[pre-commit.ci] pre-commit autoupdate

.github/pull_request_template.md

@@ -4,10 +4,10 @@
 
 <!-- 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**
 

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
       hooks:
           - id: prettier
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.8.2
+      rev: v0.8.3
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]

CODE_OF_CONDUCT.md

@@ -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
 

README.md

@@ -16,10 +16,10 @@
 
 ## 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
 

docs/contributing.md

@@ -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.
@@ -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
 

docs/index.md

@@ -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

docs/installation.md

@@ -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

pyproject.toml

@@ -99,7 +99,7 @@ docs = [
     "nbsphinx-link",
     "ipykernel",
     "ipython",
-    "ehrapy[dask,medcat]",
+    "ehrapy[dask]",
 ]
 test = [
     "ehrapy[dask]",