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BiocSetup configuration
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‎.github/workflows/publish-pypi.yml‎

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name: Publish to PyPI
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on:
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push:
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tags: "*"
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jobs:
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build:
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runs-on: ubuntu-latest
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permissions:
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id-token: write
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repository-projects: write
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contents: write
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pages: write
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.12
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uses: actions/setup-python@v5
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with:
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python-version: 3.12
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install tox
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- name: Test with tox
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run: |
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tox
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- name: Build Project and Publish
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run: |
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python -m tox -e clean,build
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# This uses the trusted publisher workflow so no token is required.
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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- name: Build docs
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run: |
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tox -e docs
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- run: touch ./docs/_build/html/.nojekyll
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- name: GH Pages Deployment
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uses: JamesIves/github-pages-deploy-action@v4
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with:
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branch: gh-pages # The branch the action should deploy to.
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folder: ./docs/_build/html
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clean: true # Automatically remove deleted files from the deploy branch

‎.github/workflows/run-tests.yml‎

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name: Test the library
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on:
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push:
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branches:
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- master # for legacy repos
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- main
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pull_request:
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branches:
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- master # for legacy repos
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- main
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workflow_dispatch: # Allow manually triggering the workflow
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schedule:
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# Run roughly every 15 days at 00:00 UTC
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# (useful to check if updates on dependencies break the package)
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- cron: "0 0 1,16 * *"
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permissions:
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contents: read
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concurrency:
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group: >-
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${{ github.workflow }}-${{ github.ref_type }}-
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${{ github.event.pull_request.number || github.sha }}
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cancel-in-progress: true
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jobs:
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test:
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strategy:
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matrix:
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python: ["3.10", "3.11", "3.12", "3.13", "3.14"]
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platform:
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- ubuntu-latest
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- macos-latest
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- windows-latest
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runs-on: ${{ matrix.platform }}
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name: Python ${{ matrix.python }}, ${{ matrix.platform }}
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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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id: setup-python
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with:
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python-version: ${{ matrix.python }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install tox coverage
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- name: Run tests
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run: >-
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pipx run --python '${{ steps.setup-python.outputs.python-path }}'
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tox
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-- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml # pytest args
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- name: Check for codecov token availability
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id: codecov-check
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shell: bash
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run: |
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if [ ${{ secrets.CODECOV_TOKEN }} != '' ]; then
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echo "codecov=true" >> $GITHUB_OUTPUT;
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else
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echo "codecov=false" >> $GITHUB_OUTPUT;
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fi
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- name: Upload coverage reports to Codecov with GitHub Action
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uses: codecov/codecov-action@v5
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if: ${{ steps.codecov-check.outputs.codecov == 'true' }}
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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slug: ${{ github.repository }}
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flags: ${{ matrix.platform }} - py${{ matrix.python }}

‎.pre-commit-config.yaml‎

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exclude: '^docs/conf.py'
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v5.0.0
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hooks:
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- id: trailing-whitespace
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- id: check-added-large-files
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- id: check-ast
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- id: check-json
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- id: check-merge-conflict
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- id: check-xml
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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: requirements-txt-fixer
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- id: mixed-line-ending
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args: ['--fix=auto'] # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
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- repo: https://github.com/astral-sh/ruff-pre-commit
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# Ruff version.
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rev: v0.8.2
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hooks:
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- id: ruff
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args: [--fix, --exit-non-zero-on-fix]
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- id: ruff-format
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## Check for misspells in documentation files:
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# - repo: https://github.com/codespell-project/codespell
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# rev: v2.2.5
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# hooks:
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# - id: codespell

‎README.md‎

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<!-- These are examples of badges you might want to add to your README:
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please update the URLs accordingly
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[![Built Status](https://api.cirrus-ci.com/github/<USER>/experimenthub.svg?branch=main)](https://cirrus-ci.com/github/<USER>/experimenthub)
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[![ReadTheDocs](https://readthedocs.org/projects/experimenthub/badge/?version=latest)](https://experimenthub.readthedocs.io/en/stable/)
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[![Coveralls](https://img.shields.io/coveralls/github/<USER>/experimenthub/main.svg)](https://coveralls.io/r/<USER>/experimenthub)
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[![PyPI-Server](https://img.shields.io/pypi/v/experimenthub.svg)](https://pypi.org/project/experimenthub/)
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[![Conda-Forge](https://img.shields.io/conda/vn/conda-forge/experimenthub.svg)](https://anaconda.org/conda-forge/experimenthub)
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[![Monthly Downloads](https://pepy.tech/badge/experimenthub/month)](https://pepy.tech/project/experimenthub)
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[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&label=Twitter)](https://twitter.com/experimenthub)
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-->
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[![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/)
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![Unit tests](https://github.com/YOUR_ORG_OR_USERNAME/experimenthub/actions/workflows/run-tests.yml/badge.svg)
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# experimenthub
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> Access Bioconductor's experimenthub resources
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A longer description of your project goes here...
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## Install
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To get started, install the package from [PyPI](https://pypi.org/project/experimenthub/)
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```bash
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pip install experimenthub
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```
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<!-- pyscaffold-notes -->
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<!-- biocsetup-notes -->
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## Note
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This project has been set up using PyScaffold 4.6. For details and usage
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information on PyScaffold see https://pyscaffold.org/.
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This project has been set up using [BiocSetup](https://github.com/biocpy/biocsetup)
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and [PyScaffold](https://pyscaffold.org/).

‎docs/conf.py‎

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"pyscaffold": ("https://pyscaffold.org/en/stable", None),
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}
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print(f"loading configurations for {project} {version} ...", file=sys.stderr)
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print(f"loading configurations for {project} {version} ...", file=sys.stderr)
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# -- Biocsetup configuration -------------------------------------------------
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# Enable execution of code chunks in markdown
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extensions.remove('myst_parser')
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extensions.append('myst_nb')
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# Less verbose api documentation
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extensions.append('sphinx_autodoc_typehints')
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autodoc_default_options = {
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"special-members": True,
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"undoc-members": True,
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"exclude-members": "__weakref__, __dict__, __str__, __module__",
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}
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autosummary_generate = True
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autosummary_imported_members = True
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html_theme = "furo"

‎docs/requirements.txt‎

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# sphinx_rtd_theme
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myst-parser[linkify]
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sphinx>=3.2.1
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myst-nb
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furo
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sphinx-autodoc-typehints

‎pyproject.toml‎

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# For smarter version schemes and other configuration options,
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# check out https://github.com/pypa/setuptools_scm
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version_scheme = "no-guess-dev"
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[tool.ruff]
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line-length = 120
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src = ["src"]
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exclude = ["tests"]
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lint.extend-ignore = ["F821"]
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[tool.ruff.lint.pydocstyle]
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convention = "google"
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[tool.ruff.format]
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docstring-code-format = true
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docstring-code-line-length = 20
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[tool.ruff.lint.per-file-ignores]
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"__init__.py" = ["E402", "F401"]

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