From f7bea87161982d7af74c780d5f064793254e3aee Mon Sep 17 00:00:00 2001 From: scverse-bot <108668866+scverse-bot@users.noreply.github.com> Date: Wed, 2 Apr 2025 18:18:50 +0000 Subject: [PATCH 1/3] Automated template update to v0.5.0 --- .bumpversion.cfg | 8 - .codecov.yaml | 22 +- .cruft.json | 62 ++-- .editorconfig | 3 + .flake8 | 57 ---- .github/ISSUE_TEMPLATE/bug_report.yml | 169 +++++----- .github/ISSUE_TEMPLATE/config.yml | 6 +- .github/ISSUE_TEMPLATE/feature_request.yml | 14 +- .github/workflows/build.yaml | 46 ++- .github/workflows/release.yaml | 34 ++ .github/workflows/test.yaml | 107 +++--- .gitignore | 12 +- .pre-commit-config.yaml | 116 +++---- .readthedocs.yaml | 22 +- .vscode/extensions.json | 18 + .vscode/launch.json | 33 ++ .vscode/settings.json | 18 + biome.jsonc | 16 + docs/_static/css/custom.css | 4 + docs/_templates/autosummary/class.rst | 12 +- docs/conf.py | 42 ++- docs/contributing.md | 214 ++++++++++++ docs/developer_docs.md | 370 --------------------- docs/extensions/typed_returns.py | 19 +- docs/make.bat | 35 -- pyproject.toml | 181 +++++----- 26 files changed, 767 insertions(+), 873 deletions(-) delete mode 100644 .bumpversion.cfg delete mode 100644 .flake8 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 create mode 100644 docs/_static/css/custom.css create mode 100644 docs/contributing.md delete mode 100644 docs/developer_docs.md delete mode 100644 docs/make.bat diff --git a/.bumpversion.cfg b/.bumpversion.cfg deleted file mode 100644 index fdba9e4..0000000 --- a/.bumpversion.cfg +++ /dev/null @@ -1,8 +0,0 @@ -[bumpversion] -current_version = 0.0.1 -tag = True -commit = True - -[bumpversion:file:./pyproject.toml] -search = version = "{current_version}" -replace = version = "{new_version}" diff --git a/.codecov.yaml b/.codecov.yaml index 829e56c..d0c0e29 100644 --- a/.codecov.yaml +++ b/.codecov.yaml @@ -1,17 +1,17 @@ # Based on pydata/xarray codecov: - require_ci_to_pass: no + require_ci_to_pass: no coverage: - status: - project: - default: - # Require 1% coverage, i.e., always succeed - target: 1 - patch: false - changes: false + status: + project: + default: + # Require 1% coverage, i.e., always succeed + target: 1 + patch: false + changes: false comment: - layout: diff, flags, files - behavior: once - require_base: no + layout: diff, flags, files + behavior: once + require_base: no diff --git a/.cruft.json b/.cruft.json index b10b394..68b131e 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,23 +1,43 @@ { - "template": "https://github.com/scverse/cookiecutter-scverse", - "commit": "f19ba436fd40fa52382687a6a1030b1507c379fc", - "checkout": null, - "context": { - "cookiecutter": { - "project_name": "cellcharter", - "package_name": "cellcharter", - "project_description": "A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.", - "author_full_name": "Marco Varrone", - "author_email": "marco.varrone@unil.ch", - "github_user": "marcovarrone", - "project_repo": "https://github.com/marcovarrone/cellcharter", - "license": "BSD 3-Clause License", - "_copy_without_render": [ - ".github/workflows/**.yaml", - "docs/_templates/autosummary/**.rst" - ], - "_template": "https://github.com/scverse/cookiecutter-scverse" - } - }, - "directory": null + "template": "https://github.com/scverse/cookiecutter-scverse", + "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1", + "checkout": "v0.5.0", + "context": { + "cookiecutter": { + "project_name": "cellcharter", + "package_name": "cellcharter", + "project_description": "A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.", + "author_full_name": "Marco Varrone", + "author_email": "marco.varrone@unil.ch", + "github_user": "marcovarrone", + "github_repo": "cellcharter", + "license": "BSD 3-Clause License", + "ide_integration": true, + "_copy_without_render": [ + ".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", + "_commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1" + } + }, + "directory": null } diff --git a/.editorconfig b/.editorconfig index 2fe0ce0..66678e3 100644 --- a/.editorconfig +++ b/.editorconfig @@ -8,5 +8,8 @@ charset = utf-8 trim_trailing_whitespace = true insert_final_newline = true +[{*.{yml,yaml,toml},.cruft.json}] +indent_size = 2 + [Makefile] indent_style = tab diff --git a/.flake8 b/.flake8 deleted file mode 100644 index 10cfc5a..0000000 --- a/.flake8 +++ /dev/null @@ -1,57 +0,0 @@ -# Can't yet be moved to the pyproject.toml due to https://github.com/PyCQA/flake8/issues/234 -[flake8] -max-line-length = 120 -ignore = - # line break before a binary operator -> black does not adhere to PEP8 - W503 - # line break occured after a binary operator -> black does not adhere to PEP8 - W504 - # line too long -> we accept long comment lines; black gets rid of long code lines - E501 - # whitespace before : -> black does not adhere to PEP8 - E203 - # line break before binary operator -> black does not adhere to PEP8 - W503 - # missing whitespace after ,', ';', or ':' -> black does not adhere to PEP8 - E231 - # continuation line over-indented for hanging indent -> black does not adhere to PEP8 - E126 - # too many leading '#' for block comment -> this is fine for indicating sections - E262 - # 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 - # Missing docstring in magic method - D105 - # format string does contain unindexed parameters - P101 - # 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 -exclude = .git,__pycache__,build,docs/_build,dist -per-file-ignores = - tests/*: D - */__init__.py: F401 -rst-roles = - class, - func, - ref, - cite:p, - cite:t, -rst-directives = - envvar, - exception, -rst-substitutions = - version, -extend-ignore = - RST307, diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 9dfd4ac..3ca1ccb 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -2,88 +2,93 @@ name: Bug report description: Report something that is broken or incorrect labels: bug body: - - type: markdown - attributes: - value: | - **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) - 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 procecure. - * 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. + - type: markdown + attributes: + value: | + **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) + 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. - - type: textarea - id: report - attributes: - label: Report - description: A clear and concise description of what the bug is. - validations: - required: true + - type: textarea + id: report + attributes: + label: Report + description: A clear and concise description of what the bug is. + validations: + required: true - - type: textarea - id: versions - attributes: - label: Version information - description: | - Please paste below the output of + - type: textarea + id: versions + attributes: + label: Versions + description: | + Which version of packages. - ```python - import session_info - session_info.show(html=False, dependencies=True) - ``` - 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 + 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_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"]) + ``` + render: python + placeholder: | + 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/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index 5cad625..5b62547 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -1,5 +1,5 @@ blank_issues_enabled: false contact_links: - - name: Scverse Community Forum - url: https://discourse.scverse.org/ - about: If you have questions about “How to do X”, please ask them here. + - name: Scverse Community Forum + url: https://discourse.scverse.org/ + about: If you have questions about “How to do X”, please ask them here. diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml index 9e5fdf4..63bf4a7 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.yml +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -2,10 +2,10 @@ name: Feature request description: Propose a new feature for cellcharter labels: enhancement body: - - type: textarea - id: description - attributes: - label: Description of feature - description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered. - validations: - required: true + - type: textarea + id: description + attributes: + label: Description of feature + description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered. + validations: + required: true diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 0242943..83e01a1 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -1,23 +1,33 @@ name: Check Build on: - push: - branches: [main] - pull_request: - branches: [main] + push: + branches: [main] + pull_request: + branches: [main] + +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@v2 - - name: Set up Python 3.10 - uses: actions/setup-python@v2 - with: - python-version: "3.10" - - name: Install build dependencies - run: python -m pip install --upgrade pip wheel twine build - - name: Build package - run: python -m build - - name: Check package - run: twine check --strict dist/*.whl + package: + runs-on: ubuntu-latest + 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: 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..9ade4b5 --- /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/cellcharter + 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 2f0ffd7..d5cfb2a 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -1,62 +1,59 @@ name: Test on: - push: - branches: [main] - pull_request: - branches: [main] + 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} jobs: - test: - runs-on: ${{ matrix.os }} - defaults: - run: - shell: bash -e {0} # -e to fail on error - - strategy: - fail-fast: false - matrix: - python: ["3.8", "3.10"] - os: [ubuntu-latest] + test: + runs-on: ${{ matrix.os }} + + 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 }} + 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: run tests using hatch env: - OS: ${{ matrix.os }} - PYTHON: ${{ matrix.python }} - - steps: - - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python }} - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python }} - - - name: Get pip cache dir - id: pip-cache-dir - run: | - echo "::set-output name=dir::$(pip cache dir)" - - name: Restore pip cache - uses: actions/cache@v2 - with: - path: ${{ steps.pip-cache-dir.outputs.dir }} - key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }} - restore-keys: | - pip-${{ runner.os }}-${{ env.pythonLocation }}- - - name: Install test dependencies - run: | - python -m pip install --upgrade pip wheel - pip install codecov - - name: Install dependencies - run: | - pip install ".[dev,test]" - - name: Test - env: - MPLBACKEND: agg - PLATFORM: ${{ matrix.os }} - DISPLAY: :42 - run: | - pytest -v --cov --color=yes - - name: Upload coverage - env: - CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }} - run: | - codecov --required --flags=unittests + 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 7bb0bd5..31e10b3 100644 --- a/.gitignore +++ b/.gitignore @@ -1,24 +1,20 @@ # Temp files .DS_Store *~ +buck-out/ # Compiled files +.venv/ __pycache__/ +.*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 59ef329..0fcce11 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,79 +1,47 @@ fail_fast: false default_language_version: - python: python3 + python: python3 default_stages: - - commit - - push + - pre-commit + - pre-push minimum_pre_commit_version: 2.16.0 repos: - - repo: https://github.com/psf/black - rev: 22.10.0 - hooks: - - id: black - - repo: https://github.com/pre-commit/mirrors-prettier - rev: v3.0.0-alpha.4 - hooks: - - id: prettier - - repo: https://github.com/asottile/blacken-docs - rev: v1.12.1 - hooks: - - id: blacken-docs - - repo: https://github.com/PyCQA/isort - rev: 5.10.1 - hooks: - - id: isort - - repo: https://github.com/asottile/yesqa - rev: v1.4.0 - hooks: - - id: yesqa - additional_dependencies: - - flake8-tidy-imports - - flake8-docstrings - - flake8-rst-docstrings - - flake8-comprehensions - - flake8-bugbear - - flake8-blind-except - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.3.0 - hooks: - - id: detect-private-key - - id: check-ast - - id: end-of-file-fixer - - id: mixed-line-ending - args: [--fix=lf] - - id: trailing-whitespace - - id: check-case-conflict - - repo: https://github.com/myint/autoflake - rev: v1.7.7 - hooks: - - id: autoflake - args: - - --in-place - - --remove-all-unused-imports - - --remove-unused-variable - - --ignore-init-module-imports - - repo: https://github.com/PyCQA/flake8 - rev: 5.0.4 - hooks: - - id: flake8 - additional_dependencies: - - flake8-tidy-imports - - flake8-docstrings - - flake8-rst-docstrings - - flake8-comprehensions - - flake8-bugbear - - flake8-blind-except - - repo: https://github.com/asottile/pyupgrade - rev: v3.2.0 - hooks: - - id: pyupgrade - args: [--py3-plus, --py38-plus, --keep-runtime-typing] - - 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$' + - repo: https://github.com/biomejs/pre-commit + rev: v1.9.4 + 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 + hooks: + - id: pyproject-fmt + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.11.2 + hooks: + - id: ruff + 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 + hooks: + - id: detect-private-key + - id: check-ast + - id: end-of-file-fixer + - id: mixed-line-ending + args: [--fix=lf] + - id: trailing-whitespace + - id: check-case-conflict + # 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$' diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 9e5d5fa..69897c3 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,16 +1,16 @@ # https://docs.readthedocs.io/en/stable/config-file/v2.html version: 2 build: - os: ubuntu-20.04 - tools: - python: "3.10" + os: ubuntu-20.04 + tools: + python: "3.10" sphinx: - configuration: docs/conf.py - # disable this for more lenient docs builds - fail_on_warning: true + configuration: docs/conf.py + # disable this for more lenient docs builds + fail_on_warning: true python: - install: - - method: pip - path: . - extra_requirements: - - doc + install: + - method: pip + path: . + extra_requirements: + - doc diff --git a/.vscode/extensions.json b/.vscode/extensions.json new file mode 100644 index 0000000..caaeb4f --- /dev/null +++ b/.vscode/extensions.json @@ -0,0 +1,18 @@ +{ + "recommendations": [ + // GitHub integration + "github.vscode-github-actions", + "github.vscode-pull-request-github", + // Language support + "ms-python.python", + "ms-python.vscode-pylance", + "ms-toolsai.jupyter", + "tamasfe.even-better-toml", + // Dependency management + "ninoseki.vscode-mogami", + // Linting and formatting + "editorconfig.editorconfig", + "charliermarsh.ruff", + "biomejs.biome", + ], +} diff --git a/.vscode/launch.json b/.vscode/launch.json new file mode 100644 index 0000000..36d1874 --- /dev/null +++ b/.vscode/launch.json @@ -0,0 +1,33 @@ +{ + // Use IntelliSense to learn about possible attributes. + // Hover to view descriptions of existing attributes. + // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 + "version": "0.2.0", + "configurations": [ + { + "name": "Python: Build Documentation", + "type": "debugpy", + "request": "launch", + "module": "sphinx", + "args": ["-M", "html", ".", "_build"], + "cwd": "${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/_static/css/custom.css b/docs/_static/css/custom.css new file mode 100644 index 0000000..b8c8d47 --- /dev/null +++ b/docs/_static/css/custom.css @@ -0,0 +1,4 @@ +/* Reduce the font size in data frames - See https://github.com/scverse/cookiecutter-scverse/issues/193 */ +div.cell_output table.dataframe { + font-size: 0.8em; +} diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst index 49f45ed..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 %} @@ -35,11 +35,9 @@ Methods table {% block attributes_documentation %} {% if attributes %} Attributes -~~~~~~~~~~~ +~~~~~~~~~~ {% for item in attributes %} -{{ item }} -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. autoattribute:: {{ [objname, item] | join(".") }} {%- endfor %} @@ -54,8 +52,6 @@ Methods {% for item in methods %} {%- if item != '__init__' %} -{{ item }} -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automethod:: {{ [objname, item] | join(".") }} {%- endif -%} diff --git a/docs/conf.py b/docs/conf.py index c8b5f86..d2323ca 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 @@ -16,12 +16,15 @@ # -- Project information ----------------------------------------------------- +# 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("cellcharter") project_name = info["Name"] author = info["Author"] copyright = f"{datetime.now():%Y}, {author}." version = info["Version"] -repository_url = f"https://github.com/marcovarrone/{project_name}" +urls = dict(pu.split(", ") for pu in info.get_all("Project-URL")) +repository_url = urls["Source"] # The full version, including alpha/beta/rc tags release = info["Version"] @@ -33,10 +36,10 @@ html_context = { "display_github": True, # Integrate GitHub - "github_user": "marcovarrone", # 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": "marcovarrone", + "github_repo": project_name, + "github_version": "main", + "conf_py_path": "/docs/", } # -- General configuration --------------------------------------------------- @@ -52,7 +55,10 @@ "sphinx.ext.napoleon", "sphinxcontrib.bibtex", "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")], ] @@ -64,7 +70,7 @@ napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True -myst_heading_anchors = 3 # create anchors for h1-h3 +myst_heading_anchors = 6 # create anchors for h1-h6 myst_enable_extensions = [ "amsmath", "colon_fence", @@ -86,11 +92,12 @@ } 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), } - # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. @@ -104,11 +111,15 @@ # html_theme = "sphinx_book_theme" html_static_path = ["_static"] +html_css_files = ["css/custom.css"] + html_title = project_name html_theme_options = { "repository_url": repository_url, "use_repository_button": True, + "path_to_docs": "docs/", + "navigation_with_keys": False, } pygments_style = "default" @@ -118,18 +129,3 @@ # you can add an exception to this list. # ("py:class", "igraph.Graph"), ] - - -def setup(app): - """App setup hook.""" - app.add_config_value( - "recommonmark_config", - { - "auto_toc_tree_section": "Contents", - "enable_auto_toc_tree": True, - "enable_math": True, - "enable_inline_math": False, - "enable_eval_rst": True, - }, - True, - ) diff --git a/docs/contributing.md b/docs/contributing.md new file mode 100644 index 0000000..10de3b3 --- /dev/null +++ b/docs/contributing.md @@ -0,0 +1,214 @@ +# 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. + +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](#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 cellcharter +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. +On every commit, pre-commit checks will either automatically fix issues with the code, or raise an error message. + +To enable pre-commit locally, simply run + +```bash +pre-commit install +``` + +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 pre-commit.ci added a commit on a branch you still have been working on locally, simply use + +```bash +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 [biome][biome-editors]. + +[pre-commit]: https://pre-commit.com/ +[pre-commit.ci]: https://pre-commit.ci/ +[ruff-editors]: https://docs.astral.sh/ruff/integrations/ +[biome-editors]: https://biomejs.dev/guides/integrate-in-editor/ + +(writing-tests)= + +## Writing tests + +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 +``` + +:::: + +::::{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. + +## 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 + +> 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. +> +> 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][]. + +[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: + +- 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. + +[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 + +The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][]. +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][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` + +(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 +(xdg-)open _build/html/index.html +``` + +:::: +::::: diff --git a/docs/developer_docs.md b/docs/developer_docs.md deleted file mode 100644 index b36437d..0000000 --- a/docs/developer_docs.md +++ /dev/null @@ -1,370 +0,0 @@ -# Developer documentation - -Welcome to the developer guidelines! This document is split into two parts: - -1. The [repository setup](#setting-up-the-repository). This section is relevant primarily for the repository maintainer and shows how to connect - continuous integration services and documents initial set-up of the repository. -2. The [contributor guide](#contributing-guide). It contains information relevant to all developers who want to make a contribution. - -## Setting up the repository - -### Documentation on _readthedocs_ - -We recommend using [readthedocs.org][] (RTD) to build and host the documentation for your project. -To enable readthedocs, head over to [their webiste][readthedocs.org] and sign in with your GitHub account. -On the RTD dashboard choose "Import a Project" and follow the instructions to add your repository. - -- Make sure to choose the correct name of the default branch. On GitHub, the default name of the default branch has - recently changed from `master` to `main`. -- We recommend to enable documentation builds for pull requests (PRs). This ensures that a PR doesn't introduce changes - that break the documentation. To do so, got to `Admin -> Advanced Settings`, check the - `Build pull requests for this projects` option, and click `Save`. For more information, please refer to - the [official RTD documentation](https://docs.readthedocs.io/en/stable/pull-requests.html). -- If you find the RTD builds are failing, you can disable the `fail_on_warning` option in `.readthedocs.yaml`. - -### Coverage tests with _Codecov_ - -Coverage tells what fraction of the code is "covered" by unit tests, thereby encouraging contributors to -[write tests](#writing-tests). -To enable coverage checks, head over to [codecov][] and sign in with your GitHub account. -You'll find more information in "getting started" section of the [codecov docs][]. - -In brief, you need to: - -1. Generate a Codecov Token by clicking _setup repo_ in the codecov dashboard. -2. Go to the _Settings_ of your newly created repository on GitHub. -3. Go to _Security > Secrets > Actions_. -4. Create new repository secret with name `CODECOV_TOKEN` and paste the token generated by codecov -5. Go back to Github Actions page an re-run previously failed jobs. - -### Pre-commit checks - -[Pre-commit][] checks are fast programs that -check code for errors, inconsistencies and code styles, before the code -is committed. - -We recommend setting up [pre-commit.ci][] to enforce consistency checks on every commit -and pull-request. - -To do so, head over to [pre-commit.ci][] and click "Sign In With GitHub". Follow -the instructions to enable pre-commit.ci for your account or your organization. You -may choose to enable the service for an entire organization or on a per-repository basis. - -Once authorized, pre-commit.ci should automatically be activated. - -#### Overview of pre-commit hooks used by the template - -The following pre-commit checks are for code style and format: - -- [black](https://black.readthedocs.io/en/stable/): standard code - formatter in Python. -- [isort](https://pycqa.github.io/isort/): sort module imports into - sections and types. -- [prettier](https://prettier.io/docs/en/index.html): standard code - formatter for non-Python files (e.g. YAML). -- [blacken-docs](https://github.com/asottile/blacken-docs): black on - python code in docs. - -The following pre-commit checks are for errors and inconsistencies: - -- [flake8](https://flake8.pycqa.org/en/latest/): standard check for errors in Python files. - - [flake8-tidy-imports](https://github.com/adamchainz/flake8-tidy-imports): - tidy module imports. - - [flake8-docstrings](https://github.com/PyCQA/flake8-docstrings): - pydocstyle extension of flake8. - - [flake8-rst-docstrings](https://github.com/peterjc/e8-rst-docstrings): - extension of `flake8-docstrings` for `rst` docs. - - [flake8-comprehensions](https://github.com/adamchainz/e8-comprehensions): - write better list/set/dict comprehensions. - - [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear): - find possible bugs and design issues in program. - - [flake8-blind-except](https://github.com/elijahandrews/flake8-blind-except): - checks for blind, catch-all `except` statements. -- [yesqa](https://github.com/asottile/yesqa): - remove unneccesary `# noqa` comments, follows additional dependencies listed above. -- [autoflake](https://github.com/PyCQA/autoflake): - remove unused imports and variables. -- [pre-commit-hooks](https://github.com/pre-commit/pre-commit-hooks): generic pre-commit hooks. - - **detect-private-key**: checks for the existence of private keys. - - **check-ast**: check whether files parse as valid python. - - **end-of-file-fixer**:check files end in a newline and only a newline. - - **mixed-line-ending**: checks mixed line ending. - - **trailing-whitespace**: trims trailing whitespace. - - **check-case-conflict**: check files that would conflict with case-insensitive file systems. -- [pyupgrade](https://github.com/asottile/pyupgrade): - upgrade syntax for newer versions of the language. -- **forbid-to-commit**: Make sure that `*.rej` files cannot be commited. These files are created by the - [automated template sync](#automated-template-sync) if there's a merge conflict and need to be addressed manually. - -#### Notes on pre-commit checks - -- To ignore lint warnigs from **flake8**, see [Ignore certain lint warnings](#ignore-certain-lint-warnings). -- You can add or remove pre-commit checks by simply deleting relevant lines in the `.pre-commit-config.yaml` file. - Some pre-commit checks have additional options that can be specified either in the `pyproject.toml` or tool-specific - config files, such as `.prettierrc.yml` for **prettier** and `.flake8` for **flake8**. - -### API design - -Scverse ecosystem packages should operate on [AnnData][] and/or [MuData][] datastructures and typically use an API -as originally [introduced by scanpy][scanpy-api] with the following submodules: - -- `pp` for preprocessing -- `tl` for tools (that, compared to `pp` generate interpretable output, often associated with a corresponding plotting - function) -- `pl` for plotting functions - -You may add additional submodules as appropriate. While we encourage to follow a scanpy-like API for ecosystem packages, -there may also be good reasons to choose a different approach, e.g. using an object-oriented API. - -[scanpy-api]: https://scanpy.readthedocs.io/en/stable/usage-principles.html - -### Ignore certain lint warnings - -The [pre-commit checks](#pre-commit-checks) include [flake8](https://flake8.pycqa.org/en/latest/) which checks -for errors in Python files, including stylistic errors. - -In some cases it might overshoot and you may have good reasons to ignore certain warnings. - -To ignore an specific error on a per-case basis, you can add a comment `# noqa` to the offending line. You can also -specify the error ID to ignore, with e.g. `# noqa: E731`. Check the [flake8 guide][] for reference. - -Alternatively, you can disable certain error messages for the entire project. To do so, edit the `.flake8` -file in the root of the repository. Add one line per linting code you wish to ignore and don't forget to add a comment. - -```toml -... -# line break before a binary operator -> black does not adhere to PEP8 -W503 -# line break occured after a binary operator -> black does not adhere to PEP8 -W504 -... -``` - -[flake8 guide]: https://flake8.pycqa.org/en/3.1.1/user/ignoring-errors.html - -### Using VCS-based versioning - -By default, the template uses hard-coded version numbers that are set in `pyproject.toml` and [managed with -bump2version](#making-a-release). If you prefer to have your project automatically infer version numbers from git -tags, it is straightforward to switch to vcs-based versioning using [hatch-vcs][]. - -In `pyproject.toml` add the following changes, and you are good to go! - -```diff ---- a/pyproject.toml -+++ b/pyproject.toml -@@ -1,11 +1,11 @@ - [build-system] - build-backend = "hatchling.build" --requires = ["hatchling"] -+requires = ["hatchling", "hatch-vcs"] - - - [project] - name = "cellcharter" --version = "0.3.1dev" -+dynamic = ["version"] - -@@ -60,6 +60,9 @@ -+[tool.hatch.version] -+source = "vcs" -+ - [tool.coverage.run] - source = ["cellcharter"] - omit = [ -``` - -Don't forget to update the [Making a release section](#making-a-release) in this document accordingly, after you are done! - -[hatch-vcs]: https://pypi.org/project/hatch-vcs/ - -## Contributing guide - -Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this repo, 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. - -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][]. - -### 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`: - -```bash -pip install "cellcharter[dev,test,doc]" -``` - -### Code-style - -This template 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. See [pre-commit checks](#pre-commit-checks) for -a full list of checks enabled for this repository. - -To enable pre-commit locally, simply run - -```bash -pre-commit install -``` - -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 pre-commit.ci added a commit on a branch you still have been working on locally, simply use - -```bash -git pull --rebase -``` - -to integrate the changes into yours. - -Finally, most editors have an _autoformat on save_ feature. Consider enabling this option for [black][black-editors] -and [prettier][prettier-editors]. - -[black-editors]: https://black.readthedocs.io/en/stable/integrations/editors.html -[prettier-editors]: https://prettier.io/docs/en/editors.html - -### Writing tests - -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 - -```bash -pytest -``` - -in the root of the repository. Continuous integration will automatically run the tests on all pull requests. - -[scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests - -### Automated template sync - -Automated template sync is enabled by default. This means that every night, a GitHub action runs [cruft][] to check -if a new version of the `scverse-cookiecutter` template got released. If there are any new changes, a pull request -proposing these changes is created automatically. This helps keeping the repository up-to-date with the latest -coding standards. - -It may happen that a template sync results in a merge conflict. If this is the case a `*.ref` file with the -diff is created. You need to manually address these changes and remove the `.rej` file when you are done. -The pull request can only be merged after all `*.rej` files have been removed. - -:::{tip} -The following hints may be useful to work with the template sync: - -- GitHub automatically disables scheduled actions if there has been not activity to the repository for 60 days. - You can re-enable or manually trigger the sync by navigating to `Actions` -> `Sync Template` in your GitHub repository. -- If you want to ignore certain files from the template update, you can add them to the `[tool.cruft]` section in the - `pyproject.toml` file in the root of your repository. More details are described in the - [cruft documentation][cruft-update-project]. -- To disable the sync entirely, simply remove the file `.github/workflows/sync.yaml`. - -::: - -[cruft]: https://cruft.github.io/cruft/ -[cruft-update-project]: https://cruft.github.io/cruft/#updating-a-project - -### Making a release - -#### Updating the version number - -Before making a release, you need to update the version number. 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. -> -> Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format. - -We use [bump2version][] to automatically update the version number in all places and automatically create a git tag. -Run one of the following commands in the root of the repository - -```bash -bump2version patch -bump2version minor -bump2version major -``` - -Once you are done, run - -``` -git push --tags -``` - -to publish the created tag on GitHub. - -[bump2version]: https://github.com/c4urself/bump2version - -#### Upload on PyPI - -Please follow the [Python packaging tutorial][]. - -It is possible to automate this with GitHub actions, see also [this feature request][pypi-feature-request] -in the cookiecutter-scverse template. - -[python packaging tutorial]: https://packaging.python.org/en/latest/tutorials/packaging-projects/#generating-distribution-archives -[pypi-feature-request]: https://github.com/scverse/cookiecutter-scverse/issues/88 - -### Writing documentation - -Please write documentation for your package. 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 - -See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information -on how to write documentation. - -### Tutorials with myst-nb and jupyter notebooks - -The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][]. -Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells. -It is your reponsibility 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. - -#### 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` - -#### Building the docs locally - -```bash -cd docs -make html -open _build/html/index.html -``` - - - -[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html -[codecov]: https://about.codecov.io/sign-up/ -[codecov docs]: https://docs.codecov.com/docs -[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 diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py index 9447813..0fbffef 100644 --- a/docs/extensions/typed_returns.py +++ b/docs/extensions/typed_returns.py @@ -1,24 +1,27 @@ # 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): +def _process_return(lines: Iterable[str]) -> Generator[str, None, None]: for line in lines: - m = re.fullmatch(r"(?P\w+)\s+:\s+(?P[\w.]+)", line) - if m: - # Once this is in scanpydoc, we can use the fancy hover stuff - yield f'-{m["param"]} (:class:`~{m["type"]}`)' + 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, section): - lines_raw = list(_process_return(self._dedent(self._consume_to_next_section()))) - lines = self._format_block(":returns: ", lines_raw) +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 diff --git a/docs/make.bat b/docs/make.bat deleted file mode 100644 index 954237b..0000000 --- a/docs/make.bat +++ /dev/null @@ -1,35 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=. -set BUILDDIR=_build - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.https://www.sphinx-doc.org/ - exit /b 1 -) - -if "%1" == "" goto help - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% - -:end -popd diff --git a/pyproject.toml b/pyproject.toml index 2b184d9..7499634 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,102 +1,135 @@ [build-system] build-backend = "hatchling.build" -requires = ["hatchling"] - +requires = [ "hatchling" ] [project] name = "cellcharter" version = "0.0.1" description = "A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data." readme = "README.md" -requires-python = ">=3.8" -license = {file = "LICENSE"} +license = { file = "LICENSE" } +maintainers = [ + { name = "Marco Varrone", email = "marco.varrone@unil.ch" }, +] authors = [ - {name = "Marco Varrone"}, + { name = "Marco Varrone" }, ] -maintainers = [ - {name = "Marco Varrone", email = "marco.varrone@unil.ch"}, +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://cellcharter.readthedocs.io/" -urls.Source = "https://github.com/marcovarrone/cellcharter" -urls.Home-page = "https://github.com/marcovarrone/cellcharter" 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 = [ - # CLI for bumping the version number - "bump2version", - "pre-commit" +optional-dependencies.dev = [ + "pre-commit", + "twine>=4.0.2", ] -doc = [ - "sphinx>=4", - "sphinx-book-theme>=0.3.3", - "myst-nb", - "sphinxcontrib-bibtex>=1.0.0", - "sphinx-autodoc-typehints", - # For notebooks - "ipykernel", - "sphinx-copybutton", +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", - "pytest-cov", +optional-dependencies.test = [ + "coverage", + "pytest", ] +# https://docs.pypi.org/project_metadata/#project-urls +urls.Documentation = "https://cellcharter.readthedocs.io/" +urls.Homepage = "https://github.com/marcovarrone/cellcharter" +urls.Source = "https://github.com/marcovarrone/cellcharter" -[tool.coverage.run] -source = ["cellcharter"] -omit = [ - "**/test_*.py", +[tool.hatch.envs.default] +installer = "uv" +features = [ "dev" ] + +[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] +line-length = 120 +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 +] +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 ] +lint.per-file-ignores."*/__init__.py" = [ "F401" ] +lint.per-file-ignores."docs/*" = [ "I" ] +lint.per-file-ignores."tests/*" = [ "D" ] +lint.pydocstyle.convention = "numpy" [tool.pytest.ini_options] -testpaths = ["tests"] +testpaths = [ "tests" ] xfail_strict = true addopts = [ - "--import-mode=importlib", # allow using test files with same name + "--import-mode=importlib", # allow using test files with same name ] -[tool.isort] -include_trailing_comma = true -multi_line_output = 3 -profile = "black" -skip_glob = ["docs/*"] - -[tool.black] -line-length = 120 -target-version = ['py38'] -include = '\.pyi?$' -exclude = ''' -( - /( - \.eggs - | \.git - | \.hg - | \.mypy_cache - | \.tox - | \.venv - | _build - | buck-out - | build - | dist - )/ -) -''' - -[tool.jupytext] -formats = "ipynb,md" +[tool.coverage.run] +source = [ "cellcharter" ] +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 bbfe9eb759d404fe86578718cb0c26295164a565 Mon Sep 17 00:00:00 2001 From: scverse-bot <108668866+scverse-bot@users.noreply.github.com> Date: Tue, 30 Sep 2025 06:20:31 +0000 Subject: [PATCH 2/3] 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 68b131e..1b23e1c 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": "cellcharter", @@ -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 10de3b3..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 cellcharter 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 7499634..28e3830 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://cellcharter.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 = [ "cellcharter" ] +patch = [ "subprocess" ] omit = [ "**/test_*.py", ] From bc12e1c0a10bc1c829a591cdafa14582a5935e2a Mon Sep 17 00:00:00 2001 From: scverse-bot <108668866+scverse-bot@users.noreply.github.com> Date: Wed, 24 Dec 2025 09:44:55 +0000 Subject: [PATCH 3/3] 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 1b23e1c..5ced892 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": "cellcharter", @@ -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 63bf4a7..513c7a4 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 cellcharter -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 9ade4b5..40b319d 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 d2323ca..acab477 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("cellcharter") -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": "marcovarrone", - "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 28e3830..e30731b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,55 +14,55 @@ maintainers = [ authors = [ { name = "Marco Varrone" }, ] -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://cellcharter.readthedocs.io/" +urls.Homepage = "https://github.com/marcovarrone/cellcharter" +urls.Source = "https://github.com/marcovarrone/cellcharter" + +[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://cellcharter.readthedocs.io/" -urls.Homepage = "https://github.com/marcovarrone/cellcharter" -urls.Source = "https://github.com/marcovarrone/cellcharter" [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 ]