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[pre-commit.ci] auto fixes from pre-commit.com hooks
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pre-commit-ci[bot] committed Dec 23, 2024
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -28,7 +28,7 @@ except in that they look similar, but not identical, to the results of InferCNV.

Please refer to the [documentation][link-docs]. In particular, the

- [API documentation][link-api].
- [API documentation][link-api].

## Installation

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18 changes: 9 additions & 9 deletions docs/contributing.md
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Expand Up @@ -99,11 +99,11 @@ Specify `vX.X.X` as a tag name and create a release. For more information, see [

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 the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
on how to write documentation.
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#### 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`

#### Building the docs locally

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