Merge branch 'main' into deprecate_napari

.pre-commit-config.yaml

@@ -7,18 +7,18 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.4.1
+      rev: v1.5.1
       hooks:
           - id: mypy
             additional_dependencies: [numpy, pandas, types-requests]
             exclude: .scripts/ci/download_data.py|squidpy/datasets/_(dataset|image).py # See https://github.com/pre-commit/mirrors-mypy/issues/33
     - repo: https://github.com/psf/black
-      rev: 23.7.0
+      rev: 23.9.1
       hooks:
           - id: black
             additional_dependencies: [toml]
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0
+      rev: v3.0.3
       hooks:
           - id: prettier
     - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -51,12 +51,12 @@ repos:
             name: Check executable files use .sh extension
             types: [shell, executable]
     - repo: https://github.com/asottile/blacken-docs
-      rev: 1.15.0
+      rev: 1.16.0
       hooks:
           - id: blacken-docs
     - repo: https://github.com/astral-sh/ruff-pre-commit
       # Ruff version.
-      rev: v0.0.281
+      rev: v0.0.292
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

README.rst

@@ -1,4 +1,4 @@
-|PyPI| |Downloads| |CI| |Docs| |Coverage| |Discourse| |Zulip|
+|PyPI| |Downloads| |CI| |Docs| |Coverage| |Discourse| |Zulip| |NumFOCUS|
 
 Squidpy - Spatial Single Cell Analysis in Python
 ================================================
@@ -10,6 +10,11 @@ tissue images if available.
 
 Visit our `documentation`_ for installation, tutorials, examples and more.
 
+Squidpy is part of the scverse project (`website`_, `governance`_) and is fiscally sponsored by `NumFOCUS`_.
+Please consider making a tax-deductible `donation`_ to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
+
+|NumFOCUS logo|
+
 Manuscript
 ----------
 Please see our manuscript `Palla, Spitzer et al. (2022)`_ in **Nature Methods** to learn more.
@@ -69,9 +74,21 @@ We are happy about any contributions! Before you start, check out our `contribut
     :target: https://scverse.zulipchat.com
     :alt: Zulip
 
+.. |NumFOCUS| image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A
+    :target: http://numfocus.org
+    :alt: NumFOCUS
+
+.. |NumFOCUS logo| image:: https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png
+    :target: https://numfocus.org/project/scverse
+    :width: 200
+
 .. _Palla, Spitzer et al. (2022): https://doi.org/10.1038/s41592-021-01358-2
 .. _scanpy: https://scanpy.readthedocs.io/en/stable/
 .. _anndata: https://anndata.readthedocs.io/en/stable/
 .. _napari: https://napari.org/
 .. _skimage: https://scikit-image.org/
 .. _documentation: https://squidpy.readthedocs.io/en/stable/
+.. _website: https://scverse.org/
+.. _governance: https://scverse.org/about/roles/
+.. _NumFOCUS: https://numfocus.org/
+.. _donation: https://numfocus.org/donate-to-scverse/

pyproject.toml

@@ -59,7 +59,7 @@ dependencies = [
    "numba>=0.56.4",
    "numpy>=1.23.0",
    "omnipath>=1.0.7",
-   "pandas>=1.5.0",
+   "pandas>=2.1.0",
    "Pillow>=8.0.0",
    "scanpy>=1.9.3",
    "scikit-image>=0.19,<=0.20",

src/squidpy/gr/_ligrec.py

@@ -508,8 +508,13 @@ def find_min_gene_in_complex(_complex: str | None) -> str | None:
                 return complexes[0]
 
             df = self._data[complexes].mean()
-
-            return str(df.index[df.argmin()])
+            try:
+                return str(df.index[df.argmin()])
+            except ValueError as e:
+                if "attempt to get argmin of an empty sequence" in str(e):
+                    return str(df.index[0])
+                else:
+                    logg.error(e)
 
         if TYPE_CHECKING:
             assert isinstance(self._interactions, pd.DataFrame)

src/squidpy/gr/_ppatterns.py

@@ -418,7 +418,7 @@ def co_occurrence(
     labs_splits = tuple(s for s in np.array_split(labs, n_splits, axis=0) if len(s))  # type: ignore[arg-type]
     # create idx array including unique combinations and self-comparison
     x, y = np.triu_indices_from(np.empty((n_splits, n_splits)))  # type: ignore[arg-type]
-    idx_splits = [(i, j) for i, j in zip(x, y)]
+    idx_splits = list(zip(x, y))
 
     n_jobs = _get_n_cores(n_jobs)
     start = logg.info(

src/squidpy/im/_container.py

@@ -883,7 +883,7 @@ def uncrop(
 
         scales.discard(None)
         if len(scales) != 1:
-            raise ValueError(f"Unable to uncrop images of different scales `{sorted((scales))}`.")
+            raise ValueError(f"Unable to uncrop images of different scales `{sorted(scales)}`.")
         scale, *_ = scales
 
         if shape is None:

tests/plotting/test_graph.py

@@ -117,7 +117,7 @@ def test_plot_cbar_kwargs(self, adata: AnnData):
         gr.spatial_neighbors(adata)
         gr.nhood_enrichment(adata, cluster_key=C_KEY)
 
-        pl.nhood_enrichment(adata, cluster_key=C_KEY, cbar_kwargs={"label": "FOOBARBAZQUUX", "filled": False})
+        pl.nhood_enrichment(adata, cluster_key=C_KEY, cbar_kwargs={"label": "FOOBARBAZQUUX"})
 
 
 class TestLigrec(PlotTester, metaclass=PlotTesterMeta):