[pre-commit.ci] pre-commit autoupdate

.github/workflows/publish-pypi.yml

@@ -52,4 +52,4 @@ jobs:
 
       # This uses the trusted publisher workflow so no token is required.
       - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.8.2
+  rev: v0.11.5
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

docs/requirements.txt

@@ -1,9 +1,9 @@
+furo
+myst-nb
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
 sphinx>=3.2.1
-myst-nb
-furo
 sphinx-autodoc-typehints

setup.py

@@ -1,10 +1,10 @@
 """
-    Setup file for SpatialFeatureExperiment.
-    Use setup.cfg to configure your project.
+Setup file for SpatialFeatureExperiment.
+Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 4.6.
-    PyScaffold helps you to put up the scaffold of your new Python project.
-    Learn more under: https://pyscaffold.org/
+This file was generated with PyScaffold 4.6.
+PyScaffold helps you to put up the scaffold of your new Python project.
+Learn more under: https://pyscaffold.org/
 """
 
 from setuptools import setup

src/spatialfeatureexperiment/SpatialFeatureExperiment.py

@@ -47,7 +47,7 @@ def _validate_geometries(geometries: Dict[str, gpd.GeoDataFrame], prop_name: str
 
     for i, geom in enumerate(geometries.values()):
         if not isinstance(geom, gpd.GeoDataFrame):
-            raise TypeError(f"Item {i} in {prop_name} is {type(geom).__name__} " f"rather than `GeoDataFrame`.\n")
+            raise TypeError(f"Item {i} in {prop_name} is {type(geom).__name__} rather than `GeoDataFrame`.\n")
 
 
 def _validate_annotgeometries(geometries, column_data):
@@ -67,7 +67,7 @@ def _validate_annotgeometries(geometries, column_data):
             missing = [s for s in samples_seen if s not in sample_ids]
             if len(missing) > 0:
                 raise ValueError(
-                    f"Samples {', '.join(missing)} in item {i} of " f"annot_geometries are absent from 'column_data'.\n"
+                    f"Samples {', '.join(missing)} in item {i} of annot_geometries are absent from 'column_data'.\n"
                 )
 
 

tests/test_pSFE.py

@@ -36,4 +36,4 @@ def test_init_with_col_geoms():
     colgeoms = {"polygons" : gpd.GeoDataFrame({"geometry": polys})}
     tspe = SpatialFeatureExperiment(assays={"spots": counts}, col_geometries=colgeoms)
 
-    assert isinstance(tspe, SpatialFeatureExperiment)
+    assert isinstance(tspe, SpatialFeatureExperiment)