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CHANGELOG.md

@@ -12,152 +12,152 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
--   Add `progress_bar` argument to {class}`scib_metrics.benchmark.Benchmarker` {pr}`152`.
--   Add ability of {class}`scib_metrics.benchmark.Benchmarker` plotting code to handle missing sets of metrics {pr}`181`.
+- Add `progress_bar` argument to {class}`scib_metrics.benchmark.Benchmarker` {pr}`152`.
+- Add ability of {class}`scib_metrics.benchmark.Benchmarker` plotting code to handle missing sets of metrics {pr}`181`.
 
 ### Changed
 
--   Changed Leiden clustering now has a seed argument for reproducibility {pr}`173`.
--   Changed passing `None` to `bio_conservation_metrics` or `batch_correction_metrics` in {class}`scib_metrics.benchmark.Benchmarker` now implies to skip this set of metrics {pr}`181`.
+- Changed Leiden clustering now has a seed argument for reproducibility {pr}`173`.
+- Changed passing `None` to `bio_conservation_metrics` or `batch_correction_metrics` in {class}`scib_metrics.benchmark.Benchmarker` now implies to skip this set of metrics {pr}`181`.
 
 ### Fixed
 
--   Fix neighbors connectivities in test to use new scanpy fn {pr}`170`.
--   Fix Kmeans test {pr}`172`.
--   Fix deprecation and future warnings {pr}`171`.
--   Fix lisi return type and docstring {pr}`182`.
+- Fix neighbors connectivities in test to use new scanpy fn {pr}`170`.
+- Fix Kmeans test {pr}`172`.
+- Fix deprecation and future warnings {pr}`171`.
+- Fix lisi return type and docstring {pr}`182`.
 
 ## 0.5.1 (2024-02-23)
 
 ### Changed
 
--   Replace removed {class}`jax.random.KeyArray` with {class}`jax.Array` {pr}`135`.
+- Replace removed {class}`jax.random.KeyArray` with {class}`jax.Array` {pr}`135`.
 
 ## 0.5.0 (2024-01-04)
 
 ### Changed
 
--   Refactor all relevant metrics to use `NeighborsResults` as input instead of sparse
-    distance/connectivity matrices {pr}`129`.
+- Refactor all relevant metrics to use `NeighborsResults` as input instead of sparse
+  distance/connectivity matrices {pr}`129`.
 
 ## 0.4.1 (2023-10-08)
 
 ### Fixed
 
--   Fix KMeans. All previous versions had a bug with KMeans and ARI/NMI metrics are not reliable
-    with this clustering {pr}`115`.
+- Fix KMeans. All previous versions had a bug with KMeans and ARI/NMI metrics are not reliable
+  with this clustering {pr}`115`.
 
 ## 0.4.0 (2023-09-19)
 
 ### Added
 
--   Update isolated labels to use newest scib methodology {pr}`108`.
+- Update isolated labels to use newest scib methodology {pr}`108`.
 
 ### Fixed
 
--   Fix jax one-hot error {pr}`107`.
+- Fix jax one-hot error {pr}`107`.
 
 ### Removed
 
--   Drop Python 3.8 {pr}`107`.
+- Drop Python 3.8 {pr}`107`.
 
 ## 0.3.3 (2023-03-29)
 
 ### Fixed
 
--   Large scale tutorial now properly uses gpu index {pr}`92`
+- Large scale tutorial now properly uses gpu index {pr}`92`
 
 ## 0.3.2 (2023-03-13)
 
 ### Changed
 
--   Switch to Ruff for linting/formatting {pr}`87`
--   Update cookiecutter template {pr}`88`
+- Switch to Ruff for linting/formatting {pr}`87`
+- Update cookiecutter template {pr}`88`
 
 ## 0.3.1 (2023-02-16)
 
 ### Changed
 
--   Expose chunk size for silhouette {pr}`82`
+- Expose chunk size for silhouette {pr}`82`
 
 ## 0.3.0 (2023-02-16)
 
 ### Changed
 
--   Rename `KmeansJax` to `Kmeans` and fix ++ initialization, use Kmeans as default in benchmarker instead of Leiden {pr}`81`.
--   Warn about joblib, add progress bar postfix str {pr}`80`
+- Rename `KmeansJax` to `Kmeans` and fix ++ initialization, use Kmeans as default in benchmarker instead of Leiden {pr}`81`.
+- Warn about joblib, add progress bar postfix str {pr}`80`
 
 ## 0.2.0 (2023-02-02)
 
 ### Added
 
--   Allow custom nearest neighbors methods in Benchmarker {pr}`78`.
+- Allow custom nearest neighbors methods in Benchmarker {pr}`78`.
 
 ## 0.1.1 (2023-01-04)
 
 ### Added
 
--   Add new tutorial and fix scalability of lisi {pr}`71`.
+- Add new tutorial and fix scalability of lisi {pr}`71`.
 
 ## 0.1.0 (2023-01-03)
 
 ### Added
 
--   Add benchmarking pipeline with plotting {pr}`52` {pr}`69`.
+- Add benchmarking pipeline with plotting {pr}`52` {pr}`69`.
 
 ### Fixed
 
--   Fix diffusion distance computation, affecting kbet {pr}`70`.
+- Fix diffusion distance computation, affecting kbet {pr}`70`.
 
 ## 0.0.9 (2022-12-16)
 
 ### Added
 
--   Add kbet {pr}`60`.
--   Add graph connectivty metric {pr}`61`.
+- Add kbet {pr}`60`.
+- Add graph connectivty metric {pr}`61`.
 
 ## 0.0.8 (2022-11-18)
 
 ### Changed
 
--   Switch to random kmeans initialization due to kmeans++ complexity issues {pr}`54`.
+- Switch to random kmeans initialization due to kmeans++ complexity issues {pr}`54`.
 
 ### Fixed
 
--   Begin fixes to make kmeans++ initialization faster {pr}`49`.
+- Begin fixes to make kmeans++ initialization faster {pr}`49`.
 
 ## 0.0.7 (2022-10-31)
 
 ### Changed
 
--   Move PCR to utils module in favor of PCR comparison {pr}`46`.
+- Move PCR to utils module in favor of PCR comparison {pr}`46`.
 
 ### Fixed
 
--   Fix memory issue in `KMeansJax` by using `_kmeans_full_run` with `map` instead of `vmap` {pr}`45`.
+- Fix memory issue in `KMeansJax` by using `_kmeans_full_run` with `map` instead of `vmap` {pr}`45`.
 
 ## 0.0.6 (2022-10-25)
 
 ### Changed
 
--   Reimplement silhouette in a memory constant way, pdist using lax scan {pr}`42`.
+- Reimplement silhouette in a memory constant way, pdist using lax scan {pr}`42`.
 
 ## 0.0.5 (2022-10-24)
 
 ### Added
 
--   Standardize language of docstring {pr}`30`.
--   Use K-means++ initialization {pr}`23`.
--   Add pc regression and pc comparsion {pr}`16` {pr}`38`.
--   Lax'd silhouette {pr}`33`.
--   Cookicutter template sync {pr}`35`.
+- Standardize language of docstring {pr}`30`.
+- Use K-means++ initialization {pr}`23`.
+- Add pc regression and pc comparsion {pr}`16` {pr}`38`.
+- Lax'd silhouette {pr}`33`.
+- Cookicutter template sync {pr}`35`.
 
 ## 0.0.4 (2022-10-10)
 
 ### Added
 
--   NMI/ARI metric with Leiden clustering resolution optimization {pr}`24`.
--   iLISI/cLISI metrics {pr}`20`.
+- NMI/ARI metric with Leiden clustering resolution optimization {pr}`24`.
+- iLISI/cLISI metrics {pr}`20`.
 
 ## 0.0.1 - 0.0.3
 

docs/contributing.md

@@ -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.
@@ -120,10 +120,10 @@ repository.
 
 #### 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/extensions/typed_returns.py

@@ -14,7 +14,7 @@
 def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
     for line in lines:
         if m := re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line):
-            yield f'-{m["param"]} (:class:`~{m["type"]}`)'
+            yield f"-{m['param']} (:class:`~{m['type']}`)"
         else:
             yield line