diff --git a/.gitattributes b/.gitattributes
index 21fe133de..4579cc53f 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,3 +1,6 @@
# Shell scripts
*.sh eol=lf
*.gif filter=lfs diff=lfs merge=lfs -text
+
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true
diff --git a/.github/workflows/python_analysis.yml b/.github/workflows/python_analysis.yml
index ac2d04dec..26cef5c65 100644
--- a/.github/workflows/python_analysis.yml
+++ b/.github/workflows/python_analysis.yml
@@ -26,14 +26,14 @@ jobs:
name: Static analysis
uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-static_analysis.yml@main
with:
- package-manager: 'poetry'
+ package-manager: 'pixi'
app-name: 'geoh5py'
python-version: '3.10'
call-workflow-pytest:
name: Pytest
uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest.yml@main
with:
- package-manager: 'poetry'
+ package-manager: 'pixi'
python-versions: '["3.10", "3.11", "3.12"]'
os: '["ubuntu-latest", "windows-latest"]'
cache-number: 1
diff --git a/.gitignore b/.gitignore
index f85336755..0aff53b7f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -145,5 +145,13 @@ dmypy.json
# geoh5 locks
*.geoh5.lock
-#version ignore
+# auto-generated version file
geoh5py/_version.py
+
+# not using poetry to lock, but pixi
+poetry.lock
+
+# pixi environments
+.pixi/*
+!.pixi/config.toml
+/docs/conf.py
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9ebd67007..4bd80b079 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,7 +15,6 @@ repos:
rev: 2.1.3
hooks:
- id: poetry-check
- args: [--lock, --no-plugins]
- repo: https://github.com/hadialqattan/pycln
rev: v2.5.0
hooks:
@@ -74,7 +73,7 @@ repos:
hooks:
- id: pylint
name: pylint
- entry: poetry run pylint
+ entry: pixi run --locked pylint
language: system
require_serial: true # pylint does its own parallelism
types: [text]
diff --git a/.readthedocs.yml b/.readthedocs.yml
index 117ec52d6..63932a35c 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -1,42 +1,37 @@
version: 2
-# Set the version of Python and other tools you might need
build:
- os: "ubuntu-22.04"
+ os: ubuntu-24.04
tools:
- python: "mambaforge-22.9"
+ python: "3.10" # pre-install for the py310 environment of pixi
jobs:
post_checkout:
- - echo "[RTD] Configure Git LFS"
+ # Download and uncompress binary for the desired version of Git LFS
- |
set -e
- # Update version of Git LFS as needed here:
LFS_VERSION="3.4.0"
wget "https://github.com/git-lfs/git-lfs/releases/download/v${LFS_VERSION}/git-lfs-linux-amd64-v${LFS_VERSION}.tar.gz"
tar xzf "git-lfs-linux-amd64-v${LFS_VERSION}.tar.gz" --strip-components=1 "git-lfs-${LFS_VERSION}/git-lfs"
rm "git-lfs-linux-amd64-v${LFS_VERSION}.tar.gz"
- - |
- set -e
- git_lfs_path="$(pwd)"
- git config filter.lfs.process "$git_lfs_path/git-lfs filter-process"
- git config filter.lfs.smudge "$git_lfs_path/git-lfs smudge -- %f"
- git config filter.lfs.clean "$git_lfs_path/git-lfs clean -- %f"
- - |
- set -e
- ./git-lfs install
- ./git-lfs fetch
- ./git-lfs checkout
+ # Modify LFS config paths to point where git-lfs binary was downloaded
+ - git config filter.lfs.process "$(pwd)/git-lfs filter-process"
+ - git config filter.lfs.smudge "$(pwd)/git-lfs smudge -- %f"
+ - git config filter.lfs.clean "$(pwd)/git-lfs clean -- %f"
+ # Make LFS available in current repository
+ - ./git-lfs install
+ # Download content from remote
+ - ./git-lfs fetch
+ # Make local files to have the real content on them
+ - ./git-lfs checkout
- pre_build:
- # Generate on-the-fly Sphinx configuration from Jupyter Book's _config.yml
- - "jupyter-book config sphinx docs/"
- - "pip install . --no-deps"
+ create_environment:
+ - asdf plugin add pixi
+ - asdf install pixi latest
+ - asdf global pixi latest
-# Build documentation in the docs/ directory with Sphinx
-sphinx:
- builder: html
- configuration: docs/conf.py
- fail_on_warning: false
+ install:
+ - pixi install -e docs
-conda:
- environment: docs/environment.yml
+ build:
+ html:
+ - pixi run --frozen -e docs build-docs html $READTHEDOCS_OUTPUT
diff --git a/docs/_config.yml b/docs/_config.yml
index ec26d789f..e861eb231 100644
--- a/docs/_config.yml
+++ b/docs/_config.yml
@@ -2,7 +2,8 @@
# Learn more at https://jupyterbook.org/customize/config.html
title: Geoh5py
-author: Mira Geoscience
+author: Mira Geoscience Ltd.
+copyright: "2025"
logo: images/geoh5py_logo.png
# Force re-execution of notebooks on each build.
@@ -13,10 +14,38 @@ execute:
sphinx:
extra_extensions:
- - 'sphinx.ext.autodoc'
+ - sphinx.ext.autodoc
+ - sphinx.ext.intersphinx
+ - sphinx.ext.todo
+ - sphinx_issues
+ - sphinxcontrib.googleanalytics
+ #- sphinx.ext.autosummary # TODO: restore? for now, tons of error
+ #- sphinx.ext.viewcode # TODO: restore? for now, tons of error
+ local_extensions:
+ dynamic_config: _ext/
+ recursive_update: true
config:
- suppress_warnings : ["etoc.toctree"]
-
+ project: geoh5py
+ html_static_path:
+ - _static/custom.css
+ html_theme: alabaster
+ autodoc_typehints: signature
+ autodoc_typehints_format: short
+ suppress_warnings:
+ - etoc.toctree
+ intersphinx_mapping:
+ # use None to auto‑fetch objects.inv
+ numpy:
+ - https://numpy.org/doc/1.26/
+ - null
+ python:
+ - https://docs.python.org/3/
+ - null
+ todo_include_todos: true
+ issues_github_path: mirageoscience/geoh5py
+ autodoc_type_aliases:
+ np.ndarray: numpy.ndarray
+ UUID: uuid.UUID
# Define the name of the latex output file for PDF builds
latex:
diff --git a/docs/_ext/Add2Build.py b/docs/_ext/Add2Build.py
deleted file mode 100644
index 3cf112b86..000000000
--- a/docs/_ext/Add2Build.py
+++ /dev/null
@@ -1,28 +0,0 @@
-import os
-import shutil
-from pathlib import Path
-
-
-def copyImages():
- # get relevant directories
- cwd = Path()
- contentdir = cwd / "content"
- buildimagesdir = cwd / "_build" / "html" / "_images"
-
- # check if images directory exists
- buildimagesdir.mkdir(exist_ok=True)
-
- # images that have been copied
- imnames = os.listdir(buildimagesdir)
-
- # search for images that have been missed
- for root, dirList, fileList in os.walk(str(contentdir)):
- if root.endswith("images"):
- for filename in fileList:
- if filename not in imnames:
- shutil.copy(Path(root) / filename, buildimagesdir)
- return
-
-
-if __name__ == "__main__":
- copyImages()
diff --git a/docs/_ext/__init__.py b/docs/_ext/__init__.py
deleted file mode 100644
index 8255d73e5..000000000
--- a/docs/_ext/__init__.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from Add2Build import copyImages
-from autodoc import make_lectures_page
-from edit_on_github import *
-from environmentSetup import supress_nonlocal_image_warn
diff --git a/docs/_ext/autodoc.py b/docs/_ext/autodoc.py
deleted file mode 100644
index 52b4af3e4..000000000
--- a/docs/_ext/autodoc.py
+++ /dev/null
@@ -1,146 +0,0 @@
-from __future__ import print_function
-
-import datetime
-import json
-from pathlib import Path
-
-fName = Path(__file__).resolve()
-# info_list = ['title', 'date', 'author', 'url', 'pdf', 'jupyter']
-pdf_root = "https://storage.googleapis.com/simpeg/eosc350lectures/"
-jupyter_root = "http://mybinder.org/repo/ubcgif/gpgLabs/notebooks/"
-youtube_channel = "https://www.youtube.com/c/geoscixyz"
-
-lecture_path = "content/appendix/"
-
-THIS_IS_AUTOGENERATED = (
- ".. --------------------------------- ..\n"
- ".. ..\n"
- ".. THIS FILE IS AUTO GENEREATED ..\n"
- ".. ..\n"
- ".. autodoc.py ..\n"
- ".. ..\n"
- ".. --------------------------------- ..\n"
-)
-
-
-def make_lectures_page(fpath=None, fout=None):
-
- if fpath is None:
- fpath = lecture_path + "lectures.json"
-
- if fout is None:
- fout = lecture_path + "lectures.rst"
-
- fpath = Path(fName).parents(2) / fpath
- fout = Path(fName).parents(2) / fout
-
- fpath = open(fpath) # file to write to
- lectures = json.load(fpath) # lecture json
-
- out = """.. _lectures:
-
-{}
-
-
-Lectures
-========
-
-
-""".format(
- THIS_IS_AUTOGENERATED
- )
-
- print("\nCreating: lectures.rst")
- f = open(fout, "w")
- f.write(out)
-
- for key in range(len(lectures.keys())): # assumes keys are ints
- lecture = lectures[f"{key}"]
- print(f" writing lecture {key}")
- date = list(map(int, lecture["date"].split("-")))
- date = datetime.date(year=date[0], month=date[1], day=date[2])
-
- if "pdf" in lecture.keys():
- pdf_name = Path(lecture["pdf"]).stem
- if "_" in pdf_name:
- pdf_name = " ".join(pdf_name.split("_")[1:])
- lecture_slides = """
-- `{title} lecture slides <{pdf}>`_
- """.format(
- title=pdf_name, pdf=pdf_root + lecture["pdf"]
- )
- else:
- lecture_slides = ""
-
- if "jupyter" in lecture.keys():
- jupyter = """
-- `Jupyter notebook: {name} <{notebook}>`_
- """.format(
- name=lecture["jupyter"].split("/")[-1],
- notebook=jupyter_root + lecture["jupyter"],
- )
- else:
- jupyter = ""
-
- if "app" in lecture.keys():
- app = """
-- `App <{app}>`_
- """.format(
- app=lecture["app"]
- )
- else:
- app = ""
-
- info_block = """
-*{0:%B} {0:%d}, {0:%Y}*
-
-{lecture_slides}
-{jupyter}
-{app}
- """.format(
- date, lecture_slides=lecture_slides, jupyter=jupyter, app=app
- )
-
- youtube_block = """
-.. raw:: html
-
-
-
-
-
-
- """.format(
- url="https://www.youtube.com/embed/" + lecture["youtube"] + "?rel=0"
- )
-
- out = """
-.. _lecture_{lecture_id}:
-
-{name}
-{underline}
-
-{info_block}
-
-{youtube_block}
-
- """.format(
- lecture_id=key,
- name=lecture["title"],
- underline=len(lecture["title"]) * "-",
- info_block=info_block,
- youtube_block=youtube_block,
- )
- f.write(out)
-
- f.close()
-
- print("Done writing lectures.rst\n")
-
-
-if __name__ == "__main__":
- """
- Run the following to create the lecture page.
- """
-
- make_lectures_page()
diff --git a/docs/_ext/dynamic_config.py b/docs/_ext/dynamic_config.py
new file mode 100644
index 000000000..5368cdef7
--- /dev/null
+++ b/docs/_ext/dynamic_config.py
@@ -0,0 +1,37 @@
+import logging
+import os
+
+from datetime import datetime
+from importlib.metadata import version as get_version
+from packaging.version import Version
+
+
+dated_copyright = f"{datetime.now().strftime('%Y, Mira Geoscience Ltd')}"
+
+def get_copyright_notice():
+ return f"Copyright {dated_copyright}."
+
+
+def setup(app):
+ # The full version, including alpha/beta/rc tags.
+ release = get_version("geoh5py")
+ # The shorter X.Y.Z version.
+ version = Version(release).base_version
+
+ app.config.project_copyright = f"{dated_copyright}"
+ app.config.release = release
+ app.config.version = version
+ app.config.html_theme_options = {
+ "description": f"version {release}",
+ "fixed_sidebar": True,
+ "logo_name": "Geoh5py",
+ "show_relbars": True,
+ }
+ app.config.rst_epilog = f"\n.. |copyright_notice| replace:: {get_copyright_notice()}\n"
+
+ app.config.googleanalytics_id = os.environ.get("GOOGLE_ANALYTICS_ID", "")
+ if not app.config.googleanalytics_id:
+ logging.warning("Environment variable GOOGLE_ANALYTICS_ID is not set")
+ app.config.googleanalytics_enabled = False
+
+ return {"version": "0.1", "parallel_read_safe": True}
diff --git a/docs/_ext/edit_on_github.py b/docs/_ext/edit_on_github.py
deleted file mode 100644
index 42a84ecaa..000000000
--- a/docs/_ext/edit_on_github.py
+++ /dev/null
@@ -1,52 +0,0 @@
-"""
-Sphinx extension to add ReadTheDocs-style "Edit on GitHub" links to the
-sidebar.
-
-Loosely based on https://github.com/astropy/astropy/pull/347
-"""
-
-from pathlib import Path
-import warnings
-
-__licence__ = "BSD (3 clause)"
-
-
-def get_github_url(app, view, path):
- if app.config.edit_on_github_directory is not None:
- return "https://github.com/{project}/{view}/{branch}/{dir}/{path}".format(
- project=app.config.edit_on_github_project,
- view=view,
- branch=app.config.edit_on_github_branch,
- dir=app.config.edit_on_github_directory,
- path=path,
- )
- else:
- return "https://github.com/{project}/{view}/{branch}/{path}".format(
- project=app.config.edit_on_github_project,
- view=view,
- branch=app.config.edit_on_github_branch,
- path=path,
- )
-
-
-def html_page_context(app, pagename, templatename, context, doctree):
- if templatename != "page.html":
- return
-
- if not app.config.edit_on_github_project:
- warnings.warn("edit_on_github_project not specified")
- return
-
- path = Path(doctree.get("source")).relative(Path(app.builder.srcdir))
- show_url = get_github_url(app, "blob", str(path))
- edit_url = get_github_url(app, "edit", str(path))
-
- # context['show_on_github_url'] = show_url
- context["edit_on_github_url"] = edit_url
-
-
-def setup(app):
- app.add_config_value("edit_on_github_project", "", True)
- app.add_config_value("edit_on_github_branch", "master", True)
- app.add_config_value("edit_on_github_directory", None, True)
- app.connect("html-page-context", html_page_context)
diff --git a/docs/_ext/environmentSetup.py b/docs/_ext/environmentSetup.py
deleted file mode 100644
index 4d554f593..000000000
--- a/docs/_ext/environmentSetup.py
+++ /dev/null
@@ -1,11 +0,0 @@
-def supress_nonlocal_image_warn():
- import sphinx.environment
-
- sphinx.environment.BuildEnvironment.warn_node = _supress_nonlocal_image_warn
-
-
-def _supress_nonlocal_image_warn(self, msg, node, **kwargs):
- from docutils.utils import get_source_line
-
- if not msg.startswith("nonlocal image URI found:"):
- self._warnfunc(msg, "%s:%s" % get_source_line(node))
diff --git a/docs/_ext/fetch_gae_sdk.py b/docs/_ext/fetch_gae_sdk.py
deleted file mode 100644
index 8c16084d5..000000000
--- a/docs/_ext/fetch_gae_sdk.py
+++ /dev/null
@@ -1,96 +0,0 @@
-#!/usr/bin/env python
-# Copyright 2015 Google Inc. All rights reserved.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# Retrieved from https://github.com/Google/oauth2client
-"""Fetch the most recent GAE SDK and decompress it in the current directory.
-Usage:
- fetch_gae_sdk.py []
-Current releases are listed here:
- https://www.googleapis.com/storage/v1/b/appengine-sdks/o?prefix=featured
-"""
-
-import json
-import sys
-import zipfile
-from pathlib import Path
-
-import StringIO
-import urllib2
-
-_SDK_URL = "https://www.googleapis.com/storage/v1/b/appengine-sdks/o?prefix=featured"
-
-
-def get_gae_versions():
- try:
- version_info_json = urllib2.urlopen(_SDK_URL).read()
- except:
- return {}
- try:
- version_info = json.loads(version_info_json)
- except:
- return {}
- return version_info.get("items", {})
-
-
-def _version_tuple(v):
- version_string = Path(v["name"]).stem.rpartition("_")[2]
- return tuple(int(x) for x in version_string.split("."))
-
-
-def get_sdk_urls(sdk_versions):
- python_releases = [
- v for v in sdk_versions if v["name"].startswith("featured/google_appengine")
- ]
- current_releases = sorted(python_releases, key=_version_tuple, reverse=True)
- return [release["mediaLink"] for release in current_releases]
-
-
-def main(argv):
- if len(argv) > 2:
- print("Usage: {} []".format(argv[0]))
- return 1
- dest_dir = Path(argv[1]) if len(argv) > 1 else Path()
- dest_dir.mkdir(exist_ok=True)
-
- if (dest_dir / "google_appengine").exists():
- print(f"GAE SDK already installed at {dest_dir}, exiting.")
- return 0
-
- sdk_versions = get_gae_versions()
- if not sdk_versions:
- print("Error fetching GAE SDK version info")
- return 1
- sdk_urls = get_sdk_urls(sdk_versions)
- for sdk_url in sdk_urls:
- try:
- sdk_contents = StringIO.StringIO(urllib2.urlopen(sdk_url).read())
- break
- except:
- pass
- else:
- print(f"Could not read SDK from any of {sdk_urls}")
- return 1
- sdk_contents.seek(0)
- try:
- zip_contents = zipfile.ZipFile(sdk_contents)
- zip_contents.extractall(dest_dir)
- print(f"GAE SDK Installed to {dest_dir}.")
- except:
- print("Error extracting SDK contents")
- return 1
-
-
-if __name__ == "__main__":
- sys.exit(main(sys.argv[:]))
diff --git a/docs/_static/custom.css b/docs/_static/custom.css
new file mode 100644
index 000000000..066ce478b
--- /dev/null
+++ b/docs/_static/custom.css
@@ -0,0 +1,736 @@
+@import url("alabaster.css");
+
+/* -- page layout ----------------------------------------------------------- */
+
+body {
+ font-family: Arial;
+ font-size: 16px;
+ background-color: #ffffff;
+ color: #000;
+ display: flex;
+ flex-direction: column;
+ min-height: 100vh;
+ text-align: justify;
+}
+
+div.document {
+ width: 1000px;
+ margin: 0 auto;
+}
+
+div.documentwrapper {
+ padding: 0;
+}
+
+div.bodywrapper {
+ padding: 0;
+}
+
+div.sphinxsidebar {
+ width: 250px;
+ font-size: 12px;
+ line-height: 1.5;
+ background: #fafafa;
+ height: 100%;
+ box-sizing: border-box;
+}
+
+hr {
+ border: 1px solid #007082;
+}
+
+div.body {
+ background-color: #ffffff;
+ color: #000000;
+ padding: 60px;
+ flex: 1;
+}
+
+div.body > .section {
+ text-align: left;
+}
+
+div.footer {
+ width: 100%;
+ font-size: 14px;
+ background: #193d6a;
+ color: #ffffff;
+ text-align: center;
+ padding: 40px;
+ margin-top: auto;
+ z-index: 1000;
+}
+
+div.footer a {
+ color: #ffffff;
+}
+
+p.caption {
+ font-family: inherit;
+ font-size: inherit;
+}
+
+div.relations {
+ display: none;
+}
+
+div.sphinxsidebar {
+ max-height: 100%;
+ overflow-y: auto;
+ margin: 0;
+}
+
+div.sphinxsidebar a {
+ color: #000000;
+ text-decoration: none;
+ border-bottom: 1.5px dotted #007082;
+}
+
+div.sphinxsidebar a:hover {
+ border-bottom: 1px solid #999;
+}
+
+div.sphinxsidebarwrapper {
+ padding: 20px 20px;
+}
+
+div.sphinxsidebarwrapper p.logo {
+ padding: 20px 20px 20px 20px;
+ margin-bottom: 20px;
+ max-width: 200px;
+ content-align: left;
+ border-bottom: 1px solid #999;
+}
+
+div.sphinxsidebarwrapper h1.logo {
+ margin-top: 0px;
+ text-align: left;
+ margin-bottom: 5px;
+}
+
+div.sphinxsidebarwrapper h1.logo-name {
+ margin-top: 0px;
+}
+
+div.sphinxsidebarwrapper p.blurb {
+ margin-bottom: 20px;
+ font-style: normal;
+ text-align: left;
+ font-size: 1rem;
+ white-space: nowrap;
+ overflow: hidden;
+ text-overflow: ellipsis;
+ max-width: 100%;
+}
+
+div.sphinxsidebar h3,
+div.sphinxsidebar h4 {
+ font-family: Arial, serif;
+ color: #193d6a;
+ font-size: 30px;
+ font-weight: normal;
+ margin: 40px 0 5px 0;
+ padding: 0;
+}
+
+div.sphinxsidebar h4 {
+ font-size: 22px;
+}
+
+div.sphinxsidebar h3 a {
+ color: #193d6a;
+}
+
+div.sphinxsidebar p.logo a,
+div.sphinxsidebar h3 a,
+div.sphinxsidebar p.logo a:hover,
+div.sphinxsidebar h3 a:hover {
+ border: none;
+}
+
+div.sphinxsidebar p {
+ color: #000000;
+ font-size: 20px;
+ font-weight: bold;
+ margin: 10px 20px;
+}
+
+div.sphinxsidebar ul {
+ margin: 10px 30px;
+ padding: 0;
+ color: #000;
+}
+
+div.sphinxsidebar ul li.toctree-l1 > a {
+ font-size: 120%;
+}
+
+div.sphinxsidebar ul li.toctree-l2 > a {
+ font-size: 110%;
+}
+
+div.sphinxsidebar input {
+ border: 1px solid #CCC;
+ font-family: Arial;
+ font-size: 1em;
+}
+
+div.sphinxsidebar #searchbox input[type="text"] {
+ width: 160px;
+}
+
+div.sphinxsidebar .search > div {
+ display: table-cell;
+ font-family: Arial;
+}
+
+div.sphinxsidebar hr {
+ border: none;
+ height: 1px;
+ color: #AAA;
+ background: #AAA;
+
+ text-align: left;
+ margin-left: 0;
+ width: 50%;
+}
+
+div.sphinxsidebar .badge {
+ border-bottom: none;
+}
+
+div.sphinxsidebar .badge:hover {
+ border-bottom: none;
+}
+
+
+/* -- body styles ----------------------------------------------------------- */
+
+a {
+ color: #007082;
+ text-decoration: underline;
+}
+
+a:hover {
+ color: #cc1f46;
+ text-decoration: underline;
+}
+
+div.body h1,
+div.body h2,
+div.body h3,
+div.body h4,
+div.body h5,
+div.body h6 {
+ font-family: Arial;
+ font-weight: bold;
+ color: #193d6a;
+ margin: 40px 0px 10px 0px;
+ padding: 0;
+}
+
+div.body h1 { margin-top: 0; padding-top: 0; font-size: 220%; }
+div.body h2 { font-size: 180%; }
+div.body h3 { font-size: 150%; }
+div.body h4 { font-size: 130%; }
+div.body h5 { font-size: 100%; }
+div.body h6 { font-size: 100%; }
+
+a.headerlink {
+ color: #007082;
+ padding: 0 4px;
+ text-decoration: none;
+}
+
+a.headerlink:hover {
+ color: #cc1f46;
+ background: #ffffff;
+}
+
+div.body p, div.body dd, div.body li {
+ line-height: 1.5em;
+}
+
+div.admonition {
+ margin: 20px 0px;
+ padding: 10px 30px;
+ background-color: #EEE;
+ border: 1px solid #CCC;
+}
+
+div.admonition tt.xref, div.admonition code.xref, div.admonition a tt {
+ background-color: #FBFBFB;
+ border-bottom: 1px solid #fafafa;
+}
+
+div.admonition p.admonition-title {
+ font-family: Arial;
+ font-weight: normal;
+ font-size: 24px;
+ margin: 0 0 10px 0;
+ padding: 0;
+ line-height: 1;
+}
+
+div.admonition p.last {
+ margin-bottom: 0;
+}
+
+div.highlight {
+ background-color: #fff;
+}
+
+dt:target, .highlight {
+ background: #FAF3E8;
+}
+
+div.warning {
+ background-color: #cc1f46;
+ color: #ffffff;
+ padding: 20px 20px 20px 20px;
+}
+
+div.danger {
+ background-color: #cc1f46;
+ color: #ffffff;
+ padding: 20px 20px 20px 20px;
+ -moz-box-shadow: 2px 2px 4px #D52C2C;
+ -webkit-box-shadow: 2px 2px 4px #D52C2C;
+ box-shadow: 2px 2px 4px #D52C2C;
+}
+
+div.error {
+ background-color: #cc1f46;
+ color: #ffffff;
+ padding: 20px 20px 20px 20px;
+ -moz-box-shadow: 2px 2px 4px #D52C2C;
+ -webkit-box-shadow: 2px 2px 4px #D52C2C;
+ box-shadow: 2px 2px 4px #D52C2C;
+}
+
+div.caution {
+ background-color: #cc1f46;
+ color: #ffffff;
+ padding: 20px 20px 20px 20px;
+}
+
+div.attention {
+ background-color: #cc1f46;
+ color: #ffffff;
+ padding: 20px 20px 20px 20px;
+}
+
+div.important {
+ background-color: #007082;
+ color: #ffffff;
+ padding: 20px 20px 20px 20px;
+}
+
+div.note {
+ background-color: #EEE;
+ border: 1px solid #CCC;
+ padding: 20px 20px 20px 20px;
+}
+
+div.tip {
+ background-color: #193d6a;
+ color: #ffffff;
+ padding: 20px 20px 20px 20px;
+}
+
+div.hint {
+ background-color: #EEE;
+ border: 1px solid #CCC;
+}
+
+div.seealso {
+ background-color: #EEE;
+ border: 1px solid #CCC;
+}
+
+div.topic {
+ background-color: #EEE;
+}
+
+p.admonition-title {
+ display: inline;
+}
+
+p.admonition-title:after {
+ content: ":";
+}
+
+pre, tt, code {
+ font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
+ font-size: 0.9em;
+}
+
+.hll {
+ background-color: #FFC;
+ margin: 0 -12px;
+ padding: 0 12px;
+ display: block;
+}
+
+img.screenshot {
+}
+
+tt.descname, tt.descclassname, code.descname, code.descclassname {
+ font-size: 0.95em;
+}
+
+tt.descname, code.descname {
+ padding-right: 0.08em;
+}
+
+img.screenshot {
+ -moz-box-shadow: 2px 2px 4px #EEE;
+ -webkit-box-shadow: 2px 2px 4px #EEE;
+ box-shadow: 2px 2px 4px #EEE;
+}
+
+table.docutils {
+ border: 1px solid #888;
+ -moz-box-shadow: 2px 2px 4px #EEE;
+ -webkit-box-shadow: 2px 2px 4px #EEE;
+ box-shadow: 2px 2px 4px #EEE;
+}
+
+table.docutils td, table.docutils th {
+ border: 1px solid #888;
+ padding: 0.25em 0.7em;
+}
+
+table.field-list, table.footnote {
+ border: none;
+ -moz-box-shadow: none;
+ -webkit-box-shadow: none;
+ box-shadow: none;
+}
+
+table.footnote {
+ margin: 0;
+ width: 100%;
+ border: 1px solid #EEE;
+ background: #FDFDFD;
+ font-size: 0.9em;
+}
+
+table.footnote + table.footnote {
+ margin-top: 0;
+ border-top: none;
+}
+
+table.field-list th {
+ padding: 0 0.8em 0 0;
+}
+
+table.field-list td {
+ padding: 0;
+}
+
+table.field-list p {
+ margin-bottom: 0.8em;
+}
+
+/* Cloned from
+ * https://github.com/sphinx-doc/sphinx/commit/ef60dbfce09286b20b7385333d63a60321784e68
+ */
+.field-name {
+ -moz-hyphens: manual;
+ -ms-hyphens: manual;
+ -webkit-hyphens: manual;
+ hyphens: manual;
+}
+
+table.footnote td.label {
+ width: .1px;
+ padding: 0;
+}
+
+table.footnote td {
+ padding: 0.3em 0.5em;
+}
+
+dl {
+ margin-left: 0;
+ margin-right: 0;
+ margin-top: 0;
+ padding: 0;
+}
+
+dl dd {
+ margin-left: 30px;
+}
+
+blockquote {
+ margin: 0 0 0 30px;
+ padding: 0;
+}
+
+ul, ol {
+ /* Matches the 30px from the narrow-screen "li > ul" selector below */
+ margin: 10px 0 10px 30px;
+ padding: 0;
+}
+
+pre {
+ background: #EEE;
+ padding: 7px 30px;
+ margin: 15px 0px;
+ line-height: 1.3em;
+}
+
+div.viewcode-block:target {
+ background: #ffd;
+}
+
+dl pre, blockquote pre, li pre {
+ margin-left: 0;
+ padding-left: 30px;
+}
+
+tt, code {
+ background-color: #ecf0f3;
+ color: #222;
+ /* padding: 1px 2px; */
+}
+
+tt.xref, code.xref, a tt {
+ background-color: #FBFBFB;
+ border-bottom: 1px solid #fff;
+}
+
+a.reference {
+ text-decoration: none;
+ border-bottom: 1px dotted #004B6B;
+}
+
+/* Don't put an underline on images */
+a.image-reference, a.image-reference:hover {
+ border-bottom: none;
+}
+
+a.reference:hover {
+ border-bottom: 1px solid #6D4100;
+}
+
+a.footnote-reference {
+ text-decoration: none;
+ font-size: 0.7em;
+ vertical-align: top;
+ border-bottom: 1px dotted #004B6B;
+}
+
+a.footnote-reference:hover {
+ border-bottom: 1px solid #6D4100;
+}
+
+a:hover tt, a:hover code {
+ background: #EEE;
+}
+
+
+@media screen and (max-width: 870px) {
+
+ div.sphinxsidebar {
+ display: grid;
+ }
+
+ div.document {
+ width: 100%;
+
+ }
+
+ div.documentwrapper {
+ margin-left: 0;
+ margin-top: 40px;
+ margin-right: 0;
+ margin-bottom: 40px;
+ }
+
+ div.bodywrapper {
+ margin-top: 40px;
+ margin-right: 0;
+ margin-bottom: 40px;
+ margin-left: 0;
+ }
+
+ ul {
+ margin-left: 0;
+ }
+
+ li > ul {
+ /* Matches the 30px from the "ul, ol" selector above */
+ margin-left: 30px;
+ }
+
+ .document {
+ width: auto;
+ }
+
+ .footer {
+ width: auto;
+ }
+
+ .bodywrapper {
+ margin: 0;
+ }
+
+ .footer {
+ width: auto;
+ }
+
+ .github {
+ display: none;
+ }
+
+
+
+}
+
+
+
+@media screen and (max-width: 875px) {
+
+ body {
+ height: 100%;
+ margin: 0;
+ padding: 30px 30px 30px 30px;
+ }
+
+ div.documentwrapper {
+ flex-direction: column;
+ height: 100%;
+ width: 100%;
+ background: #fff;
+ }
+
+ div.sphinxsidebar {
+ height: auto;
+ width: 100%;
+ margin: 0;
+ padding: 0px 10px 10px;
+ background: #fafafa;
+ color: #000000;
+ }
+
+ div.sphinxsidebar h3, div.sphinxsidebar h4, div.sphinxsidebar p,
+ div.sphinxsidebar h3 a {
+ color: #193d6a;
+ }
+
+ div.sphinxsidebar a {
+ color: #000000;
+ }
+
+ div.sphinxsidebar p.logo {
+ display: inherit;
+ }
+
+ div.document {
+ width: 100%;
+ height: 100%;
+ margin: 0;
+ flex: 1;
+ overflow-y: auto;
+ }
+
+ div.footer {
+ display: flex;
+ text-align: center;
+ width: 100%
+ height: 100%;
+ word-wrap: break-word;
+ overflow-wrap: break-word;
+ word-break: break-word;
+ }
+
+ div.bodywrapper {
+ margin: 0;
+ }
+
+ div.body {
+ min-height: 0;
+ padding: 0;
+ }
+
+ .rtd_doc_footer {
+ display: none;
+ }
+
+ .document {
+ width: auto;
+ }
+
+ .footer {
+ width: 100%;
+ }
+
+ .github {
+ display: none;
+ }
+}
+
+
+/* misc. */
+
+.revsys-inline {
+ display: none!important;
+}
+
+/* Hide ugly table cell borders in ..bibliography:: directive output */
+table.docutils.citation, table.docutils.citation td, table.docutils.citation th {
+ border: none;
+ /* Below needed in some edge cases; if not applied, bottom shadows appear */
+ -moz-box-shadow: none;
+ -webkit-box-shadow: none;
+ box-shadow: none;
+}
+
+
+/* relbar */
+
+.related {
+ line-height: 30px;
+ width: 100%;
+ font-size: 0.9rem;
+}
+
+.related.top {
+ border-bottom: 1px solid #EEE;
+ margin-bottom: 20px;
+}
+
+.related.bottom {
+ border-top: 1px solid #EEE;
+}
+
+.related ul {
+ padding: 0;
+ margin: 0;
+ list-style: none;
+}
+
+.related li {
+ display: inline;
+}
+
+nav#rellinks {
+ float: right;
+}
+
+nav#rellinks li+li:before {
+ content: "|";
+}
+
+nav#breadcrumbs li+li:before {
+ content: "\00BB";
+}
+
+/* Hide certain items when printing */
+@media print {
+ div.related {
+ display: none;
+ }
+}
diff --git a/docs/_static/logo.png b/docs/_static/logo.png
new file mode 100644
index 000000000..f9641e92d
Binary files /dev/null and b/docs/_static/logo.png differ
diff --git a/docs/conf.py b/docs/conf.py
deleted file mode 100644
index e6a44b836..000000000
--- a/docs/conf.py
+++ /dev/null
@@ -1,99 +0,0 @@
-#
-# geoh5py documentation build configuration file, created by
-# sphinx-quickstart on Tue Sep 16 16:41:10 2014.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-# on_rtd is whether we are on readthedocs.org
-import os
-import sys
-
-from datetime import datetime
-from pathlib import Path
-from importlib.metadata import version
-from packaging.version import Version
-
-sys.path.append(str(Path("_ext").resolve()))
-sys.path.append(str(Path().parent.resolve()))
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use pathlib.Path.resolve to make it absolute, like shown here.
-# sys.path.insert(0, Path().resolve())
-
-# Configuration file for the Sphinx documentation builder.
-#
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
-
-project = "geoh5py"
-author = "Mira Geoscience Ltd."
-project_copyright = "%Y, Mira Geoscience Ltd"
-
-# -- General configuration ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
-
-# The full version, including alpha/beta/rc tags.
-release = version("geoh5py")
-# The shorter X.Y.Z version.
-version = Version(release).base_version
-
-
-googleanalytics_id = "G-9EY47HMNZX"
-
-# Autosummary pages will be generated by sphinx-autogen instead of sphinx-build
-autosummary_generate = []
-autodoc_mock_imports = [
- "h5py",
- "numpy",
-]
-extensions = [
- "sphinx.ext.autodoc",
- "sphinx.ext.autosummary",
- "sphinx.ext.todo",
- "sphinxcontrib.googleanalytics",
-]
-
-templates_path = ["_templates"]
-exclude_patterns = []
-todo_include_todos = True
-
-# -- Options for auto-doc ----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#module-sphinx.ext.autodoc
-
-autodoc_typehints = "signature"
-
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-
-html_theme = "alabaster"
-html_theme_options = {
- "description": f"version {release}",
-}
-
-# Enable numref
-numfig = True
-
-
-def get_copyright_notice():
- return f"Copyright {datetime.now().strftime(project_copyright)}"
-
-
-rst_epilog = f"""
-.. |copyright_notice| replace:: {get_copyright_notice()}.
-"""
-
-# -- Edit on Github Extension ---------------------------------------------
-edit_on_github_branch = "main"
-edit_on_github_project = "mirageoscience/geoh5py"
-edit_on_github_directory = "docs"
diff --git a/docs/content/api/geoh5py.data.rst b/docs/content/api/geoh5py.data.rst
index 0d12ef764..c5733f637 100644
--- a/docs/content/api/geoh5py.data.rst
+++ b/docs/content/api/geoh5py.data.rst
@@ -108,14 +108,6 @@ geoh5py.data.numeric\_data module
:undoc-members:
:show-inheritance:
-geoh5py.data.primitive\_type\_enum module
------------------------------------------
-
-.. automodule:: geoh5py.data.primitive_type_enum
- :members:
- :undoc-members:
- :show-inheritance:
-
geoh5py.data.reference\_value\_map module
-----------------------------------------
diff --git a/docs/environment.yml b/docs/environment.yml
deleted file mode 100644
index 5930f35be..000000000
--- a/docs/environment.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-name: geoh5py_docs
-
-channels:
- - conda-forge
- - defaults
-dependencies:
- - python=3.10
- - pydantic
- - matplotlib
- - scipy
- - numpy
- - h5py
- - pip
- - jupyter-book
- - jupytext
- - notebook
- - pip:
- - sphinx
- - sphinx_issues
- - sphinx_rtd_theme
- - sphinxcontrib-bibtex
- - sphinxcontrib-googleanalytics
- - nbsphinx
- - nbstripout
- - numpydoc
- - jupyter_client
diff --git a/docs/index.rst b/docs/index.rst
index 8ea1b73e1..46ca9abd1 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -17,6 +17,8 @@ capabilities of `Geoscience ANALYST DataType | None:
+ def parent(self) -> geoh5py.data.data_type.DataType | None:
"""Parent data type"""
return self._parent
@parent.setter
- def parent(self, data_type: DataType | None):
+ def parent(self, data_type: geoh5py.data.data_type.DataType | None):
self._parent = data_type
@property
diff --git a/geoh5py/data/data.py b/geoh5py/data/data.py
index f964a814a..b61a51f67 100644
--- a/geoh5py/data/data.py
+++ b/geoh5py/data/data.py
@@ -34,6 +34,7 @@
if TYPE_CHECKING:
+ import geoh5py
from geoh5py.data.data_type import DataType, ReferenceDataType
logger = logging.getLogger(__name__)
@@ -305,7 +306,9 @@ def primitive_type(self) -> Enum:
)
return self.entity_type.primitive_type
- def validate_entity_type(self, entity_type: DataType) -> DataType:
+ def validate_entity_type(
+ self, entity_type: geoh5py.data.data_type.DataType
+ ) -> geoh5py.data.data_type.DataType:
"""
Validate the entity type.
diff --git a/geoh5py/data/data_type.py b/geoh5py/data/data_type.py
index 4e8081281..a23b3b011 100644
--- a/geoh5py/data/data_type.py
+++ b/geoh5py/data/data_type.py
@@ -22,9 +22,9 @@
from __future__ import annotations
+import uuid
from abc import ABC, abstractmethod
from typing import TYPE_CHECKING, Literal, get_args
-from uuid import UUID
import numpy as np
@@ -70,7 +70,7 @@ class DataType(EntityType):
:param transparent_no_data: If the no data values are displayed as transparent or not.
:param units: The type of the units of the data.
:param kwargs: Additional keyword arguments to set as attributes
- (see :obj:`...shared.entity_type.EntityType`).
+ (see :obj:`geoh5py.shared.entity_type.EntityType`).
"""
_attribute_map = EntityType._attribute_map.copy()
@@ -96,7 +96,7 @@ def __init__(
duplicate_on_copy: bool = False,
duplicate_type_on_copy: bool = False,
hidden: bool = False,
- mapping: ColorMapping = "equal_area",
+ mapping: ColorMapping | str = "equal_area",
number_of_bins: int | None = None,
precision: int = 2,
scale: str | None = None,
@@ -111,7 +111,7 @@ def __init__(
self.duplicate_on_copy = duplicate_on_copy
self.duplicate_type_on_copy = duplicate_type_on_copy
self.hidden = hidden
- self.mapping = mapping
+ self.mapping: ColorMapping | str = mapping
self.number_of_bins = number_of_bins
self.precision = precision
self.primitive_type = self.validate_primitive_type(primitive_type)
@@ -210,8 +210,8 @@ def find_or_create_type(
workspace: Workspace,
primitive_type: PrimitiveTypeEnum | str,
*,
- dynamic_implementation_id: str | UUID | None = None,
- uid: UUID | None = None,
+ dynamic_implementation_id: str | uuid.UUID | None = None,
+ uid: uuid.UUID | None = None,
**kwargs,
) -> DataType:
"""
@@ -566,7 +566,9 @@ class ReferencedValueMapType(ReferenceDataType):
Data container for referenced value map.
"""
- _TYPE_UID = UUID(fields=(0x2D5D6C1E, 0x4D8C, 0x4F3A, 0x9B, 0x3F, 0x2E5A0D8E1C1F))
+ _TYPE_UID = uuid.UUID(
+ fields=(0x2D5D6C1E, 0x4D8C, 0x4F3A, 0x9B, 0x3F, 0x2E5A0D8E1C1F)
+ )
def __init__(
self,
@@ -623,13 +625,13 @@ class GeometricDynamicDataType(DataType, ABC):
"Dynamic implementation ID": "dynamic_implementation_id",
}
)
- _TYPE_UID: UUID | None
- _DYNAMIC_IMPLEMENTATION_ID: UUID
+ _TYPE_UID: uuid.UUID | None
+ _DYNAMIC_IMPLEMENTATION_ID: uuid.UUID
def __init__(
self,
workspace: Workspace,
- uid: UUID | None = None,
+ uid: uuid.UUID | None = None,
**kwargs,
):
if uid is None:
@@ -638,14 +640,14 @@ def __init__(
super().__init__(workspace, uid=uid, **kwargs)
@classmethod
- def default_type_uid(cls) -> UUID | None:
+ def default_type_uid(cls) -> uuid.UUID | None:
"""
Default uuid for the entity type.
"""
return cls._TYPE_UID
@property
- def dynamic_implementation_id(self) -> UUID:
+ def dynamic_implementation_id(self) -> uuid.UUID:
"""
The dynamic implementation id.
"""
@@ -657,7 +659,7 @@ class GeometricDataValueMapType(ReferenceDataType, GeometricDynamicDataType):
Data container for value map
"""
- _DYNAMIC_IMPLEMENTATION_ID = UUID("{4b6ecb37-0623-4ea0-95f1-4873008890a8}")
+ _DYNAMIC_IMPLEMENTATION_ID = uuid.UUID("{4b6ecb37-0623-4ea0-95f1-4873008890a8}")
_TYPE_UID = None
def __init__(
@@ -790,8 +792,10 @@ class GeometricDataXType(GeometricDynamicDataType):
Data container for X values
"""
- _DYNAMIC_IMPLEMENTATION_ID = UUID("{2dbf303e-05d6-44ba-9692-39474e88d516}")
- _TYPE_UID = UUID(fields=(0xE9E6B408, 0x4109, 0x4E42, 0xB6, 0xA8, 0x685C37A802EE))
+ _DYNAMIC_IMPLEMENTATION_ID = uuid.UUID("{2dbf303e-05d6-44ba-9692-39474e88d516}")
+ _TYPE_UID = uuid.UUID(
+ fields=(0xE9E6B408, 0x4109, 0x4E42, 0xB6, 0xA8, 0x685C37A802EE)
+ )
class GeometricDataYType(GeometricDynamicDataType):
@@ -799,8 +803,10 @@ class GeometricDataYType(GeometricDynamicDataType):
Data container for Y values
"""
- _DYNAMIC_IMPLEMENTATION_ID = UUID("{d56406dc-5eeb-418d-add4-a1282a6ef668}")
- _TYPE_UID = UUID(fields=(0xF55B07BD, 0xD8A0, 0x4DFF, 0xBA, 0xE5, 0xC975D490D71C))
+ _DYNAMIC_IMPLEMENTATION_ID = uuid.UUID("{d56406dc-5eeb-418d-add4-a1282a6ef668}")
+ _TYPE_UID = uuid.UUID(
+ fields=(0xF55B07BD, 0xD8A0, 0x4DFF, 0xBA, 0xE5, 0xC975D490D71C)
+ )
class GeometricDataZType(GeometricDynamicDataType):
@@ -808,8 +814,10 @@ class GeometricDataZType(GeometricDynamicDataType):
Data container for Z values
"""
- _DYNAMIC_IMPLEMENTATION_ID = UUID("{9dacdc3b-6878-408d-93ae-e9a95e640f0c}")
- _TYPE_UID = UUID(fields=(0xDBAFB885, 0x1531, 0x410C, 0xB1, 0x8E, 0x6AC9A40B4466))
+ _DYNAMIC_IMPLEMENTATION_ID = uuid.UUID("{9dacdc3b-6878-408d-93ae-e9a95e640f0c}")
+ _TYPE_UID = uuid.UUID(
+ fields=(0xDBAFB885, 0x1531, 0x410C, 0xB1, 0x8E, 0x6AC9A40B4466)
+ )
DYNAMIC_CLASS_IDS = {
diff --git a/geoh5py/objects/curve.py b/geoh5py/objects/curve.py
index 2c6ddb33e..b7caa77f0 100644
--- a/geoh5py/objects/curve.py
+++ b/geoh5py/objects/curve.py
@@ -160,11 +160,11 @@ def unique_parts(self) -> list[int]:
return np.unique(self.parts).tolist()
def validate_cells(self, indices: list | tuple | np.ndarray | None) -> np.ndarray:
- """
+ r"""
Validate or generate cells made up of pairs of vertices making
- up line segments.
+ up line segments.
- :param indices: Array of indices, shape(*, 2). If None provided, the
+ :param indices: Array of indices, shape(\*, 2). If None provided, the
vertices are connected sequentially.
:return: Array of indices defining connected vertices.
diff --git a/geoh5py/objects/drape_model.py b/geoh5py/objects/drape_model.py
index c462e01ff..2e3b0a3ed 100644
--- a/geoh5py/objects/drape_model.py
+++ b/geoh5py/objects/drape_model.py
@@ -77,8 +77,8 @@ def z_cell_size(self) -> np.ndarray:
@property
def centroids(self) -> np.ndarray:
- """
- Cell center locations in world coordinates, shape(*, 3).
+ r"""
+ Cell center locations in world coordinates, shape(\*, 3).
.. code-block:: python
diff --git a/geoh5py/objects/surface.py b/geoh5py/objects/surface.py
index 3589e58b4..c5922058e 100644
--- a/geoh5py/objects/surface.py
+++ b/geoh5py/objects/surface.py
@@ -38,11 +38,11 @@ class Surface(CellObject):
_minimum_vertices = 3
def validate_cells(self, indices: list | tuple | np.ndarray | None) -> np.ndarray:
- """
+ r"""
Validate or generate cells made up of triplets of vertices making
up triangles.
- :param indices: Array of indices, shape(*, 3). If None provided, the
+ :param indices: Array of indices, shape(\*, 3). If None provided, the
vertices are connected sequentially.
:return: Array of indices defining connecting vertices.
diff --git a/geoh5py/shared/utils.py b/geoh5py/shared/utils.py
index 5636deee4..fbbbbecd1 100644
--- a/geoh5py/shared/utils.py
+++ b/geoh5py/shared/utils.py
@@ -657,10 +657,10 @@ def box_intersect(
def mask_by_extent(
locations: np.ndarray, extent: np.ndarray | Sequence, inverse: bool = False
) -> np.ndarray:
- """
+ r"""
Find indices of locations within a rectangular extent.
- :param locations: shape(*, 3) or shape(*, 2) Coordinates to be evaluated.
+ :param locations: shape(\*, 3) or shape(\*, 2) Coordinates to be evaluated.
:param extent: shape(2, 2) Limits defined by the South-West and
North-East corners. Extents can also be provided as 3D coordinates
with shape(2, 3) defining the top and bottom limits.
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 000000000..5016bf8f3
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,7006 @@
+version: 6
+environments:
+ default:
+ channels:
+ - url: https://repo.prefix.dev/conda-forge/
+ indexes:
+ - https://pypi.org/simple
+ packages:
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+ - conda: https://repo.prefix.dev/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
+ - conda: https://repo.prefix.dev/conda-forge/linux-64/astroid-3.3.11-py310hff52083_1.conda
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diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 000000000..a575351b6
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,125 @@
+[workspace]
+requires-pixi = ">=0.54"
+channels = ["https://repo.prefix.dev/conda-forge"]
+platforms = ["win-64", "linux-64"]
+
+[dependencies]
+# dependencies resolved from conda
+## direct dependencies:
+#----------------------
+h5py = ">=3.2.1, 3.*"
+numpy = "1.26.*"
+pillow = "10.3.*"
+pydantic = ">=2.7, 2.*"
+
+[pypi-dependencies]
+geoh5py = {path = ".", editable = true}
+
+[environments]
+#prod-py310 = {features = ["py310"], solve-group = "prod-py310"}
+#prod-py311 = {features = ["py311"], solve-group = "prod-py311"}
+#prod-py312 = {features = ["py312"], solve-group = "prod-py312"}
+#test-prod-py310 = {features = ["py310", "test"], solve-group = "prod-py310"}
+#test-prod-py311 = {features = ["py311", "test"], solve-group = "prod-py311"}
+#test-prod-py312 = {features = ["py312", "test"], solve-group = "prod-py312"}
+
+py310 = {features = ["py310", "test"], solve-group = "default"}
+py311 = {features = ["py311", "test"]}
+py312 = {features = ["py312", "test"]}
+
+default = {features = ["py310", "test", "dev"], solve-group = "default"}
+docs = {features = ["py310", "doc"], solve-group = "default"}
+
+[feature.py310.dependencies]
+python = "3.10.*"
+
+[feature.py311.dependencies]
+python = "3.11.*"
+
+[feature.py312.dependencies]
+python = "3.12.*"
+
+[feature.dev.dependencies]
+Pygments = '*'
+ipython = "*"
+
+[feature.dev.tasks]
+repl = "ipython"
+
+[feature.test.dependencies]
+h5py = '*'
+packaging = '*'
+pylint = '*'
+pytest = "*"
+pytest-cov = "*"
+pyyaml = '*'
+scipy = '*'
+
+[feature.test.tasks]
+test = "pytest --cov --cov-report=xml"
+
+[feature.test.tasks.test-local]
+args = ["packages"]
+
+depends-on = [
+ {task = "use-local-deps", args = [ "{{ packages }}" ]},
+ {task = "show-pip-source", args = [ "{{ packages }}" ]},
+ {task = "test"}
+]
+
+[feature.doc.dependencies]
+jupyter-book = "*"
+jupyter_client = "*"
+jupytext = "*"
+matplotlib-base = "*"
+nbsphinx = "*"
+nbstripout = "*"
+notebook = "*"
+numpydoc = "*"
+scipy = "*"
+sphinx = "*"
+sphinx-autodoc-typehints = "*"
+sphinx-issues = "*"
+sphinx-rtd-theme = "*"
+sphinxcontrib-bibtex = "*"
+sphinxcontrib-googleanalytics = '*'
+
+[feature.doc.tasks.config-docs]
+cmd = "jupyter-book config sphinx docs/"
+
+[feature.doc.tasks.build-docs]
+args = [
+ { arg = "builder", default = "html" },
+ { arg = "outputdir", default = "docs/_build" },
+]
+
+depends-on = ["config-docs"]
+# TODO: add -W option to fail on warnings
+cmd = "export PYTHONPATH=./docs/_ext && sphinx-build -T -n -b {{builder}} docs/ {{outputdir}}/{{builder}}"
+
+[feature.doc.tasks.jupyter-book-build]
+args = [
+ { arg = "builder", default = "html" },
+ { arg = "outputdir", default = "docs" },
+]
+
+# TODO: add -W option to fail on warnings
+cmd = "jupyter-book build -v -n --builder {{builder}} docs --path-output {{outputdir}}"
+
+[tasks.show-pip-source]
+args = ["packages"]
+cmd = "uv pip show {{packages}}"
+
+[tasks.use-local-deps]
+args = ["packages"]
+cmd = """
+uv pip install --no-deps --force-reinstall \
+{% for package in packages | split %} -e ../{{ package | trim }}{% endfor %}
+"""
+
+[tasks.test-pyvers]
+depends-on = [
+ {task = "test", environment = "py310"},
+ {task = "test", environment = "py311"},
+ {task = "test", environment = "py312"},
+]
diff --git a/poetry.lock b/poetry.lock
deleted file mode 100644
index 242411bdf..000000000
--- a/poetry.lock
+++ /dev/null
@@ -1,1385 +0,0 @@
-# This file is automatically @generated by Poetry 2.1.4 and should not be changed by hand.
-
-[[package]]
-name = "alabaster"
-version = "0.7.16"
-description = "A light, configurable Sphinx theme"
-optional = false
-python-versions = ">=3.9"
-groups = ["dev"]
-files = [
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- {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
-]
-
-[[package]]
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-version = "0.7.0"
-description = "Reusable constraint types to use with typing.Annotated"
-optional = false
-python-versions = ">=3.8"
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-[[package]]
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-description = "An abstract syntax tree for Python with inference support."
-optional = false
-python-versions = ">=3.9.0"
-groups = ["dev"]
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- {file = "astroid-3.3.11.tar.gz", hash = "sha256:1e5a5011af2920c7c67a53f65d536d65bfa7116feeaf2354d8b94f29573bb0ce"},
-]
-
-[package.dependencies]
-typing-extensions = {version = ">=4", markers = "python_version < \"3.11\""}
-
-[[package]]
-name = "babel"
-version = "2.17.0"
-description = "Internationalization utilities"
-optional = false
-python-versions = ">=3.8"
-groups = ["dev"]
-files = [
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- {file = "babel-2.17.0.tar.gz", hash = "sha256:0c54cffb19f690cdcc52a3b50bcbf71e07a808d1c80d549f2459b9d2cf0afb9d"},
-]
-
-[package.extras]
-dev = ["backports.zoneinfo ; python_version < \"3.9\"", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata ; sys_platform == \"win32\""]
-
-[[package]]
-name = "certifi"
-version = "2025.7.14"
-description = "Python package for providing Mozilla's CA Bundle."
-optional = false
-python-versions = ">=3.7"
-groups = ["dev"]
-files = [
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-
-[[package]]
-name = "charset-normalizer"
-version = "3.4.2"
-description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-optional = false
-python-versions = ">=3.7"
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-h2 = ["h2 (>=4,<5)"]
-socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
-zstd = ["zstandard (>=0.18.0)"]
-
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diff --git a/pyproject.toml b/pyproject.toml
index 2afe3a4bf..825f6c31b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,12 +15,22 @@ build-backend = "poetry_dynamic_versioning.backend"
name = "geoh5py"
requires-python = ">=3.10,<4.0"
-
description = "Python API for geoh5, an open file format for geoscientific data"
license = "LGPL-3.0-or-later"
-keywords = ["geology", "geophysics", "data", "interoperability"]
+keywords = [
+ "data",
+ "data-format",
+ "data-management",
+ "earth-sciences",
+ "geoh5",
+ "geology",
+ "geophysics",
+ "interoperability",
+ "mining",
+ "open-science",
+]
readme = "package.rst"
-dynamic = ["version", "dependencies", "classifiers"]
+dynamic = ["version", "classifiers"]
authors = [
{ name = "Mira Geoscience", email = "support@mirageoscience.com" }
]
@@ -30,6 +40,13 @@ maintainers = [
{ name = "Matthieu Cedou", email = "matthieuc@mirageoscience.com" }
]
+dependencies = [
+ "h5py >= 3.2.1, == 3.*",
+ "numpy == 1.26.*",
+ "Pillow == 10.3.*",
+ "pydantic >= 2.7, == 2.*"
+]
+
[project.urls]
homepage = "https://www.mirageoscience.com/mining-industry-software/python-integration/"
repository = "https://github.com/MiraGeoscience/geoh5py"
@@ -38,18 +55,6 @@ documentation = "https://mirageoscience-geoh5py.readthedocs-hosted.com/"
[tool.poetry]
requires-poetry = '>=2.0,<3.0'
-classifiers = [
- "Development Status :: 4 - Beta",
- "Intended Audience :: Science/Research",
- "Intended Audience :: Developers",
- "Natural Language :: English",
- "Topic :: Database",
- "Topic :: Scientific/Engineering",
- "Topic :: Scientific/Engineering :: Mathematics",
- "Topic :: Scientific/Engineering :: Physics",
- "Topic :: Software Development :: Libraries :: Python Modules"
-]
-
exclude = ["geoh5py/handlers/*", "geoh5py/interfaces/*"]
include = [
@@ -60,29 +65,23 @@ include = [
{ path = "THIRD_PARTY_SOFTWARE.rst" },
{ path = "docs/**/THIRD_PARTY_SOFTWARE.rst" },
]
-version = "0.0.0.dev0"
-[tool.poetry.dependencies]
-h5py = "^3.2.1"
-numpy = "~1.26.0"
-Pillow = "~10.3.0"
-pydantic = "^2.5.2"
-
-[tool.poetry.group.dev.dependencies]
-jinja2 = '*'
-lockfile = "^0.12.2"
-packaging = '*'
-Pygments = "*"
-pylint = "^3.3.8"
-pytest = "*"
-pytest-cov = "*"
-pyyaml = '*'
-scipy = "~1.14.0"
-sphinx = "^3.0"
-sphinx-autodoc-typehints = "^1.10"
-sphinx-rtd-theme = "^0.4.3"
-tomli = "*"
-h5py = "^3.14.0"
+classifiers = [
+ "Development Status :: 4 - Beta",
+ "Intended Audience :: Developers",
+ "Intended Audience :: Science/Research",
+ "Natural Language :: English",
+ "Operating System :: MacOS",
+ "Operating System :: Microsoft :: Windows",
+ "Operating System :: POSIX",
+ "Operating System :: Unix",
+ "Topic :: Database",
+ "Topic :: Scientific/Engineering :: Mathematics",
+ "Topic :: Scientific/Engineering :: Physics",
+ "Topic :: Scientific/Engineering",
+ "Topic :: Software Development :: Libraries :: Python Modules",
+]
+version = "0.0.0.dev0"
[tool.poetry.requires-plugins]
poetry-dynamic-versioning = { version = ">=1.9.1,<2.0.0", extras = ["plugin"] }
diff --git a/tests/version_test.py b/tests/version_test.py
index 3f59577f2..09b3a9dd4 100644
--- a/tests/version_test.py
+++ b/tests/version_test.py
@@ -26,22 +26,16 @@
import pytest
import tomli as toml
import yaml
-from jinja2 import Template
from packaging.version import InvalidVersion, Version
import geoh5py
-def get_conda_recipe_version():
- path = Path(__file__).resolve().parents[1] / "recipe.yaml"
- with open(str(path), encoding="utf-8") as file:
- content = file.read()
-
- template = Template(content)
- rendered_yaml = template.render()
-
- recipe = yaml.safe_load(rendered_yaml)
+def get_conda_recipe_version() -> str | None:
+ recipe_path = Path(__file__).resolve().parents[1] / "recipe.yaml"
+ with recipe_path.open(encoding="utf-8") as file:
+ recipe = yaml.safe_load(file)
return recipe["context"]["version"]