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[pre-commit.ci] auto fixes from pre-commit.com hooks
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pre-commit-ci[bot] committed Dec 5, 2024
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2 changes: 1 addition & 1 deletion {{cookiecutter.project_name}}/CHANGELOG.md
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Expand Up @@ -12,4 +12,4 @@ and this project adheres to [Semantic Versioning][].

### Added

- Basic tool, preprocessing and plotting functions
- Basic tool, preprocessing and plotting functions
18 changes: 9 additions & 9 deletions {{cookiecutter.project_name}}/docs/contributing.md
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Expand Up @@ -158,11 +158,11 @@ This will automatically create a git tag and trigger a Github workflow that crea
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/)
- 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.

Expand All @@ -186,10 +186,10 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu

#### 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`
- 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)=

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