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ENH: Add CI infrastructure for pre-commit checks
Introduce a noxfile with two sessions: 1. pre-commit: Runs pre-commit checks on all files except the ones generated by cookiecutter. 2. pre-commit-cookie: Runs pre-commit checks on a generated folder based on the cookiecutter template. The approach was adapted from the implementation at https://github.com/scientific-python/cookie/, originally contributed by @henryiii. Add corresponding GitHub Actions workflows in lint.yml to automate the pre-commit checks.
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‎.github/workflows/lint.yml

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name: CI (Lint)
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on:
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workflow_dispatch:
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pull_request:
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push:
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branches:
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- main
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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pre-commit:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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- uses: pre-commit/[email protected]
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pre-commit-cookie:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- run: pipx run nox -s 'pre-commit-cookie'

‎.gitignore

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/#use-with-ide
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.pdm.toml
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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### Python Patch ###
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# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
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poetry.toml
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# ruff
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.ruff_cache/
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# LSP config files
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pyrightconfig.json

‎.pre-commit-config.yaml

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exclude: "^{{cookiecutter\\.project_name}}/"
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: "v4.6.0"
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hooks:
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- id: check-added-large-files
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- id: check-case-conflict
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- id: check-merge-conflict
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- id: check-symlinks
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- id: check-toml
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- id: check-yaml
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- id: debug-statements
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- id: end-of-file-fixer
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- id: mixed-line-ending
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- id: trailing-whitespace
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- id: requirements-txt-fixer
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- repo: https://github.com/adamchainz/blacken-docs
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rev: "1.18.0"
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hooks:
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- id: blacken-docs
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additional_dependencies: [black==24.*]
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: "v0.5.7"
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hooks:
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# Run the linter.
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- id: ruff
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args: ["--fix", "--show-fixes"]
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# Run the formatter.
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- id: ruff-format
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- repo: https://github.com/rbubley/mirrors-prettier
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rev: "v3.3.3"
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hooks:
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- id: prettier
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types_or: [yaml, json]
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- repo: https://github.com/codespell-project/codespell
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rev: "v2.3.0"
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hooks:
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- id: codespell
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args: ["-Lnd", "-w"]
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- repo: https://github.com/python-jsonschema/check-jsonschema
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rev: "0.29.1"
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hooks:
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- id: check-github-workflows

‎.ruff.toml

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[lint]
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select = [
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"ARG", # flake8-unused-arguments
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"ANN", # flake8-annotations
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"B", # flake8-bugbear
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"C4", # flake8-comprehensions
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"D", # pydocstyle
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"E", "F", "W", # flake8
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"EXE", # flake8-executable
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"G", # flake8-logging-format
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"I", # isort
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"ICN", # flake8-import-conventions
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"ISC", # flake8-implicit-str-concat
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"NPY", # NumPy specific rules
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"PGH", # pygrep-hooks
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"PIE", # flake8-pie
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"PL", # pylint
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"PT", # flake8-pytest-style
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"RET", # flake8-return
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"RUF", # Ruff-specific
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"S", # flake8-bandit
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"SIM", # flake8-simplify
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"UP", # pyupgrade
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"YTT", # flake8-2020
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"W", # Warning
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]
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extend-ignore = [
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"ANN101", # missing-type-self
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"G004", # logging-f-string
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"PIE790", # unnecessary-pass
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"D10", # undocumented-public-*
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"D200", # One-line docstring should fit on one line
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# Disable linting rules conflicting with "ruff formatter"
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# See https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
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"COM812",
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"COM819",
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"D206",
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"D300",
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"E111",
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"E114",
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"E117",
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"ISC001",
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"ISC002",
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"Q000",
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"Q002",
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"Q003",
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"W191",
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]
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flake8-annotations.suppress-dummy-args = true
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flake8-annotations.suppress-none-returning = true
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pydocstyle.convention = "pep257"

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