[pre-commit.ci] pre-commit autoupdate (#140)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.4 → v0.9.1](astral-sh/ruff-pre-commit@v0.5.4...v0.9.1)
- [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.6.0...v5.0.0)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

.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

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")