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flying-sheepflying-sheep
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Modernize (#69)
1 parent d90835b commit ed3f65f

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+337
-301
lines changed

‎.editorconfig

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root = true
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[*.py]
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[*]
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charset = utf-8
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indent_size = 4
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indent_style = space
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end_of_line = lf
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insert_final_newline = true
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trim_trailing_whitespace = true
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max_line_length = 88
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indent_size = 4
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indent_style = space
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[*.{yml,yaml}]
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indent_size = 2

‎.github/workflows/ci.yml

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@@ -4,30 +4,30 @@ name: Python tests
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on:
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push:
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branches: [ master ]
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branches: [main]
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pull_request:
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branches: [ master ]
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branches: [main]
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
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python-version: ["3.8", "3.9", "3.10", "3.11"]
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steps:
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- uses: actions/checkout@v2
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- uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/cache@v2
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with:
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path: |
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~/.cache/pip
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~/.cache/pre-commit
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key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
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- name: dependencies
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run: |
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pip install --upgrade pip wheel
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pip install .[test,typehints]
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- name: tests
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run: pytest --color=yes
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- uses: actions/checkout@v2
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- uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/cache@v2
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with:
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path: |
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~/.cache/pip
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~/.cache/pre-commit
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key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
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- name: dependencies
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run: |
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pip install --upgrade pip wheel
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pip install .[test,typehints]
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- name: tests
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run: pytest --color=yes

‎.gitignore

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# Python
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__pycache__/
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_version.py
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/build/
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/dist/
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# Testing
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/.tox/
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/.coverage
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.pytest_cache/
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‎.pre-commit-config.yaml

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:
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- id: trailing-whitespace
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- repo: https://github.com/psf/black
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rev: 23.3.0
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hooks:
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- id: black
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language_version: python3
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- repo: https://github.com/pycqa/isort
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rev: 5.12.0
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hooks:
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- id: isort
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:
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- id: trailing-whitespace
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- repo: https://github.com/psf/black
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rev: "23.3.0"
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hooks:
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- id: black
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language_version: python3
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.0.276
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hooks:
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- id: ruff
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args: ["--fix"]
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: v2.7.1
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hooks:
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- id: prettier

‎.prettierrc

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{
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"overrides": [
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{
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"files": ["settings.json", ".prettierrc"],
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"options": {
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"parser": "json5",
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"quoteProps": "preserve",
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"singleQuote": false,
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"trailingComma": "all",
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},
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},
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],
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}

‎.readthedocs.yml

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version: 2
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build:
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image: latest
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sphinx:
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configuration: docs/conf.py
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os: ubuntu-22.04
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tools:
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python: "3.11"
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python:
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version: 3.8
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install:
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- method: pip
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path: .
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extra_requirements:
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- doc
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- method: pip
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path: .
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extra_requirements:
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- doc
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sphinx:
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configuration: docs/conf.py

‎.vscode/settings.json

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@@ -1,7 +1,12 @@
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{
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"editor.formatOnSave": true,
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"python.formatting.provider": "black",
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"python.testing.pytestArgs": ["-v"],
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"python.testing.unittestEnabled": false,
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"python.testing.pytestEnabled": true
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"python.testing.pytestArgs": ["-v"],
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"python.testing.unittestEnabled": false,
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"python.testing.pytestEnabled": true,
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"[python]": {
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"editor.defaultFormatter": "ms-python.black-formatter",
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"editor.formatOnSave": true,
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"editor.codeActionsOnSave": {
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"source.fixAll": true,
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},
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},
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}

‎README.rst

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@@ -14,9 +14,9 @@ Check the self-documenting documentation at https://icb-scanpydoc.readthedocs-ho
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.. |tests| image:: https://github.com/theislab/scanpydoc/actions/workflows/ci.yml/badge.svg
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:target: https://github.com/theislab/scanpydoc/actions/workflows/ci.yml
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:alt: python test status
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.. |checks| image:: https://results.pre-commit.ci/badge/github/theislab/scanpydoc/master.svg
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:target: https://results.pre-commit.ci/latest/github/theislab/scanpydoc/master
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.. |checks| image:: https://results.pre-commit.ci/badge/github/theislab/scanpydoc/main.svg
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:target: https://results.pre-commit.ci/latest/github/theislab/scanpydoc/main
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:alt: pre-commit.ci status
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.. |cov| image:: https://codecov.io/gh/theislab/scanpydoc/branch/master/graph/badge.svg
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.. |cov| image:: https://codecov.io/gh/theislab/scanpydoc/branch/main/graph/badge.svg
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:target: https://codecov.io/gh/theislab/scanpydoc
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:alt: coverage

‎docs/conf.py

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@@ -54,7 +54,7 @@
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html_theme = "scanpydoc"
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html_context = dict(
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github_user="theislab", github_repo="scanpydoc", github_version="master"
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github_user="theislab", github_repo="scanpydoc", github_version="main"
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)
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# proj/doc/conf.py/../.. → proj

‎pyproject.toml

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[build-system]
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requires = ['flit_core >=2,<4']
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build-backend = 'flit_core.buildapi'
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[tool.flit.metadata]
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module = 'scanpydoc'
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author = 'Philipp Angerer'
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author-email = 'phil.angerer@gmail.com'
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home-page = 'https://github.com/theislab/scanpydoc/'
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urls = { Documentation = 'https://icb-scanpydoc.readthedocs-hosted.com/' }
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description-file = 'README.rst'
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[project]
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name = 'scanpydoc'
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dynamic = ['version']
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description = 'A series of Sphinx extensions to get maintainable numpydoc style documentation.'
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authors = [
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{ name = 'Philipp Angerer', email = '[email protected]' },
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]
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urls.Source = 'https://github.com/theislab/scanpydoc/'
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urls.Documentation = 'https://icb-scanpydoc.readthedocs-hosted.com/'
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readme = 'README.rst'
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license = 'GPL-3.0-or-later'
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classifiers = [
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'Intended Audience :: Developers',
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'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
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'Programming Language :: Python :: 3',
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'Topic :: Documentation :: Sphinx',
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'Topic :: Software Development :: Libraries :: Python Modules',
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'Framework :: Sphinx :: Extension',
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]
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requires-python = '>=3.7'
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requires = [
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requires-python = '>=3.8.1'
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dependencies = [
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'sphinx>=3.0',
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'get_version',
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]
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[tool.flit.metadata.requires-extra]
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[project.optional-dependencies]
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dev = [
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'pre-commit',
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]
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test = [
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'pytest',
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'pytest-cov',
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'typing_extensions>=3.10; python_version<"3.8"',
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]
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doc = [
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'scanpydoc[typehints]',
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typehints = ['sphinx-autodoc-typehints>=1.15.2']
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theme = ['sphinx-rtd-theme']
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[tool.flit.entrypoints.'sphinx.html_themes']
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[project.entry-points.'sphinx.html_themes']
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scanpydoc = 'scanpydoc.theme'
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[tool.black]
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target-version = ['py37']
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[tool.ruff]
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select = [
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'E', 'W', # Pycodestyle
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'F', # Pyflakes
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'I', # isort
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'UP', # Pyupgrade
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'RUF', # Ruff’s own rules
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]
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allowed-confusables = ['’', '×', 'l']
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ignore = [
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'E741', # Ambiguous variable name
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]
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[tool.isort]
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profile = 'black'
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lines_after_imports = 2
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multi_line_output = 3
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[tool.ruff.isort]
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lines-after-imports = 2
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known-first-party = ['scanpydoc']
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[tool.tox]
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legacy_tox_ini = """
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[tox]
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envlist = py37,py38,py39
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skipsdist = True
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[tool.hatch.version]
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source = 'vcs'
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[tool.hatch.build.hooks.vcs]
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version-file = 'src/scanpydoc/_version.py'
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[testenv]
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deps =
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flit
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commands =
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flit install
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pytest
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"""
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[[tool.hatch.envs.test.matrix]]
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python = ['3.8', '3.9', '3.10', '3.11']
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[tool.hatch.envs.test]
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features = ['test', 'typehints']
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[tool.hatch.envs.test.scripts]
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test = 'pytest -vv'
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[tool.pytest.ini_options]
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addopts = [
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'--import-mode=importlib',
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'-psphinx.testing.fixtures',
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]
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[build-system]
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requires = ['hatchling', 'hatch-vcs']
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build-backend = 'hatchling.build'

‎scanpydoc/elegant_typehints/static/typehints.css

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This file was deleted.

‎scanpydoc/theme/layout.html

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This file was deleted.

‎scanpydoc/__init__.py renamed to ‎src/scanpydoc/__init__.py

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"""A series of Sphinx extensions to get easy to maintain, numpydoc style documentation.
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"""A series of Sphinx extensions to get maintainable numpydoc style documentation.
22
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This module is also an extension itself which simply sets up all included extensions.
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"""
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from __future__ import annotations
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57
from textwrap import indent
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from typing import Any, Dict
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from typing import Any
79

8-
from get_version import get_version
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from sphinx.application import Sphinx
1011

12+
from ._version import __version__
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__version__ = get_version(__file__, vcs="git")
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1415
metadata = dict(version=__version__, env_version=1, parallel_read_safe=True)
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@_setup_sig
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def setup(app: Sphinx) -> Dict[str, Any]:
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"""Set up all included extensions!"""
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def setup(app: Sphinx) -> dict[str, Any]:
35+
"""Set up all included extensions!."""
3536
app.setup_extension("scanpydoc.autosummary_generate_imported")
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app.setup_extension("scanpydoc.definition_list_typed_field")
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app.setup_extension("scanpydoc.elegant_typehints")

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