[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -2,8 +2,8 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
@@ -13,15 +13,15 @@ repos:
         # doesn't work in combination with jupytext hook yet. See https://github.com/mwouts/jupytext/issues/580
         exclude: "docs/notebooks/.*\\.md"
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.4
+    rev: v0.9.1
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
         types_or: [python, pyi, jupyter]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast

README.md

@@ -28,7 +28,7 @@ except in that they look similar, but not identical, to the results of InferCNV.
 
 Please refer to the [documentation][link-docs]. In particular, the
 
--   [API documentation][link-api].
+- [API documentation][link-api].
 
 ## Installation
 

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

@@ -12,7 +12,7 @@
 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
 

src/infercnvpy/_util.py

@@ -14,7 +14,7 @@ def _choose_mtx_rep(adata, use_raw=False, layer=None):
     is_layer = layer is not None
     if use_raw and is_layer:
         raise ValueError(
-            "Cannot use expression from both layer and raw. You provided:" f"'use_raw={use_raw}' and 'layer={layer}'"
+            f"Cannot use expression from both layer and raw. You provided:'use_raw={use_raw}' and 'layer={layer}'"
         )
     if is_layer:
         return adata.layers[layer]

src/infercnvpy/tl/_copykat.py

@@ -100,7 +100,7 @@ def copykat(
         importr("stringr")
     except ImportError:
         raise ImportError(
-            "copyKAT requires a valid R installation with the following packages: " "copykat, stringr"
+            "copyKAT requires a valid R installation with the following packages: copykat, stringr"
         ) from None
 
     logging.info("Preparing R objects")

src/infercnvpy/tl/_infercnv.py

@@ -98,7 +98,7 @@ def infercnv(
         raise ValueError("Ensure your var_names are unique!")
     if {"chromosome", "start", "end"} - set(adata.var.columns) != set():
         raise ValueError(
-            "Genomic positions not found. There need to be `chromosome`, `start`, and " "`end` columns in `adata.var`. "
+            "Genomic positions not found. There need to be `chromosome`, `start`, and `end` columns in `adata.var`. "
         )
 
     var_mask = adata.var["chromosome"].isnull()