[pre-commit.ci] pre-commit autoupdate

.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: v0.8.4
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]

CHANGELOG.md

@@ -24,31 +24,31 @@ and this project adheres to [Semantic Versioning][].
 
 ### Fixed
 
--   Fixed `KeyError: "Unable to synchronously open object (object 'X' doesn't exist)"'` when reading h5ad without X field (#40)
+- Fixed `KeyError: "Unable to synchronously open object (object 'X' doesn't exist)"'` when reading h5ad without X field (#40)
 
 ## [0.1.1] - 2024-11-25
 
 ### Added
 
--   Axis in `td.concat` can now be specified with `obs` and `var` (#40)
+- Axis in `td.concat` can now be specified with `obs` and `var` (#40)
 
 ### Changed
 
 ### Fixed
 
--   Fixed `ImportError: cannot import name '_resolve_dim' from 'anndata._core.merge'` caused by anndata update (#40)
+- Fixed `ImportError: cannot import name '_resolve_dim' from 'anndata._core.merge'` caused by anndata update (#40)
 
 ## [0.1.0] - 2024-09-27
 
 ### Added
 
 ### Changed
 
--   Encoding of `treedata` attributes in h5ad and zarr files. `label`, `allow_overlap`, `obst`, and `vart` are now separate fields in the file. (#31)
+- Encoding of `treedata` attributes in h5ad and zarr files. `label`, `allow_overlap`, `obst`, and `vart` are now separate fields in the file. (#31)
 
 ### Fixed
 
--   `TreeData` objects with `.raw` specified can now be read (#31)
+- `TreeData` objects with `.raw` specified can now be read (#31)
 
 ## [0.0.4] - 2024-09-02
 
@@ -58,39 +58,39 @@ and this project adheres to [Semantic Versioning][].
 
 ### Fixed
 
--   Fixed typing bug introduced by anndata update (#29)
+- Fixed typing bug introduced by anndata update (#29)
 
 ## [0.0.3] - 2024-08-21
 
 ### Added
 
--   Add concatenation tutorial to documentation (#27)
+- Add concatenation tutorial to documentation (#27)
 
 ### Changed
 
--   `obst` and `vart` create local copy of `nx.DiGraphs` that are added (#26)
--   `TreeData.label` value remains the same after `td.concat` as long as all `label` values are the same for all objects (#27)
+- `obst` and `vart` create local copy of `nx.DiGraphs` that are added (#26)
+- `TreeData.label` value remains the same after `td.concat` as long as all `label` values are the same for all objects (#27)
 
 ### Fixed
 
--   Fixed bug which caused key to be listed twice in `label` column after value update in `obst` or `vart` (#26)
+- Fixed bug which caused key to be listed twice in `label` column after value update in `obst` or `vart` (#26)
 
 ## [0.0.2] - 2024-06-18
 
 ### Changed
 
--   Empty trees are now allowed to avoid error on subsetting (#13)
--   How trees are stored in h5ad and zarr files (#16)
--   Format of label column with multiple trees ([1,2] -> 1,2) (#16)
+- Empty trees are now allowed to avoid error on subsetting (#13)
+- How trees are stored in h5ad and zarr files (#16)
+- Format of label column with multiple trees ([1,2] -> 1,2) (#16)
 
 ### Fixed
 
--   Fixed issue with slow read/write of large trees
+- Fixed issue with slow read/write of large trees
 
 ## [0.0.1] - 2024-05-13
 
 ### Added
 
--   TreeData class for storing and manipulating trees
--   Read/write trees to h5ad and zarr files
--   Concatenate trees with similar API to AnnData
+- TreeData class for storing and manipulating trees
+- Read/write trees to h5ad and zarr files
+- Concatenate trees with similar API to AnnData

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