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8 changes: 4 additions & 4 deletions .github/pull_request_template.md
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<!-- Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs). -->

- [ ] This comment contains a description of changes (with reason)
- [ ] Referenced issue is linked
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] Documentation in `docs` is updated
- [ ] This comment contains a description of changes (with reason)
- [ ] Referenced issue is linked
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] Documentation in `docs` is updated

**Description of changes**

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28 changes: 14 additions & 14 deletions CODE_OF_CONDUCT.md
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Expand Up @@ -14,23 +14,23 @@ religion, or sexual identity and orientation.
Examples of behavior that contributes to creating a positive environment
include:

- Using welcoming and inclusive language
- Being respectful of differing viewpoints and experiences
- Gracefully accepting constructive criticism
- Focusing on what is best for the community
- Showing empathy towards other community members
- Using welcoming and inclusive language
- Being respectful of differing viewpoints and experiences
- Gracefully accepting constructive criticism
- Focusing on what is best for the community
- Showing empathy towards other community members

Examples of unacceptable behavior by participants include:

- The use of sexualized language or imagery and unwelcome sexual
attention or advances
- Trolling, insulting/derogatory comments, and personal or political
attacks
- Public or private harassment
- Publishing others’ private information, such as a physical or
electronic address, without explicit permission
- Other conduct which could reasonably be considered inappropriate in a
professional setting
- The use of sexualized language or imagery and unwelcome sexual
attention or advances
- Trolling, insulting/derogatory comments, and personal or political
attacks
- Public or private harassment
- Publishing others’ private information, such as a physical or
electronic address, without explicit permission
- Other conduct which could reasonably be considered inappropriate in a
professional setting

## Our Responsibilities

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8 changes: 4 additions & 4 deletions README.md
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## Features

- Exploratory and targeted analysis of Electronic Health Records
- Quality control & preprocessing
- Visualization & Exploration
- Clustering & trajectory inference
- Exploratory and targeted analysis of Electronic Health Records
- Quality control & preprocessing
- Visualization & Exploration
- Clustering & trajectory inference

## Installation

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18 changes: 9 additions & 9 deletions docs/contributing.md
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Expand Up @@ -126,11 +126,11 @@ in the cookiecutter-scverse template.

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
- Google-style docstrings
- 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
- Google-style docstrings
- 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.
Expand All @@ -144,10 +144,10 @@ These notebooks come from [pert-tutorials](https://github.com/theislab/ehrapy-tu

#### 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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6 changes: 3 additions & 3 deletions docs/index.md
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Expand Up @@ -61,8 +61,8 @@ medRxiv 2023.12.11.23299816; doi: https://doi.org/10.1101/2023.12.11.23299816 ](

# Indices and tables

- {ref}`genindex`
- {ref}`modindex`
- {ref}`search`
- {ref}`genindex`
- {ref}`modindex`
- {ref}`search`

[scanpy genome biology (2018)]: https://doi.org/10.1186/s13059-017-1382-0
8 changes: 4 additions & 4 deletions docs/installation.md
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Expand Up @@ -51,10 +51,10 @@ pip install ehrapy[medcat]

Available language models are

- en_core_web_md (python -m spacy download en_core_web_md)
- en-core-sci-sm (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_sm-0.4.0.tar.gz>)
- en-core-sci-md (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_md-0.4.0.tar.gz>)
- en-core-sci-lg (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_lg-0.4.0.tar.gz>)
- en_core_web_md (python -m spacy download en_core_web_md)
- en-core-sci-sm (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_sm-0.4.0.tar.gz>)
- en-core-sci-md (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_md-0.4.0.tar.gz>)
- en-core-sci-lg (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_lg-0.4.0.tar.gz>)

[github repo]: https://github.com/theislab/ehrapy
[pip]: https://pip.pypa.io
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