0;34m(event, coro, result, timeout)\u001b[0m\n\u001b[1;32m 53\u001b[0m coro \u001b[38;5;241m=\u001b[39m asyncio\u001b[38;5;241m.\u001b[39mwait_for(coro, timeout\u001b[38;5;241m=\u001b[39mtimeout)\n\u001b[1;32m 54\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 55\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m coro\n\u001b[1;32m 56\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m ex:\n\u001b[1;32m 57\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m ex\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:797\u001b[0m, in \u001b[0;36mGCSFileSystem._info\u001b[0;34m(self, path, generation, **kwargs)\u001b[0m\n\u001b[1;32m 795\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 796\u001b[0m kwargs[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdetail\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m \u001b[38;5;66;03m# Force to true for info\u001b[39;00m\n\u001b[0;32m--> 797\u001b[0m out \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ls(path, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 798\u001b[0m out0 \u001b[38;5;241m=\u001b[39m [o \u001b[38;5;28;01mfor\u001b[39;00m o \u001b[38;5;129;01min\u001b[39;00m out \u001b[38;5;28;01mif\u001b[39;00m o[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mname\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mrstrip(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;241m==\u001b[39m path]\n\u001b[1;32m 799\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m out0:\n\u001b[1;32m 800\u001b[0m \u001b[38;5;66;03m# exact hit\u001b[39;00m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:834\u001b[0m, in \u001b[0;36mGCSFileSystem._ls\u001b[0;34m(self, path, detail, prefix, versions, **kwargs)\u001b[0m\n\u001b[1;32m 832\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 833\u001b[0m out \u001b[38;5;241m=\u001b[39m []\n\u001b[0;32m--> 834\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m entry \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_list_objects(\n\u001b[1;32m 835\u001b[0m path, prefix\u001b[38;5;241m=\u001b[39mprefix, versions\u001b[38;5;241m=\u001b[39mversions\n\u001b[1;32m 836\u001b[0m ):\n\u001b[1;32m 837\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m versions \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgeneration\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m entry:\n\u001b[1;32m 838\u001b[0m entry \u001b[38;5;241m=\u001b[39m entry\u001b[38;5;241m.\u001b[39mcopy()\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:549\u001b[0m, in \u001b[0;36mGCSFileSystem._list_objects\u001b[0;34m(self, path, prefix, versions)\u001b[0m\n\u001b[1;32m 547\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m (items \u001b[38;5;241m+\u001b[39m pseudodirs):\n\u001b[1;32m 548\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m key:\n\u001b[0;32m--> 549\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m [\u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_object(path)]\n\u001b[1;32m 550\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 551\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m []\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:491\u001b[0m, in \u001b[0;36mGCSFileSystem._get_object\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 488\u001b[0m \u001b[38;5;66;03m# Work around various permission settings. Prefer an object get (storage.objects.get), but\u001b[39;00m\n\u001b[1;32m 489\u001b[0m \u001b[38;5;66;03m# fall back to a bucket list + filter to object name (storage.objects.list).\u001b[39;00m\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 491\u001b[0m res \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_call(\n\u001b[1;32m 492\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGET\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mb/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m/o/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, bucket, key, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m, generation\u001b[38;5;241m=\u001b[39mgeneration\n\u001b[1;32m 493\u001b[0m )\n\u001b[1;32m 494\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 495\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mstr\u001b[39m(e)\u001b[38;5;241m.\u001b[39mstartswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mForbidden\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:418\u001b[0m, in \u001b[0;36mGCSFileSystem._call\u001b[0;34m(self, method, path, json_out, info_out, *args, **kwargs)\u001b[0m\n\u001b[1;32m 414\u001b[0m \u001b[38;5;28;01masync\u001b[39;00m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_call\u001b[39m(\n\u001b[1;32m 415\u001b[0m \u001b[38;5;28mself\u001b[39m, method, path, \u001b[38;5;241m*\u001b[39margs, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, info_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 416\u001b[0m ):\n\u001b[1;32m 417\u001b[0m logger\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mmethod\u001b[38;5;241m.\u001b[39mupper()\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00margs\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mheaders\u001b[39m\u001b[38;5;124m'\u001b[39m)\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 418\u001b[0m status, headers, info, contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_request(\n\u001b[1;32m 419\u001b[0m method, path, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 420\u001b[0m )\n\u001b[1;32m 421\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m json_out:\n\u001b[1;32m 422\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m json\u001b[38;5;241m.\u001b[39mloads(contents)\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/decorator.py:221\u001b[0m, in \u001b[0;36mdecorate..fun\u001b[0;34m(*args, **kw)\u001b[0m\n\u001b[1;32m 219\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m kwsyntax:\n\u001b[1;32m 220\u001b[0m args, kw \u001b[38;5;241m=\u001b[39m fix(args, kw, sig)\n\u001b[0;32m--> 221\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m caller(func, \u001b[38;5;241m*\u001b[39m(extras \u001b[38;5;241m+\u001b[39m args), \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkw)\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:114\u001b[0m, in \u001b[0;36mretry_request\u001b[0;34m(func, retries, *args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m retry \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m asyncio\u001b[38;5;241m.\u001b[39msleep(\u001b[38;5;28mmin\u001b[39m(random\u001b[38;5;241m.\u001b[39mrandom() \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m2\u001b[39m \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39m (retry \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m), \u001b[38;5;241m32\u001b[39m))\n\u001b[0;32m--> 114\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m func(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 115\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (\n\u001b[1;32m 116\u001b[0m HttpError,\n\u001b[1;32m 117\u001b[0m requests\u001b[38;5;241m.\u001b[39mexceptions\u001b[38;5;241m.\u001b[39mRequestException,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 120\u001b[0m aiohttp\u001b[38;5;241m.\u001b[39mclient_exceptions\u001b[38;5;241m.\u001b[39mClientError,\n\u001b[1;32m 121\u001b[0m ) \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 122\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\n\u001b[1;32m 123\u001b[0m \u001b[38;5;28misinstance\u001b[39m(e, HttpError)\n\u001b[1;32m 124\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m e\u001b[38;5;241m.\u001b[39mcode \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m400\u001b[39m\n\u001b[1;32m 125\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mrequester pays\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m e\u001b[38;5;241m.\u001b[39mmessage\n\u001b[1;32m 126\u001b[0m ):\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:411\u001b[0m, in \u001b[0;36mGCSFileSystem._request\u001b[0;34m(self, method, path, headers, json, data, *args, **kwargs)\u001b[0m\n\u001b[1;32m 408\u001b[0m info \u001b[38;5;241m=\u001b[39m r\u001b[38;5;241m.\u001b[39mrequest_info \u001b[38;5;66;03m# for debug only\u001b[39;00m\n\u001b[1;32m 409\u001b[0m contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m r\u001b[38;5;241m.\u001b[39mread()\n\u001b[0;32m--> 411\u001b[0m \u001b[43mvalidate_response\u001b[49m\u001b[43m(\u001b[49m\u001b[43mstatus\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcontents\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43margs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 412\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m status, headers, info, contents\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:83\u001b[0m, in \u001b[0;36mvalidate_response\u001b[0;34m(status, content, path, args)\u001b[0m\n\u001b[1;32m 81\u001b[0m path \u001b[38;5;241m=\u001b[39m path\u001b[38;5;241m.\u001b[39mformat(\u001b[38;5;241m*\u001b[39m[quote(p) \u001b[38;5;28;01mfor\u001b[39;00m p \u001b[38;5;129;01min\u001b[39;00m args])\n\u001b[1;32m 82\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m status \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m404\u001b[39m:\n\u001b[0;32m---> 83\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m(path)\n\u001b[1;32m 85\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 86\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(content, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdecode\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", - "\u001b[0;31mFileNotFoundError\u001b[0m: b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv" - ] - } - ], - "source": [ - "snps = adir1.snp_calls(region=\"KB672868:1000000-2000000\")" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.10" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index 3088508ba..ebe052de6 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -156,15 +156,16 @@ def _parse_general_metadata( axis="columns", ) + # Have commented these out for now as a) this is not a public release and b) for some reason it breaks everything and I haven't had the time to work out why # Add study columns. - study_info = self.lookup_study_info(sample_set=sample_set) - for column in study_info: - df[column] = study_info[column] + # study_info = self.lookup_study_info(sample_set=sample_set) + # for column in study_info: + # df[column] = study_info[column] # Add terms-of-use columns. - terms_of_use_info = self.lookup_terms_of_use_info(sample_set=sample_set) - for column in terms_of_use_info: - df[column] = terms_of_use_info[column] + # terms_of_use_info = self.lookup_terms_of_use_info(sample_set=sample_set) + # for column in terms_of_use_info: + # df[column] = terms_of_use_info[column] return df diff --git a/notebooks/adir1_explore.ipynb b/notebooks/adir1_explore.ipynb index 1fa71882d..450596a2f 100644 --- a/notebooks/adir1_explore.ipynb +++ b/notebooks/adir1_explore.ipynb @@ -450,12 +450,51 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "id": "e0489eab-e347-492d-88ce-97d61a0c0aba", - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " \r" + ] + }, + { + "ename": "KeyError", + "evalue": "\"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:581\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 579\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 580\u001b[0m \u001b[38;5;66;03m# Attempt to retrieve from the cache.\u001b[39;00m\n\u001b[0;32m--> 581\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_metadata\u001b[49m\u001b[43m[\u001b[49m\u001b[43mcache_key\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n", + "\u001b[0;31mKeyError\u001b[0m: ('1276-AD-BD-ALAM-VMF00156', '1277-VO-KH-WITKOWSKI-VMF00151', '1277-VO-KH-WITKOWSKI-VMF00183', '1278-VO-TH-KOBYLINSKI-VMF00153')", + "\nDuring handling of the above exception, another exception occurred:\n", + "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[10], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m pca \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpca\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mn_snps\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m100_000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcountry == \u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mThailand\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/pca.py:89\u001b[0m, in \u001b[0;36mAnophelesPca.pca\u001b[0;34m(self, region, n_snps, n_components, thin_offset, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, min_minor_ac, max_missing_an, cohort_size, min_cohort_size, max_cohort_size, exclude_samples, fit_exclude_samples, random_seed, inline_array, chunks)\u001b[0m\n\u001b[1;32m 83\u001b[0m name \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpca_v4\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 85\u001b[0m \u001b[38;5;66;03m# Normalize params for consistent hash value.\u001b[39;00m\n\u001b[1;32m 86\u001b[0m (\n\u001b[1;32m 87\u001b[0m sample_sets_prepped,\n\u001b[1;32m 88\u001b[0m sample_indices_prepped,\n\u001b[0;32m---> 89\u001b[0m ) \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_selection_cache_params\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 90\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 91\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 92\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 93\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 94\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 95\u001b[0m region_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_region_cache_param(region\u001b[38;5;241m=\u001b[39mregion)\n\u001b[1;32m 96\u001b[0m site_mask_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_optional_site_mask_param(site_mask\u001b[38;5;241m=\u001b[39msite_mask)\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:892\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._prep_sample_selection_cache_params\u001b[0;34m(self, sample_sets, sample_query, sample_query_options, sample_indices)\u001b[0m\n\u001b[1;32m 885\u001b[0m sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_sample_sets_param(sample_sets\u001b[38;5;241m=\u001b[39msample_sets)\n\u001b[1;32m 887\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_query \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 888\u001b[0m \u001b[38;5;66;03m# Resolve query to a list of integers for more cache hits - we\u001b[39;00m\n\u001b[1;32m 889\u001b[0m \u001b[38;5;66;03m# do this because there are different ways to write the same pandas\u001b[39;00m\n\u001b[1;32m 890\u001b[0m \u001b[38;5;66;03m# query, and so it's better to evaluate the query and use a list of\u001b[39;00m\n\u001b[1;32m 891\u001b[0m \u001b[38;5;66;03m# integer indices instead.\u001b[39;00m\n\u001b[0;32m--> 892\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 893\u001b[0m sample_query_options \u001b[38;5;241m=\u001b[39m sample_query_options \u001b[38;5;129;01mor\u001b[39;00m {}\n\u001b[1;32m 894\u001b[0m loc_samples \u001b[38;5;241m=\u001b[39m df_samples\u001b[38;5;241m.\u001b[39meval(sample_query, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39msample_query_options)\u001b[38;5;241m.\u001b[39mvalues\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:589\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 584\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_spinner(desc\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mLoad sample metadata\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n\u001b[1;32m 585\u001b[0m \u001b[38;5;66;03m## Build a single DataFrame using all available metadata.\u001b[39;00m\n\u001b[1;32m 586\u001b[0m \n\u001b[1;32m 587\u001b[0m \u001b[38;5;66;03m# Get the general sample metadata.\u001b[39;00m\n\u001b[1;32m 588\u001b[0m \u001b[38;5;66;03m# Note: this includes study and terms-of-use info.\u001b[39;00m\n\u001b[0;32m--> 589\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneral_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mprepped_sample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 591\u001b[0m \u001b[38;5;66;03m# Merge with the sequence QC metadata.\u001b[39;00m\n\u001b[1;32m 592\u001b[0m df_sequence_qc \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msequence_qc_metadata(\n\u001b[1;32m 593\u001b[0m sample_sets\u001b[38;5;241m=\u001b[39mprepped_sample_sets\n\u001b[1;32m 594\u001b[0m )\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:185\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.general_metadata\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 174\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 175\u001b[0m \u001b[38;5;129m@doc\u001b[39m(\n\u001b[1;32m 176\u001b[0m summary\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 183\u001b[0m \u001b[38;5;28mself\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 184\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m pd\u001b[38;5;241m.\u001b[39mDataFrame:\n\u001b[0;32m--> 185\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_metadata_paths\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 186\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath_template\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;132;43;01m{release_path}\u001b[39;49;00m\u001b[38;5;124;43m/metadata/general/\u001b[39;49m\u001b[38;5;132;43;01m{sample_set}\u001b[39;49;00m\u001b[38;5;124;43m/samples.meta.csv\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 187\u001b[0m \u001b[43m \u001b[49m\u001b[43mparse_metadata_func\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_general_metadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 188\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 189\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:119\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_metadata_paths\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 117\u001b[0m path \u001b[38;5;241m=\u001b[39m file_paths[sample_set]\n\u001b[1;32m 118\u001b[0m data \u001b[38;5;241m=\u001b[39m files[path]\n\u001b[0;32m--> 119\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[43mparse_metadata_func\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdata\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 120\u001b[0m dfs\u001b[38;5;241m.\u001b[39mappend(df)\n\u001b[1;32m 122\u001b[0m \u001b[38;5;66;03m# Concatenate all DataFrames.\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:160\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_general_metadata\u001b[0;34m(self, sample_set, data)\u001b[0m\n\u001b[1;32m 154\u001b[0m df[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mquarter\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m df\u001b[38;5;241m.\u001b[39mapply(\n\u001b[1;32m 155\u001b[0m \u001b[38;5;28;01mlambda\u001b[39;00m row: ((row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m) \u001b[38;5;241m/\u001b[39m\u001b[38;5;241m/\u001b[39m \u001b[38;5;241m3\u001b[39m) \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m,\n\u001b[1;32m 156\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcolumns\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 157\u001b[0m )\n\u001b[1;32m 159\u001b[0m \u001b[38;5;66;03m# Add study columns.\u001b[39;00m\n\u001b[0;32m--> 160\u001b[0m study_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlookup_study_info\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_set\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 161\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m column \u001b[38;5;129;01min\u001b[39;00m study_info:\n\u001b[1;32m 162\u001b[0m df[column] \u001b[38;5;241m=\u001b[39m study_info[column]\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:487\u001b[0m, in \u001b[0;36mAnophelesBase.lookup_study_info\u001b[0;34m(self, sample_set)\u001b[0m\n\u001b[1;32m 485\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 486\u001b[0m df_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets()\u001b[38;5;241m.\u001b[39mset_index(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 487\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;241m=\u001b[39m \u001b[43mdf_sample_sets\u001b[49m\u001b[43m[\u001b[49m\n\u001b[1;32m 488\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_id\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_url\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m 489\u001b[0m \u001b[43m \u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241m.\u001b[39mto_dict(orient\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 491\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info[sample_set]\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/frame.py:3766\u001b[0m, in \u001b[0;36mDataFrame.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 3764\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_iterator(key):\n\u001b[1;32m 3765\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 3766\u001b[0m indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcolumns\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_indexer_strict\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcolumns\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m[\u001b[38;5;241m1\u001b[39m]\n\u001b[1;32m 3768\u001b[0m \u001b[38;5;66;03m# take() does not accept boolean indexers\u001b[39;00m\n\u001b[1;32m 3769\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(indexer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdtype\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;241m==\u001b[39m \u001b[38;5;28mbool\u001b[39m:\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5876\u001b[0m, in \u001b[0;36mIndex._get_indexer_strict\u001b[0;34m(self, key, axis_name)\u001b[0m\n\u001b[1;32m 5873\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 5874\u001b[0m keyarr, indexer, new_indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_non_unique(keyarr)\n\u001b[0;32m-> 5876\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_raise_if_missing\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkeyarr\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindexer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis_name\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5878\u001b[0m keyarr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtake(indexer)\n\u001b[1;32m 5879\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(key, Index):\n\u001b[1;32m 5880\u001b[0m \u001b[38;5;66;03m# GH 42790 - Preserve name from an Index\u001b[39;00m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5935\u001b[0m, in \u001b[0;36mIndex._raise_if_missing\u001b[0;34m(self, key, indexer, axis_name)\u001b[0m\n\u001b[1;32m 5933\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m use_interval_msg:\n\u001b[1;32m 5934\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 5935\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNone of [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkey\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m] are in the [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00maxis_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m]\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 5937\u001b[0m not_found \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(ensure_index(key)[missing_mask\u001b[38;5;241m.\u001b[39mnonzero()[\u001b[38;5;241m0\u001b[39m]]\u001b[38;5;241m.\u001b[39munique())\n\u001b[1;32m 5938\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mnot_found\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m not in index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", + "\u001b[0;31mKeyError\u001b[0m: \"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"" + ] + } + ], "source": [ - "adir1.pca(region = \"KB672868\", n_snps = 100_000, " + "pca = adir1.pca(region = \"KB672868\", n_snps = 100_000, sample_query = \"country == 'Thailand'\")" ] } ], From b8ed3cba756c42365e9f2876847c4b3bb05451fd Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Thu, 12 Jun 2025 08:39:04 +1000 Subject: [PATCH 04/12] add annotation to commented out bit of metadata --- malariagen_data/anoph/sample_metadata.py | 34 +- notebooks/adir1_explore.ipynb | 522 ----------------------- 2 files changed, 18 insertions(+), 538 deletions(-) delete mode 100644 notebooks/adir1_explore.ipynb diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index ebe052de6..fc0d24540 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -589,29 +589,31 @@ def sample_metadata( # Note: this includes study and terms-of-use info. df_samples = self.general_metadata(sample_sets=prepped_sample_sets) + # Commented this out as it breaks some things - will fix + # Merge with the sequence QC metadata. - df_sequence_qc = self.sequence_qc_metadata( - sample_sets=prepped_sample_sets - ) + # df_sequence_qc = self.sequence_qc_metadata( + # sample_sets=prepped_sample_sets + # ) # Note: merging can change column dtypes - df_samples = df_samples.merge( - df_sequence_qc, on="sample_id", sort=False, how="left" - ) + # df_samples = df_samples.merge( + # df_sequence_qc, on="sample_id", sort=False, how="left" + # ) # If available, merge with the AIM metadata. - if self._aim_analysis: - df_aim = self.aim_metadata(sample_sets=prepped_sample_sets) - df_samples = df_samples.merge( - df_aim, on="sample_id", sort=False, how="left" - ) + # if self._aim_analysis: + # df_aim = self.aim_metadata(sample_sets=prepped_sample_sets) + # df_samples = df_samples.merge( + # df_aim, on="sample_id", sort=False, how="left" + # ) # If available, merge with the cohorts metadata. - if self._cohorts_analysis: - df_cohorts = self.cohorts_metadata(sample_sets=prepped_sample_sets) - df_samples = df_samples.merge( - df_cohorts, on="sample_id", sort=False, how="left" - ) + # if self._cohorts_analysis: + # df_cohorts = self.cohorts_metadata(sample_sets=prepped_sample_sets) + # df_samples = df_samples.merge( + # df_cohorts, on="sample_id", sort=False, how="left" + # ) # Store sample metadata in the cache. self._cache_sample_metadata[cache_key] = df_samples diff --git a/notebooks/adir1_explore.ipynb b/notebooks/adir1_explore.ipynb deleted file mode 100644 index 450596a2f..000000000 --- a/notebooks/adir1_explore.ipynb +++ /dev/null @@ -1,522 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import malariagen_data" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "application/javascript": [ - "'use strict';\n", - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " const force = true;\n", - "\n", - " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", - " root._bokeh_onload_callbacks = [];\n", - " root._bokeh_is_loading = undefined;\n", - " }\n", - "\n", - "const JS_MIME_TYPE = 'application/javascript';\n", - " const HTML_MIME_TYPE = 'text/html';\n", - " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", - " const CLASS_NAME = 'output_bokeh rendered_html';\n", - "\n", - " /**\n", - " * Render data to the DOM node\n", - " */\n", - " function render(props, node) {\n", - " const script = document.createElement(\"script\");\n", - " node.appendChild(script);\n", - " }\n", - "\n", - " /**\n", - " * Handle when an output is cleared or removed\n", - " */\n", - " function handleClearOutput(event, handle) {\n", - " function drop(id) {\n", - " const view = Bokeh.index.get_by_id(id)\n", - " if (view != null) {\n", - " view.model.document.clear()\n", - " Bokeh.index.delete(view)\n", - " }\n", - " }\n", - "\n", - " const cell = handle.cell;\n", - "\n", - " const id = cell.output_area._bokeh_element_id;\n", - " const server_id = cell.output_area._bokeh_server_id;\n", - "\n", - " // Clean up Bokeh references\n", - " if (id != null) {\n", - " drop(id)\n", - " }\n", - "\n", - " if (server_id !== undefined) {\n", - " // Clean up Bokeh references\n", - " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", - " cell.notebook.kernel.execute(cmd_clean, {\n", - " iopub: {\n", - " output: function(msg) {\n", - " const id = msg.content.text.trim()\n", - " drop(id)\n", - " }\n", - " }\n", - " });\n", - " // Destroy server and session\n", - " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", - " cell.notebook.kernel.execute(cmd_destroy);\n", - " }\n", - " }\n", - "\n", - " /**\n", - " * Handle when a new output is added\n", - " */\n", - " function handleAddOutput(event, handle) {\n", - " const output_area = handle.output_area;\n", - " const output = handle.output;\n", - "\n", - " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", - " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", - " return\n", - " }\n", - "\n", - " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", - "\n", - " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", - " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", - " // store reference to embed id on output_area\n", - " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", - " }\n", - " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", - " const bk_div = document.createElement(\"div\");\n", - " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", - " const script_attrs = bk_div.children[0].attributes;\n", - " for (let i = 0; i < script_attrs.length; i++) {\n", - " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", - " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", - " }\n", - " // store reference to server id on output_area\n", - " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", - " }\n", - " }\n", - "\n", - " function register_renderer(events, OutputArea) {\n", - "\n", - " function append_mime(data, metadata, element) {\n", - " // create a DOM node to render to\n", - " const toinsert = this.create_output_subarea(\n", - " metadata,\n", - " CLASS_NAME,\n", - " EXEC_MIME_TYPE\n", - " );\n", - " this.keyboard_manager.register_events(toinsert);\n", - " // Render to node\n", - " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", - " render(props, toinsert[toinsert.length - 1]);\n", - " element.append(toinsert);\n", - " return toinsert\n", - " }\n", - "\n", - " /* Handle when an output is cleared or removed */\n", - " events.on('clear_output.CodeCell', handleClearOutput);\n", - " events.on('delete.Cell', handleClearOutput);\n", - "\n", - " /* Handle when a new output is added */\n", - " events.on('output_added.OutputArea', handleAddOutput);\n", - "\n", - " /**\n", - " * Register the mime type and append_mime function with output_area\n", - " */\n", - " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", - " /* Is output safe? */\n", - " safe: true,\n", - " /* Index of renderer in `output_area.display_order` */\n", - " index: 0\n", - " });\n", - " }\n", - "\n", - " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", - " if (root.Jupyter !== undefined) {\n", - " const events = require('base/js/events');\n", - " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", - "\n", - " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", - " register_renderer(events, OutputArea);\n", - " }\n", - " }\n", - " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", - " root._bokeh_timeout = Date.now() + 5000;\n", - " root._bokeh_failed_load = false;\n", - " }\n", - "\n", - " const NB_LOAD_WARNING = {'data': {'text/html':\n", - " \"
\\n\"+\n", - " \"

\\n\"+\n", - " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", - " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", - " \"

\\n\"+\n", - " \"
    \\n\"+\n", - " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n", - " \"
  • use INLINE resources instead, as so:
  • \\n\"+\n", - " \"
\\n\"+\n", - " \"\\n\"+\n", - " \"from bokeh.resources import INLINE\\n\"+\n", - " \"output_notebook(resources=INLINE)\\n\"+\n", - " \"\\n\"+\n", - " \"
\"}};\n", - "\n", - " function display_loaded(error = null) {\n", - " const el = document.getElementById(null);\n", - " if (el != null) {\n", - " const html = (() => {\n", - " if (typeof root.Bokeh === \"undefined\") {\n", - " if (error == null) {\n", - " return \"BokehJS is loading ...\";\n", - " } else {\n", - " return \"BokehJS failed to load.\";\n", - " }\n", - " } else {\n", - " const prefix = `BokehJS ${root.Bokeh.version}`;\n", - " if (error == null) {\n", - " return `${prefix} successfully loaded.`;\n", - " } else {\n", - " return `${prefix} encountered errors while loading and may not function as expected.`;\n", - " }\n", - " }\n", - " })();\n", - " el.innerHTML = html;\n", - "\n", - " if (error != null) {\n", - " const wrapper = document.createElement(\"div\");\n", - " wrapper.style.overflow = \"auto\";\n", - " wrapper.style.height = \"5em\";\n", - " wrapper.style.resize = \"vertical\";\n", - " const content = document.createElement(\"div\");\n", - " content.style.fontFamily = \"monospace\";\n", - " content.style.whiteSpace = \"pre-wrap\";\n", - " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", - " content.textContent = error.stack ?? error.toString();\n", - " wrapper.append(content);\n", - " el.append(wrapper);\n", - " }\n", - " } else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(() => display_loaded(error), 100);\n", - " }\n", - " }\n", - "\n", - " function run_callbacks() {\n", - " try {\n", - " root._bokeh_onload_callbacks.forEach(function(callback) {\n", - " if (callback != null)\n", - " callback();\n", - " });\n", - " } finally {\n", - " delete root._bokeh_onload_callbacks\n", - " }\n", - " console.debug(\"Bokeh: all callbacks have finished\");\n", - " }\n", - "\n", - " function load_libs(css_urls, js_urls, callback) {\n", - " if (css_urls == null) css_urls = [];\n", - " if (js_urls == null) js_urls = [];\n", - "\n", - " root._bokeh_onload_callbacks.push(callback);\n", - " if (root._bokeh_is_loading > 0) {\n", - " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", - " return null;\n", - " }\n", - " if (js_urls == null || js_urls.length === 0) {\n", - " run_callbacks();\n", - " return null;\n", - " }\n", - " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", - " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", - "\n", - " function on_load() {\n", - " root._bokeh_is_loading--;\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", - " run_callbacks()\n", - " }\n", - " }\n", - "\n", - " function on_error(url) {\n", - " console.error(\"failed to load \" + url);\n", - " }\n", - "\n", - " for (let i = 0; i < css_urls.length; i++) {\n", - " const url = css_urls[i];\n", - " const element = document.createElement(\"link\");\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.rel = \"stylesheet\";\n", - " element.type = \"text/css\";\n", - " element.href = url;\n", - " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " for (let i = 0; i < js_urls.length; i++) {\n", - " const url = js_urls[i];\n", - " const element = document.createElement('script');\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.async = false;\n", - " element.src = url;\n", - " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", - " document.head.appendChild(element);\n", - " }\n", - " };\n", - "\n", - " function inject_raw_css(css) {\n", - " const element = document.createElement(\"style\");\n", - " element.appendChild(document.createTextNode(css));\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", - " const css_urls = [];\n", - "\n", - " const inline_js = [ function(Bokeh) {\n", - " Bokeh.set_log_level(\"info\");\n", - " },\n", - "function(Bokeh) {\n", - " }\n", - " ];\n", - "\n", - " function run_inline_js() {\n", - " if (root.Bokeh !== undefined || force === true) {\n", - " try {\n", - " for (let i = 0; i < inline_js.length; i++) {\n", - " inline_js[i].call(root, root.Bokeh);\n", - " }\n", - "\n", - " } catch (error) {throw error;\n", - " }} else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(run_inline_js, 100);\n", - " } else if (!root._bokeh_failed_load) {\n", - " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", - " root._bokeh_failed_load = true;\n", - " } else if (force !== true) {\n", - " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", - " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", - " }\n", - " }\n", - "\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", - " run_inline_js();\n", - " } else {\n", - " load_libs(css_urls, js_urls, function() {\n", - " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", - " run_inline_js();\n", - " });\n", - " }\n", - "}(window));" - ], - "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n \"
  • use INLINE resources instead, as so:
  • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/html": [ - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
MalariaGEN Adir1 API client
\n", - " Please note that data are subject to terms of use,\n", - " for more information see \n", - " the MalariaGEN website or contact support@malariagen.net.\n", - " See also the Adir1 API docs.\n", - "
\n", - " Storage URL\n", - " gs://vo_adir_production_us_central1/
\n", - " Data releases available\n", - " 1.x
\n", - " Results cache\n", - " /Users/dennistpw/Projects/malariagen_results
\n", - " Cohorts analysis\n", - " noneyet
\n", - " Site filters analysis\n", - " sc_20250610
\n", - " Software version\n", - " malariagen_data 13.3.0.post33+90e72d5a
\n", - " Client location\n", - " Queensland, Australia
\n", - " " - ], - "text/plain": [ - "\n", - "Storage URL : gs://vo_adir_production_us_central1/\n", - "Data releases available : 1.x\n", - "Results cache : /Users/dennistpw/Projects/malariagen_results\n", - "Site filters analysis : sc_20250610\n", - "Software version : malariagen_data 13.3.0.post33+90e72d5a\n", - "Client location : Queensland, Australia\n", - "---\n", - "Please note that data are subject to terms of use,\n", - "for more information see https://www.malariagen.net/data\n", - "or contact support@malariagen.net. For API documentation see \n", - "https://malariagen.github.io/malariagen-data-python/v13.3.0.post33+90e72d5a/Adir1.html" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# Init Adir1 API\n", - "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')\n", - "adir1" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - " \r" - ] - } - ], - "source": [ - "snps = adir1.snp_calls(region=\"KB672868:1000000-1010000\")" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "id": "e0489eab-e347-492d-88ce-97d61a0c0aba", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - " \r" - ] - }, - { - "ename": "KeyError", - "evalue": "\"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:581\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 579\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 580\u001b[0m \u001b[38;5;66;03m# Attempt to retrieve from the cache.\u001b[39;00m\n\u001b[0;32m--> 581\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_metadata\u001b[49m\u001b[43m[\u001b[49m\u001b[43mcache_key\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n", - "\u001b[0;31mKeyError\u001b[0m: ('1276-AD-BD-ALAM-VMF00156', '1277-VO-KH-WITKOWSKI-VMF00151', '1277-VO-KH-WITKOWSKI-VMF00183', '1278-VO-TH-KOBYLINSKI-VMF00153')", - "\nDuring handling of the above exception, another exception occurred:\n", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[10], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m pca \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpca\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mn_snps\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m100_000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcountry == \u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mThailand\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/pca.py:89\u001b[0m, in \u001b[0;36mAnophelesPca.pca\u001b[0;34m(self, region, n_snps, n_components, thin_offset, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, min_minor_ac, max_missing_an, cohort_size, min_cohort_size, max_cohort_size, exclude_samples, fit_exclude_samples, random_seed, inline_array, chunks)\u001b[0m\n\u001b[1;32m 83\u001b[0m name \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpca_v4\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 85\u001b[0m \u001b[38;5;66;03m# Normalize params for consistent hash value.\u001b[39;00m\n\u001b[1;32m 86\u001b[0m (\n\u001b[1;32m 87\u001b[0m sample_sets_prepped,\n\u001b[1;32m 88\u001b[0m sample_indices_prepped,\n\u001b[0;32m---> 89\u001b[0m ) \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_selection_cache_params\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 90\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 91\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 92\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 93\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 94\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 95\u001b[0m region_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_region_cache_param(region\u001b[38;5;241m=\u001b[39mregion)\n\u001b[1;32m 96\u001b[0m site_mask_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_optional_site_mask_param(site_mask\u001b[38;5;241m=\u001b[39msite_mask)\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:892\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._prep_sample_selection_cache_params\u001b[0;34m(self, sample_sets, sample_query, sample_query_options, sample_indices)\u001b[0m\n\u001b[1;32m 885\u001b[0m sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_sample_sets_param(sample_sets\u001b[38;5;241m=\u001b[39msample_sets)\n\u001b[1;32m 887\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_query \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 888\u001b[0m \u001b[38;5;66;03m# Resolve query to a list of integers for more cache hits - we\u001b[39;00m\n\u001b[1;32m 889\u001b[0m \u001b[38;5;66;03m# do this because there are different ways to write the same pandas\u001b[39;00m\n\u001b[1;32m 890\u001b[0m \u001b[38;5;66;03m# query, and so it's better to evaluate the query and use a list of\u001b[39;00m\n\u001b[1;32m 891\u001b[0m \u001b[38;5;66;03m# integer indices instead.\u001b[39;00m\n\u001b[0;32m--> 892\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 893\u001b[0m sample_query_options \u001b[38;5;241m=\u001b[39m sample_query_options \u001b[38;5;129;01mor\u001b[39;00m {}\n\u001b[1;32m 894\u001b[0m loc_samples \u001b[38;5;241m=\u001b[39m df_samples\u001b[38;5;241m.\u001b[39meval(sample_query, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39msample_query_options)\u001b[38;5;241m.\u001b[39mvalues\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:589\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 584\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_spinner(desc\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mLoad sample metadata\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n\u001b[1;32m 585\u001b[0m \u001b[38;5;66;03m## Build a single DataFrame using all available metadata.\u001b[39;00m\n\u001b[1;32m 586\u001b[0m \n\u001b[1;32m 587\u001b[0m \u001b[38;5;66;03m# Get the general sample metadata.\u001b[39;00m\n\u001b[1;32m 588\u001b[0m \u001b[38;5;66;03m# Note: this includes study and terms-of-use info.\u001b[39;00m\n\u001b[0;32m--> 589\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneral_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mprepped_sample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 591\u001b[0m \u001b[38;5;66;03m# Merge with the sequence QC metadata.\u001b[39;00m\n\u001b[1;32m 592\u001b[0m df_sequence_qc \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msequence_qc_metadata(\n\u001b[1;32m 593\u001b[0m sample_sets\u001b[38;5;241m=\u001b[39mprepped_sample_sets\n\u001b[1;32m 594\u001b[0m )\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:185\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.general_metadata\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 174\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 175\u001b[0m \u001b[38;5;129m@doc\u001b[39m(\n\u001b[1;32m 176\u001b[0m summary\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 183\u001b[0m \u001b[38;5;28mself\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 184\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m pd\u001b[38;5;241m.\u001b[39mDataFrame:\n\u001b[0;32m--> 185\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_metadata_paths\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 186\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath_template\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;132;43;01m{release_path}\u001b[39;49;00m\u001b[38;5;124;43m/metadata/general/\u001b[39;49m\u001b[38;5;132;43;01m{sample_set}\u001b[39;49;00m\u001b[38;5;124;43m/samples.meta.csv\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 187\u001b[0m \u001b[43m \u001b[49m\u001b[43mparse_metadata_func\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_general_metadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 188\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 189\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:119\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_metadata_paths\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 117\u001b[0m path \u001b[38;5;241m=\u001b[39m file_paths[sample_set]\n\u001b[1;32m 118\u001b[0m data \u001b[38;5;241m=\u001b[39m files[path]\n\u001b[0;32m--> 119\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[43mparse_metadata_func\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdata\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 120\u001b[0m dfs\u001b[38;5;241m.\u001b[39mappend(df)\n\u001b[1;32m 122\u001b[0m \u001b[38;5;66;03m# Concatenate all DataFrames.\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:160\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_general_metadata\u001b[0;34m(self, sample_set, data)\u001b[0m\n\u001b[1;32m 154\u001b[0m df[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mquarter\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m df\u001b[38;5;241m.\u001b[39mapply(\n\u001b[1;32m 155\u001b[0m \u001b[38;5;28;01mlambda\u001b[39;00m row: ((row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m) \u001b[38;5;241m/\u001b[39m\u001b[38;5;241m/\u001b[39m \u001b[38;5;241m3\u001b[39m) \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m,\n\u001b[1;32m 156\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcolumns\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 157\u001b[0m )\n\u001b[1;32m 159\u001b[0m \u001b[38;5;66;03m# Add study columns.\u001b[39;00m\n\u001b[0;32m--> 160\u001b[0m study_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlookup_study_info\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_set\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 161\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m column \u001b[38;5;129;01min\u001b[39;00m study_info:\n\u001b[1;32m 162\u001b[0m df[column] \u001b[38;5;241m=\u001b[39m study_info[column]\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:487\u001b[0m, in \u001b[0;36mAnophelesBase.lookup_study_info\u001b[0;34m(self, sample_set)\u001b[0m\n\u001b[1;32m 485\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 486\u001b[0m df_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets()\u001b[38;5;241m.\u001b[39mset_index(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 487\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;241m=\u001b[39m \u001b[43mdf_sample_sets\u001b[49m\u001b[43m[\u001b[49m\n\u001b[1;32m 488\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_id\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_url\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m 489\u001b[0m \u001b[43m \u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241m.\u001b[39mto_dict(orient\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 491\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info[sample_set]\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/frame.py:3766\u001b[0m, in \u001b[0;36mDataFrame.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 3764\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_iterator(key):\n\u001b[1;32m 3765\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 3766\u001b[0m indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcolumns\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_indexer_strict\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcolumns\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m[\u001b[38;5;241m1\u001b[39m]\n\u001b[1;32m 3768\u001b[0m \u001b[38;5;66;03m# take() does not accept boolean indexers\u001b[39;00m\n\u001b[1;32m 3769\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(indexer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdtype\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;241m==\u001b[39m \u001b[38;5;28mbool\u001b[39m:\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5876\u001b[0m, in \u001b[0;36mIndex._get_indexer_strict\u001b[0;34m(self, key, axis_name)\u001b[0m\n\u001b[1;32m 5873\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 5874\u001b[0m keyarr, indexer, new_indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_non_unique(keyarr)\n\u001b[0;32m-> 5876\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_raise_if_missing\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkeyarr\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindexer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis_name\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5878\u001b[0m keyarr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtake(indexer)\n\u001b[1;32m 5879\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(key, Index):\n\u001b[1;32m 5880\u001b[0m \u001b[38;5;66;03m# GH 42790 - Preserve name from an Index\u001b[39;00m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5935\u001b[0m, in \u001b[0;36mIndex._raise_if_missing\u001b[0;34m(self, key, indexer, axis_name)\u001b[0m\n\u001b[1;32m 5933\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m use_interval_msg:\n\u001b[1;32m 5934\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 5935\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNone of [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkey\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m] are in the [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00maxis_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m]\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 5937\u001b[0m not_found \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(ensure_index(key)[missing_mask\u001b[38;5;241m.\u001b[39mnonzero()[\u001b[38;5;241m0\u001b[39m]]\u001b[38;5;241m.\u001b[39munique())\n\u001b[1;32m 5938\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mnot_found\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m not in index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", - "\u001b[0;31mKeyError\u001b[0m: \"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"" - ] - } - ], - "source": [ - "pca = adir1.pca(region = \"KB672868\", n_snps = 100_000, sample_query = \"country == 'Thailand'\")" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.10" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} From 57a9b42a4af550057d3a0986e037b4ed5b9e4ca6 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Sun, 15 Jun 2025 22:28:15 -0500 Subject: [PATCH 05/12] forgot how the alphabet works d'oh --- malariagen_data/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/malariagen_data/__init__.py b/malariagen_data/__init__.py index 6bc938825..306896658 100644 --- a/malariagen_data/__init__.py +++ b/malariagen_data/__init__.py @@ -1,6 +1,6 @@ # flake8: noqa -from .af1 import Af1 from .adir1 import Adir1 +from .af1 import Af1 from .ag3 import Ag3 from .amin1 import Amin1 from .anopheles import AnophelesDataResource, Region From ced92247eefea9316d38feb4084d010b01f0f04c Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Mon, 16 Jun 2025 20:35:38 -0500 Subject: [PATCH 06/12] add hashing to roh function --- malariagen_data/adir1.py | 6 +- malariagen_data/anopheles.py | 71 +++++-- poetry.lock | 402 ++++++++++++----------------------- pyproject.toml | 1 + 4 files changed, 193 insertions(+), 287 deletions(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index 9b053ca62..c24562426 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -102,9 +102,9 @@ def __init__( aim_palettes=None, site_filters_analysis=site_filters_analysis, discordant_read_calls_analysis=discordant_read_calls_analysis, - default_site_mask="funestus", - default_phasing_analysis="funestus", - default_coverage_calls_analysis="funestus", + default_site_mask="dirus", + default_phasing_analysis="dirus", + default_coverage_calls_analysis="dirus", bokeh_output_notebook=bokeh_output_notebook, results_cache=results_cache, log=log, diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py index 0aec9bd9a..87b42a9e5 100644 --- a/malariagen_data/anopheles.py +++ b/malariagen_data/anopheles.py @@ -572,31 +572,68 @@ def roh_hmm( debug = self._log.debug resolved_region: Region = parse_single_region(self, region) - del region - debug("compute windowed heterozygosity") - sample_id, sample_set, windows, counts = self._sample_count_het( + name = "roh" + + params = dict( sample=sample, - region=resolved_region, - site_mask=site_mask, + region=region, window_size=window_size, + site_mask=site_mask, sample_set=sample_set, - chunks=chunks, - inline_array=inline_array, - ) - - debug("compute runs of homozygosity") - df_roh = self._roh_hmm_predict( - windows=windows, - counts=counts, phet_roh=phet_roh, phet_nonroh=phet_nonroh, transition=transition, - window_size=window_size, - sample_id=sample_id, - contig=resolved_region.contig, + chunks=chunks, + inline_array=inline_array, ) + del region + + try: + # Load cached numeric data, adding str / obj data again. + results = self.results_cache_get(name=name, params=params) + df_roh = pd.DataFrame(results) + df_roh["sample_id"] = sample + df_roh["contig"] = resolved_region.contig + + except CacheMiss: + debug("compute windowed heterozygosity") + sample_id, sample_set, windows, counts = self._sample_count_het( + sample=sample, + region=resolved_region, + site_mask=site_mask, + window_size=window_size, + sample_set=sample_set, + chunks=chunks, + inline_array=inline_array, + ) + + debug("compute runs of homozygosity") + df_roh = self._roh_hmm_predict( + windows=windows, + counts=counts, + phet_roh=phet_roh, + phet_nonroh=phet_nonroh, + transition=transition, + window_size=window_size, + sample_id=sample_id, + contig=resolved_region.contig, + ) + + # Specify numeric columns to save (saving obj - sample ID and contig - breaks the save. + columns_to_save = [ + "roh_start", + "roh_stop", + "roh_length", + "roh_is_marginal", + ] + self.results_cache_set( + name=name, + params=params, + results={col: df_roh[col].to_numpy() for col in columns_to_save}, + ) + return df_roh @check_types @@ -1304,7 +1341,7 @@ def ihs_gwss( ) -> Tuple[np.ndarray, np.ndarray]: # change this name if you ever change the behaviour of this function, to # invalidate any previously cached data - name = self._ihs_gwss_cache_name + name = "roh" params = dict( contig=contig, diff --git a/poetry.lock b/poetry.lock index 619febcb1..d02d5c5bc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. [[package]] name = "accessible-pygments" @@ -7,7 +7,7 @@ description = "A collection of accessible pygments styles" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "accessible_pygments-0.0.5-py3-none-any.whl", hash = "sha256:88ae3211e68a1d0b011504b2ffc1691feafce124b845bd072ab6f9f66f34d4b7"}, {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"}, @@ -27,7 +27,6 @@ description = "Async client for aws services using botocore and aiohttp" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "aiobotocore-2.15.2-py3-none-any.whl", hash = "sha256:d4d3128b4b558e2b4c369bfa963b022d7e87303adb82eec623cec8aa77ae578a"}, {file = "aiobotocore-2.15.2.tar.gz", hash = "sha256:9ac1cfcaccccc80602968174aa032bf978abe36bd4e55e6781d6500909af1375"}, @@ -50,7 +49,6 @@ description = "Happy Eyeballs for asyncio" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "aiohappyeyeballs-2.4.4-py3-none-any.whl", hash = "sha256:a980909d50efcd44795c4afeca523296716d50cd756ddca6af8c65b996e27de8"}, {file = "aiohappyeyeballs-2.4.4.tar.gz", hash = "sha256:5fdd7d87889c63183afc18ce9271f9b0a7d32c2303e394468dd45d514a757745"}, @@ -63,7 +61,6 @@ description = "Async http client/server framework (asyncio)" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "aiohttp-3.11.9-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:0411777249f25d11bd2964a230b3ffafcbed6cd65d0f2b132bc2b8f5b8c347c7"}, {file = "aiohttp-3.11.9-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:499368eb904566fbdf1a3836a1532000ef1308f34a1bcbf36e6351904cced771"}, @@ -154,7 +151,7 @@ propcache = ">=0.2.0" yarl = ">=1.17.0,<2.0" [package.extras] -speedups = ["Brotli", "aiodns (>=3.2.0)", "brotlicffi"] +speedups = ["Brotli ; platform_python_implementation == \"CPython\"", "aiodns (>=3.2.0) ; sys_platform == \"linux\" or sys_platform == \"darwin\"", "brotlicffi ; platform_python_implementation != \"CPython\""] [[package]] name = "aioitertools" @@ -163,7 +160,6 @@ description = "itertools and builtins for AsyncIO and mixed iterables" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "aioitertools-0.12.0-py3-none-any.whl", hash = "sha256:fc1f5fac3d737354de8831cbba3eb04f79dd649d8f3afb4c5b114925e662a796"}, {file = "aioitertools-0.12.0.tar.gz", hash = "sha256:c2a9055b4fbb7705f561b9d86053e8af5d10cc845d22c32008c43490b2d8dd6b"}, @@ -180,7 +176,6 @@ description = "aiosignal: a list of registered asynchronous callbacks" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "aiosignal-1.3.1-py3-none-any.whl", hash = "sha256:f8376fb07dd1e86a584e4fcdec80b36b7f81aac666ebc724e2c090300dd83b17"}, {file = "aiosignal-1.3.1.tar.gz", hash = "sha256:54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc"}, @@ -196,7 +191,7 @@ description = "A light, configurable Sphinx theme" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "alabaster-1.0.0-py3-none-any.whl", hash = "sha256:fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b"}, {file = "alabaster-1.0.0.tar.gz", hash = "sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e"}, @@ -209,7 +204,6 @@ description = "A neighbour-joining library for Python." optional = false python-versions = "<3.13,>=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "anjl-1.4.0-py3-none-any.whl", hash = "sha256:062d9b6d3d565a61a0b691fa6ae1e268e28a9ef2271d12259c1b6d42b0a1abea"}, {file = "anjl-1.4.0.tar.gz", hash = "sha256:830d6b6233d3bc9cd5631da7a8ee798e348949a07429fae87e492659b5960fba"}, @@ -233,7 +227,7 @@ description = "High level compatibility layer for multiple asynchronous event lo optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "anyio-4.6.2.post1-py3-none-any.whl", hash = "sha256:6d170c36fba3bdd840c73d3868c1e777e33676a69c3a72cf0a0d5d6d8009b61d"}, {file = "anyio-4.6.2.post1.tar.gz", hash = "sha256:4c8bc31ccdb51c7f7bd251f51c609e038d63e34219b44aa86e47576389880b4c"}, @@ -247,7 +241,7 @@ typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21.0b1)"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "truststore (>=0.9.1) ; python_version >= \"3.10\"", "uvloop (>=0.21.0b1) ; platform_python_implementation == \"CPython\" and platform_system != \"Windows\""] trio = ["trio (>=0.26.1)"] [[package]] @@ -257,7 +251,7 @@ description = "Disable App Nap on macOS >= 10.9" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" and platform_system == \"Darwin\" or python_version >= \"3.12\" and platform_system == \"Darwin\"" +markers = "platform_system == \"Darwin\"" files = [ {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"}, {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"}, @@ -270,7 +264,7 @@ description = "Argon2 for Python" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "argon2_cffi-23.1.0-py3-none-any.whl", hash = "sha256:c670642b78ba29641818ab2e68bd4e6a78ba53b7eff7b4c3815ae16abf91c7ea"}, {file = "argon2_cffi-23.1.0.tar.gz", hash = "sha256:879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08"}, @@ -292,7 +286,7 @@ description = "Low-level CFFI bindings for Argon2" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "argon2-cffi-bindings-21.2.0.tar.gz", hash = "sha256:bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3"}, {file = "argon2_cffi_bindings-21.2.0-cp36-abi3-macosx_10_9_x86_64.whl", hash = "sha256:ccb949252cb2ab3a08c02024acb77cfb179492d5701c7cbdbfd776124d4d2367"}, @@ -331,7 +325,7 @@ description = "Better dates & times for Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"}, {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"}, @@ -352,7 +346,6 @@ description = "Draws ASCII trees." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "asciitree-0.3.3.tar.gz", hash = "sha256:4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e"}, ] @@ -364,7 +357,6 @@ description = "Annotate AST trees with source code positions" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"}, {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"}, @@ -381,7 +373,7 @@ description = "Simple LRU cache for asyncio" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "async-lru-2.0.4.tar.gz", hash = "sha256:b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627"}, {file = "async_lru-2.0.4-py3-none-any.whl", hash = "sha256:ff02944ce3c288c5be660c42dbcca0742b32c3b279d6dceda655190240b99224"}, @@ -397,7 +389,7 @@ description = "Timeout context manager for asyncio programs" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "async_timeout-5.0.1-py3-none-any.whl", hash = "sha256:39e3809566ff85354557ec2398b55e096c8364bacac9405a7a1fa429e77fe76c"}, {file = "async_timeout-5.0.1.tar.gz", hash = "sha256:d9321a7a3d5a6a5e187e824d2fa0793ce379a202935782d555d6e9d2735677d3"}, @@ -410,19 +402,18 @@ description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, ] [package.extras] -benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +benchmark = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\"", "pytest-xdist[psutil]"] +cov = ["cloudpickle ; platform_python_implementation == \"CPython\"", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\"", "pytest-xdist[psutil]"] +dev = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\"", "pytest-xdist[psutil]"] docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"] -tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] +tests = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\"", "pytest-xdist[psutil]"] +tests-mypy = ["mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\""] [[package]] name = "babel" @@ -431,7 +422,7 @@ description = "Internationalization utilities" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"}, {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"}, @@ -447,7 +438,7 @@ description = "Screen-scraping library" optional = false python-versions = ">=3.6.0" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"}, {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"}, @@ -470,7 +461,6 @@ description = "Read and write the PLINK BED format, simply and efficiently." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "bed_reader-1.0.6-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:5f2e812dea71cf9aebbf8b1bf00149600948fdbf4bbdb8805c4a4ed4b1597aba"}, {file = "bed_reader-1.0.6-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:7753e3e9dcd4210aadfc071ece22264c4fef1bd53b31d34bd63ce11f217954d5"}, @@ -512,7 +502,6 @@ description = "Freely available tools for computational molecular biology." optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "biopython-1.84-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:3c8beded38884abae4c74cb6ce54142da670273fd0b2919bd0f84f6e34d3056b"}, {file = "biopython-1.84-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:b51ef31bfb79872a182a85b4113625e1b553c024bb1586c72ac98b479f8d8fe4"}, @@ -551,7 +540,7 @@ description = "An easy safelist-based HTML-sanitizing tool." optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "bleach-6.2.0-py3-none-any.whl", hash = "sha256:117d9c6097a7c3d22fd578fcd8d35ff1e125df6736f554da4e432fdd63f31e5e"}, {file = "bleach-6.2.0.tar.gz", hash = "sha256:123e894118b8a599fd80d3ec1a6d4cc7ce4e5882b1317a7e1ba69b56e95f991f"}, @@ -570,7 +559,6 @@ description = "Fast, simple object-to-object and broadcast signaling" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "blinker-1.9.0-py3-none-any.whl", hash = "sha256:ba0efaa9080b619ff2f3459d1d500c57bddea4a6b424b60a91141db6fd2f08bc"}, {file = "blinker-1.9.0.tar.gz", hash = "sha256:b4ce2265a7abece45e7cc896e98dbebe6cead56bcf805a3d23136d145f5445bf"}, @@ -583,7 +571,6 @@ description = "Interactive plots and applications in the browser from Python" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "bokeh-3.6.2-py3-none-any.whl", hash = "sha256:fddc4b91f8b40178c0e3e83dfcc33886d7803a3a1f041a840834255e435a18c2"}, {file = "bokeh-3.6.2.tar.gz", hash = "sha256:2f3043d9ecb3d5dc2e8c0ebf8ad55727617188d4e534f3e7208b36357e352396"}, @@ -607,7 +594,6 @@ description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "botocore-1.35.36-py3-none-any.whl", hash = "sha256:64241c778bf2dc863d93abab159e14024d97a926a5715056ef6411418cb9ead3"}, {file = "botocore-1.35.36.tar.gz", hash = "sha256:354ec1b766f0029b5d6ff0c45d1a0f9e5007b7d2f3ec89bcdd755b208c5bc797"}, @@ -628,7 +614,6 @@ description = "Generate complex HTML+JS pages with Python" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "branca-0.8.0-py3-none-any.whl", hash = "sha256:e78d5be39c8799a42e5c2dd1145a797a3cefc099537907bc1e4c43b6b55f7fa4"}, {file = "branca-0.8.0.tar.gz", hash = "sha256:1f8fd0d2f3b7548f2c146093932be5d3064ba21eee6cebf92d416b7f9092324f"}, @@ -644,7 +629,6 @@ description = "Extensible memoizing collections and decorators" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "cachetools-5.5.0-py3-none-any.whl", hash = "sha256:02134e8439cdc2ffb62023ce1debca2944c3f289d66bb17ead3ab3dede74b292"}, {file = "cachetools-5.5.0.tar.gz", hash = "sha256:2cc24fb4cbe39633fb7badd9db9ca6295d766d9c2995f245725a46715d050f2a"}, @@ -657,7 +641,6 @@ description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"}, {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"}, @@ -670,7 +653,7 @@ description = "Foreign Function Interface for Python calling C code." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and implementation_name == \"pypy\" or python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and implementation_name == \"pypy\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "implementation_name == \"pypy\" or extra == \"dev\"" files = [ {file = "cffi-1.17.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:df8b1c11f177bc2313ec4b2d46baec87a5f3e71fc8b45dab2ee7cae86d9aba14"}, {file = "cffi-1.17.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8f2cdc858323644ab277e9bb925ad72ae0e67f69e804f4898c070998d50b1a67"}, @@ -751,7 +734,7 @@ description = "Validate configuration and produce human readable error messages. optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, @@ -764,7 +747,6 @@ description = "The Real First Universal Charset Detector. Open, modern and activ optional = false python-versions = ">=3.7.0" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "charset_normalizer-3.4.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:4f9fc98dad6c2eaa32fc3af1417d95b5e3d08aff968df0cd320066def971f9a6"}, {file = "charset_normalizer-3.4.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0de7b687289d3c1b3e8660d0741874abe7888100efe14bd0f9fd7141bcbda92b"}, @@ -880,7 +862,6 @@ description = "Composable command line interface toolkit" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"}, {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"}, @@ -896,7 +877,6 @@ description = "Pickler class to extend the standard pickle.Pickler functionality optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "cloudpickle-3.1.0-py3-none-any.whl", hash = "sha256:fe11acda67f61aaaec473e3afe030feb131d78a43461b718185363384f1ba12e"}, {file = "cloudpickle-3.1.0.tar.gz", hash = "sha256:81a929b6e3c7335c863c771d673d105f02efdb89dfaba0c90495d1c64796601b"}, @@ -909,7 +889,7 @@ description = "Cross-platform colored terminal text." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" groups = ["main"] -markers = "python_version <= \"3.11\" and platform_system == \"Windows\" or python_version <= \"3.11\" and sys_platform == \"win32\" or python_version >= \"3.12\" and platform_system == \"Windows\" or python_version >= \"3.12\" and sys_platform == \"win32\"" +markers = "platform_system == \"Windows\" or sys_platform == \"win32\"" files = [ {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}, {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, @@ -922,7 +902,6 @@ description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus- optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "comm-0.2.2-py3-none-any.whl", hash = "sha256:e6fb86cb70ff661ee8c9c14e7d36d6de3b4066f1441be4063df9c5009f0a64d3"}, {file = "comm-0.2.2.tar.gz", hash = "sha256:3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e"}, @@ -941,7 +920,6 @@ description = "Python library for calculating contours of 2D quadrilateral grids optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "contourpy-1.3.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a045f341a77b77e1c5de31e74e966537bba9f3c4099b35bf4c2e3939dd54cdab"}, {file = "contourpy-1.3.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:500360b77259914f7805af7462e41f9cb7ca92ad38e9f94d6c8641b089338124"}, @@ -1016,7 +994,7 @@ description = "Code coverage measurement for Python" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "coverage-7.6.8-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b39e6011cd06822eb964d038d5dff5da5d98652b81f5ecd439277b32361a3a50"}, {file = "coverage-7.6.8-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:63c19702db10ad79151a059d2d6336fe0c470f2e18d0d4d1a57f7f9713875dcf"}, @@ -1086,7 +1064,7 @@ files = [ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""} [package.extras] -toml = ["tomli"] +toml = ["tomli ; python_full_version <= \"3.11.0a6\""] [[package]] name = "dash" @@ -1095,7 +1073,6 @@ description = "A Python framework for building reactive web-apps. Developed by P optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "dash-2.18.2-py3-none-any.whl", hash = "sha256:0ce0479d1bc958e934630e2de7023b8a4558f23ce1f9f5a4b34b65eb3903a869"}, {file = "dash-2.18.2.tar.gz", hash = "sha256:20e8404f73d0fe88ce2eae33c25bbc513cbe52f30d23a401fa5f24dbb44296c8"}, @@ -1130,7 +1107,6 @@ description = "Core component suite for Dash" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "dash_core_components-2.0.0-py3-none-any.whl", hash = "sha256:52b8e8cce13b18d0802ee3acbc5e888cb1248a04968f962d63d070400af2e346"}, {file = "dash_core_components-2.0.0.tar.gz", hash = "sha256:c6733874af975e552f95a1398a16c2ee7df14ce43fa60bb3718a3c6e0b63ffee"}, @@ -1143,7 +1119,6 @@ description = "A Component Library for Dash aimed at facilitating network visual optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "dash_cytoscape-1.0.2.tar.gz", hash = "sha256:a61019d2184d63a2b3b5c06d056d3b867a04223a674cc3c7cf900a561a9a59aa"}, ] @@ -1161,7 +1136,6 @@ description = "Vanilla HTML components for Dash" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "dash_html_components-2.0.0-py3-none-any.whl", hash = "sha256:b42cc903713c9706af03b3f2548bda4be7307a7cf89b7d6eae3da872717d1b63"}, {file = "dash_html_components-2.0.0.tar.gz", hash = "sha256:8703a601080f02619a6390998e0b3da4a5daabe97a1fd7a9cebc09d015f26e50"}, @@ -1174,7 +1148,6 @@ description = "Dash table" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "dash_table-5.0.0-py3-none-any.whl", hash = "sha256:19036fa352bb1c11baf38068ec62d172f0515f73ca3276c79dee49b95ddc16c9"}, {file = "dash_table-5.0.0.tar.gz", hash = "sha256:18624d693d4c8ef2ddec99a6f167593437a7ea0bf153aa20f318c170c5bc7308"}, @@ -1187,7 +1160,6 @@ description = "Parallel PyData with Task Scheduling" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "dask-2024.12.0-py3-none-any.whl", hash = "sha256:e038e87b9f06e7927b81ecde6cf2b49aa699bb902fec11abba5697cb48baeb8d"}, {file = "dask-2024.12.0.tar.gz", hash = "sha256:ffd02b06ac06b993df0b48e0ba4fe02abceb5c8b34b40bd91d63f33ec7a272a4"}, @@ -1219,7 +1191,6 @@ description = "An implementation of the Debug Adapter Protocol for Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "debugpy-1.8.9-cp310-cp310-macosx_14_0_x86_64.whl", hash = "sha256:cfe1e6c6ad7178265f74981edf1154ffce97b69005212fbc90ca22ddfe3d017e"}, {file = "debugpy-1.8.9-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ada7fb65102a4d2c9ab62e8908e9e9f12aed9d76ef44880367bc9308ebe49a0f"}, @@ -1256,7 +1227,7 @@ description = "Create decorators easily in python." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "decopatch-1.4.10-py2.py3-none-any.whl", hash = "sha256:e151f7f93de2b1b3fd3f3272dcc7cefd1a69f68ec1c2d8e288ecd9deb36dc5f7"}, {file = "decopatch-1.4.10.tar.gz", hash = "sha256:957f49c93f4150182c23f8fb51d13bb3213e0f17a79e09c8cca7057598b55720"}, @@ -1272,7 +1243,6 @@ description = "Decorators for Humans" optional = false python-versions = ">=3.5" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"}, {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"}, @@ -1285,7 +1255,7 @@ description = "XML bomb protection for Python stdlib modules" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "defusedxml-0.7.1-py2.py3-none-any.whl", hash = "sha256:a352e7e428770286cc899e2542b6cdaedb2b4953ff269a210103ec58f6198a61"}, {file = "defusedxml-0.7.1.tar.gz", hash = "sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69"}, @@ -1298,7 +1268,7 @@ description = "Distribution utilities" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "distlib-0.3.9-py2.py3-none-any.whl", hash = "sha256:47f8c22fd27c27e25a65601af709b38e4f0a45ea4fc2e710f65755fa8caaaf87"}, {file = "distlib-0.3.9.tar.gz", hash = "sha256:a60f20dea646b8a33f3e7772f74dc0b2d0772d2837ee1342a00645c81edf9403"}, @@ -1311,7 +1281,6 @@ description = "Distributed scheduler for Dask" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "distributed-2024.12.0-py3-none-any.whl", hash = "sha256:ed05aa13b6c62b69b33d1ba7d1ca95e78406c8f37163fafd07f7ca94ae036b66"}, {file = "distributed-2024.12.0.tar.gz", hash = "sha256:6a2c04e63d31973ee3c1f2160d66521ed8f08e637d6a25a450e7561582920f38"}, @@ -1341,7 +1310,7 @@ description = "Docutils -- Python Documentation Utilities" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "docutils-0.21.2-py3-none-any.whl", hash = "sha256:dafca5b9e384f0e419294eb4d2ff9fa826435bf15f15b7bd45723e8ad76811b2"}, {file = "docutils-0.21.2.tar.gz", hash = "sha256:3a6b18732edf182daa3cd12775bbb338cf5691468f91eeeb109deff6ebfa986f"}, @@ -1354,7 +1323,7 @@ description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"}, {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"}, @@ -1370,7 +1339,7 @@ description = "execnet: rapid multi-Python deployment" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "execnet-2.1.1-py3-none-any.whl", hash = "sha256:26dee51f1b80cebd6d0ca8e74dd8745419761d3bef34163928cbebbdc4749fdc"}, {file = "execnet-2.1.1.tar.gz", hash = "sha256:5189b52c6121c24feae288166ab41b32549c7e2348652736540b9e6e7d4e72e3"}, @@ -1386,14 +1355,13 @@ description = "Get the currently executing AST node of a frame, and other inform optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "executing-2.1.0-py2.py3-none-any.whl", hash = "sha256:8d63781349375b5ebccc3142f4b30350c0cd9c79f921cde38be2be4637e98eaf"}, {file = "executing-2.1.0.tar.gz", hash = "sha256:8ea27ddd260da8150fa5a708269c4a10e76161e2496ec3e587da9e3c0fe4b9ab"}, ] [package.extras] -tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"] +tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich ; python_version >= \"3.11\""] [[package]] name = "fasteners" @@ -1402,7 +1370,7 @@ description = "A python package that provides useful locks" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" and sys_platform != \"emscripten\" or python_version >= \"3.12\" and sys_platform != \"emscripten\"" +markers = "sys_platform != \"emscripten\"" files = [ {file = "fasteners-0.19-py3-none-any.whl", hash = "sha256:758819cb5d94cdedf4e836988b74de396ceacb8e2794d21f82d131fd9ee77237"}, {file = "fasteners-0.19.tar.gz", hash = "sha256:b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c"}, @@ -1415,7 +1383,7 @@ description = "Fastest Python implementation of JSON schema" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "fastjsonschema-2.21.1-py3-none-any.whl", hash = "sha256:c9e5b7e908310918cf494a434eeb31384dd84a98b57a30bcb1f535015b554667"}, {file = "fastjsonschema-2.21.1.tar.gz", hash = "sha256:794d4f0a58f848961ba16af7b9c85a3e88cd360df008c59aac6fc5ae9323b5d4"}, @@ -1431,7 +1399,7 @@ description = "A platform independent file lock." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "filelock-3.16.1-py3-none-any.whl", hash = "sha256:2082e5703d51fbf98ea75855d9d5527e33d8ff23099bec374a134febee6946b0"}, {file = "filelock-3.16.1.tar.gz", hash = "sha256:c249fbfcd5db47e5e2d6d62198e565475ee65e4831e2561c8e313fa7eb961435"}, @@ -1440,7 +1408,7 @@ files = [ [package.extras] docs = ["furo (>=2024.8.6)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4.1)"] testing = ["covdefaults (>=2.3)", "coverage (>=7.6.1)", "diff-cover (>=9.2)", "pytest (>=8.3.3)", "pytest-asyncio (>=0.24)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.26.4)"] -typing = ["typing-extensions (>=4.12.2)"] +typing = ["typing-extensions (>=4.12.2) ; python_version < \"3.11\""] [[package]] name = "flask" @@ -1449,7 +1417,6 @@ description = "A simple framework for building complex web applications." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "flask-3.0.3-py3-none-any.whl", hash = "sha256:34e815dfaa43340d1d15a5c3a02b8476004037eb4840b34910c6e21679d288f3"}, {file = "flask-3.0.3.tar.gz", hash = "sha256:ceb27b0af3823ea2737928a4d99d125a06175b8512c445cbd9a9ce200ef76842"}, @@ -1473,7 +1440,7 @@ description = "Validates fully-qualified domain names against RFC 1123, so that optional = false python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "fqdn-1.5.1-py3-none-any.whl", hash = "sha256:3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014"}, {file = "fqdn-1.5.1.tar.gz", hash = "sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f"}, @@ -1486,7 +1453,6 @@ description = "A list-like structure which implements collections.abc.MutableSeq optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "frozenlist-1.5.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:5b6a66c18b5b9dd261ca98dffcb826a525334b2f29e7caa54e182255c5f6a65a"}, {file = "frozenlist-1.5.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d1b3eb7b05ea246510b43a7e53ed1653e55c2121019a97e60cad7efb881a97bb"}, @@ -1589,7 +1555,6 @@ description = "File-system specification" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "fsspec-2024.10.0-py3-none-any.whl", hash = "sha256:03b9a6785766a4de40368b88906366755e2819e758b83705c88cd7cb5fe81871"}, {file = "fsspec-2024.10.0.tar.gz", hash = "sha256:eda2d8a4116d4f2429db8550f2457da57279247dd930bb12f821b58391359493"}, @@ -1630,7 +1595,6 @@ description = "Convenient Filesystem interface over GCS" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "gcsfs-2024.10.0-py2.py3-none-any.whl", hash = "sha256:bb2d23547e61203ea2dda5fa6c4b91a0c34b74ebe8bb6ab1926f6c33381bceb2"}, {file = "gcsfs-2024.10.0.tar.gz", hash = "sha256:5df54cfe568e8fdeea5aafa7fed695cdc69a9a674e991ca8c1ce634f5df1d314"}, @@ -1656,7 +1620,6 @@ description = "Google API client core library" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google_api_core-2.23.0-py3-none-any.whl", hash = "sha256:c20100d4c4c41070cf365f1d8ddf5365915291b5eb11b83829fbd1c999b5122f"}, {file = "google_api_core-2.23.0.tar.gz", hash = "sha256:2ceb087315e6af43f256704b871d99326b1f12a9d6ce99beaedec99ba26a0ace"}, @@ -1671,7 +1634,7 @@ requests = ">=2.18.0,<3.0.0.dev0" [package.extras] async-rest = ["google-auth[aiohttp] (>=2.35.0,<3.0.dev0)"] -grpc = ["grpcio (>=1.33.2,<2.0dev)", "grpcio (>=1.49.1,<2.0dev)", "grpcio-status (>=1.33.2,<2.0.dev0)", "grpcio-status (>=1.49.1,<2.0.dev0)"] +grpc = ["grpcio (>=1.33.2,<2.0dev)", "grpcio (>=1.49.1,<2.0dev) ; python_version >= \"3.11\"", "grpcio-status (>=1.33.2,<2.0.dev0)", "grpcio-status (>=1.49.1,<2.0.dev0) ; python_version >= \"3.11\""] grpcgcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"] grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"] @@ -1682,7 +1645,6 @@ description = "Google Authentication Library" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google_auth-2.36.0-py2.py3-none-any.whl", hash = "sha256:51a15d47028b66fd36e5c64a82d2d57480075bccc7da37cde257fc94177a61fb"}, {file = "google_auth-2.36.0.tar.gz", hash = "sha256:545e9618f2df0bcbb7dcbc45a546485b1212624716975a1ea5ae8149ce769ab1"}, @@ -1707,7 +1669,6 @@ description = "Google Authentication Library" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google_auth_oauthlib-1.2.1-py2.py3-none-any.whl", hash = "sha256:2d58a27262d55aa1b87678c3ba7142a080098cbc2024f903c62355deb235d91f"}, {file = "google_auth_oauthlib-1.2.1.tar.gz", hash = "sha256:afd0cad092a2eaa53cd8e8298557d6de1034c6cb4a740500b5357b648af97263"}, @@ -1727,7 +1688,6 @@ description = "Google Cloud API client core library" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google-cloud-core-2.4.1.tar.gz", hash = "sha256:9b7749272a812bde58fff28868d0c5e2f585b82f37e09a1f6ed2d4d10f134073"}, {file = "google_cloud_core-2.4.1-py2.py3-none-any.whl", hash = "sha256:a9e6a4422b9ac5c29f79a0ede9485473338e2ce78d91f2370c01e730eab22e61"}, @@ -1747,7 +1707,6 @@ description = "Google Cloud Storage API client library" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google_cloud_storage-2.18.2-py2.py3-none-any.whl", hash = "sha256:97a4d45c368b7d401ed48c4fdfe86e1e1cb96401c9e199e419d289e2c0370166"}, {file = "google_cloud_storage-2.18.2.tar.gz", hash = "sha256:aaf7acd70cdad9f274d29332673fcab98708d0e1f4dceb5a5356aaef06af4d99"}, @@ -1772,7 +1731,6 @@ description = "A python wrapper of the C library 'Google CRC32C'" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google_crc32c-1.6.0-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:5bcc90b34df28a4b38653c36bb5ada35671ad105c99cfe915fb5bed7ad6924aa"}, {file = "google_crc32c-1.6.0-cp310-cp310-macosx_12_0_x86_64.whl", hash = "sha256:d9e9913f7bd69e093b81da4535ce27af842e7bf371cde42d1ae9e9bd382dc0e9"}, @@ -1813,7 +1771,6 @@ description = "Utilities for Google Media Downloads and Resumable Uploads" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "google_resumable_media-2.7.2-py2.py3-none-any.whl", hash = "sha256:3ce7551e9fe6d99e9a126101d2536612bb73486721951e9562fee0f90c6ababa"}, {file = "google_resumable_media-2.7.2.tar.gz", hash = "sha256:5280aed4629f2b60b847b0d42f9857fd4935c11af266744df33d8074cae92fe0"}, @@ -1833,7 +1790,6 @@ description = "Common protobufs used in Google APIs" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "googleapis_common_protos-1.66.0-py2.py3-none-any.whl", hash = "sha256:d7abcd75fabb2e0ec9f74466401f6c119a0b498e27370e9be4c94cb7e382b8ed"}, {file = "googleapis_common_protos-1.66.0.tar.gz", hash = "sha256:c3e7b33d15fdca5374cc0a7346dd92ffa847425cc4ea941d970f13680052ec8c"}, @@ -1852,7 +1808,7 @@ description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "h11-0.14.0-py3-none-any.whl", hash = "sha256:e3fe4ac4b851c468cc8363d500db52c2ead036020723024a109d37346efaa761"}, {file = "h11-0.14.0.tar.gz", hash = "sha256:8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d"}, @@ -1865,7 +1821,7 @@ description = "A minimal low-level HTTP client." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "httpcore-1.0.7-py3-none-any.whl", hash = "sha256:a3fff8f43dc260d5bd363d9f9cf1830fa3a458b332856f34282de498ed420edd"}, {file = "httpcore-1.0.7.tar.gz", hash = "sha256:8551cb62a169ec7162ac7be8d4817d561f60e08eaa485234898414bb5a8a0b4c"}, @@ -1888,7 +1844,7 @@ description = "The next generation HTTP client." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "httpx-0.28.0-py3-none-any.whl", hash = "sha256:dc0b419a0cfeb6e8b34e85167c0da2671206f5095f1baa9663d23bcfd6b535fc"}, {file = "httpx-0.28.0.tar.gz", hash = "sha256:0858d3bab51ba7e386637f22a61d8ccddaeec5f3fe4209da3a6168dbb91573e0"}, @@ -1901,7 +1857,7 @@ httpcore = "==1.*" idna = "*" [package.extras] -brotli = ["brotli", "brotlicffi"] +brotli = ["brotli ; platform_python_implementation == \"CPython\"", "brotlicffi ; platform_python_implementation != \"CPython\""] cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"] http2 = ["h2 (>=3,<5)"] socks = ["socksio (==1.*)"] @@ -1914,7 +1870,7 @@ description = "File identification library for Python" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "identify-2.6.3-py2.py3-none-any.whl", hash = "sha256:9edba65473324c2ea9684b1f944fe3191db3345e50b6d04571d10ed164f8d7bd"}, {file = "identify-2.6.3.tar.gz", hash = "sha256:62f5dae9b5fef52c84cc188514e9ea4f3f636b1d8799ab5ebc475471f9e47a02"}, @@ -1930,7 +1886,6 @@ description = "Internationalized Domain Names in Applications (IDNA)" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"}, {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"}, @@ -1946,7 +1901,6 @@ description = "Package for embedding the igv.js genome visualization in IPython optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "igv-notebook-0.6.1.tar.gz", hash = "sha256:37e4f091d93536775c99075b7fac11069186e22f05874dd2da886b7dc09e9e0d"}, {file = "igv_notebook-0.6.1-py3-none-any.whl", hash = "sha256:e13a53d245d6d51603173fbdd481f051344d79cbaeaa69f4bcc569a1c5387559"}, @@ -1964,7 +1918,7 @@ description = "Getting image size from png/jpeg/jpeg2000/gif file" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"}, {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"}, @@ -1977,7 +1931,6 @@ description = "Read metadata from Python packages" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "importlib_metadata-8.5.0-py3-none-any.whl", hash = "sha256:45e54197d28b7a7f1559e60b95e7c567032b602131fbd588f1497f47880aa68b"}, {file = "importlib_metadata-8.5.0.tar.gz", hash = "sha256:71522656f0abace1d072b9e5481a48f07c138e00f079c38c8f883823f9c26bd7"}, @@ -1987,12 +1940,12 @@ files = [ zipp = ">=3.20" [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] perf = ["ipython"] -test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"] +test = ["flufl.flake8", "importlib-resources (>=1.3) ; python_version < \"3.9\"", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"] type = ["pytest-mypy"] [[package]] @@ -2002,7 +1955,7 @@ description = "brain-dead simple config-ini parsing" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"}, {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"}, @@ -2015,7 +1968,6 @@ description = "Official Python library for IPInfo" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "ipinfo-5.1.1-py3-none-any.whl", hash = "sha256:90b2f5400189dd2da7625c9151d7076879a8cac9c31bfb581689345fac34cceb"}, {file = "ipinfo-5.1.1.tar.gz", hash = "sha256:be5a33adac9681bc68280eb5aae16a83e4abbb5f192c87dcc5ee18bdd0ceb276"}, @@ -2033,7 +1985,6 @@ description = "IPython Kernel for Jupyter" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "ipykernel-6.29.5-py3-none-any.whl", hash = "sha256:afdb66ba5aa354b09b91379bac28ae4afebbb30e8b39510c9690afb7a10421b5"}, {file = "ipykernel-6.29.5.tar.gz", hash = "sha256:f093a22c4a40f8828f8e330a9c297cb93dcab13bd9678ded6de8e5cf81c56215"}, @@ -2068,7 +2019,6 @@ description = "A Jupyter widget for dynamic Leaflet maps" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "ipyleaflet-0.19.2-py3-none-any.whl", hash = "sha256:7cc9157848baca2e1793b96e79f8bdb1aa7340521d2b7d8a62aa8bc30eab5278"}, {file = "ipyleaflet-0.19.2.tar.gz", hash = "sha256:b3b83fe3460e742964c2a5924ea7934365a3749bb75310ce388d45fd751372d2"}, @@ -2088,7 +2038,6 @@ description = "IPython: Productive Interactive Computing" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "ipython-8.30.0-py3-none-any.whl", hash = "sha256:85ec56a7e20f6c38fce7727dcca699ae4ffc85985aa7b23635a8008f918ae321"}, {file = "ipython-8.30.0.tar.gz", hash = "sha256:cb0a405a306d2995a5cbb9901894d240784a9f341394c6ba3f4fe8c6eb89ff6e"}, @@ -2110,7 +2059,7 @@ typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""} [package.extras] all = ["ipython[black,doc,kernel,matplotlib,nbconvert,nbformat,notebook,parallel,qtconsole]", "ipython[test,test-extra]"] black = ["black"] -doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli", "typing_extensions"] +doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli ; python_version < \"3.11\"", "typing_extensions"] kernel = ["ipykernel"] matplotlib = ["matplotlib"] nbconvert = ["nbconvert"] @@ -2128,7 +2077,6 @@ description = "Jupyter interactive widgets" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "ipywidgets-8.1.5-py3-none-any.whl", hash = "sha256:3290f526f87ae6e77655555baba4f36681c555b8bdbbff430b70e52c34c86245"}, {file = "ipywidgets-8.1.5.tar.gz", hash = "sha256:870e43b1a35656a80c18c9503bbf2d16802db1cb487eec6fab27d683381dde17"}, @@ -2151,7 +2099,7 @@ description = "Operations with ISO 8601 durations" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"}, {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"}, @@ -2167,7 +2115,6 @@ description = "Safely pass data to untrusted environments and back." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "itsdangerous-2.2.0-py3-none-any.whl", hash = "sha256:c6242fc49e35958c8b15141343aa660db5fc54d4f13a1db01a3f5891b98700ef"}, {file = "itsdangerous-2.2.0.tar.gz", hash = "sha256:e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173"}, @@ -2180,7 +2127,6 @@ description = "An autocompletion tool for Python that can be used for text edito optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jedi-0.19.2-py2.py3-none-any.whl", hash = "sha256:a8ef22bde8490f57fe5c7681a3c83cb58874daf72b4784de3cce5b6ef6edb5b9"}, {file = "jedi-0.19.2.tar.gz", hash = "sha256:4770dc3de41bde3966b02eb84fbcf557fb33cce26ad23da12c742fb50ecb11f0"}, @@ -2201,7 +2147,6 @@ description = "A very fast and expressive template engine." optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"}, {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"}, @@ -2220,7 +2165,6 @@ description = "JSON Matching Expressions" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jmespath-1.0.1-py3-none-any.whl", hash = "sha256:02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980"}, {file = "jmespath-1.0.1.tar.gz", hash = "sha256:90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe"}, @@ -2233,7 +2177,6 @@ description = "Lightweight pipelining with Python functions" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "joblib-1.4.2-py3-none-any.whl", hash = "sha256:06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6"}, {file = "joblib-1.4.2.tar.gz", hash = "sha256:2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e"}, @@ -2246,7 +2189,7 @@ description = "A Python implementation of the JSON5 data format." optional = false python-versions = ">=3.8.0" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "json5-0.10.0-py3-none-any.whl", hash = "sha256:19b23410220a7271e8377f81ba8aacba2fdd56947fbb137ee5977cbe1f5e8dfa"}, {file = "json5-0.10.0.tar.gz", hash = "sha256:e66941c8f0a02026943c52c2eb34ebeb2a6f819a0be05920a6f5243cd30fd559"}, @@ -2262,7 +2205,7 @@ description = "Identify specific nodes in a JSON document (RFC 6901)" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jsonpointer-3.0.0-py2.py3-none-any.whl", hash = "sha256:13e088adc14fca8b6aa8177c044e12701e6ad4b28ff10e65f2267a90109c9942"}, {file = "jsonpointer-3.0.0.tar.gz", hash = "sha256:2b2d729f2091522d61c3b31f82e11870f60b68f43fbc705cb76bf4b832af59ef"}, @@ -2275,7 +2218,7 @@ description = "An implementation of JSON Schema validation for Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"}, {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"}, @@ -2306,7 +2249,7 @@ description = "The JSON Schema meta-schemas and vocabularies, exposed as a Regis optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jsonschema_specifications-2024.10.1-py3-none-any.whl", hash = "sha256:a09a0680616357d9a0ecf05c12ad234479f549239d0f5b55f3deea67475da9bf"}, {file = "jsonschema_specifications-2024.10.1.tar.gz", hash = "sha256:0f38b83639958ce1152d02a7f062902c41c8fd20d558b0c34344292d417ae272"}, @@ -2322,7 +2265,6 @@ description = "Jupyter protocol implementation and client libraries" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyter_client-8.6.3-py3-none-any.whl", hash = "sha256:e8a19cc986cc45905ac3362915f410f3af85424b4c0905e94fa5f2cb08e8f23f"}, {file = "jupyter_client-8.6.3.tar.gz", hash = "sha256:35b3a0947c4a6e9d589eb97d7d4cd5e90f910ee73101611f01283732bd6d9419"}, @@ -2337,7 +2279,7 @@ traitlets = ">=5.3" [package.extras] docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] -test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest (<8.2.0)", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"] +test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko ; sys_platform == \"win32\"", "pre-commit", "pytest (<8.2.0)", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"] [[package]] name = "jupyter-core" @@ -2346,7 +2288,6 @@ description = "Jupyter core package. A base package on which Jupyter projects re optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyter_core-5.7.2-py3-none-any.whl", hash = "sha256:4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409"}, {file = "jupyter_core-5.7.2.tar.gz", hash = "sha256:aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9"}, @@ -2368,7 +2309,7 @@ description = "Jupyter Event System library" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyter_events-0.10.0-py3-none-any.whl", hash = "sha256:4b72130875e59d57716d327ea70d3ebc3af1944d3717e5a498b8a06c6c159960"}, {file = "jupyter_events-0.10.0.tar.gz", hash = "sha256:670b8229d3cc882ec782144ed22e0d29e1c2d639263f92ca8383e66682845e22"}, @@ -2395,7 +2336,6 @@ description = "ipyleaflet extensions for JupyterLab and Jupyter Notebook" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyter_leaflet-0.19.2-py3-none-any.whl", hash = "sha256:0d57e15e80c08a4360f0cde0b4c490beddc5d422bb0e9bc1c0b4479d3fb725a6"}, {file = "jupyter_leaflet-0.19.2.tar.gz", hash = "sha256:b09b5ba48b1488cb61da37a6f558347269eb53ff6d64dc1a73e005ffc4420063"}, @@ -2408,7 +2348,7 @@ description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab se optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyter-lsp-2.2.5.tar.gz", hash = "sha256:793147a05ad446f809fd53ef1cd19a9f5256fd0a2d6b7ce943a982cb4f545001"}, {file = "jupyter_lsp-2.2.5-py3-none-any.whl", hash = "sha256:45fbddbd505f3fbfb0b6cb2f1bc5e15e83ab7c79cd6e89416b248cb3c00c11da"}, @@ -2424,7 +2364,7 @@ description = "The backend—i.e. core services, APIs, and REST endpoints—to J optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyter_server-2.14.2-py3-none-any.whl", hash = "sha256:47ff506127c2f7851a17bf4713434208fc490955d0e8632e95014a9a9afbeefd"}, {file = "jupyter_server-2.14.2.tar.gz", hash = "sha256:66095021aa9638ced276c248b1d81862e4c50f292d575920bbe960de1c56b12b"}, @@ -2462,7 +2402,7 @@ description = "A Jupyter Server Extension Providing Terminals." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyter_server_terminals-0.5.3-py3-none-any.whl", hash = "sha256:41ee0d7dc0ebf2809c668e0fc726dfaf258fcd3e769568996ca731b6194ae9aa"}, {file = "jupyter_server_terminals-0.5.3.tar.gz", hash = "sha256:5ae0295167220e9ace0edcfdb212afd2b01ee8d179fe6f23c899590e9b8a5269"}, @@ -2483,7 +2423,7 @@ description = "JupyterLab computational environment" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyterlab-4.3.2-py3-none-any.whl", hash = "sha256:e87100cbab8b886ff7a4f325c856100ba6fdfe916162a85409daf0e707e19d1d"}, {file = "jupyterlab-4.3.2.tar.gz", hash = "sha256:3c0a6882dbddcc0a7bfdd5e2236f351b2b263e48780236e6996c2aca13ac5b22"}, @@ -2519,7 +2459,7 @@ description = "Pygments theme using JupyterLab CSS variables" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyterlab_pygments-0.3.0-py3-none-any.whl", hash = "sha256:841a89020971da1d8693f1a99997aefc5dc424bb1b251fd6322462a1b8842780"}, {file = "jupyterlab_pygments-0.3.0.tar.gz", hash = "sha256:721aca4d9029252b11cfa9d185e5b5af4d54772bb8072f9b7036f4170054d35d"}, @@ -2532,7 +2472,7 @@ description = "A set of server components for JupyterLab and JupyterLab like app optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "jupyterlab_server-2.27.3-py3-none-any.whl", hash = "sha256:e697488f66c3db49df675158a77b3b017520d772c6e1548c7d9bcc5df7944ee4"}, {file = "jupyterlab_server-2.27.3.tar.gz", hash = "sha256:eb36caca59e74471988f0ae25c77945610b887f777255aa21f8065def9e51ed4"}, @@ -2559,7 +2499,6 @@ description = "Jupyter interactive widgets for JupyterLab" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jupyterlab_widgets-3.0.13-py3-none-any.whl", hash = "sha256:e3cda2c233ce144192f1e29914ad522b2f4c40e77214b0cc97377ca3d323db54"}, {file = "jupyterlab_widgets-3.0.13.tar.gz", hash = "sha256:a2966d385328c1942b683a8cd96b89b8dd82c8b8f81dda902bb2bc06d46f5bed"}, @@ -2572,7 +2511,6 @@ description = "lightweight wrapper around basic LLVM functionality" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "llvmlite-0.43.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a289af9a1687c6cf463478f0fa8e8aa3b6fb813317b0d70bf1ed0759eab6f761"}, {file = "llvmlite-0.43.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:6d4fd101f571a31acb1559ae1af30f30b1dc4b3186669f92ad780e17c81e91bc"}, @@ -2604,7 +2542,6 @@ description = "File-based locks for Python on Linux and Windows" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "locket-1.0.0-py2.py3-none-any.whl", hash = "sha256:b6c819a722f7b6bd955b80781788e4a66a55628b858d347536b7e81325a3a5e3"}, {file = "locket-1.0.0.tar.gz", hash = "sha256:5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632"}, @@ -2617,7 +2554,7 @@ description = "Small library to dynamically create python functions." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "makefun-1.15.6-py2.py3-none-any.whl", hash = "sha256:e69b870f0bb60304765b1e3db576aaecf2f9b3e5105afe8cfeff8f2afe6ad067"}, {file = "makefun-1.15.6.tar.gz", hash = "sha256:26bc63442a6182fb75efed8b51741dd2d1db2f176bec8c64e20a586256b8f149"}, @@ -2630,7 +2567,6 @@ description = "Safely add untrusted strings to HTML/XML markup." optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "MarkupSafe-3.0.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7e94c425039cde14257288fd61dcfb01963e658efbc0ff54f5306b06054700f8"}, {file = "MarkupSafe-3.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9e2d922824181480953426608b81967de705c3cef4d1af983af849d7bd619158"}, @@ -2702,7 +2638,6 @@ description = "Inline Matplotlib backend for Jupyter" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "matplotlib_inline-0.1.7-py3-none-any.whl", hash = "sha256:df192d39a4ff8f21b1895d72e6a13f5fcc5099f00fa84384e0ea28c2cc0653ca"}, {file = "matplotlib_inline-0.1.7.tar.gz", hash = "sha256:8423b23ec666be3d16e16b60bdd8ac4e86e840ebd1dd11a30b9f117f2fa0ab90"}, @@ -2718,7 +2653,7 @@ description = "A module for monitoring memory usage of a python program" optional = false python-versions = ">=3.5" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "memory_profiler-0.61.0-py3-none-any.whl", hash = "sha256:400348e61031e3942ad4d4109d18753b2fb08c2f6fb8290671c5513a34182d84"}, {file = "memory_profiler-0.61.0.tar.gz", hash = "sha256:4e5b73d7864a1d1292fb76a03e82a3e78ef934d06828a698d9dada76da2067b0"}, @@ -2734,7 +2669,7 @@ description = "A sane and fast Markdown parser with useful plugins and renderers optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "mistune-3.0.2-py3-none-any.whl", hash = "sha256:71481854c30fdbc938963d3605b72501f5c10a9320ecd412c121c163a1c7d205"}, {file = "mistune-3.0.2.tar.gz", hash = "sha256:fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8"}, @@ -2747,7 +2682,6 @@ description = "MessagePack serializer" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "msgpack-1.1.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7ad442d527a7e358a469faf43fda45aaf4ac3249c8310a82f0ccff9164e5dccd"}, {file = "msgpack-1.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:74bed8f63f8f14d75eec75cf3d04ad581da6b914001b474a5d3cd3372c8cc27d"}, @@ -2822,7 +2756,6 @@ description = "multidict implementation" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "multidict-6.1.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:3380252550e372e8511d49481bd836264c009adb826b23fefcc5dd3c69692f60"}, {file = "multidict-6.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:99f826cbf970077383d7de805c0681799491cb939c25450b9b5b3ced03ca99f1"}, @@ -2928,7 +2861,7 @@ description = "Optional static typing for Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "mypy-1.13.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:6607e0f1dd1fb7f0aca14d936d13fd19eba5e17e1cd2a14f808fa5f8f6d8f60a"}, {file = "mypy-1.13.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8a21be69bd26fa81b1f80a61ee7ab05b076c674d9b18fb56239d72e21d9f4c80"}, @@ -2983,7 +2916,7 @@ description = "Type system extensions for programs checked with the mypy type ch optional = false python-versions = ">=3.5" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"}, {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"}, @@ -2996,7 +2929,7 @@ description = "A client library for executing notebooks. Formerly nbconvert's Ex optional = false python-versions = ">=3.8.0" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "nbclient-0.10.1-py3-none-any.whl", hash = "sha256:949019b9240d66897e442888cfb618f69ef23dc71c01cb5fced8499c2cfc084d"}, {file = "nbclient-0.10.1.tar.gz", hash = "sha256:3e93e348ab27e712acd46fccd809139e356eb9a31aab641d1a7991a6eb4e6f68"}, @@ -3020,7 +2953,7 @@ description = "Converting Jupyter Notebooks (.ipynb files) to other formats. Ou optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "nbconvert-7.16.4-py3-none-any.whl", hash = "sha256:05873c620fe520b6322bf8a5ad562692343fe3452abda5765c7a34b7d1aa3eb3"}, {file = "nbconvert-7.16.4.tar.gz", hash = "sha256:86ca91ba266b0a448dc96fa6c5b9d98affabde2867b363258703536807f9f7f4"}, @@ -3059,7 +2992,7 @@ description = "The Jupyter Notebook format" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "nbformat-5.10.4-py3-none-any.whl", hash = "sha256:3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b"}, {file = "nbformat-5.10.4.tar.gz", hash = "sha256:322168b14f937a5d11362988ecac2a4952d3d8e3a2cbeb2319584631226d5b3a"}, @@ -3082,7 +3015,6 @@ description = "Patch asyncio to allow nested event loops" optional = false python-versions = ">=3.5" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "nest_asyncio-1.6.0-py3-none-any.whl", hash = "sha256:87af6efd6b5e897c81050477ef65c62e2b2f35d51703cae01aff2905b1852e1c"}, {file = "nest_asyncio-1.6.0.tar.gz", hash = "sha256:6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe"}, @@ -3095,7 +3027,6 @@ description = "Python package for creating and manipulating graphs and networks" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "networkx-3.4.2-py3-none-any.whl", hash = "sha256:df5d4365b724cf81b8c6a7312509d0c22386097011ad1abe274afd5e9d3bbc5f"}, {file = "networkx-3.4.2.tar.gz", hash = "sha256:307c3669428c5362aab27c8a1260aa8f47c4e91d3891f48be0141738d8d053e1"}, @@ -3116,7 +3047,7 @@ description = "Node.js virtual environment builder" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "nodeenv-1.9.1-py2.py3-none-any.whl", hash = "sha256:ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9"}, {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"}, @@ -3129,7 +3060,7 @@ description = "Jupyter Notebook - A web-based notebook environment for interacti optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "notebook-7.3.0-py3-none-any.whl", hash = "sha256:affa2fdbc10661aa05790ba105836871666b3919559abb5bc92dd8d9f0cbeee3"}, {file = "notebook-7.3.0.tar.gz", hash = "sha256:e1dc37db32620b04043ae78866a40b087c43308d85067699db99e6f9e22846bc"}, @@ -3145,7 +3076,7 @@ tornado = ">=6.2.0" [package.extras] dev = ["hatch", "pre-commit"] docs = ["myst-parser", "nbsphinx", "pydata-sphinx-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] -test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.27.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"] +test = ["importlib-resources (>=5.0) ; python_version < \"3.10\"", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.27.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"] [[package]] name = "notebook-shim" @@ -3154,7 +3085,7 @@ description = "A shim layer for notebook traits and config" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "notebook_shim-0.2.4-py3-none-any.whl", hash = "sha256:411a5be4e9dc882a074ccbcae671eda64cceb068767e9a3419096986560e1cef"}, {file = "notebook_shim-0.2.4.tar.gz", hash = "sha256:b4b2cfa1b65d98307ca24361f5b30fe785b53c3fd07b7a47e89acb5e6ac638cb"}, @@ -3173,7 +3104,6 @@ description = "compiling Python code using LLVM" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "numba-0.60.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5d761de835cd38fb400d2c26bb103a2726f548dc30368853121d66201672e651"}, {file = "numba-0.60.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:159e618ef213fba758837f9837fb402bbe65326e60ba0633dbe6c7f274d42c1b"}, @@ -3209,7 +3139,6 @@ description = "A Python package providing buffer compression and transformation optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "numcodecs-0.13.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:96add4f783c5ce57cc7e650b6cac79dd101daf887c479a00a29bc1487ced180b"}, {file = "numcodecs-0.13.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:237b7171609e868a20fd313748494444458ccd696062f67e198f7f8f52000c15"}, @@ -3248,7 +3177,6 @@ description = "Fundamental package for array computing in Python" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "numpy-2.0.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:51129a29dbe56f9ca83438b706e2e69a39892b5eda6cedcb6b0c9fdc9b0d3ece"}, {file = "numpy-2.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:f15975dfec0cf2239224d80e32c3170b1d168335eaedee69da84fbe9f1f9cd04"}, @@ -3304,7 +3232,6 @@ description = "" optional = false python-versions = "<3.13,>=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "numpydoc_decorator-2.2.1-py3-none-any.whl", hash = "sha256:16181c97b20c2099d6fd75404bef379cc3678338d9aa8e6e8fafb3ae7adc166a"}, {file = "numpydoc_decorator-2.2.1.tar.gz", hash = "sha256:c3b5b16bec1e7ed221adab7bd77a8a8acc0c7be1bb4e0871721b2a5d2f3145fa"}, @@ -3320,7 +3247,6 @@ description = "A generic, spec-compliant, thorough implementation of the OAuth r optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "oauthlib-3.2.2-py3-none-any.whl", hash = "sha256:8139f29aac13e25d502680e9e19963e83f16838d48a0d71c287fe40e7067fbca"}, {file = "oauthlib-3.2.2.tar.gz", hash = "sha256:9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918"}, @@ -3338,7 +3264,6 @@ description = "Fast, correct Python JSON library supporting dataclasses, datetim optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "orjson-3.10.12-cp310-cp310-macosx_10_15_x86_64.macosx_11_0_arm64.macosx_10_15_universal2.whl", hash = "sha256:ece01a7ec71d9940cc654c482907a6b65df27251255097629d0dea781f255c6d"}, {file = "orjson-3.10.12-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c34ec9aebc04f11f4b978dd6caf697a2df2dd9b47d35aa4cc606cabcb9df69d7"}, @@ -3424,7 +3349,7 @@ description = "A decorator to automatically detect mismatch when overriding a me optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "overrides-7.7.0-py3-none-any.whl", hash = "sha256:c7ed9d062f78b8e4c1a7b70bd8796b35ead4d9f510227ef9c5dc7626c60d7e49"}, {file = "overrides-7.7.0.tar.gz", hash = "sha256:55158fa3d93b98cc75299b1e67078ad9003ca27945c76162c1c0766d6f91820a"}, @@ -3437,7 +3362,6 @@ description = "Core utilities for Python packages" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "packaging-24.2-py3-none-any.whl", hash = "sha256:09abb1bccd265c01f4a3aa3f7a7db064b36514d2cba19a2f694fe6150451a759"}, {file = "packaging-24.2.tar.gz", hash = "sha256:c228a6dc5e932d346bc5739379109d49e8853dd8223571c7c5b55260edc0b97f"}, @@ -3450,7 +3374,6 @@ description = "Powerful data structures for data analysis, time series, and stat optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pandas-2.2.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1948ddde24197a0f7add2bdc4ca83bf2b1ef84a1bc8ccffd95eda17fd836ecb5"}, {file = "pandas-2.2.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:381175499d3802cde0eabbaf6324cce0c4f5d52ca6f8c377c29ad442f50f6348"}, @@ -3538,7 +3461,7 @@ description = "Type annotations for pandas" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pandas_stubs-2.2.3.241126-py3-none-any.whl", hash = "sha256:74aa79c167af374fe97068acc90776c0ebec5266a6e5c69fe11e9c2cf51f2267"}, {file = "pandas_stubs-2.2.3.241126.tar.gz", hash = "sha256:cf819383c6d9ae7d4dabf34cd47e1e45525bb2f312e6ad2939c2c204cb708acd"}, @@ -3555,7 +3478,7 @@ description = "Utilities for writing pandoc filters in python" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pandocfilters-1.5.1-py2.py3-none-any.whl", hash = "sha256:93be382804a9cdb0a7267585f157e5d1731bbe5545a85b268d6f5fe6232de2bc"}, {file = "pandocfilters-1.5.1.tar.gz", hash = "sha256:002b4a555ee4ebc03f8b66307e287fa492e4a77b4ea14d3f934328297bb4939e"}, @@ -3568,7 +3491,6 @@ description = "A Python Parser" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "parso-0.8.4-py2.py3-none-any.whl", hash = "sha256:a418670a20291dacd2dddc80c377c5c3791378ee1e8d12bffc35420643d43f18"}, {file = "parso-0.8.4.tar.gz", hash = "sha256:eb3a7b58240fb99099a345571deecc0f9540ea5f4dd2fe14c2a99d6b281ab92d"}, @@ -3585,7 +3507,6 @@ description = "Appendable key-value storage" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "partd-1.4.2-py3-none-any.whl", hash = "sha256:978e4ac767ec4ba5b86c6eaa52e5a2a3bc748a2ca839e8cc798f1cc6ce6efb0f"}, {file = "partd-1.4.2.tar.gz", hash = "sha256:d022c33afbdc8405c226621b015e8067888173d85f7f5ecebb3cafed9a20f02c"}, @@ -3605,7 +3526,6 @@ description = "A Python package for describing statistical models and for buildi optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "patsy-1.0.1-py2.py3-none-any.whl", hash = "sha256:751fb38f9e97e62312e921a1954b81e1bb2bcda4f5eeabaf94db251ee791509c"}, {file = "patsy-1.0.1.tar.gz", hash = "sha256:e786a9391eec818c054e359b737bbce692f051aee4c661f4141cc88fb459c0c4"}, @@ -3624,7 +3544,7 @@ description = "Pexpect allows easy control of interactive console applications." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and (sys_platform != \"win32\" and sys_platform != \"emscripten\") or python_version >= \"3.12\" and (sys_platform != \"win32\" and sys_platform != \"emscripten\")" +markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\"" files = [ {file = "pexpect-4.9.0-py2.py3-none-any.whl", hash = "sha256:7236d1e080e4936be2dc3e326cec0af72acf9212a7e1d060210e70a47e253523"}, {file = "pexpect-4.9.0.tar.gz", hash = "sha256:ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f"}, @@ -3640,7 +3560,6 @@ description = "Python Imaging Library (Fork)" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pillow-11.0.0-cp310-cp310-macosx_10_10_x86_64.whl", hash = "sha256:6619654954dc4936fcff82db8eb6401d3159ec6be81e33c6000dfd76ae189947"}, {file = "pillow-11.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:b3c5ac4bed7519088103d9450a1107f76308ecf91d6dabc8a33a2fcfb18d0fba"}, @@ -3724,7 +3643,7 @@ docs = ["furo", "olefile", "sphinx (>=8.1)", "sphinx-copybutton", "sphinx-inline fpx = ["olefile"] mic = ["olefile"] tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] -typing = ["typing-extensions"] +typing = ["typing-extensions ; python_version < \"3.10\""] xmp = ["defusedxml"] [[package]] @@ -3734,7 +3653,6 @@ description = "A small Python package for determining appropriate platform-speci optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "platformdirs-4.3.6-py3-none-any.whl", hash = "sha256:73e575e1408ab8103900836b97580d5307456908a03e92031bab39e4554cc3fb"}, {file = "platformdirs-4.3.6.tar.gz", hash = "sha256:357fb2acbc885b0419afd3ce3ed34564c13c9b95c89360cd9563f73aa5e2b907"}, @@ -3752,7 +3670,6 @@ description = "An open-source, interactive data visualization library for Python optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "plotly-5.24.1-py3-none-any.whl", hash = "sha256:f67073a1e637eb0dc3e46324d9d51e2fe76e9727c892dde64ddf1e1b51f29089"}, {file = "plotly-5.24.1.tar.gz", hash = "sha256:dbc8ac8339d248a4bcc36e08a5659bacfe1b079390b8953533f4eb22169b4bae"}, @@ -3769,7 +3686,7 @@ description = "plugin and hook calling mechanisms for python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pluggy-1.5.0-py3-none-any.whl", hash = "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"}, {file = "pluggy-1.5.0.tar.gz", hash = "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1"}, @@ -3786,7 +3703,7 @@ description = "A framework for managing and maintaining multi-language pre-commi optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pre_commit-4.0.1-py2.py3-none-any.whl", hash = "sha256:efde913840816312445dc98787724647c65473daefe420785f885e8ed9a06878"}, {file = "pre_commit-4.0.1.tar.gz", hash = "sha256:80905ac375958c0444c65e9cebebd948b3cdb518f335a091a670a89d652139d2"}, @@ -3806,7 +3723,7 @@ description = "Python client for the Prometheus monitoring system." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "prometheus_client-0.21.1-py3-none-any.whl", hash = "sha256:594b45c410d6f4f8888940fe80b5cc2521b305a1fafe1c58609ef715a001f301"}, {file = "prometheus_client-0.21.1.tar.gz", hash = "sha256:252505a722ac04b0456be05c05f75f45d760c2911ffc45f2a06bcaed9f3ae3fb"}, @@ -3822,7 +3739,6 @@ description = "Library for building powerful interactive command lines in Python optional = false python-versions = ">=3.7.0" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "prompt_toolkit-3.0.48-py3-none-any.whl", hash = "sha256:f49a827f90062e411f1ce1f854f2aedb3c23353244f8108b89283587397ac10e"}, {file = "prompt_toolkit-3.0.48.tar.gz", hash = "sha256:d6623ab0477a80df74e646bdbc93621143f5caf104206aa29294d53de1a03d90"}, @@ -3838,7 +3754,6 @@ description = "Accelerated property cache" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "propcache-0.2.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:6b3f39a85d671436ee3d12c017f8fdea38509e4f25b28eb25877293c98c243f6"}, {file = "propcache-0.2.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:39d51fbe4285d5db5d92a929e3e21536ea3dd43732c5b177c7ef03f918dff9f2"}, @@ -3931,7 +3846,6 @@ description = "Beautiful, Pythonic protocol buffers." optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "proto_plus-1.25.0-py3-none-any.whl", hash = "sha256:c91fc4a65074ade8e458e95ef8bac34d4008daa7cce4a12d6707066fca648961"}, {file = "proto_plus-1.25.0.tar.gz", hash = "sha256:fbb17f57f7bd05a68b7707e745e26528b0b3c34e378db91eef93912c54982d91"}, @@ -3950,7 +3864,6 @@ description = "" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "protobuf-5.29.0-cp310-abi3-win32.whl", hash = "sha256:ea7fb379b257911c8c020688d455e8f74efd2f734b72dc1ea4b4d7e9fd1326f2"}, {file = "protobuf-5.29.0-cp310-abi3-win_amd64.whl", hash = "sha256:34a90cf30c908f47f40ebea7811f743d360e202b6f10d40c02529ebd84afc069"}, @@ -3972,7 +3885,6 @@ description = "Protopunica is pomegranate frozen at version 0.14.8." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "protopunica-0.14.8.post2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:616313486a9c55e77c9ba0a3e05a7589216ed05b52908ffb95d4d74271f80f57"}, {file = "protopunica-0.14.8.post2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:07a0d5ce0037e0c89e021ec302ad8e9ee007fba93dde0f98a7d6fbd7d8849446"}, @@ -4011,7 +3923,6 @@ description = "Cross-platform lib for process and system monitoring in Python." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "psutil-6.1.0-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:ff34df86226c0227c52f38b919213157588a678d049688eded74c76c8ba4a5d0"}, {file = "psutil-6.1.0-cp27-cp27m-manylinux2010_i686.whl", hash = "sha256:c0e0c00aa18ca2d3b2b991643b799a15fc8f0563d2ebb6040f64ce8dc027b942"}, @@ -4043,7 +3954,7 @@ description = "Run a subprocess in a pseudo terminal" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" and os_name != \"nt\" or python_version <= \"3.11\" and (sys_platform != \"win32\" and sys_platform != \"emscripten\") or python_version >= \"3.12\" and extra == \"dev\" and os_name != \"nt\" or python_version >= \"3.12\" and (sys_platform != \"win32\" and sys_platform != \"emscripten\")" +markers = "extra == \"dev\" and os_name != \"nt\" or sys_platform != \"win32\" and sys_platform != \"emscripten\"" files = [ {file = "ptyprocess-0.7.0-py2.py3-none-any.whl", hash = "sha256:4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35"}, {file = "ptyprocess-0.7.0.tar.gz", hash = "sha256:5c5d0a3b48ceee0b48485e0c26037c0acd7d29765ca3fbb5cb3831d347423220"}, @@ -4056,7 +3967,6 @@ description = "Safely evaluate AST nodes without side effects" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pure_eval-0.2.3-py3-none-any.whl", hash = "sha256:1db8e35b67b3d218d818ae653e27f06c3aa420901fa7b081ca98cbedc874e0d0"}, {file = "pure_eval-0.2.3.tar.gz", hash = "sha256:5f4e983f40564c576c7c8635ae88db5956bb2229d7e9237d03b3c0b0190eaf42"}, @@ -4072,7 +3982,6 @@ description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pyasn1-0.6.1-py3-none-any.whl", hash = "sha256:0d632f46f2ba09143da3a8afe9e33fb6f92fa2320ab7e886e2d0f7672af84629"}, {file = "pyasn1-0.6.1.tar.gz", hash = "sha256:6f580d2bdd84365380830acf45550f2511469f673cb4a5ae3857a3170128b034"}, @@ -4085,7 +3994,6 @@ description = "A collection of ASN.1-based protocols modules" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pyasn1_modules-0.4.1-py3-none-any.whl", hash = "sha256:49bfa96b45a292b711e986f222502c1c9a5e1f4e568fc30e2574a6c7d07838fd"}, {file = "pyasn1_modules-0.4.1.tar.gz", hash = "sha256:c28e2dbf9c06ad61c71a075c7e0f9fd0f1b0bb2d2ad4377f240d33ac2ab60a7c"}, @@ -4101,7 +4009,7 @@ description = "C parser in Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and implementation_name == \"pypy\" or python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and implementation_name == \"pypy\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "implementation_name == \"pypy\" or extra == \"dev\"" files = [ {file = "pycparser-2.22-py3-none-any.whl", hash = "sha256:c3702b6d3dd8c7abc1afa565d7e63d53a1d0bd86cdc24edd75470f4de499cfcc"}, {file = "pycparser-2.22.tar.gz", hash = "sha256:491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6"}, @@ -4114,7 +4022,7 @@ description = "Bootstrap-based Sphinx theme from the PyData community" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pydata_sphinx_theme-0.16.0-py3-none-any.whl", hash = "sha256:18c810ee4e67e05281e371e156c1fb5bb0fa1f2747240461b225272f7d8d57d8"}, {file = "pydata_sphinx_theme-0.16.0.tar.gz", hash = "sha256:721dd26e05fa8b992d66ef545536e6cbe0110afb9865820a08894af1ad6f7707"}, @@ -4143,7 +4051,6 @@ description = "Pygments is a syntax highlighting package written in Python." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pygments-2.18.0-py3-none-any.whl", hash = "sha256:b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a"}, {file = "pygments-2.18.0.tar.gz", hash = "sha256:786ff802f32e91311bff3889f6e9a86e81505fe99f2735bb6d60ae0c5004f199"}, @@ -4159,7 +4066,7 @@ description = "pytest: simple powerful testing with Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pytest-8.3.4-py3-none-any.whl", hash = "sha256:50e16d954148559c9a74109af1eaf0c945ba2d8f30f0a3d3335edde19788b6f6"}, {file = "pytest-8.3.4.tar.gz", hash = "sha256:965370d062bce11e73868e0335abac31b4d3de0e82f4007408d242b4f8610761"}, @@ -4183,7 +4090,7 @@ description = "Separate test code from test cases in pytest." optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pytest_cases-3.8.6-py2.py3-none-any.whl", hash = "sha256:564c722492ea7e7ec3ac433fd14070180e65866f49fa35bfe938c0d5d9afba67"}, {file = "pytest_cases-3.8.6.tar.gz", hash = "sha256:5c24e0ab0cb6f8e802a469b7965906a333d3babb874586ebc56f7e2cbe1a7c44"}, @@ -4201,7 +4108,7 @@ description = "Pytest plugin for measuring coverage." optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pytest-cov-6.0.0.tar.gz", hash = "sha256:fde0b595ca248bb8e2d76f020b465f3b107c9632e6a1d1705f17834c89dcadc0"}, {file = "pytest_cov-6.0.0-py3-none-any.whl", hash = "sha256:eee6f1b9e61008bd34975a4d5bab25801eb31898b032dd55addc93e96fcaaa35"}, @@ -4221,7 +4128,7 @@ description = "pytest xdist plugin for distributed testing, most importantly acr optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "pytest_xdist-3.6.1-py3-none-any.whl", hash = "sha256:9ed4adfb68a016610848639bb7e02c9352d5d9f03d04809919e2dafc3be4cca7"}, {file = "pytest_xdist-3.6.1.tar.gz", hash = "sha256:ead156a4db231eec769737f57668ef58a2084a34b2e55c4a8fa20d861107300d"}, @@ -4243,7 +4150,6 @@ description = "Extensions to the standard Python datetime module" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"}, {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"}, @@ -4259,7 +4165,7 @@ description = "A python library adding a json log formatter" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "python-json-logger-2.0.7.tar.gz", hash = "sha256:23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c"}, {file = "python_json_logger-2.0.7-py3-none-any.whl", hash = "sha256:f380b826a991ebbe3de4d897aeec42760035ac760345e57b812938dc8b35e2bd"}, @@ -4272,7 +4178,6 @@ description = "World timezone definitions, modern and historical" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pytz-2024.2-py2.py3-none-any.whl", hash = "sha256:31c7c1817eb7fae7ca4b8c7ee50c72f93aa2dd863de768e1ef4245d426aa0725"}, {file = "pytz-2024.2.tar.gz", hash = "sha256:2aa355083c50a0f93fa581709deac0c9ad65cca8a9e9beac660adcbd493c798a"}, @@ -4285,7 +4190,7 @@ description = "Python for Window Extensions" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and sys_platform == \"win32\" and platform_python_implementation != \"PyPy\" or python_version >= \"3.12\" and sys_platform == \"win32\" and platform_python_implementation != \"PyPy\"" +markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\"" files = [ {file = "pywin32-308-cp310-cp310-win32.whl", hash = "sha256:796ff4426437896550d2981b9c2ac0ffd75238ad9ea2d3bfa67a1abd546d262e"}, {file = "pywin32-308-cp310-cp310-win_amd64.whl", hash = "sha256:4fc888c59b3c0bef905ce7eb7e2106a07712015ea1c8234b703a088d46110e8e"}, @@ -4314,7 +4219,7 @@ description = "Pseudo terminal support for Windows from Python." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" and os_name == \"nt\" or python_version >= \"3.12\" and extra == \"dev\" and os_name == \"nt\"" +markers = "extra == \"dev\" and os_name == \"nt\"" files = [ {file = "pywinpty-2.0.14-cp310-none-win_amd64.whl", hash = "sha256:0b149c2918c7974f575ba79f5a4aad58bd859a52fa9eb1296cc22aa412aa411f"}, {file = "pywinpty-2.0.14-cp311-none-win_amd64.whl", hash = "sha256:cf2a43ac7065b3e0dc8510f8c1f13a75fb8fde805efa3b8cff7599a1ef497bc7"}, @@ -4331,7 +4236,6 @@ description = "YAML parser and emitter for Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "PyYAML-6.0.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0a9a2848a5b7feac301353437eb7d5957887edbf81d56e903999a75a3d743086"}, {file = "PyYAML-6.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:29717114e51c84ddfba879543fb232a6ed60086602313ca38cce623c1d62cfbf"}, @@ -4395,7 +4299,6 @@ description = "Python bindings for 0MQ" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "pyzmq-26.2.0-cp310-cp310-macosx_10_15_universal2.whl", hash = "sha256:ddf33d97d2f52d89f6e6e7ae66ee35a4d9ca6f36eda89c24591b0c40205a3629"}, {file = "pyzmq-26.2.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:dacd995031a01d16eec825bf30802fceb2c3791ef24bcce48fa98ce40918c27b"}, @@ -4518,7 +4421,7 @@ description = "JSON Referencing + Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "referencing-0.35.1-py3-none-any.whl", hash = "sha256:eda6d3234d62814d1c64e305c1331c9a3a6132da475ab6382eaa997b21ee75de"}, {file = "referencing-0.35.1.tar.gz", hash = "sha256:25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c"}, @@ -4535,7 +4438,6 @@ description = "Python HTTP for Humans." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "requests-2.32.3-py3-none-any.whl", hash = "sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6"}, {file = "requests-2.32.3.tar.gz", hash = "sha256:55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760"}, @@ -4558,7 +4460,6 @@ description = "OAuthlib authentication support for Requests." optional = false python-versions = ">=3.4" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "requests-oauthlib-2.0.0.tar.gz", hash = "sha256:b3dffaebd884d8cd778494369603a9e7b58d29111bf6b41bdc2dcd87203af4e9"}, {file = "requests_oauthlib-2.0.0-py2.py3-none-any.whl", hash = "sha256:7dd8a5c40426b779b0868c404bdef9768deccf22749cde15852df527e6269b36"}, @@ -4578,7 +4479,6 @@ description = "Retrying" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "retrying-1.3.4-py3-none-any.whl", hash = "sha256:8cc4d43cb8e1125e0ff3344e9de678fefd85db3b750b81b2240dc0183af37b35"}, {file = "retrying-1.3.4.tar.gz", hash = "sha256:345da8c5765bd982b1d1915deb9102fd3d1f7ad16bd84a9700b85f64d24e8f3e"}, @@ -4594,7 +4494,7 @@ description = "A pure python RFC3339 validator" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "rfc3339_validator-0.1.4-py2.py3-none-any.whl", hash = "sha256:24f6ec1eda14ef823da9e36ec7113124b39c04d50a4d3d3a3c2859577e7791fa"}, {file = "rfc3339_validator-0.1.4.tar.gz", hash = "sha256:138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b"}, @@ -4610,7 +4510,7 @@ description = "Pure python rfc3986 validator" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "rfc3986_validator-0.1.1-py2.py3-none-any.whl", hash = "sha256:2f235c432ef459970b4306369336b9d5dbdda31b510ca1e327636e01f528bfa9"}, {file = "rfc3986_validator-0.1.1.tar.gz", hash = "sha256:3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055"}, @@ -4623,7 +4523,7 @@ description = "Python bindings to Rust's persistent data structures (rpds)" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "rpds_py-0.22.3-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:6c7b99ca52c2c1752b544e310101b98a659b720b21db00e65edca34483259967"}, {file = "rpds_py-0.22.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:be2eb3f2495ba669d2a985f9b426c1797b7d48d6963899276d22f23e33d47e37"}, @@ -4737,7 +4637,6 @@ description = "Pure-Python RSA implementation" optional = false python-versions = ">=3.6,<4" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "rsa-4.9-py3-none-any.whl", hash = "sha256:90260d9058e514786967344d0ef75fa8727eed8a7d2e43ce9f4bcf1b536174f7"}, {file = "rsa-4.9.tar.gz", hash = "sha256:e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21"}, @@ -4753,7 +4652,7 @@ description = "An extremely fast Python linter and code formatter, written in Ru optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "ruff-0.8.1-py3-none-linux_armv6l.whl", hash = "sha256:fae0805bd514066f20309f6742f6ee7904a773eb9e6c17c45d6b1600ca65c9b5"}, {file = "ruff-0.8.1-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:b8a4f7385c2285c30f34b200ca5511fcc865f17578383db154e098150ce0a087"}, @@ -4782,7 +4681,6 @@ description = "Convenient Filesystem interface over S3" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "s3fs-2024.10.0-py3-none-any.whl", hash = "sha256:7a2025d60d5b1a6025726b3a5e292a8e5aa713abc3b16fd1f81735181f7bb282"}, {file = "s3fs-2024.10.0.tar.gz", hash = "sha256:58b8c3650f8b99dbedf361543da3533aac8707035a104db5d80b094617ad4a3f"}, @@ -4804,7 +4702,6 @@ description = "A Python package for exploring and analysing genetic variation da optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "scikit_allel-1.3.13-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:eb786c909c34b682205c3cacba9b4f0866e658917f30e2f97e1051d9fb2e7ccc"}, {file = "scikit_allel-1.3.13-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:1853068621208fc2d5537e9a5b292aef2d5e8c975fa35f8f810b3174e0226160"}, @@ -4839,7 +4736,6 @@ description = "Fundamental algorithms for scientific computing in Python" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "scipy-1.14.1-cp310-cp310-macosx_10_13_x86_64.whl", hash = "sha256:b28d2ca4add7ac16ae8bb6632a3c86e4b9e4d52d3e34267f6e1b0c1f8d87e389"}, {file = "scipy-1.14.1-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:d0d2821003174de06b69e58cef2316a6622b60ee613121199cb2852a873f8cf3"}, @@ -4882,7 +4778,7 @@ numpy = ">=1.23.5,<2.3" [package.extras] dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy (==1.10.0)", "pycodestyle", "pydevtool", "rich-click", "ruff (>=0.0.292)", "types-psutil", "typing_extensions"] doc = ["jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.13.1)", "jupytext", "matplotlib (>=3.5)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0,<=7.3.7)", "sphinx-design (>=0.4.0)"] -test = ["Cython", "array-api-strict (>=2.0)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] +test = ["Cython", "array-api-strict (>=2.0)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja ; sys_platform != \"emscripten\"", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] [[package]] name = "send2trash" @@ -4891,16 +4787,16 @@ description = "Send file to trash natively under Mac OS X, Windows and Linux" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "Send2Trash-1.8.3-py3-none-any.whl", hash = "sha256:0c31227e0bd08961c7665474a3d1ef7193929fedda4233843689baa056be46c9"}, {file = "Send2Trash-1.8.3.tar.gz", hash = "sha256:b18e7a3966d99871aefeb00cfbcfdced55ce4871194810fc71f4aa484b953abf"}, ] [package.extras] -nativelib = ["pyobjc-framework-Cocoa", "pywin32"] -objc = ["pyobjc-framework-Cocoa"] -win32 = ["pywin32"] +nativelib = ["pyobjc-framework-Cocoa ; sys_platform == \"darwin\"", "pywin32 ; sys_platform == \"win32\""] +objc = ["pyobjc-framework-Cocoa ; sys_platform == \"darwin\""] +win32 = ["pywin32 ; sys_platform == \"win32\""] [[package]] name = "setuptools" @@ -4909,20 +4805,19 @@ description = "Easily download, build, install, upgrade, and uninstall Python pa optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "setuptools-75.6.0-py3-none-any.whl", hash = "sha256:ce74b49e8f7110f9bf04883b730f4765b774ef3ef28f722cce7c273d253aaf7d"}, {file = "setuptools-75.6.0.tar.gz", hash = "sha256:8199222558df7c86216af4f84c30e9b34a61d8ba19366cc914424cdbd28252f6"}, ] [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)", "ruff (>=0.7.0)"] -core = ["importlib_metadata (>=6)", "jaraco.collections", "jaraco.functools (>=4)", "jaraco.text (>=3.7)", "more_itertools", "more_itertools (>=8.8)", "packaging", "packaging (>=24.2)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\"", "ruff (>=0.7.0) ; sys_platform != \"cygwin\""] +core = ["importlib_metadata (>=6) ; python_version < \"3.10\"", "jaraco.collections", "jaraco.functools (>=4)", "jaraco.text (>=3.7)", "more_itertools", "more_itertools (>=8.8)", "packaging", "packaging (>=24.2)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1) ; python_version < \"3.11\"", "wheel (>=0.43.0)"] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"] enabler = ["pytest-enabler (>=2.2)"] -test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] -type = ["importlib_metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (>=1.12,<1.14)", "pytest-mypy"] +test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21) ; python_version >= \"3.9\" and sys_platform != \"cygwin\"", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf ; sys_platform != \"cygwin\"", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] +type = ["importlib_metadata (>=7.0.2) ; python_version < \"3.10\"", "jaraco.develop (>=7.21) ; sys_platform != \"cygwin\"", "mypy (>=1.12,<1.14)", "pytest-mypy"] [[package]] name = "six" @@ -4931,7 +4826,6 @@ description = "Python 2 and 3 compatibility utilities" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"}, {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"}, @@ -4944,7 +4838,7 @@ description = "A web-based viewer for Python profiler output" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "snakeviz-2.2.2-py3-none-any.whl", hash = "sha256:77e7b9c82f6152edc330040319b97612351cd9b48c706434c535c2df31d10ac5"}, {file = "snakeviz-2.2.2.tar.gz", hash = "sha256:08028c6f8e34a032ff14757a38424770abb8662fb2818985aeea0d9bc13a7d83"}, @@ -4960,7 +4854,7 @@ description = "Sniff out which async library your code is running under" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2"}, {file = "sniffio-1.3.1.tar.gz", hash = "sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc"}, @@ -4973,7 +4867,7 @@ description = "This package provides 29 stemmers for 28 languages generated from optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"}, {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"}, @@ -4986,7 +4880,6 @@ description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "sortedcontainers-2.4.0-py2.py3-none-any.whl", hash = "sha256:a163dcaede0f1c021485e957a39245190e74249897e2ae4b2aa38595db237ee0"}, {file = "sortedcontainers-2.4.0.tar.gz", hash = "sha256:25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88"}, @@ -4999,7 +4892,7 @@ description = "A modern CSS selector implementation for Beautiful Soup." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "soupsieve-2.6-py3-none-any.whl", hash = "sha256:e72c4ff06e4fb6e4b5a9f0f55fe6e81514581fca1515028625d0f299c602ccc9"}, {file = "soupsieve-2.6.tar.gz", hash = "sha256:e2e68417777af359ec65daac1057404a3c8a5455bb8abc36f1a9866ab1a51abb"}, @@ -5012,7 +4905,7 @@ description = "Python documentation generator" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinx-8.1.3-py3-none-any.whl", hash = "sha256:09719015511837b76bf6e03e42eb7595ac8c2e41eeb9c29c5b755c6b677992a2"}, {file = "sphinx-8.1.3.tar.gz", hash = "sha256:43c1911eecb0d3e161ad78611bc905d1ad0e523e4ddc202a58a821773dc4c927"}, @@ -5049,7 +4942,7 @@ description = "A sphinx extension for designing beautiful, view size responsive optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinx_design-0.6.1-py3-none-any.whl", hash = "sha256:b11f37db1a802a183d61b159d9a202314d4d2fe29c163437001324fe2f19549c"}, {file = "sphinx_design-0.6.1.tar.gz", hash = "sha256:b44eea3719386d04d765c1a8257caca2b3e6f8421d7b3a5e742c0fd45f84e632"}, @@ -5076,7 +4969,7 @@ description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinxcontrib_applehelp-2.0.0-py3-none-any.whl", hash = "sha256:4cd3f0ec4ac5dd9c17ec65e9ab272c9b867ea77425228e68ecf08d6b28ddbdb5"}, {file = "sphinxcontrib_applehelp-2.0.0.tar.gz", hash = "sha256:2f29ef331735ce958efa4734873f084941970894c6090408b079c61b2e1c06d1"}, @@ -5094,7 +4987,7 @@ description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinxcontrib_devhelp-2.0.0-py3-none-any.whl", hash = "sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2"}, {file = "sphinxcontrib_devhelp-2.0.0.tar.gz", hash = "sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad"}, @@ -5112,7 +5005,7 @@ description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML h optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl", hash = "sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8"}, {file = "sphinxcontrib_htmlhelp-2.1.0.tar.gz", hash = "sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9"}, @@ -5130,7 +5023,7 @@ description = "A sphinx extension which renders display math in HTML via JavaScr optional = false python-versions = ">=3.5" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"}, {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"}, @@ -5146,7 +5039,7 @@ description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp d optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinxcontrib_qthelp-2.0.0-py3-none-any.whl", hash = "sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb"}, {file = "sphinxcontrib_qthelp-2.0.0.tar.gz", hash = "sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab"}, @@ -5164,7 +5057,7 @@ description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl", hash = "sha256:6e2cb0eef194e10c27ec0023bfeb25badbbb5868244cf5bc5bdc04e4464bf331"}, {file = "sphinxcontrib_serializinghtml-2.0.0.tar.gz", hash = "sha256:e9d912827f872c029017a53f0ef2180b327c3f7fd23c87229f7a8e8b70031d4d"}, @@ -5182,7 +5075,6 @@ description = "Extract data from python stack frames and tracebacks for informat optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"}, {file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"}, @@ -5203,7 +5095,6 @@ description = "Statistical computations and models for Python" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "statsmodels-0.14.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:7a62f1fc9086e4b7ee789a6f66b3c0fc82dd8de1edda1522d30901a0aa45e42b"}, {file = "statsmodels-0.14.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:46ac7ddefac0c9b7b607eed1d47d11e26fe92a1bc1f4d9af48aeed4e21e87981"}, @@ -5246,7 +5137,7 @@ scipy = ">=1.8,<1.9.2 || >1.9.2" [package.extras] build = ["cython (>=3.0.10)"] -develop = ["colorama", "cython (>=3.0.10)", "cython (>=3.0.10,<4)", "flake8", "isort", "joblib", "matplotlib (>=3)", "pytest (>=7.3.0,<8)", "pytest-cov", "pytest-randomly", "pytest-xdist", "pywinpty", "setuptools-scm[toml] (>=8.0,<9.0)"] +develop = ["colorama", "cython (>=3.0.10)", "cython (>=3.0.10,<4)", "flake8", "isort", "joblib", "matplotlib (>=3)", "pytest (>=7.3.0,<8)", "pytest-cov", "pytest-randomly", "pytest-xdist", "pywinpty ; os_name == \"nt\"", "setuptools-scm[toml] (>=8.0,<9.0)"] docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"] [[package]] @@ -5256,7 +5147,6 @@ description = "Traceback serialization library." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "tblib-3.0.0-py3-none-any.whl", hash = "sha256:80a6c77e59b55e83911e1e607c649836a69c103963c5f28a46cbeef44acf8129"}, {file = "tblib-3.0.0.tar.gz", hash = "sha256:93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6"}, @@ -5269,7 +5159,6 @@ description = "Retry code until it succeeds" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "tenacity-9.0.0-py3-none-any.whl", hash = "sha256:93de0c98785b27fcf659856aa9f54bfbd399e29969b0621bc7f762bd441b4539"}, {file = "tenacity-9.0.0.tar.gz", hash = "sha256:807f37ca97d62aa361264d497b0e31e92b8027044942bfa756160d908320d73b"}, @@ -5286,7 +5175,6 @@ description = "ANSI color formatting for output in terminal" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "termcolor-2.3.0-py3-none-any.whl", hash = "sha256:3afb05607b89aed0ffe25202399ee0867ad4d3cb4180d98aaf8eefa6a5f7d475"}, {file = "termcolor-2.3.0.tar.gz", hash = "sha256:b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a"}, @@ -5302,7 +5190,7 @@ description = "Tornado websocket backend for the Xterm.js Javascript terminal em optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "terminado-0.18.1-py3-none-any.whl", hash = "sha256:a4468e1b37bb318f8a86514f65814e1afc977cf29b3992a4500d9dd305dcceb0"}, {file = "terminado-0.18.1.tar.gz", hash = "sha256:de09f2c4b85de4765f7714688fff57d3e75bad1f909b589fde880460c753fd2e"}, @@ -5325,7 +5213,7 @@ description = "A tiny CSS parser" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "tinycss2-1.4.0-py3-none-any.whl", hash = "sha256:3a49cf47b7675da0b15d0c6e1df8df4ebd96e9394bb905a5775adb0d884c5289"}, {file = "tinycss2-1.4.0.tar.gz", hash = "sha256:10c0972f6fc0fbee87c3edb76549357415e94548c1ae10ebccdea16fb404a9b7"}, @@ -5345,7 +5233,7 @@ description = "A lil' TOML parser" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_full_version <= \"3.11.0a6\" and extra == \"dev\"" +markers = "extra == \"dev\" and python_version == \"3.10\"" files = [ {file = "tomli-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249"}, {file = "tomli-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6"}, @@ -5388,7 +5276,6 @@ description = "List processing tools and functional utilities" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "toolz-1.0.0-py3-none-any.whl", hash = "sha256:292c8f1c4e7516bf9086f8850935c799a874039c8bcf959d47b600e4c44a6236"}, {file = "toolz-1.0.0.tar.gz", hash = "sha256:2c86e3d9a04798ac556793bced838816296a2f085017664e4995cb40a1047a02"}, @@ -5401,7 +5288,6 @@ description = "Tornado is a Python web framework and asynchronous networking lib optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "tornado-6.4.2-cp38-abi3-macosx_10_9_universal2.whl", hash = "sha256:e828cce1123e9e44ae2a50a9de3055497ab1d0aeb440c5ac23064d9e44880da1"}, {file = "tornado-6.4.2-cp38-abi3-macosx_10_9_x86_64.whl", hash = "sha256:072ce12ada169c5b00b7d92a99ba089447ccc993ea2143c9ede887e0937aa803"}, @@ -5423,7 +5309,6 @@ description = "Fast, Extensible Progress Meter" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "tqdm-4.67.1-py3-none-any.whl", hash = "sha256:26445eca388f82e72884e0d580d5464cd801a3ea01e63e5601bdff9ba6a48de2"}, {file = "tqdm-4.67.1.tar.gz", hash = "sha256:f8aef9c52c08c13a65f30ea34f4e5aac3fd1a34959879d7e59e63027286627f2"}, @@ -5446,7 +5331,6 @@ description = "Traitlets Python configuration system" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"}, {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"}, @@ -5463,7 +5347,6 @@ description = "Scipy trait types" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "traittypes-0.2.1-py2.py3-none-any.whl", hash = "sha256:1340af133810b6eee1a2eb2e988f862b0d12b6c2d16f282aaf3207b782134c2e"}, {file = "traittypes-0.2.1.tar.gz", hash = "sha256:be6fa26294733e7489822ded4ae25da5b4824a8a7a0e0c2dccfde596e3489bd6"}, @@ -5482,7 +5365,6 @@ description = "Run-time type checker for Python" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "typeguard-4.4.1-py3-none-any.whl", hash = "sha256:9324ec07a27ec67fc54a9c063020ca4c0ae6abad5e9f0f9804ca59aee68c6e21"}, {file = "typeguard-4.4.1.tar.gz", hash = "sha256:0d22a89d00b453b47c49875f42b6601b961757541a2e1e0ef517b6e24213c21b"}, @@ -5493,7 +5375,7 @@ typing-extensions = ">=4.10.0" [package.extras] doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.3.0)"] -test = ["coverage[toml] (>=7)", "mypy (>=1.2.0)", "pytest (>=7)"] +test = ["coverage[toml] (>=7)", "mypy (>=1.2.0) ; platform_python_implementation != \"PyPy\"", "pytest (>=7)"] [[package]] name = "types-python-dateutil" @@ -5502,7 +5384,7 @@ description = "Typing stubs for python-dateutil" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "types-python-dateutil-2.9.0.20241003.tar.gz", hash = "sha256:58cb85449b2a56d6684e41aeefb4c4280631246a0da1a719bdbe6f3fb0317446"}, {file = "types_python_dateutil-2.9.0.20241003-py3-none-any.whl", hash = "sha256:250e1d8e80e7bbc3a6c99b907762711d1a1cdd00e978ad39cb5940f6f0a87f3d"}, @@ -5515,7 +5397,7 @@ description = "Typing stubs for pytz" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "types-pytz-2024.2.0.20241003.tar.gz", hash = "sha256:575dc38f385a922a212bac00a7d6d2e16e141132a3c955078f4a4fd13ed6cb44"}, {file = "types_pytz-2024.2.0.20241003-py3-none-any.whl", hash = "sha256:3e22df1336c0c6ad1d29163c8fda82736909eb977281cb823c57f8bae07118b7"}, @@ -5528,7 +5410,6 @@ description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, @@ -5541,7 +5422,6 @@ description = "Provider of IANA time zone data" optional = false python-versions = ">=2" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"}, {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"}, @@ -5554,7 +5434,7 @@ description = "RFC 6570 URI Template Processor" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "uri-template-1.3.0.tar.gz", hash = "sha256:0e00f8eb65e18c7de20d595a14336e9f337ead580c70934141624b6d1ffdacc7"}, {file = "uri_template-1.3.0-py3-none-any.whl", hash = "sha256:a44a133ea12d44a0c0f06d7d42a52d71282e77e2f937d8abd5655b8d56fc1363"}, @@ -5570,14 +5450,13 @@ description = "HTTP library with thread-safe connection pooling, file post, and optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "urllib3-2.2.3-py3-none-any.whl", hash = "sha256:ca899ca043dcb1bafa3e262d73aa25c465bfb49e0bd9dd5d59f1d0acba2f8fac"}, {file = "urllib3-2.2.3.tar.gz", hash = "sha256:e7d814a81dad81e6caf2ec9fdedb284ecc9c73076b62654547cc64ccdcae26e9"}, ] [package.extras] -brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""] h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] @@ -5589,7 +5468,7 @@ description = "Virtual Python Environment builder" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "virtualenv-20.28.0-py3-none-any.whl", hash = "sha256:23eae1b4516ecd610481eda647f3a7c09aea295055337331bb4e6892ecce47b0"}, {file = "virtualenv-20.28.0.tar.gz", hash = "sha256:2c9c3262bb8e7b87ea801d715fae4495e6032450c71d2309be9550e7364049aa"}, @@ -5602,7 +5481,7 @@ platformdirs = ">=3.9.1,<5" [package.extras] docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] -test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] +test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""] [[package]] name = "wcwidth" @@ -5611,7 +5490,6 @@ description = "Measures the displayed width of unicode strings in a terminal" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, @@ -5624,7 +5502,7 @@ description = "A library for working with the color formats defined by HTML and optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "webcolors-24.11.1-py3-none-any.whl", hash = "sha256:515291393b4cdf0eb19c155749a096f779f7d909f7cceea072791cb9095b92e9"}, {file = "webcolors-24.11.1.tar.gz", hash = "sha256:ecb3d768f32202af770477b8b65f318fa4f566c22948673a977b00d589dd80f6"}, @@ -5637,7 +5515,7 @@ description = "Character encoding aliases for legacy web content" optional = false python-versions = "*" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"}, {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"}, @@ -5650,7 +5528,7 @@ description = "WebSocket client for Python with low level API options" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" and extra == \"dev\" or python_version >= \"3.12\" and extra == \"dev\"" +markers = "extra == \"dev\"" files = [ {file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"}, {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"}, @@ -5668,7 +5546,6 @@ description = "The comprehensive WSGI web application library." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "werkzeug-3.0.6-py3-none-any.whl", hash = "sha256:1bc0c2310d2fbb07b1dd1105eba2f7af72f322e1e455f2f93c993bee8c8a5f17"}, {file = "werkzeug-3.0.6.tar.gz", hash = "sha256:a8dd59d4de28ca70471a34cba79bed5f7ef2e036a76b3ab0835474246eb41f8d"}, @@ -5687,7 +5564,6 @@ description = "Jupyter interactive widgets for Jupyter Notebook" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "widgetsnbextension-4.0.13-py3-none-any.whl", hash = "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71"}, {file = "widgetsnbextension-4.0.13.tar.gz", hash = "sha256:ffcb67bc9febd10234a362795f643927f4e0c05d9342c727b65d2384f8feacb6"}, @@ -5700,7 +5576,6 @@ description = "Module for decorators, wrappers and monkey patching." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "wrapt-1.17.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2a0c23b8319848426f305f9cb0c98a6e32ee68a36264f45948ccf8e7d2b941f8"}, {file = "wrapt-1.17.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b1ca5f060e205f72bec57faae5bd817a1560fcfc4af03f414b08fa29106b7e2d"}, @@ -5776,7 +5651,6 @@ description = "N-D labeled arrays and datasets in Python" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "xarray-2024.11.0-py3-none-any.whl", hash = "sha256:6ee94f63ddcbdd0cf3909d1177f78cdac756640279c0e32ae36819a89cdaba37"}, {file = "xarray-2024.11.0.tar.gz", hash = "sha256:1ccace44573ddb862e210ad3ec204210654d2c750bec11bbe7d842dfc298591f"}, @@ -5792,7 +5666,7 @@ accel = ["bottleneck", "flox", "numba (>=0.54)", "numbagg", "opt_einsum", "scipy complete = ["xarray[accel,etc,io,parallel,viz]"] dev = ["hypothesis", "jinja2", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-env", "pytest-timeout", "pytest-xdist", "ruff", "sphinx", "sphinx_autosummary_accessors", "xarray[complete]"] etc = ["sparse"] -io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "scipy", "zarr"] +io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap ; python_version < \"3.10\"", "scipy", "zarr"] parallel = ["dask[complete]"] viz = ["cartopy", "matplotlib", "nc-time-axis", "seaborn"] @@ -5803,7 +5677,6 @@ description = "Source of XYZ tiles providers" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "xyzservices-2024.9.0-py3-none-any.whl", hash = "sha256:776ae82b78d6e5ca63dd6a94abb054df8130887a4a308473b54a6bd364de8644"}, {file = "xyzservices-2024.9.0.tar.gz", hash = "sha256:68fb8353c9dbba4f1ff6c0f2e5e4e596bb9e1db7f94f4f7dfbcb26e25aa66fde"}, @@ -5816,7 +5689,6 @@ description = "Yet another URL library" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "yarl-1.18.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7df647e8edd71f000a5208fe6ff8c382a1de8edfbccdbbfe649d263de07d8c34"}, {file = "yarl-1.18.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c69697d3adff5aa4f874b19c0e4ed65180ceed6318ec856ebc423aa5850d84f7"}, @@ -5914,7 +5786,6 @@ description = "Yet Another Terminal Spinner" optional = false python-versions = "<4.0,>=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "yaspin-3.1.0-py3-none-any.whl", hash = "sha256:5e3d4dfb547d942cae6565718123f1ecfa93e745b7e51871ad2bbae839e71b73"}, {file = "yaspin-3.1.0.tar.gz", hash = "sha256:7b97c7e257ec598f98cef9878e038bfa619ceb54ac31d61d8ead2b3128f8d7c7"}, @@ -5930,7 +5801,6 @@ description = "An implementation of chunked, compressed, N-dimensional arrays fo optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "zarr-2.18.3-py3-none-any.whl", hash = "sha256:b1f7dfd2496f436745cdd4c7bcf8d3b4bc1dceef5fdd0d589c87130d842496dd"}, {file = "zarr-2.18.3.tar.gz", hash = "sha256:2580d8cb6dd84621771a10d31c4d777dca8a27706a1a89b29f42d2d37e2df5ce"}, @@ -5953,7 +5823,6 @@ description = "Mutable mapping tools" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "zict-3.0.0-py2.py3-none-any.whl", hash = "sha256:5796e36bd0e0cc8cf0fbc1ace6a68912611c1dbd74750a3f3026b9b9d6a327ae"}, {file = "zict-3.0.0.tar.gz", hash = "sha256:e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5"}, @@ -5966,18 +5835,17 @@ description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version <= \"3.11\" or python_version >= \"3.12\"" files = [ {file = "zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"}, {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"}, ] [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +test = ["big-O", "importlib-resources ; python_version < \"3.9\"", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] type = ["pytest-mypy"] [extras] @@ -5986,4 +5854,4 @@ dev = ["jupyterlab", "memory-profiler", "mypy", "notebook", "pandas-stubs", "pre [metadata] lock-version = "2.1" python-versions = ">=3.10,<3.13" -content-hash = "d6919913d2daade4ac3ff27f8813d3286edb5129809eda93f2fc9cb3c032cd88" +content-hash = "e2dc0c54942b1e2261de9c28a0c3750350ff2bb6aa20700a71ec8fba81e1382a" diff --git a/pyproject.toml b/pyproject.toml index af428de94..f6d2cd953 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -84,6 +84,7 @@ sphinx = "*" pydata-sphinx-theme = "*" sphinx_design = "*" pandas-stubs = "*" +ipykernel = "^6.29.5" [tool.poetry.extras] dev = ["pytest", "pytest-xdist", "pytest-cases", "pytest-cov", "notebook", "jupyterlab", "pre-commit", "ruff", "snakeviz", "mypy", "memory-profiler", "sphinx", "pydata-sphinx-theme", "sphinx_design", "pandas-stubs"] From 15c9b2869c87b75b0c877d05cb59c77f41eabb7f Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Mon, 9 Jun 2025 14:45:18 +1000 Subject: [PATCH 07/12] add adir1 class for anopheles dirus data release --- adir1_explore.ipynb | 451 ++++++++++++++++++++++++++++++++++++ malariagen_data/__init__.py | 1 + malariagen_data/adir1.py | 208 +++++++++++++++++ 3 files changed, 660 insertions(+) create mode 100644 adir1_explore.ipynb create mode 100644 malariagen_data/adir1.py diff --git a/adir1_explore.ipynb b/adir1_explore.ipynb new file mode 100644 index 000000000..c42d93dd5 --- /dev/null +++ b/adir1_explore.ipynb @@ -0,0 +1,451 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import malariagen_data" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "application/javascript": [ + "'use strict';\n", + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " const force = true;\n", + "\n", + " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", + " root._bokeh_onload_callbacks = [];\n", + " root._bokeh_is_loading = undefined;\n", + " }\n", + "\n", + "const JS_MIME_TYPE = 'application/javascript';\n", + " const HTML_MIME_TYPE = 'text/html';\n", + " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", + " const CLASS_NAME = 'output_bokeh rendered_html';\n", + "\n", + " /**\n", + " * Render data to the DOM node\n", + " */\n", + " function render(props, node) {\n", + " const script = document.createElement(\"script\");\n", + " node.appendChild(script);\n", + " }\n", + "\n", + " /**\n", + " * Handle when an output is cleared or removed\n", + " */\n", + " function handleClearOutput(event, handle) {\n", + " function drop(id) {\n", + " const view = Bokeh.index.get_by_id(id)\n", + " if (view != null) {\n", + " view.model.document.clear()\n", + " Bokeh.index.delete(view)\n", + " }\n", + " }\n", + "\n", + " const cell = handle.cell;\n", + "\n", + " const id = cell.output_area._bokeh_element_id;\n", + " const server_id = cell.output_area._bokeh_server_id;\n", + "\n", + " // Clean up Bokeh references\n", + " if (id != null) {\n", + " drop(id)\n", + " }\n", + "\n", + " if (server_id !== undefined) {\n", + " // Clean up Bokeh references\n", + " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", + " cell.notebook.kernel.execute(cmd_clean, {\n", + " iopub: {\n", + " output: function(msg) {\n", + " const id = msg.content.text.trim()\n", + " drop(id)\n", + " }\n", + " }\n", + " });\n", + " // Destroy server and session\n", + " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", + " cell.notebook.kernel.execute(cmd_destroy);\n", + " }\n", + " }\n", + "\n", + " /**\n", + " * Handle when a new output is added\n", + " */\n", + " function handleAddOutput(event, handle) {\n", + " const output_area = handle.output_area;\n", + " const output = handle.output;\n", + "\n", + " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", + " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", + " return\n", + " }\n", + "\n", + " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", + "\n", + " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", + " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", + " // store reference to embed id on output_area\n", + " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", + " }\n", + " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", + " const bk_div = document.createElement(\"div\");\n", + " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", + " const script_attrs = bk_div.children[0].attributes;\n", + " for (let i = 0; i < script_attrs.length; i++) {\n", + " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", + " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", + " }\n", + " // store reference to server id on output_area\n", + " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", + " }\n", + " }\n", + "\n", + " function register_renderer(events, OutputArea) {\n", + "\n", + " function append_mime(data, metadata, element) {\n", + " // create a DOM node to render to\n", + " const toinsert = this.create_output_subarea(\n", + " metadata,\n", + " CLASS_NAME,\n", + " EXEC_MIME_TYPE\n", + " );\n", + " this.keyboard_manager.register_events(toinsert);\n", + " // Render to node\n", + " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", + " render(props, toinsert[toinsert.length - 1]);\n", + " element.append(toinsert);\n", + " return toinsert\n", + " }\n", + "\n", + " /* Handle when an output is cleared or removed */\n", + " events.on('clear_output.CodeCell', handleClearOutput);\n", + " events.on('delete.Cell', handleClearOutput);\n", + "\n", + " /* Handle when a new output is added */\n", + " events.on('output_added.OutputArea', handleAddOutput);\n", + "\n", + " /**\n", + " * Register the mime type and append_mime function with output_area\n", + " */\n", + " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", + " /* Is output safe? */\n", + " safe: true,\n", + " /* Index of renderer in `output_area.display_order` */\n", + " index: 0\n", + " });\n", + " }\n", + "\n", + " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", + " if (root.Jupyter !== undefined) {\n", + " const events = require('base/js/events');\n", + " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", + "\n", + " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", + " register_renderer(events, OutputArea);\n", + " }\n", + " }\n", + " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", + " root._bokeh_timeout = Date.now() + 5000;\n", + " root._bokeh_failed_load = false;\n", + " }\n", + "\n", + " const NB_LOAD_WARNING = {'data': {'text/html':\n", + " \"
\\n\"+\n", + " \"

\\n\"+\n", + " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", + " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", + " \"

\\n\"+\n", + " \"
    \\n\"+\n", + " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n", + " \"
  • use INLINE resources instead, as so:
  • \\n\"+\n", + " \"
\\n\"+\n", + " \"\\n\"+\n", + " \"from bokeh.resources import INLINE\\n\"+\n", + " \"output_notebook(resources=INLINE)\\n\"+\n", + " \"\\n\"+\n", + " \"
\"}};\n", + "\n", + " function display_loaded(error = null) {\n", + " const el = document.getElementById(null);\n", + " if (el != null) {\n", + " const html = (() => {\n", + " if (typeof root.Bokeh === \"undefined\") {\n", + " if (error == null) {\n", + " return \"BokehJS is loading ...\";\n", + " } else {\n", + " return \"BokehJS failed to load.\";\n", + " }\n", + " } else {\n", + " const prefix = `BokehJS ${root.Bokeh.version}`;\n", + " if (error == null) {\n", + " return `${prefix} successfully loaded.`;\n", + " } else {\n", + " return `${prefix} encountered errors while loading and may not function as expected.`;\n", + " }\n", + " }\n", + " })();\n", + " el.innerHTML = html;\n", + "\n", + " if (error != null) {\n", + " const wrapper = document.createElement(\"div\");\n", + " wrapper.style.overflow = \"auto\";\n", + " wrapper.style.height = \"5em\";\n", + " wrapper.style.resize = \"vertical\";\n", + " const content = document.createElement(\"div\");\n", + " content.style.fontFamily = \"monospace\";\n", + " content.style.whiteSpace = \"pre-wrap\";\n", + " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", + " content.textContent = error.stack ?? error.toString();\n", + " wrapper.append(content);\n", + " el.append(wrapper);\n", + " }\n", + " } else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(() => display_loaded(error), 100);\n", + " }\n", + " }\n", + "\n", + " function run_callbacks() {\n", + " try {\n", + " root._bokeh_onload_callbacks.forEach(function(callback) {\n", + " if (callback != null)\n", + " callback();\n", + " });\n", + " } finally {\n", + " delete root._bokeh_onload_callbacks\n", + " }\n", + " console.debug(\"Bokeh: all callbacks have finished\");\n", + " }\n", + "\n", + " function load_libs(css_urls, js_urls, callback) {\n", + " if (css_urls == null) css_urls = [];\n", + " if (js_urls == null) js_urls = [];\n", + "\n", + " root._bokeh_onload_callbacks.push(callback);\n", + " if (root._bokeh_is_loading > 0) {\n", + " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", + " return null;\n", + " }\n", + " if (js_urls == null || js_urls.length === 0) {\n", + " run_callbacks();\n", + " return null;\n", + " }\n", + " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", + " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", + "\n", + " function on_load() {\n", + " root._bokeh_is_loading--;\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", + " run_callbacks()\n", + " }\n", + " }\n", + "\n", + " function on_error(url) {\n", + " console.error(\"failed to load \" + url);\n", + " }\n", + "\n", + " for (let i = 0; i < css_urls.length; i++) {\n", + " const url = css_urls[i];\n", + " const element = document.createElement(\"link\");\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.rel = \"stylesheet\";\n", + " element.type = \"text/css\";\n", + " element.href = url;\n", + " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " for (let i = 0; i < js_urls.length; i++) {\n", + " const url = js_urls[i];\n", + " const element = document.createElement('script');\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.async = false;\n", + " element.src = url;\n", + " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", + " document.head.appendChild(element);\n", + " }\n", + " };\n", + "\n", + " function inject_raw_css(css) {\n", + " const element = document.createElement(\"style\");\n", + " element.appendChild(document.createTextNode(css));\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", + " const css_urls = [];\n", + "\n", + " const inline_js = [ function(Bokeh) {\n", + " Bokeh.set_log_level(\"info\");\n", + " },\n", + "function(Bokeh) {\n", + " }\n", + " ];\n", + "\n", + " function run_inline_js() {\n", + " if (root.Bokeh !== undefined || force === true) {\n", + " try {\n", + " for (let i = 0; i < inline_js.length; i++) {\n", + " inline_js[i].call(root, root.Bokeh);\n", + " }\n", + "\n", + " } catch (error) {throw error;\n", + " }} else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(run_inline_js, 100);\n", + " } else if (!root._bokeh_failed_load) {\n", + " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", + " root._bokeh_failed_load = true;\n", + " } else if (force !== true) {\n", + " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", + " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", + " }\n", + " }\n", + "\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", + " run_inline_js();\n", + " } else {\n", + " load_libs(css_urls, js_urls, function() {\n", + " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", + " run_inline_js();\n", + " });\n", + " }\n", + "}(window));" + ], + "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n \"
  • use INLINE resources instead, as so:
  • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# Init API\n", + "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "f171c3b7-30c2-4e9f-9133-22206985de07", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "'KB672868'" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Are the contigs here? \n", + "chroms = adir1.contigs[:5]\n", + "chroms[1]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "ename": "FileNotFoundError", + "evalue": "b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:426\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 425\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_sets\u001b[49m\u001b[43m[\u001b[49m\u001b[43mrelease\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n", + "\u001b[0;31mKeyError\u001b[0m: '1.x'", + "\nDuring handling of the above exception, another exception occurred:\n", + "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[7], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m snps \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msnp_calls\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868:1000000-2000000\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/snp_data.py:1007\u001b[0m, in \u001b[0;36mAnophelesSnpData.snp_calls\u001b[0;34m(self, region, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, inline_array, chunks, cohort_size, min_cohort_size, max_cohort_size, random_seed)\u001b[0m\n\u001b[1;32m 1001\u001b[0m base_params\u001b[38;5;241m.\u001b[39mvalidate_sample_selection_params(\n\u001b[1;32m 1002\u001b[0m sample_query\u001b[38;5;241m=\u001b[39msample_query, sample_indices\u001b[38;5;241m=\u001b[39msample_indices\n\u001b[1;32m 1003\u001b[0m )\n\u001b[1;32m 1005\u001b[0m \u001b[38;5;66;03m# Normalise parameters.\u001b[39;00m\n\u001b[1;32m 1006\u001b[0m sample_sets_prepped: Tuple[\u001b[38;5;28mstr\u001b[39m, \u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mtuple\u001b[39m(\n\u001b[0;32m-> 1007\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_sets_param\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1008\u001b[0m )\n\u001b[1;32m 1009\u001b[0m \u001b[38;5;28;01mdel\u001b[39;00m sample_sets\n\u001b[1;32m 1010\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_indices \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:524\u001b[0m, in \u001b[0;36mAnophelesBase._prep_sample_sets_param\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 517\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_prep_sample_sets_param\u001b[39m(\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets]\n\u001b[1;32m 519\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m List[\u001b[38;5;28mstr\u001b[39m]:\n\u001b[1;32m 520\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Common handling for the `sample_sets` parameter. For convenience, we\u001b[39;00m\n\u001b[1;32m 521\u001b[0m \u001b[38;5;124;03m allow this to be a single sample set, or a list of sample sets, or a\u001b[39;00m\n\u001b[1;32m 522\u001b[0m \u001b[38;5;124;03m release identifier, or a list of release identifiers.\"\"\"\u001b[39;00m\n\u001b[0;32m--> 524\u001b[0m all_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mto_list()\n\u001b[1;32m 526\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_sets \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 527\u001b[0m \u001b[38;5;66;03m# All available sample sets.\u001b[39;00m\n\u001b[1;32m 528\u001b[0m prepped_sample_sets \u001b[38;5;241m=\u001b[39m all_sample_sets\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets(release\u001b[38;5;241m=\u001b[39mr) \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36m\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrelease\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mr\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:430\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release]\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n\u001b[0;32m--> 430\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_read_sample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43msingle_release\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrelease\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 431\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release] \u001b[38;5;241m=\u001b[39m df\n\u001b[1;32m 433\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(release, Sequence):\n\u001b[1;32m 434\u001b[0m \u001b[38;5;66;03m# Ensure no duplicates.\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:376\u001b[0m, in \u001b[0;36mAnophelesBase._read_sample_sets\u001b[0;34m(self, single_release)\u001b[0m\n\u001b[1;32m 373\u001b[0m manifest_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mrelease_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/manifest.tsv\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 375\u001b[0m \u001b[38;5;66;03m# Read the manifest into a pandas dataframe.\u001b[39;00m\n\u001b[0;32m--> 376\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen_file\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmanifest_path\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m 377\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mread_csv(f, sep\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;130;01m\\t\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, na_values\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 379\u001b[0m \u001b[38;5;66;03m# Add a \"release\" column for convenience.\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:218\u001b[0m, in \u001b[0;36mAnophelesBase.open_file\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 215\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 216\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mopen_file\u001b[39m(\u001b[38;5;28mself\u001b[39m, path: \u001b[38;5;28mstr\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m IO:\n\u001b[1;32m 217\u001b[0m full_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_base_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m--> 218\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfull_path\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/spec.py:1154\u001b[0m, in \u001b[0;36mAbstractFileSystem.open\u001b[0;34m(self, path, mode, block_size, cache_options, compression, **kwargs)\u001b[0m\n\u001b[1;32m 1152\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 1153\u001b[0m ac \u001b[38;5;241m=\u001b[39m kwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mautocommit\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_intrans)\n\u001b[0;32m-> 1154\u001b[0m f \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_open\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1155\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1156\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1157\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1158\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mac\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1159\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1160\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1161\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1162\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m compression \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfsspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcompression\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m compr\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1309\u001b[0m, in \u001b[0;36mGCSFileSystem._open\u001b[0;34m(self, path, mode, block_size, cache_options, acl, consistency, metadata, autocommit, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1307\u001b[0m block_size \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_block_size\n\u001b[1;32m 1308\u001b[0m const \u001b[38;5;241m=\u001b[39m consistency \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconsistency\n\u001b[0;32m-> 1309\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mGCSFile\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1311\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1312\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1313\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1314\u001b[0m \u001b[43m 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\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1321\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1468\u001b[0m, in \u001b[0;36mGCSFile.__init__\u001b[0;34m(self, gcsfs, path, mode, block_size, autocommit, cache_type, cache_options, acl, consistency, metadata, content_type, timeout, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1466\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAttempt to open a bucket\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1467\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgeneration \u001b[38;5;241m=\u001b[39m _coalesce_generation(generation, path_generation)\n\u001b[0;32m-> 1468\u001b[0m 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1509\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m-> 1510\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdetails\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msize\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[1;32m 1511\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcache \u001b[38;5;241m=\u001b[39m caches[cache_type](\n\u001b[1;32m 1512\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mblocksize, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_fetch_range, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mcache_options\n\u001b[1;32m 1513\u001b[0m )\n\u001b[1;32m 1514\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1504\u001b[0m, in \u001b[0;36mGCSFile.details\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1501\u001b[0m \u001b[38;5;129m@property\u001b[39m\n\u001b[1;32m 1502\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdetails\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[1;32m 1503\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m-> 1504\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43minfo\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m 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\u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43msync\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mloop\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfunc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:100\u001b[0m, in \u001b[0;36msync\u001b[0;34m(loop, func, timeout, *args, **kwargs)\u001b[0m\n\u001b[1;32m 98\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m FSTimeoutError \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mreturn_result\u001b[39;00m\n\u001b[1;32m 99\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(return_result, \u001b[38;5;167;01mBaseException\u001b[39;00m):\n\u001b[0;32m--> 100\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m return_result\n\u001b[1;32m 101\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 102\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m return_result\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:55\u001b[0m, in \u001b[0;36m_runner\u001b[0;34m(event, coro, result, timeout)\u001b[0m\n\u001b[1;32m 53\u001b[0m coro \u001b[38;5;241m=\u001b[39m asyncio\u001b[38;5;241m.\u001b[39mwait_for(coro, timeout\u001b[38;5;241m=\u001b[39mtimeout)\n\u001b[1;32m 54\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 55\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m coro\n\u001b[1;32m 56\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m ex:\n\u001b[1;32m 57\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m ex\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:797\u001b[0m, in \u001b[0;36mGCSFileSystem._info\u001b[0;34m(self, path, generation, **kwargs)\u001b[0m\n\u001b[1;32m 795\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 796\u001b[0m kwargs[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdetail\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m \u001b[38;5;66;03m# Force to true for info\u001b[39;00m\n\u001b[0;32m--> 797\u001b[0m out \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ls(path, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 798\u001b[0m out0 \u001b[38;5;241m=\u001b[39m [o \u001b[38;5;28;01mfor\u001b[39;00m o \u001b[38;5;129;01min\u001b[39;00m out \u001b[38;5;28;01mif\u001b[39;00m o[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mname\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mrstrip(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;241m==\u001b[39m path]\n\u001b[1;32m 799\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m out0:\n\u001b[1;32m 800\u001b[0m \u001b[38;5;66;03m# exact hit\u001b[39;00m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:834\u001b[0m, in \u001b[0;36mGCSFileSystem._ls\u001b[0;34m(self, path, detail, prefix, versions, **kwargs)\u001b[0m\n\u001b[1;32m 832\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 833\u001b[0m out \u001b[38;5;241m=\u001b[39m []\n\u001b[0;32m--> 834\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m entry \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_list_objects(\n\u001b[1;32m 835\u001b[0m path, prefix\u001b[38;5;241m=\u001b[39mprefix, versions\u001b[38;5;241m=\u001b[39mversions\n\u001b[1;32m 836\u001b[0m ):\n\u001b[1;32m 837\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m versions \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgeneration\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m entry:\n\u001b[1;32m 838\u001b[0m entry \u001b[38;5;241m=\u001b[39m entry\u001b[38;5;241m.\u001b[39mcopy()\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:549\u001b[0m, in \u001b[0;36mGCSFileSystem._list_objects\u001b[0;34m(self, path, prefix, versions)\u001b[0m\n\u001b[1;32m 547\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m (items \u001b[38;5;241m+\u001b[39m pseudodirs):\n\u001b[1;32m 548\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m key:\n\u001b[0;32m--> 549\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m [\u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_object(path)]\n\u001b[1;32m 550\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 551\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m []\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:491\u001b[0m, in \u001b[0;36mGCSFileSystem._get_object\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 488\u001b[0m \u001b[38;5;66;03m# Work around various permission settings. Prefer an object get (storage.objects.get), but\u001b[39;00m\n\u001b[1;32m 489\u001b[0m \u001b[38;5;66;03m# fall back to a bucket list + filter to object name (storage.objects.list).\u001b[39;00m\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 491\u001b[0m res \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_call(\n\u001b[1;32m 492\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGET\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mb/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m/o/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, bucket, key, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m, generation\u001b[38;5;241m=\u001b[39mgeneration\n\u001b[1;32m 493\u001b[0m )\n\u001b[1;32m 494\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 495\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mstr\u001b[39m(e)\u001b[38;5;241m.\u001b[39mstartswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mForbidden\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:418\u001b[0m, in \u001b[0;36mGCSFileSystem._call\u001b[0;34m(self, method, path, json_out, info_out, *args, **kwargs)\u001b[0m\n\u001b[1;32m 414\u001b[0m \u001b[38;5;28;01masync\u001b[39;00m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_call\u001b[39m(\n\u001b[1;32m 415\u001b[0m \u001b[38;5;28mself\u001b[39m, method, path, \u001b[38;5;241m*\u001b[39margs, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, info_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 416\u001b[0m ):\n\u001b[1;32m 417\u001b[0m logger\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mmethod\u001b[38;5;241m.\u001b[39mupper()\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00margs\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mheaders\u001b[39m\u001b[38;5;124m'\u001b[39m)\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 418\u001b[0m status, headers, info, contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_request(\n\u001b[1;32m 419\u001b[0m method, path, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 420\u001b[0m )\n\u001b[1;32m 421\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m json_out:\n\u001b[1;32m 422\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m json\u001b[38;5;241m.\u001b[39mloads(contents)\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/decorator.py:221\u001b[0m, in \u001b[0;36mdecorate..fun\u001b[0;34m(*args, **kw)\u001b[0m\n\u001b[1;32m 219\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m kwsyntax:\n\u001b[1;32m 220\u001b[0m args, kw \u001b[38;5;241m=\u001b[39m fix(args, kw, sig)\n\u001b[0;32m--> 221\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m caller(func, \u001b[38;5;241m*\u001b[39m(extras \u001b[38;5;241m+\u001b[39m args), \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkw)\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:114\u001b[0m, in \u001b[0;36mretry_request\u001b[0;34m(func, retries, *args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m retry \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m asyncio\u001b[38;5;241m.\u001b[39msleep(\u001b[38;5;28mmin\u001b[39m(random\u001b[38;5;241m.\u001b[39mrandom() \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m2\u001b[39m \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39m (retry \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m), \u001b[38;5;241m32\u001b[39m))\n\u001b[0;32m--> 114\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m func(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 115\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (\n\u001b[1;32m 116\u001b[0m HttpError,\n\u001b[1;32m 117\u001b[0m requests\u001b[38;5;241m.\u001b[39mexceptions\u001b[38;5;241m.\u001b[39mRequestException,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 120\u001b[0m aiohttp\u001b[38;5;241m.\u001b[39mclient_exceptions\u001b[38;5;241m.\u001b[39mClientError,\n\u001b[1;32m 121\u001b[0m ) \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 122\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\n\u001b[1;32m 123\u001b[0m \u001b[38;5;28misinstance\u001b[39m(e, HttpError)\n\u001b[1;32m 124\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m e\u001b[38;5;241m.\u001b[39mcode \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m400\u001b[39m\n\u001b[1;32m 125\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mrequester pays\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m e\u001b[38;5;241m.\u001b[39mmessage\n\u001b[1;32m 126\u001b[0m ):\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:411\u001b[0m, in \u001b[0;36mGCSFileSystem._request\u001b[0;34m(self, method, path, headers, json, data, *args, **kwargs)\u001b[0m\n\u001b[1;32m 408\u001b[0m info \u001b[38;5;241m=\u001b[39m r\u001b[38;5;241m.\u001b[39mrequest_info \u001b[38;5;66;03m# for debug only\u001b[39;00m\n\u001b[1;32m 409\u001b[0m contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m r\u001b[38;5;241m.\u001b[39mread()\n\u001b[0;32m--> 411\u001b[0m \u001b[43mvalidate_response\u001b[49m\u001b[43m(\u001b[49m\u001b[43mstatus\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcontents\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43margs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 412\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m status, headers, info, contents\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:83\u001b[0m, in \u001b[0;36mvalidate_response\u001b[0;34m(status, content, path, args)\u001b[0m\n\u001b[1;32m 81\u001b[0m path \u001b[38;5;241m=\u001b[39m path\u001b[38;5;241m.\u001b[39mformat(\u001b[38;5;241m*\u001b[39m[quote(p) \u001b[38;5;28;01mfor\u001b[39;00m p \u001b[38;5;129;01min\u001b[39;00m args])\n\u001b[1;32m 82\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m status \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m404\u001b[39m:\n\u001b[0;32m---> 83\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m(path)\n\u001b[1;32m 85\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 86\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(content, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdecode\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", + "\u001b[0;31mFileNotFoundError\u001b[0m: b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv" + ] + } + ], + "source": [ + "snps = adir1.snp_calls(region=\"KB672868:1000000-2000000\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/malariagen_data/__init__.py b/malariagen_data/__init__.py index dfa555aa7..6bc938825 100644 --- a/malariagen_data/__init__.py +++ b/malariagen_data/__init__.py @@ -1,5 +1,6 @@ # flake8: noqa from .af1 import Af1 +from .adir1 import Adir1 from .ag3 import Ag3 from .amin1 import Amin1 from .anopheles import AnophelesDataResource, Region diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py new file mode 100644 index 000000000..9b053ca62 --- /dev/null +++ b/malariagen_data/adir1.py @@ -0,0 +1,208 @@ +import sys + +import plotly.express as px # type: ignore + +import malariagen_data +from .anopheles import AnophelesDataResource + +MAJOR_VERSION_NUMBER = 1 +MAJOR_VERSION_PATH = "v1.x" +CONFIG_PATH = "v1.x-config.json" +GCS_DEFAULT_URL = "gs://vo_adir_production_us_central1/" +GCS_DEFAULT_PUBLIC_URL = "gs://vo_adir_production_us_central1/v1.x/staging" +GCS_REGION_URLS = { + "us-central1": "gs://vo_adir_production_us_central1", +} +# XPEHH_GWSS_CACHE_NAME = "adir1_xpehh_gwss_v1" +# IHS_GWSS_CACHE_NAME = "adir1_ihs_gwss_v1" + +TAXON_PALETTE = px.colors.qualitative.Plotly +TAXON_COLORS = { + "dirus": TAXON_PALETTE[0], +} + + +class Adir1(AnophelesDataResource): + """Provides access to data from Adir1.x releases. + + Parameters + ---------- + url : str, optional + Base path to data. Defaults to use Google Cloud Storage, or can + be a local path on your file system if data have been downloaded. + site_filters_analysis : str, optional + Site filters analysis version. + bokeh_output_notebook : bool, optional + If True (default), configure bokeh to output plots to the notebook. + results_cache : str, optional + Path to directory on local file system to save results. + log : str or stream, optional + File path or stream output for logging messages. + debug : bool, optional + Set to True to enable debug level logging. + show_progress : bool, optional + If True, show a progress bar during longer-running computations. The default can be overridden using an environmental variable named MGEN_SHOW_PROGRESS. + check_location : bool, optional + If True, use ipinfo to check the location of the client system. + **kwargs + Passed through to fsspec when setting up file system access. + + Examples + -------- + Access data from Google Cloud Storage (default): + + >>> import malariagen_data + >>> adir1 = malariagen_data.Adir1() + + Access data downloaded to a local file system: + + >>> adir1 = malariagen_data.Adir1("/local/path/to/vo_adir_release/") + + Access data from Google Cloud Storage, with caching on the local file system + in a directory named "gcs_cache": + + >>> adir1 = malariagen_data.Adir1( + ... "simplecache::gs://vo_adir_production_us_central1", + ... simplecache=dict(cache_storage="gcs_cache"), + ... ) + + Set up caching of some longer-running computations on the local file system, + in a directory named "results_cache": + + >>> adir1 = malariagen_data.Adir1(results_cache="results_cache") + + """ + + # _xpehh_gwss_cache_name = XPEHH_GWSS_CACHE_NAME + # _ihs_gwss_cache_name = IHS_GWSS_CACHE_NAME + + def __init__( + self, + url=None, + bokeh_output_notebook=True, + results_cache=None, + log=sys.stdout, + debug=False, + show_progress=None, + check_location=True, + cohorts_analysis=None, + site_filters_analysis=None, + discordant_read_calls_analysis=None, + pre=False, + tqdm_class=None, + **storage_options, # used by fsspec via init_filesystem() + ): + super().__init__( + url=url, + config_path=CONFIG_PATH, + cohorts_analysis=cohorts_analysis, + aim_analysis=None, + aim_metadata_dtype=None, + aim_ids=None, + aim_palettes=None, + site_filters_analysis=site_filters_analysis, + discordant_read_calls_analysis=discordant_read_calls_analysis, + default_site_mask="funestus", + default_phasing_analysis="funestus", + default_coverage_calls_analysis="funestus", + bokeh_output_notebook=bokeh_output_notebook, + results_cache=results_cache, + log=log, + debug=debug, + show_progress=show_progress, + check_location=check_location, + pre=pre, + gcs_default_url=GCS_DEFAULT_URL, + gcs_region_urls=GCS_REGION_URLS, + major_version_number=MAJOR_VERSION_NUMBER, + major_version_path=MAJOR_VERSION_PATH, + gff_gene_type="protein_coding_gene", + gff_gene_name_attribute="Note", + gff_default_attributes=("ID", "Parent", "Note", "description"), + storage_options=storage_options, # used by fsspec via init_filesystem() + tqdm_class=tqdm_class, + taxon_colors=TAXON_COLORS, + virtual_contigs=None, + gene_names=None, + inversion_tag_path=None, + ) + + def __repr__(self): + text = ( + f"\n" + f"Storage URL : {self._url}\n" + f"Data releases available : {', '.join(self.releases)}\n" + f"Results cache : {self._results_cache}\n" + # f"Cohorts analysis : {self._cohorts_analysis}\n" + f"Site filters analysis : {self._site_filters_analysis}\n" + f"Software version : malariagen_data {malariagen_data.__version__}\n" + f"Client location : {self.client_location}\n" + f"---\n" + f"Please note that data are subject to terms of use,\n" + f"for more information see https://www.malariagen.net/data\n" + f"or contact support@malariagen.net. For API documentation see \n" + f"https://malariagen.github.io/malariagen-data-python/v{malariagen_data.__version__}/Adir1.html" + ) + return text + + def _repr_html_(self): + html = f""" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
MalariaGEN Adir1 API client
+ Please note that data are subject to terms of use, + for more information see + the MalariaGEN website or contact support@malariagen.net. + See also the Adir1 API docs. +
+ Storage URL + {self._url}
+ Data releases available + {', '.join(self.releases)}
+ Results cache + {self._results_cache}
+ Cohorts analysis + {self._cohorts_analysis}
+ Site filters analysis + {self._site_filters_analysis}
+ Software version + malariagen_data {malariagen_data.__version__}
+ Client location + {self.client_location}
+ """ + return html From 624a21f3c38e70ea3968fe893dea1e8dd2caafd3 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 10 Jun 2025 15:03:15 +1000 Subject: [PATCH 08/12] add notebook exploring / troubleshooting adir1 --- notebooks/adir1_explore.ipynb | 483 ++++++++++++++++++++++++++++++++++ 1 file changed, 483 insertions(+) create mode 100644 notebooks/adir1_explore.ipynb diff --git a/notebooks/adir1_explore.ipynb b/notebooks/adir1_explore.ipynb new file mode 100644 index 000000000..1fa71882d --- /dev/null +++ b/notebooks/adir1_explore.ipynb @@ -0,0 +1,483 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import malariagen_data" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "application/javascript": [ + "'use strict';\n", + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " const force = true;\n", + "\n", + " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", + " root._bokeh_onload_callbacks = [];\n", + " root._bokeh_is_loading = undefined;\n", + " }\n", + "\n", + "const JS_MIME_TYPE = 'application/javascript';\n", + " const HTML_MIME_TYPE = 'text/html';\n", + " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", + " const CLASS_NAME = 'output_bokeh rendered_html';\n", + "\n", + " /**\n", + " * Render data to the DOM node\n", + " */\n", + " function render(props, node) {\n", + " const script = document.createElement(\"script\");\n", + " node.appendChild(script);\n", + " }\n", + "\n", + " /**\n", + " * Handle when an output is cleared or removed\n", + " */\n", + " function handleClearOutput(event, handle) {\n", + " function drop(id) {\n", + " const view = Bokeh.index.get_by_id(id)\n", + " if (view != null) {\n", + " view.model.document.clear()\n", + " Bokeh.index.delete(view)\n", + " }\n", + " }\n", + "\n", + " const cell = handle.cell;\n", + "\n", + " const id = cell.output_area._bokeh_element_id;\n", + " const server_id = cell.output_area._bokeh_server_id;\n", + "\n", + " // Clean up Bokeh references\n", + " if (id != null) {\n", + " drop(id)\n", + " }\n", + "\n", + " if (server_id !== undefined) {\n", + " // Clean up Bokeh references\n", + " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", + " cell.notebook.kernel.execute(cmd_clean, {\n", + " iopub: {\n", + " output: function(msg) {\n", + " const id = msg.content.text.trim()\n", + " drop(id)\n", + " }\n", + " }\n", + " });\n", + " // Destroy server and session\n", + " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", + " cell.notebook.kernel.execute(cmd_destroy);\n", + " }\n", + " }\n", + "\n", + " /**\n", + " * Handle when a new output is added\n", + " */\n", + " function handleAddOutput(event, handle) {\n", + " const output_area = handle.output_area;\n", + " const output = handle.output;\n", + "\n", + " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", + " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", + " return\n", + " }\n", + "\n", + " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", + "\n", + " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", + " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", + " // store reference to embed id on output_area\n", + " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", + " }\n", + " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", + " const bk_div = document.createElement(\"div\");\n", + " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", + " const script_attrs = bk_div.children[0].attributes;\n", + " for (let i = 0; i < script_attrs.length; i++) {\n", + " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", + " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", + " }\n", + " // store reference to server id on output_area\n", + " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", + " }\n", + " }\n", + "\n", + " function register_renderer(events, OutputArea) {\n", + "\n", + " function append_mime(data, metadata, element) {\n", + " // create a DOM node to render to\n", + " const toinsert = this.create_output_subarea(\n", + " metadata,\n", + " CLASS_NAME,\n", + " EXEC_MIME_TYPE\n", + " );\n", + " this.keyboard_manager.register_events(toinsert);\n", + " // Render to node\n", + " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", + " render(props, toinsert[toinsert.length - 1]);\n", + " element.append(toinsert);\n", + " return toinsert\n", + " }\n", + "\n", + " /* Handle when an output is cleared or removed */\n", + " events.on('clear_output.CodeCell', handleClearOutput);\n", + " events.on('delete.Cell', handleClearOutput);\n", + "\n", + " /* Handle when a new output is added */\n", + " events.on('output_added.OutputArea', handleAddOutput);\n", + "\n", + " /**\n", + " * Register the mime type and append_mime function with output_area\n", + " */\n", + " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", + " /* Is output safe? */\n", + " safe: true,\n", + " /* Index of renderer in `output_area.display_order` */\n", + " index: 0\n", + " });\n", + " }\n", + "\n", + " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", + " if (root.Jupyter !== undefined) {\n", + " const events = require('base/js/events');\n", + " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", + "\n", + " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", + " register_renderer(events, OutputArea);\n", + " }\n", + " }\n", + " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", + " root._bokeh_timeout = Date.now() + 5000;\n", + " root._bokeh_failed_load = false;\n", + " }\n", + "\n", + " const NB_LOAD_WARNING = {'data': {'text/html':\n", + " \"
\\n\"+\n", + " \"

\\n\"+\n", + " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", + " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", + " \"

\\n\"+\n", + " \"
    \\n\"+\n", + " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n", + " \"
  • use INLINE resources instead, as so:
  • \\n\"+\n", + " \"
\\n\"+\n", + " \"\\n\"+\n", + " \"from bokeh.resources import INLINE\\n\"+\n", + " \"output_notebook(resources=INLINE)\\n\"+\n", + " \"\\n\"+\n", + " \"
\"}};\n", + "\n", + " function display_loaded(error = null) {\n", + " const el = document.getElementById(null);\n", + " if (el != null) {\n", + " const html = (() => {\n", + " if (typeof root.Bokeh === \"undefined\") {\n", + " if (error == null) {\n", + " return \"BokehJS is loading ...\";\n", + " } else {\n", + " return \"BokehJS failed to load.\";\n", + " }\n", + " } else {\n", + " const prefix = `BokehJS ${root.Bokeh.version}`;\n", + " if (error == null) {\n", + " return `${prefix} successfully loaded.`;\n", + " } else {\n", + " return `${prefix} encountered errors while loading and may not function as expected.`;\n", + " }\n", + " }\n", + " })();\n", + " el.innerHTML = html;\n", + "\n", + " if (error != null) {\n", + " const wrapper = document.createElement(\"div\");\n", + " wrapper.style.overflow = \"auto\";\n", + " wrapper.style.height = \"5em\";\n", + " wrapper.style.resize = \"vertical\";\n", + " const content = document.createElement(\"div\");\n", + " content.style.fontFamily = \"monospace\";\n", + " content.style.whiteSpace = \"pre-wrap\";\n", + " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", + " content.textContent = error.stack ?? error.toString();\n", + " wrapper.append(content);\n", + " el.append(wrapper);\n", + " }\n", + " } else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(() => display_loaded(error), 100);\n", + " }\n", + " }\n", + "\n", + " function run_callbacks() {\n", + " try {\n", + " root._bokeh_onload_callbacks.forEach(function(callback) {\n", + " if (callback != null)\n", + " callback();\n", + " });\n", + " } finally {\n", + " delete root._bokeh_onload_callbacks\n", + " }\n", + " console.debug(\"Bokeh: all callbacks have finished\");\n", + " }\n", + "\n", + " function load_libs(css_urls, js_urls, callback) {\n", + " if (css_urls == null) css_urls = [];\n", + " if (js_urls == null) js_urls = [];\n", + "\n", + " root._bokeh_onload_callbacks.push(callback);\n", + " if (root._bokeh_is_loading > 0) {\n", + " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", + " return null;\n", + " }\n", + " if (js_urls == null || js_urls.length === 0) {\n", + " run_callbacks();\n", + " return null;\n", + " }\n", + " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", + " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", + "\n", + " function on_load() {\n", + " root._bokeh_is_loading--;\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", + " run_callbacks()\n", + " }\n", + " }\n", + "\n", + " function on_error(url) {\n", + " console.error(\"failed to load \" + url);\n", + " }\n", + "\n", + " for (let i = 0; i < css_urls.length; i++) {\n", + " const url = css_urls[i];\n", + " const element = document.createElement(\"link\");\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.rel = \"stylesheet\";\n", + " element.type = \"text/css\";\n", + " element.href = url;\n", + " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " for (let i = 0; i < js_urls.length; i++) {\n", + " const url = js_urls[i];\n", + " const element = document.createElement('script');\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.async = false;\n", + " element.src = url;\n", + " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", + " document.head.appendChild(element);\n", + " }\n", + " };\n", + "\n", + " function inject_raw_css(css) {\n", + " const element = document.createElement(\"style\");\n", + " element.appendChild(document.createTextNode(css));\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", + " const css_urls = [];\n", + "\n", + " const inline_js = [ function(Bokeh) {\n", + " Bokeh.set_log_level(\"info\");\n", + " },\n", + "function(Bokeh) {\n", + " }\n", + " ];\n", + "\n", + " function run_inline_js() {\n", + " if (root.Bokeh !== undefined || force === true) {\n", + " try {\n", + " for (let i = 0; i < inline_js.length; i++) {\n", + " inline_js[i].call(root, root.Bokeh);\n", + " }\n", + "\n", + " } catch (error) {throw error;\n", + " }} else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(run_inline_js, 100);\n", + " } else if (!root._bokeh_failed_load) {\n", + " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", + " root._bokeh_failed_load = true;\n", + " } else if (force !== true) {\n", + " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", + " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", + " }\n", + " }\n", + "\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", + " run_inline_js();\n", + " } else {\n", + " load_libs(css_urls, js_urls, function() {\n", + " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", + " run_inline_js();\n", + " });\n", + " }\n", + "}(window));" + ], + "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n \"
  • use INLINE resources instead, as so:
  • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
MalariaGEN Adir1 API client
\n", + " Please note that data are subject to terms of use,\n", + " for more information see \n", + " the MalariaGEN website or contact support@malariagen.net.\n", + " See also the Adir1 API docs.\n", + "
\n", + " Storage URL\n", + " gs://vo_adir_production_us_central1/
\n", + " Data releases available\n", + " 1.x
\n", + " Results cache\n", + " /Users/dennistpw/Projects/malariagen_results
\n", + " Cohorts analysis\n", + " noneyet
\n", + " Site filters analysis\n", + " sc_20250610
\n", + " Software version\n", + " malariagen_data 13.3.0.post33+90e72d5a
\n", + " Client location\n", + " Queensland, Australia
\n", + " " + ], + "text/plain": [ + "\n", + "Storage URL : gs://vo_adir_production_us_central1/\n", + "Data releases available : 1.x\n", + "Results cache : /Users/dennistpw/Projects/malariagen_results\n", + "Site filters analysis : sc_20250610\n", + "Software version : malariagen_data 13.3.0.post33+90e72d5a\n", + "Client location : Queensland, Australia\n", + "---\n", + "Please note that data are subject to terms of use,\n", + "for more information see https://www.malariagen.net/data\n", + "or contact support@malariagen.net. For API documentation see \n", + "https://malariagen.github.io/malariagen-data-python/v13.3.0.post33+90e72d5a/Adir1.html" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Init Adir1 API\n", + "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')\n", + "adir1" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " \r" + ] + } + ], + "source": [ + "snps = adir1.snp_calls(region=\"KB672868:1000000-1010000\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e0489eab-e347-492d-88ce-97d61a0c0aba", + "metadata": {}, + "outputs": [], + "source": [ + "adir1.pca(region = \"KB672868\", n_snps = 100_000, " + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From 6cbce3aeeb82b43fdd7888bca6fb33c570f83b2d Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Tue, 10 Jun 2025 15:21:09 +1000 Subject: [PATCH 09/12] comment out TOU lookups for metadata --- adir1_explore.ipynb | 451 ----------------------- malariagen_data/anoph/sample_metadata.py | 13 +- notebooks/adir1_explore.ipynb | 47 ++- 3 files changed, 50 insertions(+), 461 deletions(-) delete mode 100644 adir1_explore.ipynb diff --git a/adir1_explore.ipynb b/adir1_explore.ipynb deleted file mode 100644 index c42d93dd5..000000000 --- a/adir1_explore.ipynb +++ /dev/null @@ -1,451 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import malariagen_data" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "application/javascript": [ - "'use strict';\n", - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " const force = true;\n", - "\n", - " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", - " root._bokeh_onload_callbacks = [];\n", - " root._bokeh_is_loading = undefined;\n", - " }\n", - "\n", - "const JS_MIME_TYPE = 'application/javascript';\n", - " const HTML_MIME_TYPE = 'text/html';\n", - " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", - " const CLASS_NAME = 'output_bokeh rendered_html';\n", - "\n", - " /**\n", - " * Render data to the DOM node\n", - " */\n", - " function render(props, node) {\n", - " const script = document.createElement(\"script\");\n", - " node.appendChild(script);\n", - " }\n", - "\n", - " /**\n", - " * Handle when an output is cleared or removed\n", - " */\n", - " function handleClearOutput(event, handle) {\n", - " function drop(id) {\n", - " const view = Bokeh.index.get_by_id(id)\n", - " if (view != null) {\n", - " view.model.document.clear()\n", - " Bokeh.index.delete(view)\n", - " }\n", - " }\n", - "\n", - " const cell = handle.cell;\n", - "\n", - " const id = cell.output_area._bokeh_element_id;\n", - " const server_id = cell.output_area._bokeh_server_id;\n", - "\n", - " // Clean up Bokeh references\n", - " if (id != null) {\n", - " drop(id)\n", - " }\n", - "\n", - " if (server_id !== undefined) {\n", - " // Clean up Bokeh references\n", - " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", - " cell.notebook.kernel.execute(cmd_clean, {\n", - " iopub: {\n", - " output: function(msg) {\n", - " const id = msg.content.text.trim()\n", - " drop(id)\n", - " }\n", - " }\n", - " });\n", - " // Destroy server and session\n", - " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", - " cell.notebook.kernel.execute(cmd_destroy);\n", - " }\n", - " }\n", - "\n", - " /**\n", - " * Handle when a new output is added\n", - " */\n", - " function handleAddOutput(event, handle) {\n", - " const output_area = handle.output_area;\n", - " const output = handle.output;\n", - "\n", - " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", - " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", - " return\n", - " }\n", - "\n", - " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", - "\n", - " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", - " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", - " // store reference to embed id on output_area\n", - " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", - " }\n", - " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", - " const bk_div = document.createElement(\"div\");\n", - " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", - " const script_attrs = bk_div.children[0].attributes;\n", - " for (let i = 0; i < script_attrs.length; i++) {\n", - " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", - " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", - " }\n", - " // store reference to server id on output_area\n", - " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", - " }\n", - " }\n", - "\n", - " function register_renderer(events, OutputArea) {\n", - "\n", - " function append_mime(data, metadata, element) {\n", - " // create a DOM node to render to\n", - " const toinsert = this.create_output_subarea(\n", - " metadata,\n", - " CLASS_NAME,\n", - " EXEC_MIME_TYPE\n", - " );\n", - " this.keyboard_manager.register_events(toinsert);\n", - " // Render to node\n", - " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", - " render(props, toinsert[toinsert.length - 1]);\n", - " element.append(toinsert);\n", - " return toinsert\n", - " }\n", - "\n", - " /* Handle when an output is cleared or removed */\n", - " events.on('clear_output.CodeCell', handleClearOutput);\n", - " events.on('delete.Cell', handleClearOutput);\n", - "\n", - " /* Handle when a new output is added */\n", - " events.on('output_added.OutputArea', handleAddOutput);\n", - "\n", - " /**\n", - " * Register the mime type and append_mime function with output_area\n", - " */\n", - " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", - " /* Is output safe? */\n", - " safe: true,\n", - " /* Index of renderer in `output_area.display_order` */\n", - " index: 0\n", - " });\n", - " }\n", - "\n", - " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", - " if (root.Jupyter !== undefined) {\n", - " const events = require('base/js/events');\n", - " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", - "\n", - " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", - " register_renderer(events, OutputArea);\n", - " }\n", - " }\n", - " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", - " root._bokeh_timeout = Date.now() + 5000;\n", - " root._bokeh_failed_load = false;\n", - " }\n", - "\n", - " const NB_LOAD_WARNING = {'data': {'text/html':\n", - " \"
\\n\"+\n", - " \"

\\n\"+\n", - " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", - " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", - " \"

\\n\"+\n", - " \"
    \\n\"+\n", - " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n", - " \"
  • use INLINE resources instead, as so:
  • \\n\"+\n", - " \"
\\n\"+\n", - " \"\\n\"+\n", - " \"from bokeh.resources import INLINE\\n\"+\n", - " \"output_notebook(resources=INLINE)\\n\"+\n", - " \"\\n\"+\n", - " \"
\"}};\n", - "\n", - " function display_loaded(error = null) {\n", - " const el = document.getElementById(null);\n", - " if (el != null) {\n", - " const html = (() => {\n", - " if (typeof root.Bokeh === \"undefined\") {\n", - " if (error == null) {\n", - " return \"BokehJS is loading ...\";\n", - " } else {\n", - " return \"BokehJS failed to load.\";\n", - " }\n", - " } else {\n", - " const prefix = `BokehJS ${root.Bokeh.version}`;\n", - " if (error == null) {\n", - " return `${prefix} successfully loaded.`;\n", - " } else {\n", - " return `${prefix} encountered errors while loading and may not function as expected.`;\n", - " }\n", - " }\n", - " })();\n", - " el.innerHTML = html;\n", - "\n", - " if (error != null) {\n", - " const wrapper = document.createElement(\"div\");\n", - " wrapper.style.overflow = \"auto\";\n", - " wrapper.style.height = \"5em\";\n", - " wrapper.style.resize = \"vertical\";\n", - " const content = document.createElement(\"div\");\n", - " content.style.fontFamily = \"monospace\";\n", - " content.style.whiteSpace = \"pre-wrap\";\n", - " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", - " content.textContent = error.stack ?? error.toString();\n", - " wrapper.append(content);\n", - " el.append(wrapper);\n", - " }\n", - " } else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(() => display_loaded(error), 100);\n", - " }\n", - " }\n", - "\n", - " function run_callbacks() {\n", - " try {\n", - " root._bokeh_onload_callbacks.forEach(function(callback) {\n", - " if (callback != null)\n", - " callback();\n", - " });\n", - " } finally {\n", - " delete root._bokeh_onload_callbacks\n", - " }\n", - " console.debug(\"Bokeh: all callbacks have finished\");\n", - " }\n", - "\n", - " function load_libs(css_urls, js_urls, callback) {\n", - " if (css_urls == null) css_urls = [];\n", - " if (js_urls == null) js_urls = [];\n", - "\n", - " root._bokeh_onload_callbacks.push(callback);\n", - " if (root._bokeh_is_loading > 0) {\n", - " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", - " return null;\n", - " }\n", - " if (js_urls == null || js_urls.length === 0) {\n", - " run_callbacks();\n", - " return null;\n", - " }\n", - " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", - " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", - "\n", - " function on_load() {\n", - " root._bokeh_is_loading--;\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", - " run_callbacks()\n", - " }\n", - " }\n", - "\n", - " function on_error(url) {\n", - " console.error(\"failed to load \" + url);\n", - " }\n", - "\n", - " for (let i = 0; i < css_urls.length; i++) {\n", - " const url = css_urls[i];\n", - " const element = document.createElement(\"link\");\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.rel = \"stylesheet\";\n", - " element.type = \"text/css\";\n", - " element.href = url;\n", - " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " for (let i = 0; i < js_urls.length; i++) {\n", - " const url = js_urls[i];\n", - " const element = document.createElement('script');\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.async = false;\n", - " element.src = url;\n", - " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", - " document.head.appendChild(element);\n", - " }\n", - " };\n", - "\n", - " function inject_raw_css(css) {\n", - " const element = document.createElement(\"style\");\n", - " element.appendChild(document.createTextNode(css));\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", - " const css_urls = [];\n", - "\n", - " const inline_js = [ function(Bokeh) {\n", - " Bokeh.set_log_level(\"info\");\n", - " },\n", - "function(Bokeh) {\n", - " }\n", - " ];\n", - "\n", - " function run_inline_js() {\n", - " if (root.Bokeh !== undefined || force === true) {\n", - " try {\n", - " for (let i = 0; i < inline_js.length; i++) {\n", - " inline_js[i].call(root, root.Bokeh);\n", - " }\n", - "\n", - " } catch (error) {throw error;\n", - " }} else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(run_inline_js, 100);\n", - " } else if (!root._bokeh_failed_load) {\n", - " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", - " root._bokeh_failed_load = true;\n", - " } else if (force !== true) {\n", - " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", - " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", - " }\n", - " }\n", - "\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", - " run_inline_js();\n", - " } else {\n", - " load_libs(css_urls, js_urls, function() {\n", - " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", - " run_inline_js();\n", - " });\n", - " }\n", - "}(window));" - ], - "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n \"
  • use INLINE resources instead, as so:
  • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "# Init API\n", - "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "f171c3b7-30c2-4e9f-9133-22206985de07", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "'KB672868'" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# Are the contigs here? \n", - "chroms = adir1.contigs[:5]\n", - "chroms[1]" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "ename": "FileNotFoundError", - "evalue": "b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:426\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 425\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_sets\u001b[49m\u001b[43m[\u001b[49m\u001b[43mrelease\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n", - "\u001b[0;31mKeyError\u001b[0m: '1.x'", - "\nDuring handling of the above exception, another exception occurred:\n", - "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[7], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m snps \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msnp_calls\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868:1000000-2000000\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/snp_data.py:1007\u001b[0m, in \u001b[0;36mAnophelesSnpData.snp_calls\u001b[0;34m(self, region, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, inline_array, chunks, cohort_size, min_cohort_size, max_cohort_size, random_seed)\u001b[0m\n\u001b[1;32m 1001\u001b[0m base_params\u001b[38;5;241m.\u001b[39mvalidate_sample_selection_params(\n\u001b[1;32m 1002\u001b[0m sample_query\u001b[38;5;241m=\u001b[39msample_query, sample_indices\u001b[38;5;241m=\u001b[39msample_indices\n\u001b[1;32m 1003\u001b[0m )\n\u001b[1;32m 1005\u001b[0m \u001b[38;5;66;03m# Normalise parameters.\u001b[39;00m\n\u001b[1;32m 1006\u001b[0m sample_sets_prepped: Tuple[\u001b[38;5;28mstr\u001b[39m, \u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mtuple\u001b[39m(\n\u001b[0;32m-> 1007\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_sets_param\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1008\u001b[0m )\n\u001b[1;32m 1009\u001b[0m \u001b[38;5;28;01mdel\u001b[39;00m sample_sets\n\u001b[1;32m 1010\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_indices \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:524\u001b[0m, in \u001b[0;36mAnophelesBase._prep_sample_sets_param\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 517\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_prep_sample_sets_param\u001b[39m(\n\u001b[1;32m 518\u001b[0m \u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets]\n\u001b[1;32m 519\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m List[\u001b[38;5;28mstr\u001b[39m]:\n\u001b[1;32m 520\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Common handling for the `sample_sets` parameter. For convenience, we\u001b[39;00m\n\u001b[1;32m 521\u001b[0m \u001b[38;5;124;03m allow this to be a single sample set, or a list of sample sets, or a\u001b[39;00m\n\u001b[1;32m 522\u001b[0m \u001b[38;5;124;03m release identifier, or a list of release identifiers.\"\"\"\u001b[39;00m\n\u001b[0;32m--> 524\u001b[0m all_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mto_list()\n\u001b[1;32m 526\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_sets \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 527\u001b[0m \u001b[38;5;66;03m# All available sample sets.\u001b[39;00m\n\u001b[1;32m 528\u001b[0m prepped_sample_sets \u001b[38;5;241m=\u001b[39m all_sample_sets\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets(release\u001b[38;5;241m=\u001b[39mr) \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:439\u001b[0m, in \u001b[0;36m\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 435\u001b[0m releases \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msorted\u001b[39m(\u001b[38;5;28mset\u001b[39m(release))\n\u001b[1;32m 437\u001b[0m \u001b[38;5;66;03m# Retrieve and concatenate sample sets from multiple releases.\u001b[39;00m\n\u001b[1;32m 438\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mconcat(\n\u001b[0;32m--> 439\u001b[0m [\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrelease\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mr\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m releases],\n\u001b[1;32m 440\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m,\n\u001b[1;32m 441\u001b[0m ignore_index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 442\u001b[0m )\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:430\u001b[0m, in \u001b[0;36mAnophelesBase.sample_sets\u001b[0;34m(self, release)\u001b[0m\n\u001b[1;32m 426\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release]\n\u001b[1;32m 428\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[38;5;66;03m# Read and cache dataframe for performance.\u001b[39;00m\n\u001b[0;32m--> 430\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_read_sample_sets\u001b[49m\u001b[43m(\u001b[49m\u001b[43msingle_release\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrelease\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 431\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_sets[release] \u001b[38;5;241m=\u001b[39m df\n\u001b[1;32m 433\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(release, Sequence):\n\u001b[1;32m 434\u001b[0m \u001b[38;5;66;03m# Ensure no duplicates.\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:376\u001b[0m, in \u001b[0;36mAnophelesBase._read_sample_sets\u001b[0;34m(self, single_release)\u001b[0m\n\u001b[1;32m 373\u001b[0m manifest_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mrelease_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/manifest.tsv\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 375\u001b[0m \u001b[38;5;66;03m# Read the manifest into a pandas dataframe.\u001b[39;00m\n\u001b[0;32m--> 376\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen_file\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmanifest_path\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m 377\u001b[0m df \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mread_csv(f, sep\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;130;01m\\t\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, na_values\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 379\u001b[0m \u001b[38;5;66;03m# Add a \"release\" column for convenience.\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:218\u001b[0m, in \u001b[0;36mAnophelesBase.open_file\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 215\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 216\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mopen_file\u001b[39m(\u001b[38;5;28mself\u001b[39m, path: \u001b[38;5;28mstr\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m IO:\n\u001b[1;32m 217\u001b[0m full_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_base_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m--> 218\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfull_path\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/spec.py:1154\u001b[0m, in \u001b[0;36mAbstractFileSystem.open\u001b[0;34m(self, path, mode, block_size, cache_options, compression, **kwargs)\u001b[0m\n\u001b[1;32m 1152\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 1153\u001b[0m ac \u001b[38;5;241m=\u001b[39m kwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mautocommit\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_intrans)\n\u001b[0;32m-> 1154\u001b[0m f \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_open\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1155\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1156\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1157\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1158\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mac\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1159\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1160\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1161\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1162\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m compression \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfsspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcompression\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m compr\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1309\u001b[0m, in \u001b[0;36mGCSFileSystem._open\u001b[0;34m(self, path, mode, block_size, cache_options, acl, consistency, metadata, autocommit, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1307\u001b[0m block_size \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_block_size\n\u001b[1;32m 1308\u001b[0m const \u001b[38;5;241m=\u001b[39m consistency \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconsistency\n\u001b[0;32m-> 1309\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mGCSFile\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1310\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1311\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1312\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1313\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1314\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1315\u001b[0m \u001b[43m \u001b[49m\u001b[43mconsistency\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mconst\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1316\u001b[0m \u001b[43m \u001b[49m\u001b[43mmetadata\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmetadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1317\u001b[0m \u001b[43m \u001b[49m\u001b[43macl\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43macl\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1318\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mautocommit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1319\u001b[0m \u001b[43m \u001b[49m\u001b[43mfixed_key_metadata\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfixed_key_metadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1320\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1321\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1468\u001b[0m, in \u001b[0;36mGCSFile.__init__\u001b[0;34m(self, gcsfs, path, mode, block_size, autocommit, cache_type, cache_options, acl, consistency, metadata, content_type, timeout, fixed_key_metadata, generation, **kwargs)\u001b[0m\n\u001b[1;32m 1466\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAttempt to open a bucket\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1467\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgeneration \u001b[38;5;241m=\u001b[39m _coalesce_generation(generation, path_generation)\n\u001b[0;32m-> 1468\u001b[0m \u001b[38;5;28;43msuper\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1469\u001b[0m \u001b[43m \u001b[49m\u001b[43mgcsfs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1470\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1471\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1472\u001b[0m \u001b[43m \u001b[49m\u001b[43mblock_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1473\u001b[0m \u001b[43m \u001b[49m\u001b[43mautocommit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mautocommit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1474\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_type\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_type\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1475\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1476\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1477\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1478\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgcsfs \u001b[38;5;241m=\u001b[39m gcsfs\n\u001b[1;32m 1479\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mbucket \u001b[38;5;241m=\u001b[39m bucket\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/spec.py:1510\u001b[0m, in \u001b[0;36mAbstractBufferedFile.__init__\u001b[0;34m(self, fs, path, mode, block_size, autocommit, cache_type, cache_options, size, **kwargs)\u001b[0m\n\u001b[1;32m 1508\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize \u001b[38;5;241m=\u001b[39m size\n\u001b[1;32m 1509\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m-> 1510\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdetails\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msize\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[1;32m 1511\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcache \u001b[38;5;241m=\u001b[39m caches[cache_type](\n\u001b[1;32m 1512\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mblocksize, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_fetch_range, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msize, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mcache_options\n\u001b[1;32m 1513\u001b[0m )\n\u001b[1;32m 1514\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:1504\u001b[0m, in \u001b[0;36mGCSFile.details\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1501\u001b[0m \u001b[38;5;129m@property\u001b[39m\n\u001b[1;32m 1502\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdetails\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[1;32m 1503\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m-> 1504\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43minfo\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mgeneration\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneration\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1505\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_details\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:115\u001b[0m, in \u001b[0;36msync_wrapper..wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 114\u001b[0m \u001b[38;5;28mself\u001b[39m \u001b[38;5;241m=\u001b[39m obj \u001b[38;5;129;01mor\u001b[39;00m args[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m--> 115\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43msync\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mloop\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfunc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:100\u001b[0m, in \u001b[0;36msync\u001b[0;34m(loop, func, timeout, *args, **kwargs)\u001b[0m\n\u001b[1;32m 98\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m FSTimeoutError \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mreturn_result\u001b[39;00m\n\u001b[1;32m 99\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(return_result, \u001b[38;5;167;01mBaseException\u001b[39;00m):\n\u001b[0;32m--> 100\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m return_result\n\u001b[1;32m 101\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 102\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m return_result\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/fsspec/asyn.py:55\u001b[0m, in \u001b[0;36m_runner\u001b[0;34m(event, coro, result, timeout)\u001b[0m\n\u001b[1;32m 53\u001b[0m coro \u001b[38;5;241m=\u001b[39m asyncio\u001b[38;5;241m.\u001b[39mwait_for(coro, timeout\u001b[38;5;241m=\u001b[39mtimeout)\n\u001b[1;32m 54\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 55\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m coro\n\u001b[1;32m 56\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m ex:\n\u001b[1;32m 57\u001b[0m result[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m=\u001b[39m ex\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:797\u001b[0m, in \u001b[0;36mGCSFileSystem._info\u001b[0;34m(self, path, generation, **kwargs)\u001b[0m\n\u001b[1;32m 795\u001b[0m \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[1;32m 796\u001b[0m kwargs[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdetail\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m \u001b[38;5;66;03m# Force to true for info\u001b[39;00m\n\u001b[0;32m--> 797\u001b[0m out \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ls(path, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 798\u001b[0m out0 \u001b[38;5;241m=\u001b[39m [o \u001b[38;5;28;01mfor\u001b[39;00m o \u001b[38;5;129;01min\u001b[39;00m out \u001b[38;5;28;01mif\u001b[39;00m o[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mname\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mrstrip(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;241m==\u001b[39m path]\n\u001b[1;32m 799\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m out0:\n\u001b[1;32m 800\u001b[0m \u001b[38;5;66;03m# exact hit\u001b[39;00m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:834\u001b[0m, in \u001b[0;36mGCSFileSystem._ls\u001b[0;34m(self, path, detail, prefix, versions, **kwargs)\u001b[0m\n\u001b[1;32m 832\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 833\u001b[0m out \u001b[38;5;241m=\u001b[39m []\n\u001b[0;32m--> 834\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m entry \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_list_objects(\n\u001b[1;32m 835\u001b[0m path, prefix\u001b[38;5;241m=\u001b[39mprefix, versions\u001b[38;5;241m=\u001b[39mversions\n\u001b[1;32m 836\u001b[0m ):\n\u001b[1;32m 837\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m versions \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgeneration\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m entry:\n\u001b[1;32m 838\u001b[0m entry \u001b[38;5;241m=\u001b[39m entry\u001b[38;5;241m.\u001b[39mcopy()\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:549\u001b[0m, in \u001b[0;36mGCSFileSystem._list_objects\u001b[0;34m(self, path, prefix, versions)\u001b[0m\n\u001b[1;32m 547\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m (items \u001b[38;5;241m+\u001b[39m pseudodirs):\n\u001b[1;32m 548\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m key:\n\u001b[0;32m--> 549\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m [\u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_object(path)]\n\u001b[1;32m 550\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 551\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m []\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:491\u001b[0m, in \u001b[0;36mGCSFileSystem._get_object\u001b[0;34m(self, path)\u001b[0m\n\u001b[1;32m 488\u001b[0m \u001b[38;5;66;03m# Work around various permission settings. Prefer an object get (storage.objects.get), but\u001b[39;00m\n\u001b[1;32m 489\u001b[0m \u001b[38;5;66;03m# fall back to a bucket list + filter to object name (storage.objects.list).\u001b[39;00m\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 491\u001b[0m res \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_call(\n\u001b[1;32m 492\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGET\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mb/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m/o/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, bucket, key, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m, generation\u001b[38;5;241m=\u001b[39mgeneration\n\u001b[1;32m 493\u001b[0m )\n\u001b[1;32m 494\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mOSError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 495\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mstr\u001b[39m(e)\u001b[38;5;241m.\u001b[39mstartswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mForbidden\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:418\u001b[0m, in \u001b[0;36mGCSFileSystem._call\u001b[0;34m(self, method, path, json_out, info_out, *args, **kwargs)\u001b[0m\n\u001b[1;32m 414\u001b[0m \u001b[38;5;28;01masync\u001b[39;00m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_call\u001b[39m(\n\u001b[1;32m 415\u001b[0m \u001b[38;5;28mself\u001b[39m, method, path, \u001b[38;5;241m*\u001b[39margs, json_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, info_out\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 416\u001b[0m ):\n\u001b[1;32m 417\u001b[0m logger\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mmethod\u001b[38;5;241m.\u001b[39mupper()\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00margs\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mheaders\u001b[39m\u001b[38;5;124m'\u001b[39m)\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 418\u001b[0m status, headers, info, contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_request(\n\u001b[1;32m 419\u001b[0m method, path, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 420\u001b[0m )\n\u001b[1;32m 421\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m json_out:\n\u001b[1;32m 422\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m json\u001b[38;5;241m.\u001b[39mloads(contents)\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/decorator.py:221\u001b[0m, in \u001b[0;36mdecorate..fun\u001b[0;34m(*args, **kw)\u001b[0m\n\u001b[1;32m 219\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m kwsyntax:\n\u001b[1;32m 220\u001b[0m args, kw \u001b[38;5;241m=\u001b[39m fix(args, kw, sig)\n\u001b[0;32m--> 221\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m caller(func, \u001b[38;5;241m*\u001b[39m(extras \u001b[38;5;241m+\u001b[39m args), \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkw)\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:114\u001b[0m, in \u001b[0;36mretry_request\u001b[0;34m(func, retries, *args, **kwargs)\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m retry \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 113\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m asyncio\u001b[38;5;241m.\u001b[39msleep(\u001b[38;5;28mmin\u001b[39m(random\u001b[38;5;241m.\u001b[39mrandom() \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m2\u001b[39m \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39m (retry \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m), \u001b[38;5;241m32\u001b[39m))\n\u001b[0;32m--> 114\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m func(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 115\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (\n\u001b[1;32m 116\u001b[0m HttpError,\n\u001b[1;32m 117\u001b[0m requests\u001b[38;5;241m.\u001b[39mexceptions\u001b[38;5;241m.\u001b[39mRequestException,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 120\u001b[0m aiohttp\u001b[38;5;241m.\u001b[39mclient_exceptions\u001b[38;5;241m.\u001b[39mClientError,\n\u001b[1;32m 121\u001b[0m ) \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 122\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\n\u001b[1;32m 123\u001b[0m \u001b[38;5;28misinstance\u001b[39m(e, HttpError)\n\u001b[1;32m 124\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m e\u001b[38;5;241m.\u001b[39mcode \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m400\u001b[39m\n\u001b[1;32m 125\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mrequester pays\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m e\u001b[38;5;241m.\u001b[39mmessage\n\u001b[1;32m 126\u001b[0m ):\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/core.py:411\u001b[0m, in \u001b[0;36mGCSFileSystem._request\u001b[0;34m(self, method, path, headers, json, data, *args, **kwargs)\u001b[0m\n\u001b[1;32m 408\u001b[0m info \u001b[38;5;241m=\u001b[39m r\u001b[38;5;241m.\u001b[39mrequest_info \u001b[38;5;66;03m# for debug only\u001b[39;00m\n\u001b[1;32m 409\u001b[0m contents \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m r\u001b[38;5;241m.\u001b[39mread()\n\u001b[0;32m--> 411\u001b[0m \u001b[43mvalidate_response\u001b[49m\u001b[43m(\u001b[49m\u001b[43mstatus\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcontents\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43margs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 412\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m status, headers, info, contents\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/gcsfs/retry.py:83\u001b[0m, in \u001b[0;36mvalidate_response\u001b[0;34m(status, content, path, args)\u001b[0m\n\u001b[1;32m 81\u001b[0m path \u001b[38;5;241m=\u001b[39m path\u001b[38;5;241m.\u001b[39mformat(\u001b[38;5;241m*\u001b[39m[quote(p) \u001b[38;5;28;01mfor\u001b[39;00m p \u001b[38;5;129;01min\u001b[39;00m args])\n\u001b[1;32m 82\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m status \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m404\u001b[39m:\n\u001b[0;32m---> 83\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m(path)\n\u001b[1;32m 85\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 86\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(content, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdecode\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", - "\u001b[0;31mFileNotFoundError\u001b[0m: b/vo_adir_production_us_central1/o/v1.x%2Fmanifest.tsv" - ] - } - ], - "source": [ - "snps = adir1.snp_calls(region=\"KB672868:1000000-2000000\")" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.10" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index 62baa6870..c8bfbf601 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -180,15 +180,16 @@ def _parse_general_metadata( axis="columns", ) + # Have commented these out for now as a) this is not a public release and b) for some reason it breaks everything and I haven't had the time to work out why # Add study columns. - study_info = self.lookup_study_info(sample_set=sample_set) - for column in study_info: - df[column] = study_info[column] + # study_info = self.lookup_study_info(sample_set=sample_set) + # for column in study_info: + # df[column] = study_info[column] # Add terms-of-use columns. - terms_of_use_info = self.lookup_terms_of_use_info(sample_set=sample_set) - for column in terms_of_use_info: - df[column] = terms_of_use_info[column] + # terms_of_use_info = self.lookup_terms_of_use_info(sample_set=sample_set) + # for column in terms_of_use_info: + # df[column] = terms_of_use_info[column] return df diff --git a/notebooks/adir1_explore.ipynb b/notebooks/adir1_explore.ipynb index 1fa71882d..450596a2f 100644 --- a/notebooks/adir1_explore.ipynb +++ b/notebooks/adir1_explore.ipynb @@ -450,12 +450,51 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "id": "e0489eab-e347-492d-88ce-97d61a0c0aba", - "metadata": {}, - "outputs": [], + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " \r" + ] + }, + { + "ename": "KeyError", + "evalue": "\"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:581\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 579\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 580\u001b[0m \u001b[38;5;66;03m# Attempt to retrieve from the cache.\u001b[39;00m\n\u001b[0;32m--> 581\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_metadata\u001b[49m\u001b[43m[\u001b[49m\u001b[43mcache_key\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n", + "\u001b[0;31mKeyError\u001b[0m: ('1276-AD-BD-ALAM-VMF00156', '1277-VO-KH-WITKOWSKI-VMF00151', '1277-VO-KH-WITKOWSKI-VMF00183', '1278-VO-TH-KOBYLINSKI-VMF00153')", + "\nDuring handling of the above exception, another exception occurred:\n", + "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[10], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m pca \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpca\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mn_snps\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m100_000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcountry == \u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mThailand\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/pca.py:89\u001b[0m, in \u001b[0;36mAnophelesPca.pca\u001b[0;34m(self, region, n_snps, n_components, thin_offset, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, min_minor_ac, max_missing_an, cohort_size, min_cohort_size, max_cohort_size, exclude_samples, fit_exclude_samples, random_seed, inline_array, chunks)\u001b[0m\n\u001b[1;32m 83\u001b[0m name \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpca_v4\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 85\u001b[0m \u001b[38;5;66;03m# Normalize params for consistent hash value.\u001b[39;00m\n\u001b[1;32m 86\u001b[0m (\n\u001b[1;32m 87\u001b[0m sample_sets_prepped,\n\u001b[1;32m 88\u001b[0m sample_indices_prepped,\n\u001b[0;32m---> 89\u001b[0m ) \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_selection_cache_params\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 90\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 91\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 92\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 93\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 94\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 95\u001b[0m region_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_region_cache_param(region\u001b[38;5;241m=\u001b[39mregion)\n\u001b[1;32m 96\u001b[0m site_mask_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_optional_site_mask_param(site_mask\u001b[38;5;241m=\u001b[39msite_mask)\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:892\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._prep_sample_selection_cache_params\u001b[0;34m(self, sample_sets, sample_query, sample_query_options, sample_indices)\u001b[0m\n\u001b[1;32m 885\u001b[0m sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_sample_sets_param(sample_sets\u001b[38;5;241m=\u001b[39msample_sets)\n\u001b[1;32m 887\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_query \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 888\u001b[0m \u001b[38;5;66;03m# Resolve query to a list of integers for more cache hits - we\u001b[39;00m\n\u001b[1;32m 889\u001b[0m \u001b[38;5;66;03m# do this because there are different ways to write the same pandas\u001b[39;00m\n\u001b[1;32m 890\u001b[0m \u001b[38;5;66;03m# query, and so it's better to evaluate the query and use a list of\u001b[39;00m\n\u001b[1;32m 891\u001b[0m \u001b[38;5;66;03m# integer indices instead.\u001b[39;00m\n\u001b[0;32m--> 892\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 893\u001b[0m sample_query_options \u001b[38;5;241m=\u001b[39m sample_query_options \u001b[38;5;129;01mor\u001b[39;00m {}\n\u001b[1;32m 894\u001b[0m loc_samples \u001b[38;5;241m=\u001b[39m df_samples\u001b[38;5;241m.\u001b[39meval(sample_query, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39msample_query_options)\u001b[38;5;241m.\u001b[39mvalues\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:589\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 584\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_spinner(desc\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mLoad sample metadata\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n\u001b[1;32m 585\u001b[0m \u001b[38;5;66;03m## Build a single DataFrame using all available metadata.\u001b[39;00m\n\u001b[1;32m 586\u001b[0m \n\u001b[1;32m 587\u001b[0m \u001b[38;5;66;03m# Get the general sample metadata.\u001b[39;00m\n\u001b[1;32m 588\u001b[0m \u001b[38;5;66;03m# Note: this includes study and terms-of-use info.\u001b[39;00m\n\u001b[0;32m--> 589\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneral_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mprepped_sample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 591\u001b[0m \u001b[38;5;66;03m# Merge with the sequence QC metadata.\u001b[39;00m\n\u001b[1;32m 592\u001b[0m df_sequence_qc \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msequence_qc_metadata(\n\u001b[1;32m 593\u001b[0m sample_sets\u001b[38;5;241m=\u001b[39mprepped_sample_sets\n\u001b[1;32m 594\u001b[0m )\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:185\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.general_metadata\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 174\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 175\u001b[0m \u001b[38;5;129m@doc\u001b[39m(\n\u001b[1;32m 176\u001b[0m summary\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 183\u001b[0m \u001b[38;5;28mself\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 184\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m pd\u001b[38;5;241m.\u001b[39mDataFrame:\n\u001b[0;32m--> 185\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_metadata_paths\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 186\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath_template\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;132;43;01m{release_path}\u001b[39;49;00m\u001b[38;5;124;43m/metadata/general/\u001b[39;49m\u001b[38;5;132;43;01m{sample_set}\u001b[39;49;00m\u001b[38;5;124;43m/samples.meta.csv\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 187\u001b[0m \u001b[43m \u001b[49m\u001b[43mparse_metadata_func\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_general_metadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 188\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 189\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:119\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_metadata_paths\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 117\u001b[0m path \u001b[38;5;241m=\u001b[39m file_paths[sample_set]\n\u001b[1;32m 118\u001b[0m data \u001b[38;5;241m=\u001b[39m files[path]\n\u001b[0;32m--> 119\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[43mparse_metadata_func\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdata\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 120\u001b[0m dfs\u001b[38;5;241m.\u001b[39mappend(df)\n\u001b[1;32m 122\u001b[0m \u001b[38;5;66;03m# Concatenate all DataFrames.\u001b[39;00m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:160\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_general_metadata\u001b[0;34m(self, sample_set, data)\u001b[0m\n\u001b[1;32m 154\u001b[0m df[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mquarter\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m df\u001b[38;5;241m.\u001b[39mapply(\n\u001b[1;32m 155\u001b[0m \u001b[38;5;28;01mlambda\u001b[39;00m row: ((row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m) \u001b[38;5;241m/\u001b[39m\u001b[38;5;241m/\u001b[39m \u001b[38;5;241m3\u001b[39m) \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m,\n\u001b[1;32m 156\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcolumns\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 157\u001b[0m )\n\u001b[1;32m 159\u001b[0m \u001b[38;5;66;03m# Add study columns.\u001b[39;00m\n\u001b[0;32m--> 160\u001b[0m study_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlookup_study_info\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_set\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 161\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m column \u001b[38;5;129;01min\u001b[39;00m study_info:\n\u001b[1;32m 162\u001b[0m df[column] \u001b[38;5;241m=\u001b[39m study_info[column]\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:487\u001b[0m, in \u001b[0;36mAnophelesBase.lookup_study_info\u001b[0;34m(self, sample_set)\u001b[0m\n\u001b[1;32m 485\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 486\u001b[0m df_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets()\u001b[38;5;241m.\u001b[39mset_index(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 487\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;241m=\u001b[39m \u001b[43mdf_sample_sets\u001b[49m\u001b[43m[\u001b[49m\n\u001b[1;32m 488\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_id\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_url\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m 489\u001b[0m \u001b[43m \u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241m.\u001b[39mto_dict(orient\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 491\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info[sample_set]\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/frame.py:3766\u001b[0m, in \u001b[0;36mDataFrame.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 3764\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_iterator(key):\n\u001b[1;32m 3765\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 3766\u001b[0m indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcolumns\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_indexer_strict\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcolumns\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m[\u001b[38;5;241m1\u001b[39m]\n\u001b[1;32m 3768\u001b[0m \u001b[38;5;66;03m# take() does not accept boolean indexers\u001b[39;00m\n\u001b[1;32m 3769\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(indexer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdtype\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;241m==\u001b[39m \u001b[38;5;28mbool\u001b[39m:\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5876\u001b[0m, in \u001b[0;36mIndex._get_indexer_strict\u001b[0;34m(self, key, axis_name)\u001b[0m\n\u001b[1;32m 5873\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 5874\u001b[0m keyarr, indexer, new_indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_non_unique(keyarr)\n\u001b[0;32m-> 5876\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_raise_if_missing\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkeyarr\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindexer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis_name\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5878\u001b[0m keyarr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtake(indexer)\n\u001b[1;32m 5879\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(key, Index):\n\u001b[1;32m 5880\u001b[0m \u001b[38;5;66;03m# GH 42790 - Preserve name from an Index\u001b[39;00m\n", + "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5935\u001b[0m, in \u001b[0;36mIndex._raise_if_missing\u001b[0;34m(self, key, indexer, axis_name)\u001b[0m\n\u001b[1;32m 5933\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m use_interval_msg:\n\u001b[1;32m 5934\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 5935\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNone of [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkey\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m] are in the [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00maxis_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m]\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 5937\u001b[0m not_found \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(ensure_index(key)[missing_mask\u001b[38;5;241m.\u001b[39mnonzero()[\u001b[38;5;241m0\u001b[39m]]\u001b[38;5;241m.\u001b[39munique())\n\u001b[1;32m 5938\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mnot_found\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m not in index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", + "\u001b[0;31mKeyError\u001b[0m: \"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"" + ] + } + ], "source": [ - "adir1.pca(region = \"KB672868\", n_snps = 100_000, " + "pca = adir1.pca(region = \"KB672868\", n_snps = 100_000, sample_query = \"country == 'Thailand'\")" ] } ], From fcbb281cdd7595d4fc06194f74e4a97aaeca55ea Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Thu, 12 Jun 2025 08:39:04 +1000 Subject: [PATCH 10/12] add annotation to commented out bit of metadata --- malariagen_data/anoph/sample_metadata.py | 34 +- notebooks/adir1_explore.ipynb | 522 ----------------------- 2 files changed, 18 insertions(+), 538 deletions(-) delete mode 100644 notebooks/adir1_explore.ipynb diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index c8bfbf601..399998524 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -618,29 +618,31 @@ def sample_metadata( # Note: this includes study and terms-of-use info. df_samples = self.general_metadata(sample_sets=prepped_sample_sets) + # Commented this out as it breaks some things - will fix + # Merge with the sequence QC metadata. - df_sequence_qc = self.sequence_qc_metadata( - sample_sets=prepped_sample_sets - ) + # df_sequence_qc = self.sequence_qc_metadata( + # sample_sets=prepped_sample_sets + # ) # Note: merging can change column dtypes - df_samples = df_samples.merge( - df_sequence_qc, on="sample_id", sort=False, how="left" - ) + # df_samples = df_samples.merge( + # df_sequence_qc, on="sample_id", sort=False, how="left" + # ) # If available, merge with the AIM metadata. - if self._aim_analysis: - df_aim = self.aim_metadata(sample_sets=prepped_sample_sets) - df_samples = df_samples.merge( - df_aim, on="sample_id", sort=False, how="left" - ) + # if self._aim_analysis: + # df_aim = self.aim_metadata(sample_sets=prepped_sample_sets) + # df_samples = df_samples.merge( + # df_aim, on="sample_id", sort=False, how="left" + # ) # If available, merge with the cohorts metadata. - if self._cohorts_analysis: - df_cohorts = self.cohorts_metadata(sample_sets=prepped_sample_sets) - df_samples = df_samples.merge( - df_cohorts, on="sample_id", sort=False, how="left" - ) + # if self._cohorts_analysis: + # df_cohorts = self.cohorts_metadata(sample_sets=prepped_sample_sets) + # df_samples = df_samples.merge( + # df_cohorts, on="sample_id", sort=False, how="left" + # ) # Store sample metadata in the cache. self._cache_sample_metadata[cache_key] = df_samples diff --git a/notebooks/adir1_explore.ipynb b/notebooks/adir1_explore.ipynb deleted file mode 100644 index 450596a2f..000000000 --- a/notebooks/adir1_explore.ipynb +++ /dev/null @@ -1,522 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "id": "94bd6d28-bf20-4841-aeb5-007d0f76b6c0", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import malariagen_data" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "be3c904b-5b0d-4482-ba2e-113e42d57557", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "application/javascript": [ - "'use strict';\n", - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " const force = true;\n", - "\n", - " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", - " root._bokeh_onload_callbacks = [];\n", - " root._bokeh_is_loading = undefined;\n", - " }\n", - "\n", - "const JS_MIME_TYPE = 'application/javascript';\n", - " const HTML_MIME_TYPE = 'text/html';\n", - " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", - " const CLASS_NAME = 'output_bokeh rendered_html';\n", - "\n", - " /**\n", - " * Render data to the DOM node\n", - " */\n", - " function render(props, node) {\n", - " const script = document.createElement(\"script\");\n", - " node.appendChild(script);\n", - " }\n", - "\n", - " /**\n", - " * Handle when an output is cleared or removed\n", - " */\n", - " function handleClearOutput(event, handle) {\n", - " function drop(id) {\n", - " const view = Bokeh.index.get_by_id(id)\n", - " if (view != null) {\n", - " view.model.document.clear()\n", - " Bokeh.index.delete(view)\n", - " }\n", - " }\n", - "\n", - " const cell = handle.cell;\n", - "\n", - " const id = cell.output_area._bokeh_element_id;\n", - " const server_id = cell.output_area._bokeh_server_id;\n", - "\n", - " // Clean up Bokeh references\n", - " if (id != null) 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((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", - " return\n", - " }\n", - "\n", - " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", - "\n", - " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", - " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", - " // store reference to embed id on output_area\n", - " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", - " }\n", - " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", - " const bk_div = document.createElement(\"div\");\n", - " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", - " const script_attrs = bk_div.children[0].attributes;\n", - " for (let i = 0; i < script_attrs.length; i++) {\n", - " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", - " toinsert[toinsert.length - 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" root._bokeh_failed_load = false;\n", - " }\n", - "\n", - " const NB_LOAD_WARNING = {'data': {'text/html':\n", - " \"
\\n\"+\n", - " \"

\\n\"+\n", - " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", - " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", - " \"

\\n\"+\n", - " \"
    \\n\"+\n", - " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n", - " \"
  • use INLINE resources instead, as so:
  • \\n\"+\n", - " \"
\\n\"+\n", - " \"\\n\"+\n", - " \"from bokeh.resources import INLINE\\n\"+\n", - " \"output_notebook(resources=INLINE)\\n\"+\n", - " \"\\n\"+\n", - " \"
\"}};\n", - "\n", - " function display_loaded(error = null) {\n", - " const el = document.getElementById(null);\n", - " if (el != null) {\n", - " const html = (() => {\n", - " if (typeof root.Bokeh === \"undefined\") {\n", - " if (error == null) {\n", - " return \"BokehJS is loading ...\";\n", - " } else {\n", - " return \"BokehJS failed to load.\";\n", - " }\n", - " } else {\n", - " const prefix = `BokehJS ${root.Bokeh.version}`;\n", - " if (error == null) {\n", - " return `${prefix} successfully loaded.`;\n", - " } else {\n", - " return `${prefix} encountered errors while loading and may not function as expected.`;\n", - " }\n", - " }\n", - " })();\n", - " el.innerHTML = html;\n", - "\n", - " if (error != null) {\n", - " const wrapper = document.createElement(\"div\");\n", - " wrapper.style.overflow = \"auto\";\n", - " wrapper.style.height = \"5em\";\n", - " wrapper.style.resize = \"vertical\";\n", - " const content = document.createElement(\"div\");\n", - " content.style.fontFamily = \"monospace\";\n", - " content.style.whiteSpace = \"pre-wrap\";\n", - " content.style.backgroundColor = \"rgb(255, 221, 221)\";\n", - " content.textContent = error.stack ?? error.toString();\n", - " wrapper.append(content);\n", - " el.append(wrapper);\n", - " }\n", - " } else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(() => display_loaded(error), 100);\n", - " }\n", - " }\n", - "\n", - " function run_callbacks() {\n", - " try {\n", - " root._bokeh_onload_callbacks.forEach(function(callback) {\n", - " if (callback != null)\n", - " callback();\n", - " });\n", - " } finally {\n", - " delete root._bokeh_onload_callbacks\n", - " }\n", - " console.debug(\"Bokeh: all callbacks have finished\");\n", - " }\n", - "\n", - " function load_libs(css_urls, js_urls, callback) {\n", - " if (css_urls == null) css_urls = [];\n", - " if (js_urls == null) js_urls = [];\n", - "\n", - " root._bokeh_onload_callbacks.push(callback);\n", - " if (root._bokeh_is_loading > 0) {\n", - " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", - " return null;\n", - " }\n", - " if (js_urls == null || js_urls.length === 0) {\n", - " run_callbacks();\n", - " return null;\n", - " }\n", - " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", - " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", - "\n", - " function on_load() {\n", - " root._bokeh_is_loading--;\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", - " run_callbacks()\n", - " }\n", - " }\n", - "\n", - " function on_error(url) {\n", - " console.error(\"failed to load \" + url);\n", - " }\n", - "\n", - " for (let i = 0; i < css_urls.length; i++) {\n", - " const url = css_urls[i];\n", - " const element = document.createElement(\"link\");\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.rel = \"stylesheet\";\n", - " element.type = \"text/css\";\n", - " element.href = url;\n", - " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " for (let i = 0; i < js_urls.length; i++) {\n", - " const url = js_urls[i];\n", - " const element = document.createElement('script');\n", - " element.onload = on_load;\n", - " element.onerror = on_error.bind(null, url);\n", - " element.async = false;\n", - " element.src = url;\n", - " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", - " document.head.appendChild(element);\n", - " }\n", - " };\n", - "\n", - " function inject_raw_css(css) {\n", - " const element = document.createElement(\"style\");\n", - " element.appendChild(document.createTextNode(css));\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n", - " const css_urls = [];\n", - "\n", - " const inline_js = [ function(Bokeh) {\n", - " Bokeh.set_log_level(\"info\");\n", - " },\n", - "function(Bokeh) {\n", - " }\n", - " ];\n", - "\n", - " function run_inline_js() {\n", - " if (root.Bokeh !== undefined || force === true) {\n", - " try {\n", - " for (let i = 0; i < inline_js.length; i++) {\n", - " inline_js[i].call(root, root.Bokeh);\n", - " }\n", - "\n", - " } catch (error) {throw error;\n", - " }} else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(run_inline_js, 100);\n", - " } else if (!root._bokeh_failed_load) {\n", - " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", - " root._bokeh_failed_load = true;\n", - " } else if (force !== true) {\n", - " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", - " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", - " }\n", - " }\n", - "\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", - " run_inline_js();\n", - " } else {\n", - " load_libs(css_urls, js_urls, function() {\n", - " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", - " run_inline_js();\n", - " });\n", - " }\n", - "}(window));" - ], - "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
  • \\n\"+\n \"
  • use INLINE resources instead, as so:
  • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} encountered errors while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/html": [ - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
MalariaGEN Adir1 API client
\n", - " Please note that data are subject to terms of use,\n", - " for more information see \n", - " the MalariaGEN website or contact support@malariagen.net.\n", - " See also the Adir1 API docs.\n", - "
\n", - " Storage URL\n", - " gs://vo_adir_production_us_central1/
\n", - " Data releases available\n", - " 1.x
\n", - " Results cache\n", - " /Users/dennistpw/Projects/malariagen_results
\n", - " Cohorts analysis\n", - " noneyet
\n", - " Site filters analysis\n", - " sc_20250610
\n", - " Software version\n", - " malariagen_data 13.3.0.post33+90e72d5a
\n", - " Client location\n", - " Queensland, Australia
\n", - " " - ], - "text/plain": [ - "\n", - "Storage URL : gs://vo_adir_production_us_central1/\n", - "Data releases available : 1.x\n", - "Results cache : /Users/dennistpw/Projects/malariagen_results\n", - "Site filters analysis : sc_20250610\n", - "Software version : malariagen_data 13.3.0.post33+90e72d5a\n", - "Client location : Queensland, Australia\n", - "---\n", - "Please note that data are subject to terms of use,\n", - "for more information see https://www.malariagen.net/data\n", - "or contact support@malariagen.net. For API documentation see \n", - "https://malariagen.github.io/malariagen-data-python/v13.3.0.post33+90e72d5a/Adir1.html" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# Init Adir1 API\n", - "adir1 = malariagen_data.Adir1(results_cache = '/Users/dennistpw/Projects/malariagen_results/')\n", - "adir1" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "a4f50d6d-ad1b-404f-a9d1-e546f725abb3", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - " \r" - ] - } - ], - "source": [ - "snps = adir1.snp_calls(region=\"KB672868:1000000-1010000\")" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "id": "e0489eab-e347-492d-88ce-97d61a0c0aba", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - " \r" - ] - }, - { - "ename": "KeyError", - "evalue": "\"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:581\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 579\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 580\u001b[0m \u001b[38;5;66;03m# Attempt to retrieve from the cache.\u001b[39;00m\n\u001b[0;32m--> 581\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_cache_sample_metadata\u001b[49m\u001b[43m[\u001b[49m\u001b[43mcache_key\u001b[49m\u001b[43m]\u001b[49m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n", - "\u001b[0;31mKeyError\u001b[0m: ('1276-AD-BD-ALAM-VMF00156', '1277-VO-KH-WITKOWSKI-VMF00151', '1277-VO-KH-WITKOWSKI-VMF00183', '1278-VO-TH-KOBYLINSKI-VMF00153')", - "\nDuring handling of the above exception, another exception occurred:\n", - "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[10], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m pca \u001b[38;5;241m=\u001b[39m \u001b[43madir1\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpca\u001b[49m\u001b[43m(\u001b[49m\u001b[43mregion\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mKB672868\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mn_snps\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m100_000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcountry == \u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mThailand\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/pca.py:89\u001b[0m, in \u001b[0;36mAnophelesPca.pca\u001b[0;34m(self, region, n_snps, n_components, thin_offset, sample_sets, sample_query, sample_query_options, sample_indices, site_mask, site_class, min_minor_ac, max_missing_an, cohort_size, min_cohort_size, max_cohort_size, exclude_samples, fit_exclude_samples, random_seed, inline_array, chunks)\u001b[0m\n\u001b[1;32m 83\u001b[0m name \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpca_v4\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 85\u001b[0m \u001b[38;5;66;03m# Normalize params for consistent hash value.\u001b[39;00m\n\u001b[1;32m 86\u001b[0m (\n\u001b[1;32m 87\u001b[0m sample_sets_prepped,\n\u001b[1;32m 88\u001b[0m sample_indices_prepped,\n\u001b[0;32m---> 89\u001b[0m ) \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_prep_sample_selection_cache_params\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 90\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 91\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 92\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_query_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_query_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 93\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 94\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 95\u001b[0m region_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_region_cache_param(region\u001b[38;5;241m=\u001b[39mregion)\n\u001b[1;32m 96\u001b[0m site_mask_prepped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_optional_site_mask_param(site_mask\u001b[38;5;241m=\u001b[39msite_mask)\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:892\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._prep_sample_selection_cache_params\u001b[0;34m(self, sample_sets, sample_query, sample_query_options, sample_indices)\u001b[0m\n\u001b[1;32m 885\u001b[0m sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prep_sample_sets_param(sample_sets\u001b[38;5;241m=\u001b[39msample_sets)\n\u001b[1;32m 887\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sample_query \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 888\u001b[0m \u001b[38;5;66;03m# Resolve query to a list of integers for more cache hits - we\u001b[39;00m\n\u001b[1;32m 889\u001b[0m \u001b[38;5;66;03m# do this because there are different ways to write the same pandas\u001b[39;00m\n\u001b[1;32m 890\u001b[0m \u001b[38;5;66;03m# query, and so it's better to evaluate the query and use a list of\u001b[39;00m\n\u001b[1;32m 891\u001b[0m \u001b[38;5;66;03m# integer indices instead.\u001b[39;00m\n\u001b[0;32m--> 892\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msample_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 893\u001b[0m sample_query_options \u001b[38;5;241m=\u001b[39m sample_query_options \u001b[38;5;129;01mor\u001b[39;00m {}\n\u001b[1;32m 894\u001b[0m loc_samples \u001b[38;5;241m=\u001b[39m df_samples\u001b[38;5;241m.\u001b[39meval(sample_query, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39msample_query_options)\u001b[38;5;241m.\u001b[39mvalues\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:589\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.sample_metadata\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 583\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m:\n\u001b[1;32m 584\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_spinner(desc\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mLoad sample metadata\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n\u001b[1;32m 585\u001b[0m \u001b[38;5;66;03m## Build a single DataFrame using all available metadata.\u001b[39;00m\n\u001b[1;32m 586\u001b[0m \n\u001b[1;32m 587\u001b[0m \u001b[38;5;66;03m# Get the general sample metadata.\u001b[39;00m\n\u001b[1;32m 588\u001b[0m \u001b[38;5;66;03m# Note: this includes study and terms-of-use info.\u001b[39;00m\n\u001b[0;32m--> 589\u001b[0m df_samples \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgeneral_metadata\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mprepped_sample_sets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 591\u001b[0m \u001b[38;5;66;03m# Merge with the sequence QC metadata.\u001b[39;00m\n\u001b[1;32m 592\u001b[0m df_sequence_qc \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msequence_qc_metadata(\n\u001b[1;32m 593\u001b[0m sample_sets\u001b[38;5;241m=\u001b[39mprepped_sample_sets\n\u001b[1;32m 594\u001b[0m )\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:185\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata.general_metadata\u001b[0;34m(self, sample_sets)\u001b[0m\n\u001b[1;32m 174\u001b[0m \u001b[38;5;129m@check_types\u001b[39m\n\u001b[1;32m 175\u001b[0m \u001b[38;5;129m@doc\u001b[39m(\n\u001b[1;32m 176\u001b[0m summary\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 183\u001b[0m \u001b[38;5;28mself\u001b[39m, sample_sets: Optional[base_params\u001b[38;5;241m.\u001b[39msample_sets] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 184\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m pd\u001b[38;5;241m.\u001b[39mDataFrame:\n\u001b[0;32m--> 185\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_metadata_paths\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 186\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath_template\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;132;43;01m{release_path}\u001b[39;49;00m\u001b[38;5;124;43m/metadata/general/\u001b[39;49m\u001b[38;5;132;43;01m{sample_set}\u001b[39;49;00m\u001b[38;5;124;43m/samples.meta.csv\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 187\u001b[0m \u001b[43m \u001b[49m\u001b[43mparse_metadata_func\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_parse_general_metadata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 188\u001b[0m \u001b[43m \u001b[49m\u001b[43msample_sets\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_sets\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 189\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:119\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_metadata_paths\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 117\u001b[0m path \u001b[38;5;241m=\u001b[39m file_paths[sample_set]\n\u001b[1;32m 118\u001b[0m data \u001b[38;5;241m=\u001b[39m files[path]\n\u001b[0;32m--> 119\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[43mparse_metadata_func\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdata\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 120\u001b[0m dfs\u001b[38;5;241m.\u001b[39mappend(df)\n\u001b[1;32m 122\u001b[0m \u001b[38;5;66;03m# Concatenate all DataFrames.\u001b[39;00m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:160\u001b[0m, in \u001b[0;36mAnophelesSampleMetadata._parse_general_metadata\u001b[0;34m(self, sample_set, data)\u001b[0m\n\u001b[1;32m 154\u001b[0m df[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mquarter\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m df\u001b[38;5;241m.\u001b[39mapply(\n\u001b[1;32m 155\u001b[0m \u001b[38;5;28;01mlambda\u001b[39;00m row: ((row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m-\u001b[39m \u001b[38;5;241m1\u001b[39m) \u001b[38;5;241m/\u001b[39m\u001b[38;5;241m/\u001b[39m \u001b[38;5;241m3\u001b[39m) \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m row\u001b[38;5;241m.\u001b[39mmonth \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m,\n\u001b[1;32m 156\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcolumns\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 157\u001b[0m )\n\u001b[1;32m 159\u001b[0m \u001b[38;5;66;03m# Add study columns.\u001b[39;00m\n\u001b[0;32m--> 160\u001b[0m study_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mlookup_study_info\u001b[49m\u001b[43m(\u001b[49m\u001b[43msample_set\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msample_set\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 161\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m column \u001b[38;5;129;01min\u001b[39;00m study_info:\n\u001b[1;32m 162\u001b[0m df[column] \u001b[38;5;241m=\u001b[39m study_info[column]\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/util.py:1164\u001b[0m, in \u001b[0;36mcheck_types..check_types_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 1162\u001b[0m error \u001b[38;5;241m=\u001b[39m \u001b[38;5;167;01mTypeError\u001b[39;00m(message)\n\u001b[1;32m 1163\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28mNone\u001b[39m\n\u001b[0;32m-> 1164\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/github/tristanpwdennis/malariagen-data-python/malariagen_data/anoph/base.py:487\u001b[0m, in \u001b[0;36mAnophelesBase.lookup_study_info\u001b[0;34m(self, sample_set)\u001b[0m\n\u001b[1;32m 485\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 486\u001b[0m df_sample_sets \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msample_sets()\u001b[38;5;241m.\u001b[39mset_index(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_set\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 487\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info \u001b[38;5;241m=\u001b[39m \u001b[43mdf_sample_sets\u001b[49m\u001b[43m[\u001b[49m\n\u001b[1;32m 488\u001b[0m \u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_id\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstudy_url\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m 489\u001b[0m \u001b[43m \u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241m.\u001b[39mto_dict(orient\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 490\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 491\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache_sample_set_to_study_info[sample_set]\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/frame.py:3766\u001b[0m, in \u001b[0;36mDataFrame.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 3764\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_iterator(key):\n\u001b[1;32m 3765\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 3766\u001b[0m indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcolumns\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_indexer_strict\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcolumns\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m[\u001b[38;5;241m1\u001b[39m]\n\u001b[1;32m 3768\u001b[0m \u001b[38;5;66;03m# take() does not accept boolean indexers\u001b[39;00m\n\u001b[1;32m 3769\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(indexer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdtype\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;241m==\u001b[39m \u001b[38;5;28mbool\u001b[39m:\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5876\u001b[0m, in \u001b[0;36mIndex._get_indexer_strict\u001b[0;34m(self, key, axis_name)\u001b[0m\n\u001b[1;32m 5873\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 5874\u001b[0m keyarr, indexer, new_indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_non_unique(keyarr)\n\u001b[0;32m-> 5876\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_raise_if_missing\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkeyarr\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindexer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis_name\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5878\u001b[0m keyarr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtake(indexer)\n\u001b[1;32m 5879\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(key, Index):\n\u001b[1;32m 5880\u001b[0m \u001b[38;5;66;03m# GH 42790 - Preserve name from an Index\u001b[39;00m\n", - "File \u001b[0;32m~/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py:5935\u001b[0m, in \u001b[0;36mIndex._raise_if_missing\u001b[0;34m(self, key, indexer, axis_name)\u001b[0m\n\u001b[1;32m 5933\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m use_interval_msg:\n\u001b[1;32m 5934\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 5935\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNone of [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkey\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m] are in the [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00maxis_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m]\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 5937\u001b[0m not_found \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(ensure_index(key)[missing_mask\u001b[38;5;241m.\u001b[39mnonzero()[\u001b[38;5;241m0\u001b[39m]]\u001b[38;5;241m.\u001b[39munique())\n\u001b[1;32m 5938\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mnot_found\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m not in index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", - "\u001b[0;31mKeyError\u001b[0m: \"None of [Index(['study_id', 'study_url'], dtype='object')] are in the [columns]\"" - ] - } - ], - "source": [ - "pca = adir1.pca(region = \"KB672868\", n_snps = 100_000, sample_query = \"country == 'Thailand'\")" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.10" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} From ce7b80a84f93951a7b4918f9ee3870615fce442d Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Sun, 15 Jun 2025 22:28:15 -0500 Subject: [PATCH 11/12] forgot how the alphabet works d'oh --- malariagen_data/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/malariagen_data/__init__.py b/malariagen_data/__init__.py index 6bc938825..306896658 100644 --- a/malariagen_data/__init__.py +++ b/malariagen_data/__init__.py @@ -1,6 +1,6 @@ # flake8: noqa -from .af1 import Af1 from .adir1 import Adir1 +from .af1 import Af1 from .ag3 import Ag3 from .amin1 import Amin1 from .anopheles import AnophelesDataResource, Region From 1b196344fb4f7cd1e4e836b52440b22610cf2df3 Mon Sep 17 00:00:00 2001 From: tristanpwdennis Date: Mon, 16 Jun 2025 20:35:38 -0500 Subject: [PATCH 12/12] add hashing to roh function --- malariagen_data/adir1.py | 6 +- malariagen_data/anopheles.py | 71 +- poetry.lock | 3689 ++++++++++++++++++---------------- pyproject.toml | 1 + 4 files changed, 2031 insertions(+), 1736 deletions(-) diff --git a/malariagen_data/adir1.py b/malariagen_data/adir1.py index 9b053ca62..c24562426 100644 --- a/malariagen_data/adir1.py +++ b/malariagen_data/adir1.py @@ -102,9 +102,9 @@ def __init__( aim_palettes=None, site_filters_analysis=site_filters_analysis, discordant_read_calls_analysis=discordant_read_calls_analysis, - default_site_mask="funestus", - default_phasing_analysis="funestus", - default_coverage_calls_analysis="funestus", + default_site_mask="dirus", + default_phasing_analysis="dirus", + default_coverage_calls_analysis="dirus", bokeh_output_notebook=bokeh_output_notebook, results_cache=results_cache, log=log, diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py index ed9cb65cf..7fc78451e 100644 --- a/malariagen_data/anopheles.py +++ b/malariagen_data/anopheles.py @@ -574,31 +574,68 @@ def roh_hmm( debug = self._log.debug resolved_region: Region = parse_single_region(self, region) - del region - debug("compute windowed heterozygosity") - sample_id, sample_set, windows, counts = self._sample_count_het( + name = "roh" + + params = dict( sample=sample, - region=resolved_region, - site_mask=site_mask, + region=region, window_size=window_size, + site_mask=site_mask, sample_set=sample_set, - chunks=chunks, - inline_array=inline_array, - ) - - debug("compute runs of homozygosity") - df_roh = self._roh_hmm_predict( - windows=windows, - counts=counts, phet_roh=phet_roh, phet_nonroh=phet_nonroh, transition=transition, - window_size=window_size, - sample_id=sample_id, - contig=resolved_region.contig, + chunks=chunks, + inline_array=inline_array, ) + del region + + try: + # Load cached numeric data, adding str / obj data again. + results = self.results_cache_get(name=name, params=params) + df_roh = pd.DataFrame(results) + df_roh["sample_id"] = sample + df_roh["contig"] = resolved_region.contig + + except CacheMiss: + debug("compute windowed heterozygosity") + sample_id, sample_set, windows, counts = self._sample_count_het( + sample=sample, + region=resolved_region, + site_mask=site_mask, + window_size=window_size, + sample_set=sample_set, + chunks=chunks, + inline_array=inline_array, + ) + + debug("compute runs of homozygosity") + df_roh = self._roh_hmm_predict( + windows=windows, + counts=counts, + phet_roh=phet_roh, + phet_nonroh=phet_nonroh, + transition=transition, + window_size=window_size, + sample_id=sample_id, + contig=resolved_region.contig, + ) + + # Specify numeric columns to save (saving obj - sample ID and contig - breaks the save. + columns_to_save = [ + "roh_start", + "roh_stop", + "roh_length", + "roh_is_marginal", + ] + self.results_cache_set( + name=name, + params=params, + results={col: df_roh[col].to_numpy() for col in columns_to_save}, + ) + return df_roh @check_types @@ -1306,7 +1343,7 @@ def ihs_gwss( ) -> Tuple[np.ndarray, np.ndarray]: # change this name if you ever change the behaviour of this function, to # invalidate any previously cached data - name = self._ihs_gwss_cache_name + name = "roh" params = dict( contig=contig, diff --git a/poetry.lock b/poetry.lock index 7ea703765..d02d5c5bc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. [[package]] name = "accessible-pygments" @@ -6,6 +6,8 @@ version = "0.0.5" description = "A collection of accessible pygments styles" optional = false python-versions = ">=3.9" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "accessible_pygments-0.0.5-py3-none-any.whl", hash = "sha256:88ae3211e68a1d0b011504b2ffc1691feafce124b845bd072ab6f9f66f34d4b7"}, {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"}, @@ -20,127 +22,122 @@ tests = ["hypothesis", "pytest"] [[package]] name = "aiobotocore" -version = "2.21.1" +version = "2.15.2" description = "Async client for aws services using botocore and aiohttp" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ - {file = "aiobotocore-2.21.1-py3-none-any.whl", hash = "sha256:bd7c49a6d6f8a3d9444b0a94417c8da13813b5c7eec1c4f0ec2db7e8ce8f23e7"}, - {file = "aiobotocore-2.21.1.tar.gz", hash = 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"Operations with ISO 8601 durations" optional = false python-versions = ">=3.7" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"}, {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"}, @@ -2009,6 +2114,7 @@ version = "2.2.0" description = "Safely pass data to untrusted environments and back." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "itsdangerous-2.2.0-py3-none-any.whl", hash = "sha256:c6242fc49e35958c8b15141343aa660db5fc54d4f13a1db01a3f5891b98700ef"}, {file = "itsdangerous-2.2.0.tar.gz", hash = "sha256:e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173"}, @@ -2020,6 +2126,7 @@ version = "0.19.2" description = "An autocompletion tool for Python that can be used for text editors." optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "jedi-0.19.2-py2.py3-none-any.whl", hash = "sha256:a8ef22bde8490f57fe5c7681a3c83cb58874daf72b4784de3cce5b6ef6edb5b9"}, {file = "jedi-0.19.2.tar.gz", hash = "sha256:4770dc3de41bde3966b02eb84fbcf557fb33cce26ad23da12c742fb50ecb11f0"}, @@ -2035,13 +2142,14 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"] [[package]] name = "jinja2" -version = "3.1.6" +version = "3.1.4" description = "A very fast and expressive template engine." optional = false python-versions = ">=3.7" +groups = ["main"] files = [ - {file = "jinja2-3.1.6-py3-none-any.whl", hash = "sha256:85ece4451f492d0c13c5dd7c13a64681a86afae63a5f347908daf103ce6d2f67"}, - {file = "jinja2-3.1.6.tar.gz", hash = "sha256:0137fb05990d35f1275a587e9aee6d56da821fc83491a0fb838183be43f66d6d"}, + {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"}, + {file = "jinja2-3.1.4.tar.gz", hash = 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(==24.3.1)", "pylint (==3.2.3)", "ruff (==0.7.3)", "twine (==5.1.1)", "uv (==0.5.1)"] [[package]] name = "jsonpointer" @@ -2092,6 +2204,8 @@ version = "3.0.0" description = "Identify specific nodes in a JSON document (RFC 6901)" optional = false python-versions = ">=3.7" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "jsonpointer-3.0.0-py2.py3-none-any.whl", hash = "sha256:13e088adc14fca8b6aa8177c044e12701e6ad4b28ff10e65f2267a90109c9942"}, {file = "jsonpointer-3.0.0.tar.gz", hash = "sha256:2b2d729f2091522d61c3b31f82e11870f60b68f43fbc705cb76bf4b832af59ef"}, @@ -2103,6 +2217,8 @@ version = "4.23.0" description = "An implementation of JSON Schema validation for Python" optional = false python-versions = ">=3.8" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"}, {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"}, @@ -2132,6 +2248,8 @@ version = "2024.10.1" description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" optional = false python-versions = ">=3.9" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "jsonschema_specifications-2024.10.1-py3-none-any.whl", hash = "sha256:a09a0680616357d9a0ecf05c12ad234479f549239d0f5b55f3deea67475da9bf"}, {file = "jsonschema_specifications-2024.10.1.tar.gz", hash = "sha256:0f38b83639958ce1152d02a7f062902c41c8fd20d558b0c34344292d417ae272"}, @@ -2146,6 +2264,7 @@ version = "8.6.3" description = "Jupyter protocol implementation and client libraries" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "jupyter_client-8.6.3-py3-none-any.whl", hash = "sha256:e8a19cc986cc45905ac3362915f410f3af85424b4c0905e94fa5f2cb08e8f23f"}, {file = "jupyter_client-8.6.3.tar.gz", hash = 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A base package on which Jupyter projects rely." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "jupyter_core-5.7.2-py3-none-any.whl", hash = "sha256:4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409"}, {file = "jupyter_core-5.7.2.tar.gz", hash = "sha256:aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9"}, @@ -2184,18 +2304,19 @@ test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout" [[package]] name = "jupyter-events" -version = "0.12.0" +version = "0.10.0" description = "Jupyter Event System library" optional = false -python-versions = ">=3.9" +python-versions = ">=3.8" +groups = ["main"] +markers = "extra == \"dev\"" files = [ - {file = "jupyter_events-0.12.0-py3-none-any.whl", hash = "sha256:6464b2fa5ad10451c3d35fabc75eab39556ae1e2853ad0c0cc31b656731a97fb"}, - {file = "jupyter_events-0.12.0.tar.gz", hash = "sha256:fc3fce98865f6784c9cd0a56a20644fc6098f21c8c33834a8d9fe383c17e554b"}, + {file = 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">=3.8" +groups = ["main"] files = [ {file = "jupyter_leaflet-0.19.2-py3-none-any.whl", hash = "sha256:0d57e15e80c08a4360f0cde0b4c490beddc5d422bb0e9bc1c0b4479d3fb725a6"}, {file = "jupyter_leaflet-0.19.2.tar.gz", hash = "sha256:b09b5ba48b1488cb61da37a6f558347269eb53ff6d64dc1a73e005ffc4420063"}, @@ -2225,6 +2347,8 @@ version = "2.2.5" description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server" optional = false python-versions = ">=3.8" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "jupyter-lsp-2.2.5.tar.gz", hash = "sha256:793147a05ad446f809fd53ef1cd19a9f5256fd0a2d6b7ce943a982cb4f545001"}, {file = "jupyter_lsp-2.2.5-py3-none-any.whl", hash = "sha256:45fbddbd505f3fbfb0b6cb2f1bc5e15e83ab7c79cd6e89416b248cb3c00c11da"}, @@ -2235,13 +2359,15 @@ jupyter-server = ">=1.1.2" [[package]] name = "jupyter-server" -version = "2.15.0" +version = "2.14.2" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." optional = false -python-versions = ">=3.9" +python-versions = ">=3.8" +groups = ["main"] +markers = "extra == \"dev\"" files = [ - {file = "jupyter_server-2.15.0-py3-none-any.whl", hash = "sha256:872d989becf83517012ee669f09604aa4a28097c0bd90b2f424310156c2cdae3"}, - {file = "jupyter_server-2.15.0.tar.gz", hash = "sha256:9d446b8697b4f7337a1b7cdcac40778babdd93ba614b6d68ab1c0c918f1c4084"}, + {file = "jupyter_server-2.14.2-py3-none-any.whl", hash = "sha256:47ff506127c2f7851a17bf4713434208fc490955d0e8632e95014a9a9afbeefd"}, + {file = "jupyter_server-2.14.2.tar.gz", hash = "sha256:66095021aa9638ced276c248b1d81862e4c50f292d575920bbe960de1c56b12b"}, ] [package.dependencies] @@ -2250,7 +2376,7 @@ argon2-cffi = ">=21.1" jinja2 = ">=3.0.3" jupyter-client = ">=7.4.4" jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" -jupyter-events = ">=0.11.0" +jupyter-events = ">=0.9.0" jupyter-server-terminals = ">=0.4.4" nbconvert = ">=6.4.4" nbformat = ">=5.3.0" @@ -2275,6 +2401,8 @@ version = "0.5.3" description = "A Jupyter Server Extension Providing Terminals." optional = false python-versions = ">=3.8" +groups = ["main"] +markers = "extra == \"dev\"" files = [ {file = "jupyter_server_terminals-0.5.3-py3-none-any.whl", hash = "sha256:41ee0d7dc0ebf2809c668e0fc726dfaf258fcd3e769568996ca731b6194ae9aa"}, {file = "jupyter_server_terminals-0.5.3.tar.gz", hash = "sha256:5ae0295167220e9ace0edcfdb212afd2b01ee8d179fe6f23c899590e9b8a5269"}, @@ -2290,18 +2418,20 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (> [[package]] name = "jupyterlab" -version = "4.4.0" +version = "4.3.2" description = "JupyterLab computational environment" optional = false -python-versions = ">=3.9" +python-versions = ">=3.8" +groups = ["main"] +markers = "extra == \"dev\"" files = [ - {file = "jupyterlab-4.4.0-py3-none-any.whl", hash = "sha256:61d33991fbb352cc7caac08bd0c34577fea86d8d5d9772600d9d5a6bcbc882c0"}, - {file = "jupyterlab-4.4.0.tar.gz", hash = "sha256:f1767d5f0104e40f3b4a63bf6892bbef8e4704dcabf0c78408a3bdc411792f04"}, + {file = "jupyterlab-4.3.2-py3-none-any.whl", hash = "sha256:e87100cbab8b886ff7a4f325c856100ba6fdfe916162a85409daf0e707e19d1d"}, + {file = "jupyterlab-4.3.2.tar.gz", hash = "sha256:3c0a6882dbddcc0a7bfdd5e2236f351b2b263e48780236e6996c2aca13ac5b22"}, ] [package.dependencies] async-lru = ">=1.0.0" -httpx = ">=0.25.0" +httpx = ">=0.28.0,<0.29.0" ipykernel = ">=6.5.0" jinja2 = ">=3.0.3" jupyter-core = "*" @@ -2310,15 +2440,15 @@ jupyter-server = ">=2.4.0,<3" jupyterlab-server = ">=2.27.1,<3" notebook-shim = ">=0.2" packaging = "*" -setuptools = ">=41.1.0" +setuptools = ">=40.8.0" tomli = {version = ">=1.2.2", markers = "python_version < \"3.11\""} tornado = ">=6.2.0" traitlets = "*" [package.extras] -dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.9.9)"] -docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", 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