diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 4214c3b8..0bafff61 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -4,10 +4,10 @@ -- [ ] 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** diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 423780fb..12e5ab31 100644 --- a/.pre-commit-config.yaml +++ b/.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] diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index d6209cca..39816a93 100644 --- a/CODE_OF_CONDUCT.md +++ b/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 diff --git a/README.md b/README.md index 32e66dec..6c4533b4 100644 --- a/README.md +++ b/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 diff --git a/docs/contributing.md b/docs/contributing.md index ce5858eb..0a5b318e 100644 --- a/docs/contributing.md +++ b/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 diff --git a/docs/index.md b/docs/index.md index 56cc3037..03a0987d 100644 --- a/docs/index.md +++ b/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 diff --git a/docs/installation.md b/docs/installation.md index ba7010a9..b349394e 100644 --- a/docs/installation.md +++ b/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 ) -- en-core-sci-md (pip install ) -- en-core-sci-lg (pip install ) +- en_core_web_md (python -m spacy download en_core_web_md) +- en-core-sci-sm (pip install ) +- en-core-sci-md (pip install ) +- en-core-sci-lg (pip install ) [github repo]: https://github.com/theislab/ehrapy [pip]: https://pip.pypa.io diff --git a/pyproject.toml b/pyproject.toml index 78931dcc..7bc35d29 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -99,7 +99,7 @@ docs = [ "nbsphinx-link", "ipykernel", "ipython", - "ehrapy[dask,medcat]", + "ehrapy[dask]", ] test = [ "ehrapy[dask]",