diff --git a/.cruft.json b/.cruft.json index 29f98c6..c590332 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,7 +1,7 @@ { "template": "https://github.com/scverse/cookiecutter-scverse", - "commit": "f25cfb52557bd87017094a129d403b284b6dbba1", - "checkout": null, + "commit": "87a407a65408d75a949c0b54b19fd287475a56f8", + "checkout": "v0.4.0", "context": { "cookiecutter": { "project_name": "binsparse", @@ -13,9 +13,15 @@ "project_repo": "https://github.com/ivirshup/binsparse", "license": "MIT License", "_copy_without_render": [ - ".github/workflows/**.yaml", + ".github/workflows/build.yaml", + ".github/workflows/test.yaml", "docs/_templates/autosummary/**.rst" ], + "_render_devdocs": false, + "_jinja2_env_vars": { + "lstrip_blocks": true, + "trim_blocks": true + }, "_template": "https://github.com/scverse/cookiecutter-scverse" } }, diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index 9352d04..ebaa612 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -1,30 +1,29 @@ name: Release on: - push: - tags: - - "*.*.*" + release: + types: [published] +# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/ jobs: release: - name: Release + name: Upload release to PyPI runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/binsparse + permissions: + id-token: write # IMPORTANT: this permission is mandatory for trusted publishing steps: - - name: Checkout code - uses: actions/checkout@v3 - - - name: Set up Python 3.10 - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 with: - python-version: "3.10" - - - name: Install hatch - run: pip install hatch - - - name: Build project for distribution - run: hatch build - - - name: Publish a Python distribution to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + filter: blob:none + fetch-depth: 0 + - uses: actions/setup-python@v4 with: - password: ${{ secrets.PYPI_API_TOKEN }} + python-version: "3.x" + cache: "pip" + - run: pip install build + - run: python -m 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 965660e..941e337 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -5,6 +5,8 @@ on: branches: [main] pull_request: branches: [main] + schedule: + - cron: "0 5 1,15 * *" concurrency: group: ${{ github.workflow }}-${{ github.ref }} @@ -54,6 +56,9 @@ jobs: PLATFORM: ${{ matrix.os }} DISPLAY: :42 run: | - pytest -v --cov --color=yes + coverage run -m pytest -v --color=yes + - name: Report coverage + run: | + coverage report - name: Upload coverage uses: codecov/codecov-action@v3 diff --git a/.github/workflows/test.yaml.rej b/.github/workflows/test.yaml.rej new file mode 100644 index 0000000..376646b --- /dev/null +++ b/.github/workflows/test.yaml.rej @@ -0,0 +1,21 @@ +diff a/.github/workflows/test.yaml b/.github/workflows/test.yaml (rejected hunks) +@@ -21,13 +23,16 @@ jobs: + fail-fast: false + matrix: + include: +- - os: ubuntu-latest +- python: "3.9" + - os: ubuntu-latest + python: "3.10" + - os: ubuntu-latest +- python: "3.10" ++ 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 }} diff --git a/.gitignore b/.gitignore index dcdc618..eeec7e2 100644 --- a/.gitignore +++ b/.gitignore @@ -18,6 +18,7 @@ __pycache__/ /.pytest_cache/ /.cache/ /data/ +/node_modules/ # docs /docs/generated/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 989a909..9cacaf6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -39,6 +39,9 @@ repos: 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 diff --git a/.pre-commit-config.yaml.rej b/.pre-commit-config.yaml.rej new file mode 100644 index 0000000..5f9ac18 --- /dev/null +++ b/.pre-commit-config.yaml.rej @@ -0,0 +1,34 @@ +diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml (rejected hunks) +@@ -6,29 +6,18 @@ default_stages: + - push + minimum_pre_commit_version: 2.16.0 + repos: +- - repo: https://github.com/psf/black +- rev: "24.4.2" +- hooks: +- - id: black +- - repo: https://github.com/asottile/blacken-docs +- rev: 1.16.0 +- hooks: +- - id: blacken-docs + - repo: https://github.com/pre-commit/mirrors-prettier + rev: v4.0.0-alpha.8 + hooks: + - id: prettier +- # Newer versions of node don't work on systems that have an older version of GLIBC +- # (in particular Ubuntu 18.04 and Centos 7) +- # EOL of Centos 7 is in 2024-06, we can probably get rid of this then. +- # See https://github.com/scverse/cookiecutter-scverse/issues/143 and +- # https://github.com/jupyterlab/jupyterlab/issues/12675 +- language_version: "17.9.1" + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.4.4 + 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: v4.6.0 + hooks: diff --git a/README.md.rej b/README.md.rej new file mode 100644 index 0000000..8b3fddb --- /dev/null +++ b/README.md.rej @@ -0,0 +1,10 @@ +diff a/README.md b/README.md (rejected hunks) +@@ -17,7 +17,7 @@ Please refer to the [documentation][link-docs]. In particular, the + + ## Installation + +-You need to have Python 3.9 or newer installed on your system. If you don't have ++You need to have Python 3.10 or newer installed on your system. If you don't have + Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge). + + There are several alternative options to install binsparse: 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/conf.py b/docs/conf.py index 3b0cfad..78f40a4 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,5 +1,5 @@ # Configuration file for the Sphinx documentation builder. -# + # This file only contains a selection of the most common options. For a full # list see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html @@ -36,10 +36,10 @@ html_context = { "display_github": True, # Integrate GitHub - "github_user": "ivirshup", # 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": "ivirshup", + "github_repo": "https://github.com/ivirshup/binsparse", + "github_version": "main", + "conf_py_path": "/docs/", } # -- General configuration --------------------------------------------------- @@ -115,12 +115,15 @@ # 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" @@ -131,18 +134,3 @@ # 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 index 36f33b6..37aa3b8 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -1,6 +1,6 @@ # Contributing guide -Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this repo, too. +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. @@ -19,9 +19,8 @@ pip install -e ".[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](template_usage.md#pre-commit-checks) for -a full list of checks enabled for this repository. +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 @@ -43,16 +42,16 @@ 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 [black][black-editors] +Finally, most editors have an _autoformat on save_ feature. Consider enabling this option for [ruff][ruff-editors] and [prettier][prettier-editors]. -[black-editors]: https://black.readthedocs.io/en/stable/integrations/editors.html +[ruff-editors]: https://docs.astral.sh/ruff/integrations/ [prettier-editors]: https://prettier.io/docs/en/editors.html ## Writing tests ```{note} -Remember to first install the package with `pip install '-e[dev,test]'` +Remember to first install the package with `pip install -e '.[dev,test]'` ``` This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added @@ -65,7 +64,17 @@ command line by executing pytest ``` -in the root of the repository. Continuous integration will automatically run the tests on all pull requests. +in the root of the repository. + +### Continuous integration + +Continuous integration will automatically run the tests on all pull requests and test +against the minimum and maximum supported Python version. + +Additionally, there's a CI job that tests against pre-releases of all dependencies +(if there are any). The purpose of this check is to detect incompatibilities +of new package versions early on and gives you time to fix the issue or reach +out to the developers of the dependency before the package is released to a wider audience. [scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests @@ -83,55 +92,8 @@ Before making a release, you need to update the version number in the `pyproject > > Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format. -Once you are done, run - -``` -git push --tags -``` - -to publish the created tag on GitHub. Alternatively, it is possible to create a tag through the Github web interface. For more information, see [managing Github releases][]. This will automatically trigger a Github workflow that creates a release on PyPI. - -### The release Github workflow - -#### Behind the scenes - -This section explains how releases can be created manually purely for educational purposes. Experienced developers may skip this section. -Python packages are not distributed as source code, but as _distributions_. The most common distribution format is the so-called _wheel_. To build a _wheel_, run - -```bash -python -m build -``` - -This command creates a _source archive_ and a _wheel_, which are required for publishing your package to [PyPI][]. These files are created directly in the root of the repository. - -Before uploading them to [PyPI][] you can check that your _distribution_ is valid by running: - -```bash -twine check dist/* -``` - -and finally publishing it with: - -```bash -twine upload dist/* -``` - -Provide your username and password when requested and then go check out your package on [PyPI][]! - -For more information, follow the [Python packaging tutorial][]. - -#### Configuring the Github workflow - -Tags adhering to `"*.*.*"` that are pushed to the `main` branch will trigger the release Github workflow that automatically builds and uploads the Python package to [PyPI][]. -For this to work, the `PYPI_API_TOKEN` Github secret needs to be set to the value of the [PyPI][] token. -See [Creating PyPI tokens][] for instructions on how to create a [PyPI][] token. -Finally, set your `PYPI_API_TOKEN` Github secret equal to the value of the just created [PyPI][] token by following [creating Github secrets][]. - -[creating github secrets]: https://docs.github.com/en/actions/security-guides/encrypted-secrets -[creating pypi tokens]: https://pypi.org/help/#apitoken -[managing github releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository -[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 +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. ## Writing documentation @@ -195,3 +157,4 @@ open _build/html/index.html [numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html [sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints [pypi]: https://pypi.org/ +[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository diff --git a/docs/index.md.rej b/docs/index.md.rej new file mode 100644 index 0000000..14a8d31 --- /dev/null +++ b/docs/index.md.rej @@ -0,0 +1,9 @@ +diff a/docs/index.md b/docs/index.md (rejected hunks) +@@ -8,7 +8,6 @@ + + api.md + changelog.md +-template_usage.md + contributing.md + references.md + diff --git a/pyproject.toml b/pyproject.toml index 5807306..da9b3a4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,12 +67,15 @@ addopts = [ "--import-mode=importlib", # allow using test files with same name ] -[tool.black] -line-length = 120 - [tool.ruff] -src = ["src"] line-length = 120 +src = ["src"] +extend-include = ["*.ipynb"] + +[tool.ruff.format] +docstring-code-format = true + +[tool.ruff.lint] select = [ "F", # Errors detected by Pyflakes "E", # Error detected by Pycodestyle @@ -87,7 +90,7 @@ select = [ "RUF100", # Report unused noqa directives ] ignore = [ - # line too long -> we accept long comment lines; black gets rid of long code lines + # line too long -> we accept long comment lines; formatter gets rid of long code lines "E501", # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient "E731", @@ -101,7 +104,7 @@ ignore = [ "D107", # Errors from function calls in argument defaults. These are fine when the result is immutable. "B008", - # __magic__ methods are are often self-explanatory, allow missing docstrings + # __magic__ methods are often self-explanatory, allow missing docstrings "D105", # first line should end with a period [Bug: doesn't work with single-line docstrings] "D400", @@ -114,10 +117,10 @@ ignore = [ "D213", ] -[tool.ruff.pydocstyle] +[tool.ruff.lint.pydocstyle] convention = "numpy" -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "docs/*" = ["I"] "tests/*" = ["D"] "*/__init__.py" = ["F401"] @@ -130,5 +133,5 @@ skip = [ "docs/changelog.md", "docs/references.bib", "docs/references.md", - "docs/notebooks/example.ipynb" + "docs/notebooks/example.ipynb", ] diff --git a/pyproject.toml.rej b/pyproject.toml.rej new file mode 100644 index 0000000..7350813 --- /dev/null +++ b/pyproject.toml.rej @@ -0,0 +1,47 @@ +diff a/pyproject.toml b/pyproject.toml (rejected hunks) +@@ -7,7 +7,7 @@ name = "binsparse" + version = "0.0.1" + description = "binsparse implementation in python" + readme = "README.md" +-requires-python = ">=3.9" ++requires-python = ">=3.10" + license = {file = "LICENSE"} + authors = [ + {name = "Isaac Virshup"}, +@@ -21,20 +21,19 @@ urls.Home-page = "https://github.com/ivirshup/binsparse" + dependencies = [ + "anndata", + # for debug logging (referenced from the issue template) +- "session-info" ++ "session-info", + ] + + [project.optional-dependencies] + dev = [ +- # CLI for bumping the version number + "pre-commit", +- "twine>=4.0.2" ++ "twine>=4.0.2", + ] + doc = [ + "docutils>=0.8,!=0.18.*,!=0.19.*", + "sphinx>=4", + "sphinx-book-theme>=1.0.0", +- "myst-nb", ++ "myst-nb>=1.1.0", + "sphinxcontrib-bibtex>=1.0.0", + "sphinx-autodoc-typehints", + "sphinxext-opengraph", +@@ -42,10 +41,11 @@ doc = [ + "ipykernel", + "ipython", + "sphinx-copybutton", ++ "pandas", + ] + test = [ + "pytest", +- "pytest-cov", ++ "coverage", + ] + + [tool.coverage.run]