Merge branch 'main' into bugfix/issue1115-pkg_resources-not-founded-deprecated-since-python-312

Author: timtreis

.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: v2.3.10
+    rev: v2.3.15
     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: v2.11.1
+    rev: v2.16.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.11
+    rev: v0.15.1
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]

pyproject.toml

@@ -15,8 +15,8 @@ keywords = [
 ]
 license = "BSD-3-Clause"
 maintainers = [
-  { name = "Tim Treis", email = "tim.treis@scverse.org" },
   { name = "Selman Ozleyen", email = "selman.ozleyen@helmholtz-munich.de" },
+  { name = "Tim Treis", email = "tim.treis@scverse.org" },
 ]
 authors = [
   { name = "scverse" },
@@ -76,7 +76,6 @@ dependencies = [
   "xarray>=2024.10",
   "zarr>=3",
 ]
-
 optional-dependencies.dev = [
   "hatch>=1.9",
   "ipykernel",
@@ -128,17 +127,11 @@ include-package-data = true
 
 [tool.setuptools_scm]
 
-[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.hatch]
+build.hooks.vcs.version-file = "_version.py"
+build.targets.wheel.packages = [ "src/squidpy" ]
+metadata.allow-direct-references = true
+version.source = "vcs"
 
 [tool.ruff]
 line-length = 120
@@ -151,7 +144,6 @@ exclude = [
   "docs/_build",
   "setup.py",
 ]
-
 format.docstring-code-format = true
 lint.select = [
   "B",   # flake8-bugbear
@@ -161,8 +153,8 @@ lint.select = [
   "F",   # pyflakes
   "I",   # isort
   # below are not autofixed
-  "UP", # pyupgrade
-  "W",  # pycodestyle
+  "UP",  # pyupgrade
+  "W",   # pycodestyle
 ]
 # "squidpy/*.py"= ["RST303"]
 lint.ignore = [
@@ -234,84 +226,46 @@ 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",
 ]
-python_files = "test_*.py"
-testpaths = [ "tests/" ]
-xfail_strict = true
-addopts = [
+ini_options.python_files = "test_*.py"
+ini_options.testpaths = [ "tests/" ]
+ini_options.xfail_strict = true
+ini_options.addopts = [
   "--ignore=tests/plotting/test_interactive.py",
   "--ignore=docs",
 ]
 
-[tool.coverage.run]
-branch = true
-parallel = true
-source = [ "squidpy" ]
-omit = [
+[tool.coverage]
+run.branch = true
+run.omit = [
   "*/__init__.py",
   "*/_version.py",
   "squidpy/pl/_interactive/*",
   "tox/*",
 ]
-
-[tool.coverage.paths]
-source = [
+run.parallel = true
+run.source = [ "squidpy" ]
+paths.source = [
   "squidpy",
   "*/site-packages/squidpy",
 ]
-
-[tool.coverage.report]
-exclude_lines = [
+report.exclude_lines = [
   "\\#.*pragma:\\s*no.?cover",
-  "^if __name__ == .__main__.:$",
   "^\\s*raise AssertionError\\b",
   "^\\s*raise NotImplementedError\\b",
   "^\\s*return NotImplemented\\b",
+  "^if __name__ == .__main__.:$",
 ]
-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"
+report.precision = 2
+report.show_missing = true
+report.skip_empty = true
+report.sort = "Miss"
 
 [tool.cruft]
 skip = [
@@ -324,3 +278,24 @@ 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/_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