Formatting (#3414)

Co-authored-by: Ilan Gold <[email protected]>

.gitignore

@@ -42,7 +42,6 @@ Thumbs.db
 
 # IDEs and editors
 /.idea/
-/.vscode/
 
 # asv benchmark files
 /benchmarks/.asv

.pre-commit-config.yaml

@@ -3,14 +3,11 @@ repos:
     rev: v0.8.6
     hooks:
     -   id: ruff
-        types_or: [python, pyi, jupyter]
         args: ["--fix"]
     -   id: ruff-format
-        types_or: [python, pyi, jupyter]
     # The following can be removed once PLR0917 is out of preview
     -   name: ruff preview rules
         id: ruff
-        types_or: [python, pyi, jupyter]
         args: ["--preview", "--select=PLR0917"]
 -   repo: https://github.com/flying-sheep/bibfmt
     rev: v4.3.0
@@ -19,6 +16,15 @@ repos:
         args:
         - --sort-by-bibkey
         - --drop=abstract
+-   repo: https://github.com/biomejs/pre-commit
+    rev: v0.6.1
+    hooks:
+    -   id: biome-format
+        additional_dependencies: ["@biomejs/[email protected]"]
+-   repo: https://github.com/ComPWA/taplo-pre-commit
+    rev: v0.9.3
+    hooks:
+    -   id: taplo-format
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
@@ -34,6 +40,3 @@ repos:
     -   id: detect-private-key
     -   id: no-commit-to-branch
         args: ["--branch=main"]
-
-ci:
-    autofix_prs: false

.taplo.toml

@@ -0,0 +1,5 @@
+[formatting]
+array_auto_collapse = false
+column_width = 120
+compact_arrays = false
+indent_string = '    '

.vscode/launch.json

@@ -0,0 +1,26 @@
+{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Documentation",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": { "PYTEST_ADDOPTS": "--color=yes" },
+            "presentation": { "hidden": true },
+        },
+    ],
+}

.vscode/settings.json

@@ -0,0 +1,22 @@
+{
+    "[python][toml][json][jsonc]": {
+        "editor.formatOnSave": true,
+        "editor.codeActionsOnSave": {
+            "source.organizeImports": "explicit",
+            "source.fixAll": "explicit",
+        },
+    },
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+    },
+    "[toml]": {
+        "editor.defaultFormatter": "tamasfe.even-better-toml",
+    },
+    "[json][jsonc]": {
+        "editor.defaultFormatter": "biomejs.biome",
+    },
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestArgs": ["-vv", "--color=yes"],
+    "python.testing.pytestEnabled": true,
+    "python.terminal.activateEnvironment": true,
+}

biome.jsonc

@@ -0,0 +1,21 @@
+{
+    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "formatter": {
+        "indentStyle": "space",
+        "indentWidth": 4,
+    },
+    "overrides": [
+        {
+            "include": ["./.vscode/*.json", "**/*.jsonc", "**/asv.conf.json"],
+            "json": {
+                "formatter": {
+                    "trailingCommas": "all",
+                },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}

hatch.toml

@@ -1,9 +1,9 @@
 [envs.default]
 installer = "uv"
-features = ["dev"]
+features = [ "dev" ]
 
 [envs.docs]
-features = ["doc"]
+features = [ "doc" ]
 scripts.build = "sphinx-build -M html docs docs/_build -W --keep-going {args}"
 scripts.open = "python3 -m webbrowser -t docs/_build/html/index.html"
 scripts.clean = "git clean -fdX -- {args:docs}"
@@ -14,23 +14,23 @@ scripts.build = "python3 ci/scripts/towncrier_automation.py {args}"
 scripts.clean = "git restore --source=HEAD --staged --worktree -- docs/release-notes"
 
 [envs.hatch-test]
-default-args = []
-features = ["test", "dask-ml"]
-extra-dependencies = ["ipykernel"]
+default-args = [  ]
+features = [ "test", "dask-ml" ]
+extra-dependencies = [ "ipykernel" ]
 overrides.matrix.deps.env-vars = [
-    { if = ["pre"], key = "UV_PRERELEASE", value = "allow" },
-    { if = ["min"], key = "UV_CONSTRAINT", value = "ci/scanpy-min-deps.txt" },
+    { if = [ "pre" ], key = "UV_PRERELEASE", value = "allow" },
+    { if = [ "min" ], key = "UV_CONSTRAINT", value = "ci/scanpy-min-deps.txt" },
 ]
 overrides.matrix.deps.pre-install-commands = [
-    { if = ["min"], value = "uv run ci/scripts/min-deps.py pyproject.toml --all-extras -o ci/scanpy-min-deps.txt" },
+    { if = [ "min" ], value = "uv run ci/scripts/min-deps.py pyproject.toml --all-extras -o ci/scanpy-min-deps.txt" },
 ]
 overrides.matrix.deps.python = [
-    { if = ["min"], value = "3.10" },
-    { if = ["stable", "full", "pre"], value = "3.12" },
+    { if = [ "min" ], value = "3.10" },
+    { if = [ "stable", "full", "pre" ], value = "3.12" },
 ]
 overrides.matrix.deps.features = [
-    { if = ["full"], value = "test-full" },
+    { if = [ "full" ], value = "test-full" },
 ]
 
 [[envs.hatch-test.matrix]]
-deps = ["stable", "full", "pre", "min"]
+deps = [ "stable", "full", "pre", "min" ]

pyproject.toml

@@ -1,30 +1,30 @@
 [build-system]
 build-backend = "hatchling.build"
-requires = ["hatchling", "hatch-vcs"]
+requires = [ "hatchling", "hatch-vcs" ]
 
 [project]
 name = "scanpy"
 description = "Single-Cell Analysis in Python."
 requires-python = ">=3.10"
 license = "BSD-3-clause"
 authors = [
-    {name = "Alex Wolf"},
-    {name = "Philipp Angerer"},
-    {name = "Fidel Ramirez"},
-    {name = "Isaac Virshup"},
-    {name = "Sergei Rybakov"},
-    {name = "Gokcen Eraslan"},
-    {name = "Tom White"},
-    {name = "Malte Luecken"},
-    {name = "Davide Cittaro"},
-    {name = "Tobias Callies"},
-    {name = "Marius Lange"},
-    {name = "Andrés R. Muñoz-Rojas"},
+    { name = "Alex Wolf" },
+    { name = "Philipp Angerer" },
+    { name = "Fidel Ramirez" },
+    { name = "Isaac Virshup" },
+    { name = "Sergei Rybakov" },
+    { name = "Gokcen Eraslan" },
+    { name = "Tom White" },
+    { name = "Malte Luecken" },
+    { name = "Davide Cittaro" },
+    { name = "Tobias Callies" },
+    { name = "Marius Lange" },
+    { name = "Andrés R. Muñoz-Rojas" },
 ]
 maintainers = [
-    {name = "Philipp Angerer", email = "[email protected]"},
-    {name = "Ilan Gold"},
-    {name = "Severin Dicks"},
+    { name = "Philipp Angerer", email = "[email protected]" },
+    { name = "Ilan Gold", email = "[email protected]" },
+    { name = "Severin Dicks" },
 ]
 readme = "README.md"
 classifiers = [
@@ -56,7 +56,7 @@ dependencies = [
     "tqdm",
     "scikit-learn>=1.1,<1.6.0",
     "statsmodels>=0.13",
-    "patsy!=1.0.0", # https://github.com/pydata/patsy/issues/215
+    "patsy!=1.0.0",                               # https://github.com/pydata/patsy/issues/215
     "networkx>=2.7",
     "natsort",
     "joblib",
@@ -65,10 +65,10 @@ dependencies = [
     "pynndescent>=0.5",
     "packaging>=21.3",
     "session-info2",
-    "legacy-api-wrap>=1.4",  # for positional API deprecations
+    "legacy-api-wrap>=1.4",                       # for positional API deprecations
     "typing-extensions; python_version < '3.13'",
 ]
-dynamic = ["version"]
+dynamic = [ "version" ]
 
 # https://docs.pypi.org/project_metadata/#project-urls
 [project.urls]
@@ -120,13 +120,13 @@ doc = [
     "sphinx-design",
     "sphinx-tabs",
     "readthedocs-sphinx-search",
-    "sphinxext-opengraph", # for nice cards when sharing on social
+    "sphinxext-opengraph",              # for nice cards when sharing on social
     "sphinx-copybutton",
     "nbsphinx>=0.9",
-    "ipython>=7.20",  # for nbsphinx code highlighting
+    "ipython>=7.20",                    # for nbsphinx code highlighting
     "matplotlib!=3.6.1",
     "sphinxcontrib-bibtex",
-    "setuptools", # undeclared dependency of sphinxcontrib-bibtex→pybtex
+    "setuptools",                       # undeclared dependency of sphinxcontrib-bibtex→pybtex
     # TODO: remove necessity for being able to import doc-linked classes
     "scanpy[paga,dask-ml]",
     "sam-algorithm",
@@ -139,22 +139,22 @@ dev = [
     "towncrier",
 ]
 # Algorithms
-paga = ["igraph"]
-louvain = ["igraph", "louvain>=0.6.0,!=0.6.2"]  # Louvain community detection
-leiden = ["igraph>=0.10", "leidenalg>=0.9.0"]  # Leiden community detection
-bbknn = ["bbknn"]  # Batch balanced KNN (batch correction)
-magic = ["magic-impute>=2.0"]  # MAGIC imputation method
-skmisc = ["scikit-misc>=0.1.3"]  # highly_variable_genes method 'seurat_v3'
-harmony = ["harmonypy"]  # Harmony dataset integration
-scanorama = ["scanorama"]  # Scanorama dataset integration
-scrublet = ["scikit-image"]  # Doublet detection with automatic thresholds
+paga = [ "igraph" ]
+louvain = [ "igraph", "louvain>=0.6.0,!=0.6.2" ] # Louvain community detection
+leiden = [ "igraph>=0.10", "leidenalg>=0.9.0" ]  # Leiden community detection
+bbknn = [ "bbknn" ]                              # Batch balanced KNN (batch correction)
+magic = [ "magic-impute>=2.0" ]                  # MAGIC imputation method
+skmisc = [ "scikit-misc>=0.1.3" ]                # highly_variable_genes method 'seurat_v3'
+harmony = [ "harmonypy" ]                        # Harmony dataset integration
+scanorama = [ "scanorama" ]                      # Scanorama dataset integration
+scrublet = [ "scikit-image" ]                    # Doublet detection with automatic thresholds
 # Acceleration
-rapids = ["cudf>=0.9", "cuml>=0.9", "cugraph>=0.9"]  # GPU accelerated calculation of neighbors
-dask = ["dask[array]>=2022.09.2,<2024.8.0"]  # Use the Dask parallelization engine
-dask-ml = ["dask-ml", "scanpy[dask]"]  # Dask-ML for sklearn-like API
+rapids = [ "cudf>=0.9", "cuml>=0.9", "cugraph>=0.9" ] # GPU accelerated calculation of neighbors
+dask = [ "dask[array]>=2022.09.2,<2024.8.0" ]         # Use the Dask parallelization engine
+dask-ml = [ "dask-ml", "scanpy[dask]" ]               # Dask-ML for sklearn-like API
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/testing", "src/scanpy"]
+packages = [ "src/testing", "src/scanpy" ]
 [tool.hatch.version]
 source = "vcs"
 raw-options.version_scheme = "release-branch-semver"
@@ -169,8 +169,8 @@ addopts = [
     "-ptesting.scanpy._pytest",
     "--pyargs",
 ]
-testpaths = ["./tests", "./ci", "scanpy"]
-norecursedirs = ["tests/_images"]
+testpaths = [ "./tests", "./ci", "scanpy" ]
+norecursedirs = [ "tests/_images" ]
 xfail_strict = true
 nunit_attach_on = "fail"
 markers = [
@@ -203,12 +203,12 @@ filterwarnings = [
 
 [tool.coverage.run]
 data_file = "test-data/coverage"
-source_pkgs = ["scanpy"]
-omit = ["tests/*", "src/testing/*"]
+source_pkgs = [ "scanpy" ]
+omit = [ "tests/*", "src/testing/*" ]
 [tool.coverage.xml]
 output = "test-data/coverage.xml"
 [tool.coverage.paths]
-source = [".", "**/site-packages"]
+source = [ ".", "**/site-packages" ]
 [tool.coverage.report]
 exclude_also = [
     "if __name__ == .__main__.:",
@@ -218,7 +218,7 @@ exclude_also = [
 ]
 
 [tool.ruff]
-src = ["src"]
+src = [ "src" ]
 
 [tool.ruff.format]
 docstring-code-format = true
@@ -254,10 +254,10 @@ ignore = [
 ]
 [tool.ruff.lint.per-file-ignores]
 # Do not assign a lambda expression, use a def
-"src/scanpy/tools/_rank_genes_groups.py" = ["E731"]
+"src/scanpy/tools/_rank_genes_groups.py" = [ "E731" ]
 [tool.ruff.lint.isort]
-known-first-party = ["scanpy", "testing.scanpy"]
-required-imports = ["from __future__ import annotations"]
+known-first-party = [ "scanpy", "testing.scanpy" ]
+required-imports = [ "from __future__ import annotations" ]
 [tool.ruff.lint.flake8-tidy-imports.banned-api]
 "pytest.importorskip".msg = "Use the “@needs” decorator/mark instead"
 "pandas.api.types.is_categorical_dtype".msg = "Use isinstance(s.dtype, CategoricalDtype) instead"
@@ -267,7 +267,7 @@ required-imports = ["from __future__ import annotations"]
 "numba.jit".msg = "Use `scanpy._compat.njit` instead"
 "numba.njit".msg = "Use `scanpy._compat.njit` instead"
 [tool.ruff.lint.flake8-type-checking]
-exempt-modules = []
+exempt-modules = [  ]
 strict = true
 
 [tool.towncrier]

tests/_data/visium_data/1.0.0/spatial/scalefactors_json.json

@@ -1 +1,6 @@
-{"spot_diameter_fullres": 89.42751063343188, "tissue_hires_scalef": 0.150015, "fiducial_diameter_fullres": 144.45982486939, "tissue_lowres_scalef": 0.045004502}
+{
+    "spot_diameter_fullres": 89.42751063343188,
+    "tissue_hires_scalef": 0.150015,
+    "fiducial_diameter_fullres": 144.45982486939,
+    "tissue_lowres_scalef": 0.045004502
+}