Revert unrelated config and source changes to match main

Restores pyproject.toml, hatch.toml, test.yaml, pre-commit config,
and gr/ source files that were inadvertently modified by earlier
merge commits on this branch.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: timtreis

.github/workflows/test.yaml

@@ -100,13 +100,10 @@ jobs:
             env: { name: hatch-test.py3.11-stable }
           - os: macos-latest
             env: { name: hatch-test.py3.12-stable }
-          - os: macos-latest
-            env: { name: hatch-test.py3.13-pre } # pre-release only needs one OS
           - os: ubuntu-latest
             env: { name: hatch-test.py3.13-stable } # skipping because we run this as a coverage job
     name: ${{ matrix.env.label }} (${{ matrix.os }})
     runs-on: ${{ matrix.os }}
-    continue-on-error: ${{ contains(matrix.env.name, 'pre') }}
     steps:
       - uses: actions/checkout@v5
         with:

.pre-commit-config.yaml

@@ -7,16 +7,16 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.3.15
+    rev: v2.3.10
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.16.0
+    rev: v2.11.1
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.1
+    rev: v0.14.11
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]

hatch.toml

@@ -39,14 +39,17 @@ download = "python ./.scripts/ci/download_data.py {args}"
 deps = ["stable"]
 python = ["3.11", "3.12", "3.13"]
 
-[[envs.hatch-test.matrix]]
-deps = ["pre"]
-python = ["3.13"]
+# Test the newest supported Python version also with pre-release deps
+# [[envs.hatch-test.matrix]]
+# deps = [ "pre" ]
+# python = [ "3.13" ]
 
-[envs.hatch-test.overrides]
-matrix.deps.env-vars = [
-  { key = "UV_PRERELEASE", value = "allow", if = ["pre"] },
-]
+# [envs.hatch-test.overrides]
+# If the matrix variable `deps` is set to "pre",
+# set the environment variable `UV_PRERELEASE` to "allow".
+# matrix.deps.env-vars = [
+#   { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
+# ]
 
 [envs.notebooks]
 extra-dependencies = [

pyproject.toml

@@ -15,8 +15,8 @@ keywords = [
 ]
 license = "BSD-3-Clause"
 maintainers = [
-  { name = "Selman Ozleyen", email = "selman.ozleyen@helmholtz-munich.de" },
   { name = "Tim Treis", email = "tim.treis@scverse.org" },
+  { name = "Selman Ozleyen", email = "selman.ozleyen@helmholtz-munich.de" },
 ]
 authors = [
   { name = "scverse" },
@@ -67,7 +67,7 @@ dependencies = [
   # due to https://github.com/scikit-image/scikit-image/issues/6850 breaks rescale ufunc
   "scikit-learn>=0.24",
   "spatialdata>=0.7.1",
-  "spatialdata-plot>=0.2.13",
+  "spatialdata-plot",
   "statsmodels>=0.12",
   # https://github.com/scverse/squidpy/issues/526
   "tifffile!=2022.4.22",
@@ -76,6 +76,7 @@ dependencies = [
   "xarray>=2024.10",
   "zarr>=3",
 ]
+
 optional-dependencies.dev = [
   "hatch>=1.9",
   "ipykernel",
@@ -127,11 +128,17 @@ include-package-data = true
 
 [tool.setuptools_scm]
 
-[tool.hatch]
-build.hooks.vcs.version-file = "_version.py"
-build.targets.wheel.packages = [ "src/squidpy" ]
-metadata.allow-direct-references = true
-version.source = "vcs"
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "_version.py"
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = [ "src/squidpy" ]
 
 [tool.ruff]
 line-length = 120
@@ -144,6 +151,7 @@ exclude = [
   "docs/_build",
   "setup.py",
 ]
+
 format.docstring-code-format = true
 lint.select = [
   "B",   # flake8-bugbear
@@ -153,8 +161,8 @@ lint.select = [
   "F",   # pyflakes
   "I",   # isort
   # below are not autofixed
-  "UP",  # pyupgrade
-  "W",   # pycodestyle
+  "UP", # pyupgrade
+  "W",  # pycodestyle
 ]
 # "squidpy/*.py"= ["RST303"]
 lint.ignore = [
@@ -226,46 +234,84 @@ lint.unfixable = [
 lint.flake8-tidy-imports.ban-relative-imports = "all"
 lint.isort.required-imports = [ "from __future__ import annotations" ]
 
-[tool.pytest]
-ini_options.filterwarnings = [
+[tool.pytest.ini_options]
+filterwarnings = [
   "error::numba.NumbaPerformanceWarning",
   "ignore::UserWarning",
   "ignore::anndata.OldFormatWarning",
   "ignore:.*pkg_resources:DeprecationWarning",
 ]
-ini_options.python_files = "test_*.py"
-ini_options.testpaths = [ "tests/" ]
-ini_options.xfail_strict = true
-ini_options.addopts = [
+python_files = "test_*.py"
+testpaths = [ "tests/" ]
+xfail_strict = true
+addopts = [
   "--ignore=tests/plotting/test_interactive.py",
   "--ignore=docs",
 ]
 
-[tool.coverage]
-run.branch = true
-run.omit = [
+[tool.coverage.run]
+branch = true
+parallel = true
+source = [ "squidpy" ]
+omit = [
   "*/__init__.py",
   "*/_version.py",
   "squidpy/pl/_interactive/*",
   "tox/*",
 ]
-run.parallel = true
-run.source = [ "squidpy" ]
-paths.source = [
+
+[tool.coverage.paths]
+source = [
   "squidpy",
   "*/site-packages/squidpy",
 ]
-report.exclude_lines = [
+
+[tool.coverage.report]
+exclude_lines = [
   "\\#.*pragma:\\s*no.?cover",
+  "^if __name__ == .__main__.:$",
   "^\\s*raise AssertionError\\b",
   "^\\s*raise NotImplementedError\\b",
   "^\\s*return NotImplemented\\b",
-  "^if __name__ == .__main__.:$",
 ]
-report.precision = 2
-report.show_missing = true
-report.skip_empty = true
-report.sort = "Miss"
+show_missing = true
+precision = 2
+skip_empty = true
+sort = "Miss"
+
+[tool.pixi.workspace]
+channels = [ "conda-forge" ]
+platforms = [ "osx-arm64", "linux-64" ]
+
+[tool.pixi.dependencies]
+python = ">=3.11"
+
+[tool.pixi.pypi-dependencies]
+squidpy = { path = ".", editable = true }
+
+[tool.pixi.feature.py311.dependencies]
+python = "3.11.*"
+
+[tool.pixi.feature.py313.dependencies]
+python = "3.13.*"
+
+[tool.pixi.environments]
+dev-py311 = { features = [ "dev", "test", "py311" ], solve-group = "py311" }
+docs-py311 = { features = [ "docs", "py311" ], solve-group = "py311" }
+
+default = { features = [ "py313" ], solve-group = "py313" }
+dev-py313 = { features = [ "dev", "test", "py313" ], solve-group = "py313" }
+docs-py313 = { features = [ "docs", "py313" ], solve-group = "py313" }
+test-py313 = { features = [ "test", "py313" ], solve-group = "py313" }
+
+[tool.pixi.tasks]
+lab = "jupyter lab"
+kernel-install = "python -m ipykernel install --user --name pixi-dev --display-name \"squidpy (dev)\""
+test = "pytest -v --color=yes --tb=short --durations=10"
+lint = "ruff check ."
+format = "ruff format ."
+pre-commit-install = "pre-commit install"
+pre-commit = "pre-commit run"
 
 [tool.cruft]
 skip = [
@@ -278,24 +324,3 @@ skip = [
   "docs/references.md",
   "docs/notebooks/example.ipynb",
 ]
-
-[tool.pixi]
-dependencies.python = ">=3.11"
-environments.dev-py311 = { features = [ "dev", "test", "py311" ], solve-group = "py311" }
-environments.docs-py311 = { features = [ "docs", "py311" ], solve-group = "py311" }
-environments.default = { features = [ "py313" ], solve-group = "py313" }
-environments.dev-py313 = { features = [ "dev", "test", "py313" ], solve-group = "py313" }
-environments.docs-py313 = { features = [ "docs", "py313" ], solve-group = "py313" }
-environments.test-py313 = { features = [ "test", "py313" ], solve-group = "py313" }
-feature.py311.dependencies.python = "3.11.*"
-feature.py313.dependencies.python = "3.13.*"
-pypi-dependencies.squidpy = { path = ".", editable = true }
-tasks.lab = "jupyter lab"
-tasks.kernel-install = 'python -m ipykernel install --user --name pixi-dev --display-name "squidpy (dev)"'
-tasks.test = "pytest -v --color=yes --tb=short --durations=10"
-tasks.lint = "ruff check ."
-tasks.format = "ruff format ."
-tasks.pre-commit-install = "pre-commit install"
-tasks.pre-commit = "pre-commit run"
-workspace.channels = [ "conda-forge" ]
-workspace.platforms = [ "osx-arm64", "linux-64" ]

src/squidpy/gr/_ligrec.py

@@ -25,6 +25,7 @@
     _assert_categorical_obs,
     _assert_positive,
     _check_tuple_needles,
+    _create_sparse_df,
     _genesymbols,
     _save_data,
 )
@@ -211,7 +212,7 @@ def __init__(self, adata: AnnData, use_raw: bool = True):
 
         self._data = pd.DataFrame.sparse.from_spmatrix(
             csc_matrix(adata.X), index=adata.obs_names, columns=adata.var_names
-        ).fillna(0.0)
+        )
 
         self._interactions: pd.DataFrame | None = None
         self._filtered_data: pd.DataFrame | None = None
@@ -425,16 +426,18 @@ def test(
             numba_parallel=numba_parallel,
             **kwargs,
         )
-        index = pd.MultiIndex.from_frame(interactions, names=[SOURCE, TARGET])
-        columns = pd.MultiIndex.from_tuples(clusters, names=["cluster_1", "cluster_2"])
         res = {
-            "means": pd.DataFrame(
-                {c: pd.arrays.SparseArray(res.means[:, i], fill_value=0) for i, c in enumerate(columns)},
-                index=index,
+            "means": _create_sparse_df(
+                res.means,
+                index=pd.MultiIndex.from_frame(interactions, names=[SOURCE, TARGET]),
+                columns=pd.MultiIndex.from_tuples(clusters, names=["cluster_1", "cluster_2"]),
+                fill_value=0,
             ),
-            "pvalues": pd.DataFrame(
-                {c: pd.arrays.SparseArray(res.pvalues[:, i], fill_value=np.nan) for i, c in enumerate(columns)},
-                index=index,
+            "pvalues": _create_sparse_df(
+                res.pvalues,
+                index=pd.MultiIndex.from_frame(interactions, names=[SOURCE, TARGET]),
+                columns=pd.MultiIndex.from_tuples(clusters, names=["cluster_1", "cluster_2"]),
+                fill_value=np.nan,
             ),
             "metadata": self.interactions[self.interactions.columns.difference([SOURCE, TARGET])],
         }
@@ -735,11 +738,8 @@ def extractor(res: Sequence[TempResult]) -> TempResult:
 
         return TempResult(means=means, pvalues=pvalues)
 
-    clustering = np.array(data["clusters"].values, dtype=np.int32)
-    # densify the data earlier to avoid concatenating sparse arrays
-    # with multiple fill values: '[0.0, nan]' (which leads to PerformanceWarning)
-    data = data.astype({c: np.float64 for c in data.columns if c != "clusters"})
     groups = data.groupby("clusters", observed=True)
+    clustering = np.array(data["clusters"].values, dtype=np.int32)
 
     mean = groups.mean().values.T  # (n_genes, n_clusters)
     # see https://github.com/scverse/squidpy/pull/991#issuecomment-2888506296

src/squidpy/gr/_niche.py

@@ -245,7 +245,7 @@ def calculate_niche(
             for col in result_columns:
                 if col in lib_result.obs.columns:
                     prefixed_values = lib_result.obs[col].apply(
-                        lambda x, lib=lib_id: f"lib={lib}_{x}" if x != "not_a_niche" else x
+                        lambda x, lib=lib_id: (f"lib={lib}_{x}" if x != "not_a_niche" else x)
                     )
 
                     adata.obs.loc[lib_indices, col] = prefixed_values.values