From 5c23cb4525016a3da11c0a8c09dc2eda93126bc2 Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Wed, 2 Apr 2025 18:21:44 +0000
Subject: [PATCH 1/4] Automated template update to v0.5.0
---
.cruft.json | 27 +++-
.editorconfig | 5 +-
.github/ISSUE_TEMPLATE/bug_report.yml | 123 ++++++++-------
.github/workflows/build.yaml | 76 +++------
.github/workflows/release.yaml | 34 +++++
.github/workflows/test.yaml | 74 +++++----
.gitignore | 12 +-
.pre-commit-config.yaml | 19 ++-
.vscode/extensions.json | 18 +++
.vscode/launch.json | 33 ++++
.vscode/settings.json | 18 +++
biome.jsonc | 16 ++
docs/_templates/autosummary/class.rst | 8 +-
docs/conf.py | 12 +-
docs/contributing.md | 193 ++++++++++++++---------
docs/extensions/typed_returns.py | 2 +-
pyproject.toml | 212 +++++++++++++-------------
17 files changed, 530 insertions(+), 352 deletions(-)
create mode 100644 .github/workflows/release.yaml
create mode 100644 .vscode/extensions.json
create mode 100644 .vscode/launch.json
create mode 100644 .vscode/settings.json
create mode 100644 biome.jsonc
diff --git a/.cruft.json b/.cruft.json
index c800e9e..348a054 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,27 +1,42 @@
{
"template": "https://github.com/scverse/cookiecutter-scverse",
- "commit": "6a1f5a101d3de6ef0c48821eaaa00d078ad223a1",
- "checkout": null,
+ "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
+ "checkout": "v0.5.0",
"context": {
"cookiecutter": {
"project_name": "Nimbus-Inference",
"package_name": "nimbus_inference",
- "project_description": "A very interesting piece of code",
+ "project_description": "A model for classification of cells into marker positive / negative",
"author_full_name": "Lorenz Rumberger",
"author_email": "jlrumber@stanford.edu",
"github_user": "angelolab",
- "project_repo": "https://github.com/angelolab/Nimbus-Inference",
+ "github_repo": "Nimbus-Inference",
"license": "MIT License",
+ "ide_integration": true,
"_copy_without_render": [
- ".github/workflows/**.yaml",
+ ".github/workflows/build.yaml",
+ ".github/workflows/test.yaml",
"docs/_templates/autosummary/**.rst"
],
+ "_exclude_on_template_update": [
+ "CHANGELOG.md",
+ "LICENSE",
+ "README.md",
+ "docs/api.md",
+ "docs/index.md",
+ "docs/notebooks/example.ipynb",
+ "docs/references.bib",
+ "docs/references.md",
+ "src/**",
+ "tests/**"
+ ],
"_render_devdocs": false,
"_jinja2_env_vars": {
"lstrip_blocks": true,
"trim_blocks": true
},
- "_template": "https://github.com/scverse/cookiecutter-scverse"
+ "_template": "https://github.com/scverse/cookiecutter-scverse",
+ "_commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
}
},
"directory": null
diff --git a/.editorconfig b/.editorconfig
index 050f911..66678e3 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -8,10 +8,7 @@ charset = utf-8
trim_trailing_whitespace = true
insert_final_newline = true
-[*.{yml,yaml}]
-indent_size = 2
-
-[.cruft.json]
+[{*.{yml,yaml,toml},.cruft.json}]
indent_size = 2
[Makefile]
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index a5a20e6..3ca1ccb 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -23,67 +23,72 @@ body:
- type: textarea
id: versions
attributes:
- label: Version information
+ label: Versions
description: |
- Please paste below the output of
+ Which version of packages.
+
+ Please install `session-info2`, run the following command in a notebook,
+ click the “Copy as Markdown” button, then paste the results into the text box below.
+
+ ```python
+ In[1]: import session_info2; session_info2.session_info(dependencies=True)
+ ```
+
+ Alternatively, run this in a console:
```python
- import session_info
- session_info.show(html=False, dependencies=True)
+ >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
```
+ render: python
placeholder: |
- -----
- anndata 0.8.0rc2.dev27+ge524389
- session_info 1.0.0
- -----
- asttokens NA
- awkward 1.8.0
- backcall 0.2.0
- cython_runtime NA
- dateutil 2.8.2
- debugpy 1.6.0
- decorator 5.1.1
- entrypoints 0.4
- executing 0.8.3
- h5py 3.7.0
- ipykernel 6.15.0
- jedi 0.18.1
- mpl_toolkits NA
- natsort 8.1.0
- numpy 1.22.4
- packaging 21.3
- pandas 1.4.2
- parso 0.8.3
- pexpect 4.8.0
- pickleshare 0.7.5
- pkg_resources NA
- prompt_toolkit 3.0.29
- psutil 5.9.1
- ptyprocess 0.7.0
- pure_eval 0.2.2
- pydev_ipython NA
- pydevconsole NA
- pydevd 2.8.0
- pydevd_file_utils NA
- pydevd_plugins NA
- pydevd_tracing NA
- pygments 2.12.0
- pytz 2022.1
- scipy 1.8.1
- setuptools 62.5.0
- setuptools_scm NA
- six 1.16.0
- stack_data 0.3.0
- tornado 6.1
- traitlets 5.3.0
- wcwidth 0.2.5
- zmq 23.1.0
- -----
- IPython 8.4.0
- jupyter_client 7.3.4
- jupyter_core 4.10.0
- -----
- Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
- Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
- -----
- Session information updated at 2022-07-07 17:55
+ anndata 0.11.3
+ ---- ----
+ charset-normalizer 3.4.1
+ coverage 7.7.0
+ psutil 7.0.0
+ dask 2024.7.1
+ jaraco.context 5.3.0
+ numcodecs 0.15.1
+ jaraco.functools 4.0.1
+ Jinja2 3.1.6
+ sphinxcontrib-jsmath 1.0.1
+ sphinxcontrib-htmlhelp 2.1.0
+ toolz 1.0.0
+ session-info2 0.1.2
+ PyYAML 6.0.2
+ llvmlite 0.44.0
+ scipy 1.15.2
+ pandas 2.2.3
+ sphinxcontrib-devhelp 2.0.0
+ h5py 3.13.0
+ tblib 3.0.0
+ setuptools-scm 8.2.0
+ more-itertools 10.3.0
+ msgpack 1.1.0
+ sparse 0.15.5
+ wrapt 1.17.2
+ jaraco.collections 5.1.0
+ numba 0.61.0
+ pyarrow 19.0.1
+ pytz 2025.1
+ MarkupSafe 3.0.2
+ crc32c 2.7.1
+ sphinxcontrib-qthelp 2.0.0
+ sphinxcontrib-serializinghtml 2.0.0
+ zarr 2.18.4
+ asciitree 0.3.3
+ six 1.17.0
+ sphinxcontrib-applehelp 2.0.0
+ numpy 2.1.3
+ cloudpickle 3.1.1
+ sphinxcontrib-bibtex 2.6.3
+ natsort 8.4.0
+ jaraco.text 3.12.1
+ setuptools 76.1.0
+ Deprecated 1.2.18
+ packaging 24.2
+ python-dateutil 2.9.0.post0
+ ---- ----
+ Python 3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
+ OS Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
+ Updated 2025-03-18 15:47
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index a22eaf1..83e01a1 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -1,61 +1,33 @@
-name: Build
+name: Check Build
on:
- workflow_call:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
-permissions:
- contents: read # to fetch code (actions/checkout)
+concurrency:
+ group: ${{ github.workflow }}-${{ github.ref }}
+ cancel-in-progress: true
-jobs:
- build_wheels:
- name: ${{ matrix.os }} Wheels
- runs-on: ${{ matrix.os }}
- strategy:
- # Ensure that a wheel builder finishes even if another fails
- fail-fast: false
- matrix:
- os: [ubuntu-latest, windows-latest, macos-latest]
+defaults:
+ run:
+ # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+ shell: bash -euo pipefail {0}
+jobs:
+ package:
+ runs-on: ubuntu-latest
steps:
- - name: Checkout ${{ github.repository }}
- uses: actions/checkout@v4
+ - uses: actions/checkout@v4
with:
+ filter: blob:none
fetch-depth: 0
-
- - name: Set up QEMU (For Linux ARM)
- if: runner.os == 'Linux'
- uses: docker/setup-qemu-action@v3
- with:
- platforms: arm64
-
- - name: Build Wheels
- uses: pypa/cibuildwheel@v2.16.2
- with:
- package-dir: .
- output-dir: wheelhouse
- config-file: "{package}/pyproject.toml"
-
- - name: Store Wheel Artifacts
- uses: actions/upload-artifact@v4
- with:
- name: distributions
- path: wheelhouse/*.whl
-
- build_sdist:
- name: Source Distribution
- runs-on: ubuntu-latest
- steps:
- - name: Checkout ${{ github.repository }}
- uses: actions/checkout@v4
-
- - name: Build sdist
- run: pipx run build --sdist
-
- - name: Check sdist Metadata
- run: pipx run twine check dist/*
-
- - name: Store sdist Artifacts
- uses: actions/upload-artifact@v4
+ - name: Install uv
+ uses: astral-sh/setup-uv@v5
with:
- name: distributions
- path: dist/*.tar.gz
+ cache-dependency-glob: pyproject.toml
+ - name: Build package
+ run: uv build
+ - name: Check package
+ run: uvx twine check --strict dist/*.whl
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
new file mode 100644
index 0000000..87e5c38
--- /dev/null
+++ b/.github/workflows/release.yaml
@@ -0,0 +1,34 @@
+name: Release
+
+on:
+ release:
+ types: [published]
+
+defaults:
+ run:
+ # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+ shell: bash -euo pipefail {0}
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+ release:
+ name: Upload release to PyPI
+ runs-on: ubuntu-latest
+ environment:
+ name: pypi
+ url: https://pypi.org/p/nimbus_inference
+ permissions:
+ id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+ steps:
+ - uses: actions/checkout@v4
+ with:
+ filter: blob:none
+ fetch-depth: 0
+ - name: Install uv
+ uses: astral-sh/setup-uv@v5
+ with:
+ cache-dependency-glob: pyproject.toml
+ - name: Build package
+ run: uv build
+ - name: Publish package distributions to PyPI
+ uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 7aff0c4..d5cfb2a 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -1,45 +1,59 @@
name: Test
on:
- workflow_call:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+ schedule:
+ - cron: "0 5 1,15 * *"
+
+concurrency:
+ group: ${{ github.workflow }}-${{ github.ref }}
+ cancel-in-progress: true
+
+defaults:
+ run:
+ # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+ shell: bash -euo pipefail {0}
-permissions:
- contents: read # to fetch code (actions/checkout)
jobs:
test:
- name: ${{ matrix.os }} - ${{ matrix.python-version }}
runs-on: ${{ matrix.os }}
+
strategy:
- # Ensure that if any job fails, all jobs are cancelled.
fail-fast: false
matrix:
- python-version: ["3.9", "3.10", "3.11", "3.12"]
- os: [ubuntu-latest, macos-latest, windows-latest]
+ include:
+ - os: ubuntu-latest
+ python: "3.10"
+ - os: ubuntu-latest
+ python: "3.12"
+ - os: ubuntu-latest
+ python: "3.12"
+ pip-flags: "--pre"
+ name: PRE-RELEASE DEPENDENCIES
+
+ name: ${{ matrix.name }} Python ${{ matrix.python }}
+
+ env:
+ OS: ${{ matrix.os }}
+ PYTHON: ${{ matrix.python }}
steps:
- - name: Checkout ${{ github.repository }}
- uses: actions/checkout@v3
+ - uses: actions/checkout@v4
with:
+ filter: blob:none
fetch-depth: 0
-
- - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
- with:
- python-version: ${{ matrix.python-version }}
- cache-dependency-path: "**/pyproject.toml"
- cache: "pip"
-
- - name: Install Dependencies and ${{ github.repository }}
- run: |
- pip install .[test]
-
- - name: Run Tests
- run: |
- pytest
-
- - name: Archive Coverage
- uses: actions/upload-artifact@v4
+ - name: Install uv
+ uses: astral-sh/setup-uv@v5
with:
- name: coverage-${{ join(matrix.*, '-') }}
- path: |
- coverage.lcov
+ cache-dependency-glob: pyproject.toml
+ - name: run tests using hatch
+ env:
+ MPLBACKEND: agg
+ PLATFORM: ${{ matrix.os }}
+ DISPLAY: :42
+ run: uvx hatch test --cover --python ${{ matrix.python }}
+ - name: Upload coverage
+ uses: codecov/codecov-action@v4
diff --git a/.gitignore b/.gitignore
index dcdc618..31e10b3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,23 +6,15 @@ buck-out/
# Compiled files
.venv/
__pycache__/
-.mypy_cache/
-.ruff_cache/
+.*cache/
# Distribution / packaging
-/build/
/dist/
-/*.egg-info/
# Tests and coverage
-/.pytest_cache/
-/.cache/
/data/
+/node_modules/
# docs
/docs/generated/
/docs/_build/
-
-# IDEs
-/.idea/
-/.vscode/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 383a6e1..0fcce11 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,16 +2,21 @@ fail_fast: false
default_language_version:
python: python3
default_stages:
- - commit
- - push
+ - pre-commit
+ - pre-push
minimum_pre_commit_version: 2.16.0
repos:
- - repo: https://github.com/pre-commit/mirrors-prettier
- rev: v4.0.0-alpha.8
+ - repo: https://github.com/biomejs/pre-commit
+ rev: v1.9.4
hooks:
- - id: prettier
+ - id: biome-format
+ exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
+ - repo: https://github.com/tox-dev/pyproject-fmt
+ rev: v2.5.1
+ hooks:
+ - id: pyproject-fmt
- repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.1.11
+ rev: v0.11.2
hooks:
- id: ruff
types_or: [python, pyi, jupyter]
@@ -19,7 +24,7 @@ repos:
- id: ruff-format
types_or: [python, pyi, jupyter]
- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.5.0
+ rev: v5.0.0
hooks:
- id: detect-private-key
- id: check-ast
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
new file mode 100644
index 0000000..caaeb4f
--- /dev/null
+++ b/.vscode/extensions.json
@@ -0,0 +1,18 @@
+{
+ "recommendations": [
+ // GitHub integration
+ "github.vscode-github-actions",
+ "github.vscode-pull-request-github",
+ // Language support
+ "ms-python.python",
+ "ms-python.vscode-pylance",
+ "ms-toolsai.jupyter",
+ "tamasfe.even-better-toml",
+ // Dependency management
+ "ninoseki.vscode-mogami",
+ // Linting and formatting
+ "editorconfig.editorconfig",
+ "charliermarsh.ruff",
+ "biomejs.biome",
+ ],
+}
diff --git a/.vscode/launch.json b/.vscode/launch.json
new file mode 100644
index 0000000..36d1874
--- /dev/null
+++ b/.vscode/launch.json
@@ -0,0 +1,33 @@
+{
+ // Use IntelliSense to learn about possible attributes.
+ // Hover to view descriptions of existing attributes.
+ // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+ "version": "0.2.0",
+ "configurations": [
+ {
+ "name": "Python: Build Documentation",
+ "type": "debugpy",
+ "request": "launch",
+ "module": "sphinx",
+ "args": ["-M", "html", ".", "_build"],
+ "cwd": "${workspaceFolder}/docs",
+ "console": "internalConsole",
+ "justMyCode": false,
+ },
+ {
+ "name": "Python: Debug Test",
+ "type": "debugpy",
+ "request": "launch",
+ "program": "${file}",
+ "purpose": ["debug-test"],
+ "console": "internalConsole",
+ "justMyCode": false,
+ "env": {
+ "PYTEST_ADDOPTS": "--color=yes",
+ },
+ "presentation": {
+ "hidden": true,
+ },
+ },
+ ],
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000..e034b91
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,18 @@
+{
+ "[python][json][jsonc]": {
+ "editor.formatOnSave": true,
+ },
+ "[python]": {
+ "editor.defaultFormatter": "charliermarsh.ruff",
+ "editor.codeActionsOnSave": {
+ "source.fixAll": "always",
+ "source.organizeImports": "always",
+ },
+ },
+ "[json][jsonc]": {
+ "editor.defaultFormatter": "biomejs.biome",
+ },
+ "python.analysis.typeCheckingMode": "basic",
+ "python.testing.pytestEnabled": true,
+ "python.testing.pytestArgs": ["-vv", "--color=yes"],
+}
diff --git a/biome.jsonc b/biome.jsonc
new file mode 100644
index 0000000..2175c16
--- /dev/null
+++ b/biome.jsonc
@@ -0,0 +1,16 @@
+{
+ "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+ "formatter": { "useEditorconfig": true },
+ "overrides": [
+ {
+ "include": ["./.vscode/*.json", "**/*.jsonc"],
+ "json": {
+ "formatter": { "trailingCommas": "all" },
+ "parser": {
+ "allowComments": true,
+ "allowTrailingCommas": true,
+ },
+ },
+ },
+ ],
+}
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
index e4665df..7b4a0cf 100644
--- a/docs/_templates/autosummary/class.rst
+++ b/docs/_templates/autosummary/class.rst
@@ -9,11 +9,11 @@
{% block attributes %}
{% if attributes %}
Attributes table
-~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~
.. autosummary::
{% for item in attributes %}
- ~{{ fullname }}.{{ item }}
+ ~{{ name }}.{{ item }}
{%- endfor %}
{% endif %}
{% endblock %}
@@ -26,7 +26,7 @@ Methods table
.. autosummary::
{% for item in methods %}
{%- if item != '__init__' %}
- ~{{ fullname }}.{{ item }}
+ ~{{ name }}.{{ item }}
{%- endif -%}
{%- endfor %}
{% endif %}
@@ -35,7 +35,7 @@ Methods table
{% block attributes_documentation %}
{% if attributes %}
Attributes
-~~~~~~~~~~~
+~~~~~~~~~~
{% for item in attributes %}
diff --git a/docs/conf.py b/docs/conf.py
index 07fe101..a1e3e58 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,5 +1,5 @@
# Configuration file for the Sphinx documentation builder.
-#
+
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
@@ -36,10 +36,10 @@
html_context = {
"display_github": True, # Integrate GitHub
- "github_user": "angelolab", # Username
- "github_repo": project_name, # Repo name
- "github_version": "main", # Version
- "conf_py_path": "/docs/", # Path in the checkout to the docs root
+ "github_user": "angelolab",
+ "github_repo": project_name,
+ "github_version": "main",
+ "conf_py_path": "/docs/",
}
# -- General configuration ---------------------------------------------------
@@ -55,6 +55,7 @@
"sphinx.ext.napoleon",
"sphinxcontrib.bibtex",
"sphinx_autodoc_typehints",
+ "sphinx_tabs.tabs",
"sphinx.ext.mathjax",
"IPython.sphinxext.ipython_console_highlighting",
"sphinxext.opengraph",
@@ -93,6 +94,7 @@
intersphinx_mapping = {
"python": ("https://docs.python.org/3", None),
"anndata": ("https://anndata.readthedocs.io/en/stable/", None),
+ "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
"numpy": ("https://numpy.org/doc/stable/", None),
}
diff --git a/docs/contributing.md b/docs/contributing.md
index 1ce0855..bf3833c 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -1,22 +1,45 @@
# Contributing guide
Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this project, too.
-This document will not reproduce the entire content from there. Instead, it aims at summarizing the most important
-information to get you started on contributing.
+This document will not reproduce the entire content from there.
+Instead, it aims at summarizing the most important information to get you started on contributing.
-We assume that you are already familiar with git and with making pull requests on GitHub. If not, please refer
-to the [scanpy developer guide][].
+We assume that you are already familiar with git and with making pull requests on GitHub.
+If not, please refer to the [scanpy developer guide][].
+
+[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
## Installing dev dependencies
-In addition to the packages needed to _use_ this package, you need additional python packages to _run tests_ and _build
-the documentation_. It's easy to install them using `pip`:
+In addition to the packages needed to _use_ this package,
+you need additional python packages to [run tests](#writing-tests) and [build the documentation](#docs-building).
+
+:::::{tabs}
+::::{group-tab} Hatch
+The easiest way is to get familiar with [hatch environments][], with which these tasks are simply:
+
+```bash
+hatch test # defined in the table [tool.hatch.envs.hatch-test] in pyproject.toml
+hatch run docs:build # defined in the table [tool.hatch.envs.docs]
+```
+
+::::
+
+::::{group-tab} Pip
+If you prefer managing environments manually, you can use `pip`:
```bash
cd Nimbus-Inference
+python3 -m venv .venv
+source .venv/bin/activate
pip install -e ".[dev,test,doc]"
```
+::::
+:::::
+
+[hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+
## Code-style
This package uses [pre-commit][] to enforce consistent code-styles.
@@ -28,10 +51,11 @@ To enable pre-commit locally, simply run
pre-commit install
```
-in the root of the repository. Pre-commit will automatically download all dependencies when it is run for the first time.
+in the root of the repository.
+Pre-commit will automatically download all dependencies when it is run for the first time.
-Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub. If you didn't run `pre-commit` before
-pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
+Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub.
+If you didn't run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
@@ -42,71 +66,108 @@ git pull --rebase
to integrate the changes into yours.
While the [pre-commit.ci][] is useful, we strongly encourage installing and running pre-commit locally first to understand its usage.
-Finally, most editors have an _autoformat on save_ feature. Consider enabling this option for [ruff][ruff-editors]
-and [prettier][prettier-editors].
+Finally, most editors have an _autoformat on save_ feature.
+Consider enabling this option for [ruff][ruff-editors] and [biome][biome-editors].
+[pre-commit]: https://pre-commit.com/
+[pre-commit.ci]: https://pre-commit.ci/
[ruff-editors]: https://docs.astral.sh/ruff/integrations/
-[prettier-editors]: https://prettier.io/docs/en/editors.html
+[biome-editors]: https://biomejs.dev/guides/integrate-in-editor/
+
+(writing-tests)=
## Writing tests
-```{note}
-Remember to first install the package with `pip install '-e[dev,test]'`
+This package uses [pytest][] for automated testing.
+Please write {doc}`scanpy:dev/testing` for every function added to the package.
+
+Most IDEs integrate with pytest and provide a GUI to run tests.
+Just point yours to one of the environments returned by
+
+```bash
+hatch env create hatch-test # create test environments for all supported versions
+hatch env find hatch-test # list all possible test environment paths
+```
+
+Alternatively, you can run all tests from the command line by executing
+
+:::::{tabs}
+::::{group-tab} Hatch
+
+```bash
+hatch test # test with the highest supported Python version
+# or
+hatch test --all # test with all supported Python versions
```
-This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added
-to the package.
+::::
-Most IDEs integrate with pytest and provide a GUI to run tests. Alternatively, you can run all tests from the
-command line by executing
+::::{group-tab} Pip
```bash
+source .venv/bin/activate
pytest
```
+::::
+:::::
+
in the root of the repository.
+[pytest]: https://docs.pytest.org/
+
### Continuous integration
Continuous integration will automatically run the tests on all pull requests and test
against the minimum and maximum supported Python version.
-Additionally, there's a CI job that tests against pre-releases of all dependencies
-(if there are any). The purpose of this check is to detect incompatibilities
-of new package versions early on and gives you time to fix the issue or reach
-out to the developers of the dependency before the package is released to a wider audience.
-
-[scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests
+Additionally, there's a CI job that tests against pre-releases of all dependencies (if there are any).
+The purpose of this check is to detect incompatibilities of new package versions early on and
+gives you time to fix the issue or reach out to the developers of the dependency before the package is released to a wider audience.
## Publishing a release
### Updating the version number
-Before making a release, you need to update the version number in the `pyproject.toml` file. Please adhere to [Semantic Versioning][semver], in brief
+Before making a release, you need to update the version number in the `pyproject.toml` file.
+Please adhere to [Semantic Versioning][semver], in brief
> Given a version number MAJOR.MINOR.PATCH, increment the:
>
-> 1. MAJOR version when you make incompatible API changes,
-> 2. MINOR version when you add functionality in a backwards compatible manner, and
-> 3. PATCH version when you make backwards compatible bug fixes.
+> 1. MAJOR version when you make incompatible API changes,
+> 2. MINOR version when you add functionality in a backwards compatible manner, and
+> 3. PATCH version when you make backwards compatible bug fixes.
>
> Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
-Specify `vX.X.X` as a tag name and create a release. For more information, see [managing Github releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
+Specify `vX.X.X` as a tag name and create a release.
+For more information, see [managing GitHub releases][].
+This will automatically create a git tag and trigger a Github workflow that creates a release on [PyPI][].
+
+[semver]: https://semver.org/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository
+[pypi]: https://pypi.org/
## Writing documentation
-Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
+Please write documentation for new or changed features and use-cases.
+This project uses [sphinx][] with the following features:
+
+- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
+- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
+- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
-- the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
-- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
-- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
-- [Sphinx autodoc typehints][], to automatically reference annotated input and output types
-- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own.
-See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
-on how to write documentation.
+[sphinx]: https://www.sphinx-doc.org/en/master/
+[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
+[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
+[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
+[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
+[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
### Tutorials with myst-nb and jupyter notebooks
@@ -114,46 +175,40 @@ The documentation is set-up to render jupyter notebooks stored in the `docs/note
Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
It is your responsibility to update and re-run the notebook whenever necessary.
-If you are interested in automatically running notebooks as part of the continuous integration, please check
-out [this feature request](https://github.com/scverse/cookiecutter-scverse/issues/40) in the `cookiecutter-scverse`
-repository.
+If you are interested in automatically running notebooks as part of the continuous integration,
+please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
+
+[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
#### Hints
-- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
- if you do so can sphinx automatically create a link to the external documentation.
-- If building the documentation fails because of a missing link that is outside your control, you can add an entry to
- the `nitpick_ignore` list in `docs/conf.py`
+- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`.
+ Only if you do so can sphinx automatically create a link to the external documentation.
+- If building the documentation fails because of a missing link that is outside your control,
+ you can add an entry to the `nitpick_ignore` list in `docs/conf.py`
+
+(docs-building)=
#### Building the docs locally
+:::::{tabs}
+::::{group-tab} Hatch
+
```bash
+hatch run docs:build
+hatch run docs:open
+```
+
+::::
+
+::::{group-tab} Pip
+
+```bash
+source .venv/bin/activate
cd docs
make html
-open _build/html/index.html
+(xdg-)open _build/html/index.html
```
-
-
-[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
-[cookiecutter-scverse-instance]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html
-[github quickstart guide]: https://docs.github.com/en/get-started/quickstart/create-a-repo?tool=webui
-[codecov]: https://about.codecov.io/sign-up/
-[codecov docs]: https://docs.codecov.com/docs
-[codecov bot]: https://docs.codecov.com/docs/team-bot
-[codecov app]: https://github.com/apps/codecov
-[pre-commit.ci]: https://pre-commit.ci/
-[readthedocs.org]: https://readthedocs.org/
-[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
-[jupytext]: https://jupytext.readthedocs.io/en/latest/
-[pre-commit]: https://pre-commit.com/
-[anndata]: https://github.com/scverse/anndata
-[mudata]: https://github.com/scverse/mudata
-[pytest]: https://docs.pytest.org/
-[semver]: https://semver.org/
-[sphinx]: https://www.sphinx-doc.org/en/master/
-[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
-[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
-[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
-[sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
-[pypi]: https://pypi.org/
+::::
+:::::
diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
index 1135204..0fbffef 100644
--- a/docs/extensions/typed_returns.py
+++ b/docs/extensions/typed_returns.py
@@ -12,7 +12,7 @@
def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
for line in lines:
if m := re.fullmatch(r"(?P\w+)\s+:\s+(?P[\w.]+)", line):
- yield f'-{m["param"]} (:class:`~{m["type"]}`)'
+ yield f"-{m['param']} (:class:`~{m['type']}`)"
else:
yield line
diff --git a/pyproject.toml b/pyproject.toml
index 0293da8..6b423b0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,133 +1,135 @@
[build-system]
build-backend = "hatchling.build"
-requires = ["hatchling"]
+requires = [ "hatchling" ]
[project]
name = "Nimbus-Inference"
version = "0.0.1"
-description = "A very interesting piece of code"
+description = "A model for classification of cells into marker positive / negative"
readme = "README.md"
-requires-python = ">=3.9"
-license = {file = "LICENSE"}
+license = { file = "LICENSE" }
+maintainers = [
+ { name = "Lorenz Rumberger", email = "jlrumber@stanford.edu" },
+]
authors = [
- {name = "Lorenz Rumberger"},
- {name = "Noah F. Greenwald"},
+ { name = "Lorenz Rumberger" },
]
-maintainers = [
- {name = "Lorenz Rumberger", email = "jlrumber@stanford.edu"},
- {name = "Noah F. Greenwald", email = "nfgreen@stanford.edu"},
- {name = "Sricharan Reddy Varra", email = "srivarra@stanford.edu"}
+requires-python = ">=3.10"
+classifiers = [
+ "Programming Language :: Python :: 3 :: Only",
+ "Programming Language :: Python :: 3.10",
+ "Programming Language :: Python :: 3.11",
+ "Programming Language :: Python :: 3.12",
+ "Programming Language :: Python :: 3.13",
]
-urls.Documentation = "https://Nimbus-Inference.readthedocs.io/"
-urls.Source = "https://github.com/angelolab/Nimbus-Inference"
-urls.Home-page = "https://github.com/angelolab/Nimbus-Inference"
dependencies = [
- "anndata",
- # for debug logging (referenced from the issue template)
- "session-info",
+ "anndata",
+ # for debug logging (referenced from the issue template)
+ "session-info2",
]
-
-[project.optional-dependencies]
-dev = [
- "pre-commit",
- "twine>=4.0.2",
+optional-dependencies.dev = [
+ "pre-commit",
+ "twine>=4.0.2",
]
-doc = [
- "docutils>=0.8,!=0.18.*,!=0.19.*",
- "sphinx>=4",
- "sphinx-book-theme>=1.0.0",
- "myst-nb",
- "sphinxcontrib-bibtex>=1.0.0",
- "sphinx-autodoc-typehints",
- "sphinxext-opengraph",
- # For notebooks
- "ipykernel",
- "ipython",
- "sphinx-copybutton",
- "pandas",
+optional-dependencies.doc = [
+ "docutils>=0.8,!=0.18.*,!=0.19.*",
+ "ipykernel",
+ "ipython",
+ "myst-nb>=1.1",
+ "pandas",
+ # Until pybtex >0.24.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
+ "setuptools",
+ "sphinx>=4",
+ "sphinx-autodoc-typehints",
+ "sphinx-book-theme>=1",
+ "sphinx-copybutton",
+ "sphinx-tabs",
+ "sphinxcontrib-bibtex>=1",
+ "sphinxext-opengraph",
]
-test = [
- "pytest",
- "coverage",
+optional-dependencies.test = [
+ "coverage",
+ "pytest",
]
+# https://docs.pypi.org/project_metadata/#project-urls
+urls.Documentation = "https://Nimbus-Inference.readthedocs.io/"
+urls.Homepage = "https://github.com/angelolab/Nimbus-Inference"
+urls.Source = "https://github.com/angelolab/Nimbus-Inference"
-[tool.coverage.run]
-source = ["nimbus_inference"]
-omit = [
- "**/test_*.py",
-]
+[tool.hatch.envs.default]
+installer = "uv"
+features = [ "dev" ]
-[tool.pytest.ini_options]
-testpaths = ["tests"]
-xfail_strict = true
-addopts = [
- "--import-mode=importlib", # allow using test files with same name
-]
+[tool.hatch.envs.docs]
+features = [ "doc" ]
+scripts.build = "sphinx-build -M html docs docs/_build {args}"
+scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
+scripts.clean = "git clean -fdX -- {args:docs}"
+
+[tool.hatch.envs.hatch-test]
+features = [ "test" ]
[tool.ruff]
-src = ["src"]
line-length = 120
-select = [
- "F", # Errors detected by Pyflakes
- "E", # Error detected by Pycodestyle
- "W", # Warning detected by Pycodestyle
- "I", # isort
- "D", # pydocstyle
- "B", # flake8-bugbear
- "TID", # flake8-tidy-imports
- "C4", # flake8-comprehensions
- "BLE", # flake8-blind-except
- "UP", # pyupgrade
- "RUF100", # Report unused noqa directives
+src = [ "src" ]
+extend-include = [ "*.ipynb" ]
+
+format.docstring-code-format = true
+
+lint.select = [
+ "B", # flake8-bugbear
+ "BLE", # flake8-blind-except
+ "C4", # flake8-comprehensions
+ "D", # pydocstyle
+ "E", # Error detected by Pycodestyle
+ "F", # Errors detected by Pyflakes
+ "I", # isort
+ "RUF100", # Report unused noqa directives
+ "TID", # flake8-tidy-imports
+ "UP", # pyupgrade
+ "W", # Warning detected by Pycodestyle
]
-ignore = [
- # line too long -> we accept long comment lines; formatter gets rid of long code lines
- "E501",
- # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
- "E731",
- # allow I, O, l as variable names -> I is the identity matrix
- "E741",
- # Missing docstring in public package
- "D104",
- # Missing docstring in public module
- "D100",
- # Missing docstring in __init__
- "D107",
- # Errors from function calls in argument defaults. These are fine when the result is immutable.
- "B008",
- # __magic__ methods are are often self-explanatory, allow missing docstrings
- "D105",
- # first line should end with a period [Bug: doesn't work with single-line docstrings]
- "D400",
- # First line should be in imperative mood; try rephrasing
- "D401",
- ## Disable one in each pair of mutually incompatible rules
- # We don’t want a blank line before a class docstring
- "D203",
- # We want docstrings to start immediately after the opening triple quote
- "D213",
+lint.ignore = [
+ "B008", # Errors from function calls in argument defaults. These are fine when the result is immutable.
+ "D100", # Missing docstring in public module
+ "D104", # Missing docstring in public package
+ "D105", # __magic__ methods are often self-explanatory, allow missing docstrings
+ "D107", # Missing docstring in __init__
+ # Disable one in each pair of mutually incompatible rules
+ "D203", # We don’t want a blank line before a class docstring
+ "D213", # <> We want docstrings to start immediately after the opening triple quote
+ "D400", # first line should end with a period [Bug: doesn’t work with single-line docstrings]
+ "D401", # First line should be in imperative mood; try rephrasing
+ "E501", # line too long -> we accept long comment lines; formatter gets rid of long code lines
+ "E731", # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
+ "E741", # allow I, O, l as variable names -> I is the identity matrix
]
-extend-include = ["*.ipynb"]
-
-[tool.ruff.format]
-docstring-code-format = true
+lint.per-file-ignores."*/__init__.py" = [ "F401" ]
+lint.per-file-ignores."docs/*" = [ "I" ]
+lint.per-file-ignores."tests/*" = [ "D" ]
+lint.pydocstyle.convention = "numpy"
-[tool.ruff.pydocstyle]
-convention = "numpy"
+[tool.pytest.ini_options]
+testpaths = [ "tests" ]
+xfail_strict = true
+addopts = [
+ "--import-mode=importlib", # allow using test files with same name
+]
-[tool.ruff.per-file-ignores]
-"docs/*" = ["I"]
-"tests/*" = ["D"]
-"*/__init__.py" = ["F401"]
+[tool.coverage.run]
+source = [ "nimbus_inference" ]
+omit = [
+ "**/test_*.py",
+]
[tool.cruft]
skip = [
- "tests",
- "src/**/__init__.py",
- "src/**/basic.py",
- "docs/api.md",
- "docs/changelog.md",
- "docs/references.bib",
- "docs/references.md",
- "docs/notebooks/example.ipynb",
+ "tests",
+ "src/**/__init__.py",
+ "src/**/basic.py",
+ "docs/api.md",
+ "docs/changelog.md",
+ "docs/references.bib",
+ "docs/references.md",
+ "docs/notebooks/example.ipynb",
]
From f4ad923bec71061a25c9aa3fdd3b167409b13d8d Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Tue, 30 Sep 2025 06:24:30 +0000
Subject: [PATCH 2/4] Automated template update to v0.6.0
---
.cruft.json | 6 +-
.github/workflows/test.yaml | 80 +++++++++++++++-----
.gitignore | 1 +
.pre-commit-config.yaml | 19 ++---
.readthedocs.yaml | 23 +++---
biome.jsonc | 5 +-
docs/Makefile | 20 -----
docs/contributing.md | 144 ++++++++++++++++++++++++++++++++----
pyproject.toml | 27 ++++++-
9 files changed, 238 insertions(+), 87 deletions(-)
delete mode 100644 docs/Makefile
diff --git a/.cruft.json b/.cruft.json
index 348a054..fd552f0 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,7 +1,7 @@
{
"template": "https://github.com/scverse/cookiecutter-scverse",
- "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
- "checkout": "v0.5.0",
+ "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
+ "checkout": "v0.6.0",
"context": {
"cookiecutter": {
"project_name": "Nimbus-Inference",
@@ -36,7 +36,7 @@
"trim_blocks": true
},
"_template": "https://github.com/scverse/cookiecutter-scverse",
- "_commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
+ "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
}
},
"directory": null
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index d5cfb2a..0bd76e8 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -18,27 +18,48 @@ defaults:
shell: bash -euo pipefail {0}
jobs:
+ # Get the test environment from hatch as defined in pyproject.toml.
+ # This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
+ # run locally and on continuous integration.
+ # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
+ # more details.
+ get-environments:
+ runs-on: ubuntu-latest
+ outputs:
+ envs: ${{ steps.get-envs.outputs.envs }}
+ steps:
+ - uses: actions/checkout@v4
+ with:
+ filter: blob:none
+ fetch-depth: 0
+ - name: Install uv
+ uses: astral-sh/setup-uv@v5
+ - name: Get test environments
+ id: get-envs
+ run: |
+ ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
+ | map(
+ select(.key | startswith("hatch-test"))
+ | {
+ name: .key,
+ label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
+ python: .value.python
+ }
+ )')
+ echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+
+ # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
test:
- runs-on: ${{ matrix.os }}
+ needs: get-environments
strategy:
fail-fast: false
matrix:
- include:
- - os: ubuntu-latest
- python: "3.10"
- - os: ubuntu-latest
- python: "3.12"
- - os: ubuntu-latest
- python: "3.12"
- pip-flags: "--pre"
- name: PRE-RELEASE DEPENDENCIES
-
- name: ${{ matrix.name }} Python ${{ matrix.python }}
-
- env:
- OS: ${{ matrix.os }}
- PYTHON: ${{ matrix.python }}
+ os: [ubuntu-latest]
+ env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+
+ name: ${{ matrix.env.label }}
+ runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
@@ -48,12 +69,35 @@ jobs:
- name: Install uv
uses: astral-sh/setup-uv@v5
with:
+ python-version: ${{ matrix.env.python }}
cache-dependency-glob: pyproject.toml
+ - name: create hatch environment
+ run: uvx hatch env create ${{ matrix.env.name }}
- name: run tests using hatch
env:
MPLBACKEND: agg
PLATFORM: ${{ matrix.os }}
DISPLAY: :42
- run: uvx hatch test --cover --python ${{ matrix.python }}
+ run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
+ - name: generate coverage report
+ run: |
+ # See https://coverage.readthedocs.io/en/latest/config.html#run-patch
+ test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
+ uvx hatch run ${{ matrix.env.name }}:cov-report # report visibly
+ uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
- name: Upload coverage
- uses: codecov/codecov-action@v4
+ uses: codecov/codecov-action@v5
+
+ # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
+ # protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
+ check:
+ name: Tests pass in all hatch environments
+ if: always()
+ needs:
+ - get-environments
+ - test
+ runs-on: ubuntu-latest
+ steps:
+ - uses: re-actors/alls-green@release/v1
+ with:
+ jobs: ${{ toJSON(needs) }}
diff --git a/.gitignore b/.gitignore
index 31e10b3..bd24e4e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,6 +14,7 @@ __pycache__/
# Tests and coverage
/data/
/node_modules/
+/.coverage*
# docs
/docs/generated/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0fcce11..b9de3fe 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,24 +7,24 @@ default_stages:
minimum_pre_commit_version: 2.16.0
repos:
- repo: https://github.com/biomejs/pre-commit
- rev: v1.9.4
+ rev: v2.2.4
hooks:
- id: biome-format
exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
- repo: https://github.com/tox-dev/pyproject-fmt
- rev: v2.5.1
+ rev: v2.6.0
hooks:
- id: pyproject-fmt
- repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.11.2
+ rev: v0.13.2
hooks:
- - id: ruff
+ - id: ruff-check
types_or: [python, pyi, jupyter]
args: [--fix, --exit-non-zero-on-fix]
- id: ruff-format
types_or: [python, pyi, jupyter]
- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v5.0.0
+ rev: v6.0.0
hooks:
- id: detect-private-key
- id: check-ast
@@ -36,12 +36,3 @@ repos:
# Check that there are no merge conflicts (could be generated by template sync)
- id: check-merge-conflict
args: [--assume-in-merge]
- - repo: local
- hooks:
- - id: forbid-to-commit
- name: Don't commit rej files
- entry: |
- Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
- Fix the merge conflicts manually and remove the .rej files.
- language: fail
- files: '.*\.rej$'
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 69897c3..c3f3f96 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,16 +1,15 @@
# https://docs.readthedocs.io/en/stable/config-file/v2.html
version: 2
build:
- os: ubuntu-20.04
+ os: ubuntu-24.04
tools:
- python: "3.10"
-sphinx:
- configuration: docs/conf.py
- # disable this for more lenient docs builds
- fail_on_warning: true
-python:
- install:
- - method: pip
- path: .
- extra_requirements:
- - doc
+ python: "3.12"
+ jobs:
+ create_environment:
+ - asdf plugin add uv
+ - asdf install uv latest
+ - asdf global uv latest
+ build:
+ html:
+ - uvx hatch run docs:build
+ - mv docs/_build $READTHEDOCS_OUTPUT
diff --git a/biome.jsonc b/biome.jsonc
index 2175c16..9f8f220 100644
--- a/biome.jsonc
+++ b/biome.jsonc
@@ -1,9 +1,10 @@
{
- "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+ "$schema": "https://biomejs.dev/schemas/2.2.0/schema.json",
+ "vcs": { "enabled": true, "clientKind": "git", "useIgnoreFile": true },
"formatter": { "useEditorconfig": true },
"overrides": [
{
- "include": ["./.vscode/*.json", "**/*.jsonc"],
+ "includes": ["./.vscode/*.json", "**/*.jsonc"],
"json": {
"formatter": { "trailingCommas": "all" },
"parser": {
diff --git a/docs/Makefile b/docs/Makefile
deleted file mode 100644
index d4bb2cb..0000000
--- a/docs/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS ?=
-SPHINXBUILD ?= sphinx-build
-SOURCEDIR = .
-BUILDDIR = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
- @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
- @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/contributing.md b/docs/contributing.md
index bf3833c..699d942 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -1,14 +1,33 @@
# Contributing guide
-Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this project, too.
-This document will not reproduce the entire content from there.
-Instead, it aims at summarizing the most important information to get you started on contributing.
-
+This document aims at summarizing the most important information for getting you started on contributing to this project.
We assume that you are already familiar with git and with making pull requests on GitHub.
-If not, please refer to the [scanpy developer guide][].
+For more extensive tutorials, that also cover the absolute basics,
+please refer to other resources such as the [pyopensci tutorials][],
+the [scientific Python tutorials][], or the [scanpy developer guide][].
+
+[pyopensci tutorials]: https://www.pyopensci.org/learn.html
+[scientific Python tutorials]: https://learn.scientific-python.org/development/tutorials/
[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
+:::{tip} The *hatch* project manager
+
+We highly recommend to familiarize yourself with [`hatch`][hatch].
+Hatch is a Python project manager that
+
+- manages virtual environments, separately for development, testing and building the documentation.
+ Separating the environments is useful to avoid dependency conflicts.
+- allows to run tests locally in different environments (e.g. different python versions)
+- allows to run tasks defined in `pyproject.toml`, e.g. to build documentation.
+
+While the project is setup with `hatch` in mind,
+it is still possible to use different tools to manage dependencies, such as `uv` or `pip`.
+
+:::
+
+[hatch]: https://hatch.pypa.io/latest/
+
## Installing dev dependencies
In addition to the packages needed to _use_ this package,
@@ -16,29 +35,103 @@ you need additional python packages to [run tests](#writing-tests) and [build th
:::::{tabs}
::::{group-tab} Hatch
-The easiest way is to get familiar with [hatch environments][], with which these tasks are simply:
+
+On the command line, you typically interact with hatch through its command line interface (CLI).
+Running one of the following commands will automatically resolve the environments for testing and
+building the documentation in the background:
```bash
hatch test # defined in the table [tool.hatch.envs.hatch-test] in pyproject.toml
hatch run docs:build # defined in the table [tool.hatch.envs.docs]
```
+When using an IDE such as VS Code,
+you’ll have to point the editor at the paths to the virtual environments manually.
+The environment you typically want to use as your main development environment is the `hatch-test`
+environment with the latest Python version.
+
+To get a list of all environments for your projects, run
+
+```bash
+hatch env show -i
+```
+
+This will list “Standalone” environments and a table of “Matrix” environments like the following:
+
+```
++------------+---------+--------------------------+----------+---------------------------------+-------------+
+| Name | Type | Envs | Features | Dependencies | Scripts |
++------------+---------+--------------------------+----------+---------------------------------+-------------+
+| hatch-test | virtual | hatch-test.py3.10-stable | dev | coverage-enable-subprocess==1.0 | cov-combine |
+| | | hatch-test.py3.13-stable | test | coverage[toml]~=7.4 | cov-report |
+| | | hatch-test.py3.13-pre | | pytest-mock~=3.12 | run |
+| | | | | pytest-randomly~=3.15 | run-cov |
+| | | | | pytest-rerunfailures~=14.0 | |
+| | | | | pytest-xdist[psutil]~=3.5 | |
+| | | | | pytest~=8.1 | |
++------------+---------+--------------------------+----------+---------------------------------+-------------+
+```
+
+From the `Envs` column, select the environment name you want to use for development.
+In this example, it would be `hatch-test.py3.13-stable`.
+
+Next, create the environment with
+
+```bash
+hatch env create hatch-test.py3.13-stable
+```
+
+Then, obtain the path to the environment using
+
+```bash
+hatch env find hatch-test.py3.13-stable
+```
+
+In case you are using VScode, now open the command palette (Ctrl+Shift+P) and search for `Python: Select Interpreter`.
+Choose `Enter Interpreter Path` and paste the path to the virtual environment from above.
+
+In this future, this may become easier through a hatch vscode extension.
+
+::::
+
+::::{group-tab} uv
+
+A popular choice for managing virtual environments is [uv][].
+The main disadvantage compared to hatch is that it supports only a single environment per project at a time,
+which requires you to mix the dependencies for running tests and building docs.
+This can have undesired side-effects,
+such as requiring to install a lower version of a library your project depends on,
+only because an outdated sphinx plugin pins an older version.
+
+To initalize a virtual environment in the `.venv` directory of your project, simply run
+
+```bash
+uv sync --all-extras
+```
+
+The `.venv` directory is typically automatically discovered by IDEs such as VS Code.
+
::::
::::{group-tab} Pip
-If you prefer managing environments manually, you can use `pip`:
+
+Pip is nowadays mostly superseded by environment manager such as [hatch][].
+However, for the sake of completeness, and since it’s ubiquitously available,
+we describe how you can manage environments manually using `pip`:
```bash
-cd Nimbus-Inference
python3 -m venv .venv
source .venv/bin/activate
pip install -e ".[dev,test,doc]"
```
+The `.venv` directory is typically automatically discovered by IDEs such as VS Code.
+
::::
:::::
[hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+[uv]: https://docs.astral.sh/uv/
## Code-style
@@ -55,7 +148,7 @@ in the root of the repository.
Pre-commit will automatically download all dependencies when it is run for the first time.
Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub.
-If you didn't run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
+If you didn’t run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
@@ -102,6 +195,14 @@ hatch test --all # test with all supported Python versions
::::
+::::{group-tab} uv
+
+```bash
+uv run pytest
+```
+
+::::
+
::::{group-tab} Pip
```bash
@@ -118,12 +219,17 @@ in the root of the repository.
### Continuous integration
-Continuous integration will automatically run the tests on all pull requests and test
+Continuous integration via GitHub actions will automatically run the tests on all pull requests and test
against the minimum and maximum supported Python version.
-Additionally, there's a CI job that tests against pre-releases of all dependencies (if there are any).
+Additionally, there’s a CI job that tests against pre-releases of all dependencies (if there are any).
The purpose of this check is to detect incompatibilities of new package versions early on and
-gives you time to fix the issue or reach out to the developers of the dependency before the package is released to a wider audience.
+gives you time to fix the issue or reach out to the developers of the dependency before the package
+is released to a wider audience.
+
+The CI job is defined in `.github/workflows/test.yaml`,
+however the single point of truth for CI jobs is the Hatch test matrix defined in `pyproject.toml`.
+This means that local testing via hatch and remote testing on CI tests against the same python versions and uses the same environments.
## Publishing a release
@@ -189,7 +295,7 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu
(docs-building)=
-#### Building the docs locally
+### Building the docs locally
:::::{tabs}
::::{group-tab} Hatch
@@ -201,12 +307,22 @@ hatch run docs:open
::::
+::::{group-tab} uv
+
+```bash
+cd docs
+uv run sphinx-build -M html . _build -W
+(xdg-)open _build/html/index.html
+```
+
+::::
+
::::{group-tab} Pip
```bash
source .venv/bin/activate
cd docs
-make html
+sphinx-build -M html . _build -W
(xdg-)open _build/html/index.html
```
diff --git a/pyproject.toml b/pyproject.toml
index 6b423b0..b59703d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,7 @@ optional-dependencies.doc = [
"pandas",
# Until pybtex >0.24.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
"setuptools",
- "sphinx>=4",
+ "sphinx>=8.1",
"sphinx-autodoc-typehints",
"sphinx-book-theme>=1",
"sphinx-copybutton",
@@ -48,8 +48,9 @@ optional-dependencies.doc = [
"sphinxext-opengraph",
]
optional-dependencies.test = [
- "coverage",
+ "coverage>=7.10",
"pytest",
+ "pytest-cov", # For VS Code’s coverage functionality
]
# https://docs.pypi.org/project_metadata/#project-urls
urls.Documentation = "https://Nimbus-Inference.readthedocs.io/"
@@ -62,12 +63,29 @@ features = [ "dev" ]
[tool.hatch.envs.docs]
features = [ "doc" ]
-scripts.build = "sphinx-build -M html docs docs/_build {args}"
+scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
scripts.clean = "git clean -fdX -- {args:docs}"
+# Test the lowest and highest supported Python versions with normal deps
+[[tool.hatch.envs.hatch-test.matrix]]
+deps = [ "stable" ]
+python = [ "3.10", "3.13" ]
+
+# Test the newest supported Python version also with pre-release deps
+[[tool.hatch.envs.hatch-test.matrix]]
+deps = [ "pre" ]
+python = [ "3.13" ]
+
[tool.hatch.envs.hatch-test]
-features = [ "test" ]
+features = [ "dev", "test" ]
+
+[tool.hatch.envs.hatch-test.overrides]
+# If the matrix variable `deps` is set to "pre",
+# set the environment variable `UV_PRERELEASE` to "allow".
+matrix.deps.env-vars = [
+ { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
+]
[tool.ruff]
line-length = 120
@@ -118,6 +136,7 @@ addopts = [
[tool.coverage.run]
source = [ "nimbus_inference" ]
+patch = [ "subprocess" ]
omit = [
"**/test_*.py",
]
From 68fe586b4f7418626c9e94ed91c8ddc1d62b30ec Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Wed, 24 Dec 2025 09:50:16 +0000
Subject: [PATCH 3/4] Automated template update to v0.7.0
---
.cruft.json | 6 +--
.github/ISSUE_TEMPLATE/bug_report.yml | 5 +--
.github/ISSUE_TEMPLATE/feature_request.yml | 2 +-
.github/workflows/build.yaml | 11 +-----
.github/workflows/release.yaml | 11 +-----
.github/workflows/test.yaml | 20 +++++-----
.pre-commit-config.yaml | 6 +--
.readthedocs.yaml | 3 +-
docs/conf.py | 15 ++++---
docs/contributing.md | 12 +++---
pyproject.toml | 46 +++++++++++-----------
11 files changed, 64 insertions(+), 73 deletions(-)
diff --git a/.cruft.json b/.cruft.json
index fd552f0..21f0c1b 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,7 +1,7 @@
{
"template": "https://github.com/scverse/cookiecutter-scverse",
- "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
- "checkout": "v0.6.0",
+ "commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95",
+ "checkout": "v0.7.0",
"context": {
"cookiecutter": {
"project_name": "Nimbus-Inference",
@@ -36,7 +36,7 @@
"trim_blocks": true
},
"_template": "https://github.com/scverse/cookiecutter-scverse",
- "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
+ "_commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95"
}
},
"directory": null
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 3ca1ccb..6104b9e 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -1,6 +1,6 @@
name: Bug report
description: Report something that is broken or incorrect
-labels: bug
+type: Bug
body:
- type: markdown
attributes:
@@ -9,8 +9,7 @@ body:
detailing how to provide the necessary information for us to reproduce your bug. In brief:
* Please provide exact steps how to reproduce the bug in a clean Python environment.
* In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
- * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
- available datasets or to share a subset of your data.
+ * Replicate problems on public datasets or share data subsets when full sharing isn't possible.
- type: textarea
id: report
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
index 6576689..88b2cbb 100644
--- a/.github/ISSUE_TEMPLATE/feature_request.yml
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,6 +1,6 @@
name: Feature request
description: Propose a new feature for Nimbus-Inference
-labels: enhancement
+type: Enhancement
body:
- type: textarea
id: description
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index 83e01a1..c6ecc2f 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -10,23 +10,16 @@ concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
-defaults:
- run:
- # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
- shell: bash -euo pipefail {0}
-
jobs:
package:
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout@v4
+ - uses: actions/checkout@v5
with:
filter: blob:none
fetch-depth: 0
- name: Install uv
- uses: astral-sh/setup-uv@v5
- with:
- cache-dependency-glob: pyproject.toml
+ uses: astral-sh/setup-uv@v7
- name: Build package
run: uv build
- name: Check package
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index 87e5c38..1ca179b 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -4,11 +4,6 @@ on:
release:
types: [published]
-defaults:
- run:
- # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
- shell: bash -euo pipefail {0}
-
# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
jobs:
release:
@@ -20,14 +15,12 @@ jobs:
permissions:
id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
steps:
- - uses: actions/checkout@v4
+ - uses: actions/checkout@v5
with:
filter: blob:none
fetch-depth: 0
- name: Install uv
- uses: astral-sh/setup-uv@v5
- with:
- cache-dependency-glob: pyproject.toml
+ uses: astral-sh/setup-uv@v7
- name: Build package
run: uv build
- name: Publish package distributions to PyPI
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 0bd76e8..6bf473b 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -12,11 +12,6 @@ concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
-defaults:
- run:
- # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
- shell: bash -euo pipefail {0}
-
jobs:
# Get the test environment from hatch as defined in pyproject.toml.
# This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
@@ -28,12 +23,12 @@ jobs:
outputs:
envs: ${{ steps.get-envs.outputs.envs }}
steps:
- - uses: actions/checkout@v4
+ - uses: actions/checkout@v5
with:
filter: blob:none
fetch-depth: 0
- name: Install uv
- uses: astral-sh/setup-uv@v5
+ uses: astral-sh/setup-uv@v7
- name: Get test environments
id: get-envs
run: |
@@ -51,6 +46,8 @@ jobs:
# Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
test:
needs: get-environments
+ permissions:
+ id-token: write # for codecov OIDC
strategy:
fail-fast: false
@@ -60,17 +57,17 @@ jobs:
name: ${{ matrix.env.label }}
runs-on: ${{ matrix.os }}
+ continue-on-error: ${{ contains(matrix.env.name, 'pre') }} # make "all-green" pass even if pre-release job fails
steps:
- - uses: actions/checkout@v4
+ - uses: actions/checkout@v5
with:
filter: blob:none
fetch-depth: 0
- name: Install uv
- uses: astral-sh/setup-uv@v5
+ uses: astral-sh/setup-uv@v7
with:
python-version: ${{ matrix.env.python }}
- cache-dependency-glob: pyproject.toml
- name: create hatch environment
run: uvx hatch env create ${{ matrix.env.name }}
- name: run tests using hatch
@@ -87,6 +84,9 @@ jobs:
uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
- name: Upload coverage
uses: codecov/codecov-action@v5
+ with:
+ fail_ci_if_error: true
+ use_oidc: true
# Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
# protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b9de3fe..27d8a95 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,16 +7,16 @@ default_stages:
minimum_pre_commit_version: 2.16.0
repos:
- repo: https://github.com/biomejs/pre-commit
- rev: v2.2.4
+ rev: v2.3.10
hooks:
- id: biome-format
exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
- repo: https://github.com/tox-dev/pyproject-fmt
- rev: v2.6.0
+ rev: v2.11.1
hooks:
- id: pyproject-fmt
- repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.13.2
+ rev: v0.14.10
hooks:
- id: ruff-check
types_or: [python, pyi, jupyter]
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index c3f3f96..6c28477 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -3,7 +3,8 @@ version: 2
build:
os: ubuntu-24.04
tools:
- python: "3.12"
+ python: "3.13"
+ nodejs: latest
jobs:
create_environment:
- asdf plugin add uv
diff --git a/docs/conf.py b/docs/conf.py
index a1e3e58..d67e598 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -5,11 +5,14 @@
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
+import shutil
import sys
from datetime import datetime
from importlib.metadata import metadata
from pathlib import Path
+from sphinxcontrib import katex
+
HERE = Path(__file__).parent
sys.path.insert(0, str(HERE / "extensions"))
@@ -19,7 +22,7 @@
# NOTE: If you installed your project in editable mode, this might be stale.
# If this is the case, reinstall it to refresh the metadata
info = metadata("Nimbus-Inference")
-project_name = info["Name"]
+project = info["Name"]
author = info["Author"]
copyright = f"{datetime.now():%Y}, {author}."
version = info["Version"]
@@ -37,7 +40,7 @@
html_context = {
"display_github": True, # Integrate GitHub
"github_user": "angelolab",
- "github_repo": project_name,
+ "github_repo": project,
"github_version": "main",
"conf_py_path": "/docs/",
}
@@ -54,9 +57,9 @@
"sphinx.ext.autosummary",
"sphinx.ext.napoleon",
"sphinxcontrib.bibtex",
+ "sphinxcontrib.katex",
"sphinx_autodoc_typehints",
"sphinx_tabs.tabs",
- "sphinx.ext.mathjax",
"IPython.sphinxext.ipython_console_highlighting",
"sphinxext.opengraph",
*[p.stem for p in (HERE / "extensions").glob("*.py")],
@@ -92,7 +95,8 @@
}
intersphinx_mapping = {
- "python": ("https://docs.python.org/3", None),
+ # TODO: replace `3.13` with `3` once ReadTheDocs supports building with Python 3.14
+ "python": ("https://docs.python.org/3.13", None),
"anndata": ("https://anndata.readthedocs.io/en/stable/", None),
"scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
"numpy": ("https://numpy.org/doc/stable/", None),
@@ -113,7 +117,7 @@
html_static_path = ["_static"]
html_css_files = ["css/custom.css"]
-html_title = project_name
+html_title = project
html_theme_options = {
"repository_url": repository_url,
@@ -123,6 +127,7 @@
}
pygments_style = "default"
+katex_prerender = shutil.which(katex.NODEJS_BINARY) is not None
nitpick_ignore = [
# If building the documentation fails because of a missing link that is outside your control,
diff --git a/docs/contributing.md b/docs/contributing.md
index 699d942..b172fd1 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -62,9 +62,9 @@ This will list “Standalone” environments and a table of “Matrix” environ
+------------+---------+--------------------------+----------+---------------------------------+-------------+
| Name | Type | Envs | Features | Dependencies | Scripts |
+------------+---------+--------------------------+----------+---------------------------------+-------------+
-| hatch-test | virtual | hatch-test.py3.10-stable | dev | coverage-enable-subprocess==1.0 | cov-combine |
-| | | hatch-test.py3.13-stable | test | coverage[toml]~=7.4 | cov-report |
-| | | hatch-test.py3.13-pre | | pytest-mock~=3.12 | run |
+| hatch-test | virtual | hatch-test.py3.11-stable | dev | coverage-enable-subprocess==1.0 | cov-combine |
+| | | hatch-test.py3.14-stable | test | coverage[toml]~=7.4 | cov-report |
+| | | hatch-test.py3.14-pre | | pytest-mock~=3.12 | run |
| | | | | pytest-randomly~=3.15 | run-cov |
| | | | | pytest-rerunfailures~=14.0 | |
| | | | | pytest-xdist[psutil]~=3.5 | |
@@ -73,18 +73,18 @@ This will list “Standalone” environments and a table of “Matrix” environ
```
From the `Envs` column, select the environment name you want to use for development.
-In this example, it would be `hatch-test.py3.13-stable`.
+In this example, it would be `hatch-test.py3.14-stable`.
Next, create the environment with
```bash
-hatch env create hatch-test.py3.13-stable
+hatch env create hatch-test.py3.14-stable
```
Then, obtain the path to the environment using
```bash
-hatch env find hatch-test.py3.13-stable
+hatch env find hatch-test.py3.14-stable
```
In case you are using VScode, now open the command palette (Ctrl+Shift+P) and search for `Python: Select Interpreter`.
diff --git a/pyproject.toml b/pyproject.toml
index b59703d..ea3dc5e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,55 +14,55 @@ maintainers = [
authors = [
{ name = "Lorenz Rumberger" },
]
-requires-python = ">=3.10"
+requires-python = ">=3.11"
classifiers = [
"Programming Language :: Python :: 3 :: Only",
- "Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
+ "Programming Language :: Python :: 3.14",
]
dependencies = [
"anndata",
# for debug logging (referenced from the issue template)
"session-info2",
]
-optional-dependencies.dev = [
+# https://docs.pypi.org/project_metadata/#project-urls
+urls.Documentation = "https://Nimbus-Inference.readthedocs.io/"
+urls.Homepage = "https://github.com/angelolab/Nimbus-Inference"
+urls.Source = "https://github.com/angelolab/Nimbus-Inference"
+
+[dependency-groups]
+dev = [
"pre-commit",
"twine>=4.0.2",
]
-optional-dependencies.doc = [
- "docutils>=0.8,!=0.18.*,!=0.19.*",
+test = [
+ "coverage>=7.10",
+ "pytest",
+ "pytest-cov", # For VS Code’s coverage functionality
+]
+doc = [
"ipykernel",
"ipython",
"myst-nb>=1.1",
"pandas",
- # Until pybtex >0.24.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
- "setuptools",
"sphinx>=8.1",
"sphinx-autodoc-typehints",
"sphinx-book-theme>=1",
"sphinx-copybutton",
"sphinx-tabs",
"sphinxcontrib-bibtex>=1",
+ "sphinxcontrib-katex",
"sphinxext-opengraph",
]
-optional-dependencies.test = [
- "coverage>=7.10",
- "pytest",
- "pytest-cov", # For VS Code’s coverage functionality
-]
-# https://docs.pypi.org/project_metadata/#project-urls
-urls.Documentation = "https://Nimbus-Inference.readthedocs.io/"
-urls.Homepage = "https://github.com/angelolab/Nimbus-Inference"
-urls.Source = "https://github.com/angelolab/Nimbus-Inference"
[tool.hatch.envs.default]
installer = "uv"
-features = [ "dev" ]
+dependency-groups = [ "dev" ]
[tool.hatch.envs.docs]
-features = [ "doc" ]
+dependency-groups = [ "doc" ]
scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
scripts.clean = "git clean -fdX -- {args:docs}"
@@ -70,15 +70,15 @@ scripts.clean = "git clean -fdX -- {args:docs}"
# Test the lowest and highest supported Python versions with normal deps
[[tool.hatch.envs.hatch-test.matrix]]
deps = [ "stable" ]
-python = [ "3.10", "3.13" ]
+python = [ "3.11", "3.14" ]
# Test the newest supported Python version also with pre-release deps
[[tool.hatch.envs.hatch-test.matrix]]
deps = [ "pre" ]
-python = [ "3.13" ]
+python = [ "3.14" ]
[tool.hatch.envs.hatch-test]
-features = [ "dev", "test" ]
+dependency-groups = [ "dev", "test" ]
[tool.hatch.envs.hatch-test.overrides]
# If the matrix variable `deps` is set to "pre",
@@ -127,9 +127,9 @@ lint.per-file-ignores."docs/*" = [ "I" ]
lint.per-file-ignores."tests/*" = [ "D" ]
lint.pydocstyle.convention = "numpy"
-[tool.pytest.ini_options]
+[tool.pytest]
+strict = true
testpaths = [ "tests" ]
-xfail_strict = true
addopts = [
"--import-mode=importlib", # allow using test files with same name
]
From a77fd5e409259b4f8774dcffa5cc9df4b8df71a3 Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Fri, 17 Jul 2026 07:13:31 +0000
Subject: [PATCH 4/4] Automated template update to v0.8.0
---
.cruft.json | 17 ++--
.github/ISSUE_TEMPLATE/bug_report.yml | 2 +-
.github/ISSUE_TEMPLATE/feature_request.yml | 2 +-
.github/dependabot.yml | 12 +++
.github/workflows/build.yaml | 8 +-
.github/workflows/release.yaml | 12 ++-
.github/workflows/test.yaml | 24 ++++--
.pre-commit-config.yaml | 12 ++-
.readthedocs.yaml | 4 +-
docs/_templates/autosummary/class.rst | 61 --------------
docs/conf.py | 13 +--
docs/contributing.md | 97 +++++++++++++---------
docs/extensions/typed_returns.py | 32 -------
pyproject.toml | 65 ++++++---------
14 files changed, 157 insertions(+), 204 deletions(-)
create mode 100644 .github/dependabot.yml
delete mode 100644 docs/_templates/autosummary/class.rst
delete mode 100644 docs/extensions/typed_returns.py
diff --git a/.cruft.json b/.cruft.json
index 21f0c1b..8dd481e 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,7 +1,7 @@
{
- "template": "https://github.com/scverse/cookiecutter-scverse",
- "commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95",
- "checkout": "v0.7.0",
+ "template": "/tmp/tmpvf8ta0q7",
+ "commit": "6518dfa1abde7379ea7255daf0ce09c23f2b4c94",
+ "checkout": "v0.8.0",
"context": {
"cookiecutter": {
"project_name": "Nimbus-Inference",
@@ -13,6 +13,7 @@
"github_repo": "Nimbus-Inference",
"license": "MIT License",
"ide_integration": true,
+ "issue_categorization": "",
"_copy_without_render": [
".github/workflows/build.yaml",
".github/workflows/test.yaml",
@@ -35,9 +36,11 @@
"lstrip_blocks": true,
"trim_blocks": true
},
- "_template": "https://github.com/scverse/cookiecutter-scverse",
- "_commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95"
- }
+ "_template": "/tmp/tmpvf8ta0q7",
+ "_commit": "4d6aa34fd5be7523ca3bd49fbd81a882dde01d1f"
+ },
+ "_commit": "6518dfa1abde7379ea7255daf0ce09c23f2b4c94",
+ "_template": "https://github.com/scverse/cookiecutter-scverse"
},
"directory": null
-}
+}
\ No newline at end of file
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 6104b9e..cc32eda 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -1,6 +1,6 @@
name: Bug report
description: Report something that is broken or incorrect
-type: Bug
+labels: bug
body:
- type: markdown
attributes:
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
index 88b2cbb..6576689 100644
--- a/.github/ISSUE_TEMPLATE/feature_request.yml
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,6 +1,6 @@
name: Feature request
description: Propose a new feature for Nimbus-Inference
-type: Enhancement
+labels: enhancement
body:
- type: textarea
id: description
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 0000000..914ad69
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,12 @@
+version: 2
+updates:
+ - package-ecosystem: github-actions
+ directory: /
+ schedule:
+ interval: weekly
+ cooldown:
+ default-days: 7
+ groups:
+ actions-deps:
+ patterns:
+ - "*"
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index c6ecc2f..6cca7d4 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -10,16 +10,20 @@ concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
+permissions:
+ contents: read
+
jobs:
package:
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout@v5
+ - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
with:
filter: blob:none
fetch-depth: 0
+ persist-credentials: false
- name: Install uv
- uses: astral-sh/setup-uv@v7
+ uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
- name: Build package
run: uv build
- name: Check package
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index 1ca179b..67faa7f 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -5,6 +5,8 @@ on:
types: [published]
# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+permissions: {}
+
jobs:
release:
name: Upload release to PyPI
@@ -13,15 +15,19 @@ jobs:
name: pypi
url: https://pypi.org/p/nimbus_inference
permissions:
+ contents: read
id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
steps:
- - uses: actions/checkout@v5
+ - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
with:
filter: blob:none
fetch-depth: 0
+ persist-credentials: false
- name: Install uv
- uses: astral-sh/setup-uv@v7
+ uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+ with:
+ enable-cache: false
- name: Build package
run: uv build
- name: Publish package distributions to PyPI
- uses: pypa/gh-action-pypi-publish@release/v1
+ uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 6bf473b..0075425 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -12,6 +12,9 @@ concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
+permissions:
+ contents: read
+
jobs:
# Get the test environment from hatch as defined in pyproject.toml.
# This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
@@ -19,16 +22,17 @@ jobs:
# Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
# more details.
get-environments:
- runs-on: ubuntu-latest
+ runs-on: ubuntu-slim
outputs:
envs: ${{ steps.get-envs.outputs.envs }}
steps:
- - uses: actions/checkout@v5
+ - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
with:
filter: blob:none
fetch-depth: 0
+ persist-credentials: false
- name: Install uv
- uses: astral-sh/setup-uv@v7
+ uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
- name: Get test environments
id: get-envs
run: |
@@ -48,6 +52,7 @@ jobs:
needs: get-environments
permissions:
id-token: write # for codecov OIDC
+ contents: read
strategy:
fail-fast: false
@@ -60,16 +65,19 @@ jobs:
continue-on-error: ${{ contains(matrix.env.name, 'pre') }} # make "all-green" pass even if pre-release job fails
steps:
- - uses: actions/checkout@v5
+ - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
with:
filter: blob:none
fetch-depth: 0
+ persist-credentials: false
- name: Install uv
- uses: astral-sh/setup-uv@v7
+ uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
with:
python-version: ${{ matrix.env.python }}
- name: create hatch environment
run: uvx hatch env create ${{ matrix.env.name }}
+ - name: list all all installed package versions
+ run: uvx hatch run ${{ matrix.env.name }}:uv pip list
- name: run tests using hatch
env:
MPLBACKEND: agg
@@ -78,12 +86,12 @@ jobs:
run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
- name: generate coverage report
run: |
- # See https://coverage.readthedocs.io/en/latest/config.html#run-patch
+ # See https://coverage.readthedocs.io/page/config.html#run-patch
test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
uvx hatch run ${{ matrix.env.name }}:cov-report # report visibly
uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
- name: Upload coverage
- uses: codecov/codecov-action@v5
+ uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
with:
fail_ci_if_error: true
use_oidc: true
@@ -98,6 +106,6 @@ jobs:
- test
runs-on: ubuntu-latest
steps:
- - uses: re-actors/alls-green@release/v1
+ - uses: re-actors/alls-green@05ac9388f0aebcb5727afa17fcccfecd6f8ec5fe # v1.2.2
with:
jobs: ${{ toJSON(needs) }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 27d8a95..3a84322 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,16 +7,16 @@ default_stages:
minimum_pre_commit_version: 2.16.0
repos:
- repo: https://github.com/biomejs/pre-commit
- rev: v2.3.10
+ rev: v2.5.3
hooks:
- id: biome-format
exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
- repo: https://github.com/tox-dev/pyproject-fmt
- rev: v2.11.1
+ rev: v2.25.3
hooks:
- id: pyproject-fmt
- repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.14.10
+ rev: v0.15.21
hooks:
- id: ruff-check
types_or: [python, pyi, jupyter]
@@ -36,3 +36,9 @@ repos:
# Check that there are no merge conflicts (could be generated by template sync)
- id: check-merge-conflict
args: [--assume-in-merge]
+
+ - repo: https://github.com/zizmorcore/zizmor-pre-commit
+ rev: v1.24.1
+ hooks:
+ - id: zizmor
+ args: [--no-progress, --fix]
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 6c28477..67eb948 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,9 +1,9 @@
-# https://docs.readthedocs.io/en/stable/config-file/v2.html
+# https://docs.readthedocs.io/page/config-file/v2.html
version: 2
build:
os: ubuntu-24.04
tools:
- python: "3.13"
+ python: "3.14"
nodejs: latest
jobs:
create_environment:
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
deleted file mode 100644
index 7b4a0cf..0000000
--- a/docs/_templates/autosummary/class.rst
+++ /dev/null
@@ -1,61 +0,0 @@
-{{ fullname | escape | underline}}
-
-.. currentmodule:: {{ module }}
-
-.. add toctree option to make autodoc generate the pages
-
-.. autoclass:: {{ objname }}
-
-{% block attributes %}
-{% if attributes %}
-Attributes table
-~~~~~~~~~~~~~~~~
-
-.. autosummary::
-{% for item in attributes %}
- ~{{ name }}.{{ item }}
-{%- endfor %}
-{% endif %}
-{% endblock %}
-
-{% block methods %}
-{% if methods %}
-Methods table
-~~~~~~~~~~~~~
-
-.. autosummary::
-{% for item in methods %}
- {%- if item != '__init__' %}
- ~{{ name }}.{{ item }}
- {%- endif -%}
-{%- endfor %}
-{% endif %}
-{% endblock %}
-
-{% block attributes_documentation %}
-{% if attributes %}
-Attributes
-~~~~~~~~~~
-
-{% for item in attributes %}
-
-.. autoattribute:: {{ [objname, item] | join(".") }}
-{%- endfor %}
-
-{% endif %}
-{% endblock %}
-
-{% block methods_documentation %}
-{% if methods %}
-Methods
-~~~~~~~
-
-{% for item in methods %}
-{%- if item != '__init__' %}
-
-.. automethod:: {{ [objname, item] | join(".") }}
-{%- endif -%}
-{%- endfor %}
-
-{% endif %}
-{% endblock %}
diff --git a/docs/conf.py b/docs/conf.py
index d67e598..d96395c 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -2,7 +2,7 @@
# This file only contains a selection of the most common options. For a full
# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
+# https://www.sphinx-doc.org/page/usage/configuration.html
# -- Path setup --------------------------------------------------------------
import shutil
@@ -59,9 +59,10 @@
"sphinxcontrib.bibtex",
"sphinxcontrib.katex",
"sphinx_autodoc_typehints",
- "sphinx_tabs.tabs",
+ "sphinx_design",
"IPython.sphinxext.ipython_console_highlighting",
"sphinxext.opengraph",
+ "scverse_misc.sphinx_ext",
*[p.stem for p in (HERE / "extensions").glob("*.py")],
]
@@ -87,6 +88,7 @@
nb_execution_mode = "off"
nb_merge_streams = True
typehints_defaults = "braces"
+always_use_bars_union = True # use `|` instead of `Union` in types even when building with Python ≤3.14
source_suffix = {
".rst": "restructuredtext",
@@ -95,10 +97,9 @@
}
intersphinx_mapping = {
- # TODO: replace `3.13` with `3` once ReadTheDocs supports building with Python 3.14
- "python": ("https://docs.python.org/3.13", None),
- "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
- "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+ "python": ("https://docs.python.org/3", None),
+ "anndata": ("https://anndata.scverse.org/en/stable/", None),
+ "scanpy": ("https://scanpy.scverse.org/en/stable/", None),
"numpy": ("https://numpy.org/doc/stable/", None),
}
diff --git a/docs/contributing.md b/docs/contributing.md
index b172fd1..33afd7d 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -9,7 +9,7 @@ the [scientific Python tutorials][], or the [scanpy developer guide][].
[pyopensci tutorials]: https://www.pyopensci.org/learn.html
[scientific Python tutorials]: https://learn.scientific-python.org/development/tutorials/
-[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
+[scanpy developer guide]: https://scanpy.scverse.org/page/dev/
:::{tip} The *hatch* project manager
@@ -33,8 +33,9 @@ it is still possible to use different tools to manage dependencies, such as `uv`
In addition to the packages needed to _use_ this package,
you need additional python packages to [run tests](#writing-tests) and [build the documentation](#docs-building).
-:::::{tabs}
-::::{group-tab} Hatch
+:::::{tab-set}
+::::{tab-item} Hatch
+:sync: hatch
On the command line, you typically interact with hatch through its command line interface (CLI).
Running one of the following commands will automatically resolve the environments for testing and
@@ -45,11 +46,21 @@ hatch test # defined in the table [tool.hatch.envs.hatch-test] in pyproject.tom
hatch run docs:build # defined in the table [tool.hatch.envs.docs]
```
-When using an IDE such as VS Code,
-you’ll have to point the editor at the paths to the virtual environments manually.
-The environment you typically want to use as your main development environment is the `hatch-test`
-environment with the latest Python version.
+### VS Code
+If you are using VS code, install the [hatch-code][] extension.
+Additionally, make sure that the `vscode-python-environments` extension is installed (should be by default)
+and `"python.useEnvironmentsExtension": true` is activated in your `settings.json`.
+
+Next, open the "Python Environment Managers" sidebar.
+You can do so by opening the command palette (Ctrl+Shift+P) and searching for `Python: Focus on Environment Managers View`.
+It will show a collapsible list where you can expand "Hatch"
+and activate an environment by clicking on the checkmark next to it.
+As the main development environment, we recommend to use `hatch-test` with the latest supported Python version.
+
+### Other IDEs
+
+For other IDEs, you’ll have to point the editor at the paths to the virtual environments manually.
To get a list of all environments for your projects, run
```bash
@@ -62,7 +73,7 @@ This will list “Standalone” environments and a table of “Matrix” environ
+------------+---------+--------------------------+----------+---------------------------------+-------------+
| Name | Type | Envs | Features | Dependencies | Scripts |
+------------+---------+--------------------------+----------+---------------------------------+-------------+
-| hatch-test | virtual | hatch-test.py3.11-stable | dev | coverage-enable-subprocess==1.0 | cov-combine |
+| hatch-test | virtual | hatch-test.py3.12-stable | dev | coverage-enable-subprocess==1.0 | cov-combine |
| | | hatch-test.py3.14-stable | test | coverage[toml]~=7.4 | cov-report |
| | | hatch-test.py3.14-pre | | pytest-mock~=3.12 | run |
| | | | | pytest-randomly~=3.15 | run-cov |
@@ -73,6 +84,7 @@ This will list “Standalone” environments and a table of “Matrix” environ
```
From the `Envs` column, select the environment name you want to use for development.
+As the main development environment, we recommend to use `hatch-test` with the latest supported Python version.
In this example, it would be `hatch-test.py3.14-stable`.
Next, create the environment with
@@ -87,14 +99,13 @@ Then, obtain the path to the environment using
hatch env find hatch-test.py3.14-stable
```
-In case you are using VScode, now open the command palette (Ctrl+Shift+P) and search for `Python: Select Interpreter`.
-Choose `Enter Interpreter Path` and paste the path to the virtual environment from above.
+and manually point it to the python binary.
-In this future, this may become easier through a hatch vscode extension.
::::
-::::{group-tab} uv
+::::{tab-item} uv
+:sync: uv
A popular choice for managing virtual environments is [uv][].
The main disadvantage compared to hatch is that it supports only a single environment per project at a time,
@@ -103,7 +114,7 @@ This can have undesired side-effects,
such as requiring to install a lower version of a library your project depends on,
only because an outdated sphinx plugin pins an older version.
-To initalize a virtual environment in the `.venv` directory of your project, simply run
+To initialize a virtual environment in the `.venv` directory of your project, simply run
```bash
uv sync --all-extras
@@ -113,7 +124,8 @@ The `.venv` directory is typically automatically discovered by IDEs such as VS C
::::
-::::{group-tab} Pip
+::::{tab-item} Pip
+:sync: pip
Pip is nowadays mostly superseded by environment manager such as [hatch][].
However, for the sake of completeness, and since it’s ubiquitously available,
@@ -131,24 +143,26 @@ The `.venv` directory is typically automatically discovered by IDEs such as VS C
:::::
[hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+[hatch-code]: https://marketplace.visualstudio.com/items?itemName=PyPA.hatch
[uv]: https://docs.astral.sh/uv/
## Code-style
-This package uses [pre-commit][] to enforce consistent code-styles.
-On every commit, pre-commit checks will either automatically fix issues with the code, or raise an error message.
+This package uses [pre-commit][]-style hooks to enforce consistent code-styles.
+We recommend running them with [prek][], a fast, drop-in replacement for `pre-commit` that reads the same `.pre-commit-config.yaml`.
+On every commit, the checks will either automatically fix issues with the code, or raise an error message.
-To enable pre-commit locally, simply run
+To enable the checks locally, install [prek][] (e.g. with `uv tool install prek`) and run
```bash
-pre-commit install
+prek install
```
in the root of the repository.
-Pre-commit will automatically download all dependencies when it is run for the first time.
+prek will automatically download all dependencies when it is run for the first time.
Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub.
-If you didn’t run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
+If you didn’t run the checks before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
@@ -157,12 +171,13 @@ git pull --rebase
```
to integrate the changes into yours.
-While the [pre-commit.ci][] is useful, we strongly encourage installing and running pre-commit locally first to understand its usage.
+While the [pre-commit.ci][] is useful, we strongly encourage installing and running the checks locally first to understand their usage.
Finally, most editors have an _autoformat on save_ feature.
Consider enabling this option for [ruff][ruff-editors] and [biome][biome-editors].
[pre-commit]: https://pre-commit.com/
+[prek]: https://prek.j178.dev/
[pre-commit.ci]: https://pre-commit.ci/
[ruff-editors]: https://docs.astral.sh/ruff/integrations/
[biome-editors]: https://biomejs.dev/guides/integrate-in-editor/
@@ -175,17 +190,14 @@ This package uses [pytest][] for automated testing.
Please write {doc}`scanpy:dev/testing` for every function added to the package.
Most IDEs integrate with pytest and provide a GUI to run tests.
-Just point yours to one of the environments returned by
-
-```bash
-hatch env create hatch-test # create test environments for all supported versions
-hatch env find hatch-test # list all possible test environment paths
-```
+If you set up your virtual environments as described in [installing dev dependencies](#installing-dev-dependencies),
+test cases should be automatically discovered by your IDE.
Alternatively, you can run all tests from the command line by executing
-:::::{tabs}
-::::{group-tab} Hatch
+:::::{tab-set}
+::::{tab-item} Hatch
+:sync: hatch
```bash
hatch test # test with the highest supported Python version
@@ -195,7 +207,8 @@ hatch test --all # test with all supported Python versions
::::
-::::{group-tab} uv
+::::{tab-item} uv
+:sync: uv
```bash
uv run pytest
@@ -203,7 +216,8 @@ uv run pytest
::::
-::::{group-tab} Pip
+::::{tab-item} Pip
+:sync: pip
```bash
source .venv/bin/activate
@@ -268,11 +282,11 @@ This project uses [sphinx][] with the following features:
See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own.
-[sphinx]: https://www.sphinx-doc.org/en/master/
-[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
-[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
-[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
-[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
+[sphinx]: https://www.sphinx-doc.org/
+[myst]: https://myst-parser.readthedocs.io/page/intro.html
+[myst-nb]: https://myst-nb.readthedocs.io/
+[numpydoc-napoleon]: https://www.sphinx-doc.org/page/usage/extensions/napoleon.html
+[numpydoc]: https://numpydoc.readthedocs.io/page/format.html
[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
### Tutorials with myst-nb and jupyter notebooks
@@ -297,8 +311,9 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu
### Building the docs locally
-:::::{tabs}
-::::{group-tab} Hatch
+:::::{tab-set}
+::::{tab-item} Hatch
+:sync: hatch
```bash
hatch run docs:build
@@ -307,7 +322,8 @@ hatch run docs:open
::::
-::::{group-tab} uv
+::::{tab-item} uv
+:sync: uv
```bash
cd docs
@@ -317,7 +333,8 @@ uv run sphinx-build -M html . _build -W
::::
-::::{group-tab} Pip
+::::{tab-item} Pip
+:sync: pip
```bash
source .venv/bin/activate
diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
deleted file mode 100644
index 0fbffef..0000000
--- a/docs/extensions/typed_returns.py
+++ /dev/null
@@ -1,32 +0,0 @@
-# code from https://github.com/theislab/scanpy/blob/master/docs/extensions/typed_returns.py
-# with some minor adjustment
-from __future__ import annotations
-
-import re
-from collections.abc import Generator, Iterable
-
-from sphinx.application import Sphinx
-from sphinx.ext.napoleon import NumpyDocstring
-
-
-def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
- for line in lines:
- if m := re.fullmatch(r"(?P\w+)\s+:\s+(?P[\w.]+)", line):
- yield f"-{m['param']} (:class:`~{m['type']}`)"
- else:
- yield line
-
-
-def _parse_returns_section(self: NumpyDocstring, section: str) -> list[str]:
- lines_raw = self._dedent(self._consume_to_next_section())
- if lines_raw[0] == ":":
- del lines_raw[0]
- lines = self._format_block(":returns: ", list(_process_return(lines_raw)))
- if lines and lines[-1]:
- lines.append("")
- return lines
-
-
-def setup(app: Sphinx):
- """Set app."""
- NumpyDocstring._parse_returns_section = _parse_returns_section
diff --git a/pyproject.toml b/pyproject.toml
index ea3dc5e..34480f0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,10 +14,9 @@ maintainers = [
authors = [
{ name = "Lorenz Rumberger" },
]
-requires-python = ">=3.11"
+requires-python = ">=3.12"
classifiers = [
"Programming Language :: Python :: 3 :: Only",
- "Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Programming Language :: Python :: 3.14",
@@ -34,7 +33,7 @@ urls.Source = "https://github.com/angelolab/Nimbus-Inference"
[dependency-groups]
dev = [
- "pre-commit",
+ "prek",
"twine>=4.0.2",
]
test = [
@@ -47,53 +46,42 @@ doc = [
"ipython",
"myst-nb>=1.1",
"pandas",
+ "scverse-misc[sphinx]>=0.1.2",
"sphinx>=8.1",
"sphinx-autodoc-typehints",
"sphinx-book-theme>=1",
"sphinx-copybutton",
- "sphinx-tabs",
+ "sphinx-design",
"sphinxcontrib-bibtex>=1",
"sphinxcontrib-katex",
"sphinxext-opengraph",
]
-[tool.hatch.envs.default]
-installer = "uv"
-dependency-groups = [ "dev" ]
-
-[tool.hatch.envs.docs]
-dependency-groups = [ "doc" ]
-scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
-scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
-scripts.clean = "git clean -fdX -- {args:docs}"
-
-# Test the lowest and highest supported Python versions with normal deps
-[[tool.hatch.envs.hatch-test.matrix]]
-deps = [ "stable" ]
-python = [ "3.11", "3.14" ]
-
-# Test the newest supported Python version also with pre-release deps
-[[tool.hatch.envs.hatch-test.matrix]]
-deps = [ "pre" ]
-python = [ "3.14" ]
-
-[tool.hatch.envs.hatch-test]
-dependency-groups = [ "dev", "test" ]
-
-[tool.hatch.envs.hatch-test.overrides]
+[tool.hatch]
+envs.default.installer = "uv"
+envs.default.dependency-groups = [ "dev" ]
+envs.docs.scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
+envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
+envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
+envs.docs.dependency-groups = [ "doc" ]
+envs.hatch-test.matrix = [
+ # Test the lowest and highest supported Python versions with normal deps
+ { deps = [ "stable" ], python = [ "3.12", "3.14" ] },
+ # Test the newest supported Python version also with pre-release deps
+ { deps = [ "pre" ], python = [ "3.14" ] },
+]
# If the matrix variable `deps` is set to "pre",
# set the environment variable `UV_PRERELEASE` to "allow".
-matrix.deps.env-vars = [
- { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
+envs.hatch-test.overrides.matrix.deps.env-vars = [
+ { value = "allow", key = "UV_PRERELEASE", if = [ "pre" ] },
]
+envs.hatch-test.dependency-groups = [ "dev", "test" ]
[tool.ruff]
line-length = 120
src = [ "src" ]
extend-include = [ "*.ipynb" ]
-
format.docstring-code-format = true
-
lint.select = [
"B", # flake8-bugbear
"BLE", # flake8-blind-except
@@ -128,21 +116,22 @@ lint.per-file-ignores."tests/*" = [ "D" ]
lint.pydocstyle.convention = "numpy"
[tool.pytest]
-strict = true
-testpaths = [ "tests" ]
addopts = [
"--import-mode=importlib", # allow using test files with same name
]
+strict = true
+testpaths = [ "tests" ]
-[tool.coverage.run]
-source = [ "nimbus_inference" ]
-patch = [ "subprocess" ]
-omit = [
+[tool.coverage]
+run.omit = [
"**/test_*.py",
]
+run.patch = [ "subprocess" ]
+run.source = [ "nimbus_inference" ]
[tool.cruft]
skip = [
+ ".git",
"tests",
"src/**/__init__.py",
"src/**/basic.py",