Update instance repo from cookiecutter template

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.1
+    rev: v0.8.3
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]

CHANGELOG.md

@@ -12,4 +12,4 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
--   Basic tool, preprocessing and plotting functions
+- Basic tool, preprocessing and plotting functions

docs/contributing.md

@@ -156,11 +156,11 @@ 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.
 
@@ -184,10 +184,10 @@ 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)=
 

docs/template_usage.md

@@ -168,13 +168,13 @@ We recommend using [readthedocs.org][] (RTD) to build and host the documentation
 To enable readthedocs, head over to [their website][readthedocs.org] and sign in with your GitHub account.
 On the RTD dashboard choose "Import a Project" and follow the instructions to add your repository.
 
--   Make sure to choose the correct name of the default branch.
-    On GitHub, the name of the default branch should be `main` (it has recently changed from `master` to `main`).
--   We recommend enabling documentation builds for pull requests (PRs).
-    This ensures that a PR doesn't introduce changes that break the documentation.
-    To do so, got to `Admin -> Advanced Settings`, check the `Build pull requests for this projects` option, and click `Save`.
-    For more information, please refer to the [official RTD documentation][rtd-prs].
--   If you find the RTD builds are failing, you can disable the `fail_on_warning` option in `.readthedocs.yaml`.
+- Make sure to choose the correct name of the default branch.
+  On GitHub, the name of the default branch should be `main` (it has recently changed from `master` to `main`).
+- We recommend enabling documentation builds for pull requests (PRs).
+  This ensures that a PR doesn't introduce changes that break the documentation.
+  To do so, got to `Admin -> Advanced Settings`, check the `Build pull requests for this projects` option, and click `Save`.
+  For more information, please refer to the [official RTD documentation][rtd-prs].
+- If you find the RTD builds are failing, you can disable the `fail_on_warning` option in `.readthedocs.yaml`.
 
 If your project is private, there are ways to enable docs rendering on [readthedocs.org][] but it is more cumbersome and requires a different subscription for read the docs.
 See a guide [here](https://docs.readthedocs.io/en/stable/guides/importing-private-repositories.html).
@@ -259,44 +259,44 @@ Once authorized, pre-commit.ci should automatically be activated.
 
 The following pre-commit hooks are for code style and format:
 
--   [prettier](https://prettier.io/docs/en/index.html):
-    standard code formatter for non-Python files (e.g. YAML).
--   [ruff][] formatting (`ruff-format`)
--   [ruff][] based checks:
-    -   [isort](https://beta.ruff.rs/docs/rules/#isort-i) (rule category: `I`):
-        sort module imports into sections and types.
-    -   [pydocstyle](https://beta.ruff.rs/docs/rules/#pydocstyle-d) (rule category: `D`):
-        pydocstyle extension of flake8.
-    -   [flake8-tidy-imports](https://beta.ruff.rs/docs/rules/#flake8-tidy-imports-tid) (rule category: `TID`):
-        tidy module imports.
-    -   [flake8-comprehensions](https://beta.ruff.rs/docs/rules/#flake8-comprehensions-c4) (rule category: `C4`):
-        write better list/set/dict comprehensions.
-    -   [pyupgrade](https://beta.ruff.rs/docs/rules/#pyupgrade-up) (rule category: `UP`):
-        upgrade syntax for newer versions of the language.
+- [prettier](https://prettier.io/docs/en/index.html):
+  standard code formatter for non-Python files (e.g. YAML).
+- [ruff][] formatting (`ruff-format`)
+- [ruff][] based checks:
+    - [isort](https://beta.ruff.rs/docs/rules/#isort-i) (rule category: `I`):
+      sort module imports into sections and types.
+    - [pydocstyle](https://beta.ruff.rs/docs/rules/#pydocstyle-d) (rule category: `D`):
+      pydocstyle extension of flake8.
+    - [flake8-tidy-imports](https://beta.ruff.rs/docs/rules/#flake8-tidy-imports-tid) (rule category: `TID`):
+      tidy module imports.
+    - [flake8-comprehensions](https://beta.ruff.rs/docs/rules/#flake8-comprehensions-c4) (rule category: `C4`):
+      write better list/set/dict comprehensions.
+    - [pyupgrade](https://beta.ruff.rs/docs/rules/#pyupgrade-up) (rule category: `UP`):
+      upgrade syntax for newer versions of the language.
 
 The following pre-commit hooks are for errors and inconsistencies:
 
--   [pre-commit-hooks](https://github.com/pre-commit/pre-commit-hooks): generic pre-commit hooks for text files.
-    -   **detect-private-key**: checks for the existence of private keys.
-    -   **check-ast**: check whether files parse as valid python.
-    -   **end-of-file-fixer**: check files end in a newline and only a newline.
-    -   **mixed-line-ending**: checks mixed line ending.
-    -   **trailing-whitespace**: trims trailing whitespace.
-    -   **check-case-conflict**: check files that would conflict with case-insensitive file systems.
-    -   **forbid-to-commit**: Make sure that `*.rej` files cannot be commited.
-        These files are created by the [automated template sync](#automated-template-sync)
-        if there's a merge conflict and need to be addressed manually.
--   [ruff][] based checks:
-    -   [pyflakes](https://beta.ruff.rs/docs/rules/#pyflakes-f) (rule category: `F`):
-        various checks for errors.
-    -   [pycodestyle](https://beta.ruff.rs/docs/rules/#pycodestyle-e-w) (rule category: `E`, `W`):
-        various checks for errors.
-    -   [flake8-bugbear](https://beta.ruff.rs/docs/rules/#flake8-bugbear-b) (rule category: `B`):
-        find possible bugs and design issues in program.
-    -   [flake8-blind-except](https://beta.ruff.rs/docs/rules/#flake8-blind-except-ble) (rule category: `BLE`):
-        checks for blind, catch-all `except` statements.
-    -   [Ruff-specific rules](https://beta.ruff.rs/docs/rules/#ruff-specific-rules-ruf) (rule category: `RUF`):
-        -   `RUF100`: remove unneccesary `# noqa` comments ()
+- [pre-commit-hooks](https://github.com/pre-commit/pre-commit-hooks): generic pre-commit hooks for text files.
+    - **detect-private-key**: checks for the existence of private keys.
+    - **check-ast**: check whether files parse as valid python.
+    - **end-of-file-fixer**: check files end in a newline and only a newline.
+    - **mixed-line-ending**: checks mixed line ending.
+    - **trailing-whitespace**: trims trailing whitespace.
+    - **check-case-conflict**: check files that would conflict with case-insensitive file systems.
+    - **forbid-to-commit**: Make sure that `*.rej` files cannot be commited.
+      These files are created by the [automated template sync](#automated-template-sync)
+      if there's a merge conflict and need to be addressed manually.
+- [ruff][] based checks:
+    - [pyflakes](https://beta.ruff.rs/docs/rules/#pyflakes-f) (rule category: `F`):
+      various checks for errors.
+    - [pycodestyle](https://beta.ruff.rs/docs/rules/#pycodestyle-e-w) (rule category: `E`, `W`):
+      various checks for errors.
+    - [flake8-bugbear](https://beta.ruff.rs/docs/rules/#flake8-bugbear-b) (rule category: `B`):
+      find possible bugs and design issues in program.
+    - [flake8-blind-except](https://beta.ruff.rs/docs/rules/#flake8-blind-except-ble) (rule category: `BLE`):
+      checks for blind, catch-all `except` statements.
+    - [Ruff-specific rules](https://beta.ruff.rs/docs/rules/#ruff-specific-rules-ruf) (rule category: `RUF`):
+        - `RUF100`: remove unneccesary `# noqa` comments ()
 
 #### How to add or remove pre-commit checks
 
@@ -373,9 +373,9 @@ add it to Ruff’s [`external = [...]`][ruff-external] setting to prevent `RUF10
 Scverse ecosystem packages should operate on [AnnData][] and/or [MuData][] data structures and typically use an API
 as originally [introduced by scanpy][scanpy-api] with the following submodules:
 
--   `pp` for preprocessing
--   `tl` for tools (that, compared to `pp` generate interpretable output, often associated with a corresponding plotting function)
--   `pl` for plotting functions
+- `pp` for preprocessing
+- `tl` for tools (that, compared to `pp` generate interpretable output, often associated with a corresponding plotting function)
+- `pl` for plotting functions
 
 You may add additional submodules as appropriate.
 While we encourage to follow a scanpy-like API for ecosystem packages,
@@ -439,12 +439,12 @@ The pull request can only be merged after all `*.rej` files have been removed.
 :::{tip}
 The following hints may be useful to work with the template sync:
 
--   GitHub automatically disables scheduled actions if there has been not activity to the repository for 60 days.
-    You can re-enable or manually trigger the sync by navigating to `Actions` -> `Sync Template` in your GitHub repository.
--   If you want to ignore certain files from the template update,
-    you can add them to the `[tool.cruft]` section in the `pyproject.toml` file in the root of your repository.
-    More details are described in the [cruft documentation][cruft-update-project].
--   To disable the sync entirely, simply remove the file `.github/workflows/sync.yaml`.
+- GitHub automatically disables scheduled actions if there has been not activity to the repository for 60 days.
+  You can re-enable or manually trigger the sync by navigating to `Actions` -> `Sync Template` in your GitHub repository.
+- If you want to ignore certain files from the template update,
+  you can add them to the `[tool.cruft]` section in the `pyproject.toml` file in the root of your repository.
+  More details are described in the [cruft documentation][cruft-update-project].
+- To disable the sync entirely, simply remove the file `.github/workflows/sync.yaml`.
 
 :::