Format TOML with taplo (#1898)

Author: flying-sheep

.pre-commit-config.yaml

@@ -9,6 +9,10 @@ repos:
     rev: v1.9.4
     hooks:
       - id: biome-format
+  - 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:

.taplo.toml

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

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}"
@@ -14,21 +14,21 @@ 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 = ["dev", "test"]
-extra-dependencies = ["ipykernel"]
+default-args = [  ]
+features = [ "dev", "test" ]
+extra-dependencies = [ "ipykernel" ]
 env-vars.UV_CONSTRAINT = "ci/constraints.txt"
 overrides.matrix.deps.env-vars = [
-    { if = ["pre"], key = "UV_PRERELEASE", value = "allow" },
-    { if = ["min"], key = "UV_CONSTRAINT", value = "ci/constraints.txt ci/min-deps.txt" },
+    { if = [ "pre" ], key = "UV_PRERELEASE", value = "allow" },
+    { if = [ "min" ], key = "UV_CONSTRAINT", value = "ci/constraints.txt ci/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/min-deps.txt" },
+    { if = [ "min" ], value = "uv run ci/scripts/min-deps.py pyproject.toml --all-extras -o ci/min-deps.txt" },
 ]
 overrides.matrix.deps.python = [
-    { if = ["min"], value = "3.11" },
-    { if = ["stable", "pre"], value = "3.13" },
+    { if = [ "min" ], value = "3.11" },
+    { if = [ "stable", "pre" ], value = "3.13" },
 ]
 
 [[envs.hatch-test.matrix]]
-deps = ["stable", "pre", "min"]
+deps = [ "stable", "pre", "min" ]

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
 build-backend = "hatchling.build"
-requires = ["hatchling", "hatch-vcs"]
+requires = [ "hatchling", "hatch-vcs" ]
 
 [project]
 name = "anndata"
@@ -49,7 +49,7 @@ dependencies = [
     "legacy-api-wrap",
     "zarr >=2.15.0, !=3.0.0, !=3.0.1, !=3.0.2, !=3.0.3",
 ]
-dynamic = ["version"]
+dynamic = [ "version" ]
 
 [project.urls]
 Documentation = "https://anndata.readthedocs.io/"
@@ -74,14 +74,14 @@ doc = [
     "nbsphinx",
     "scanpydoc[theme,typehints] >=0.15.1",
     "awkward>=2.3",
-    "IPython",                          # For syntax highlighting in notebooks
+    "IPython",                             # For syntax highlighting in notebooks
     "myst_parser",
     "sphinx_design>=0.5.0",
     "readthedocs-sphinx-search",
     # for unreleased changes
     "anndata[dev-doc]",
 ]
-dev-doc = ["towncrier>=24.8.0"] # release notes tool
+dev-doc = [ "towncrier>=24.8.0" ] # release notes tool
 test = [
     "loompy>=3.0.5",
     "pytest>=8.2,<8.3.4",
@@ -92,36 +92,36 @@ test = [
     "joblib",
     "boltons",
     "scanpy>=1.10",
-    "httpx", # For data downloading
+    "httpx",              # For data downloading
     "dask[distributed]",
     "awkward>=2.3",
     "pyarrow",
     "pytest_memray",
     "pytest-mock",
     "anndata[dask]",
 ]
-dev-test = ["pytest-xdist"] # local test speedups
-gpu = ["cupy"]
-cu12 = ["cupy-cuda12x"]
-cu11 = ["cupy-cuda11x"]
+dev-test = [ "pytest-xdist" ] # local test speedups
+gpu = [ "cupy" ]
+cu12 = [ "cupy-cuda12x" ]
+cu11 = [ "cupy-cuda11x" ]
 # https://github.com/dask/dask/issues/11290
 # https://github.com/dask/dask/issues/11752
-dask = ["dask[array]>=2023.5.1,!=2024.8.*,!=2024.9.*,<2025.2.0"]
+dask = [ "dask[array]>=2023.5.1,!=2024.8.*,!=2024.9.*,<2025.2.0" ]
 
 [tool.hatch.version]
 source = "vcs"
 raw-options.version_scheme = "release-branch-semver"
 [tool.hatch.build.targets.wheel]
-packages = ["src/anndata", "src/testing"]
+packages = [ "src/anndata", "src/testing" ]
 
 [tool.coverage.run]
 data_file = "test-data/coverage"
-source_pkgs = ["anndata"]
-omit = ["src/anndata/_version.py", "**/test_*.py"]
+source_pkgs = [ "anndata" ]
+omit = [ "src/anndata/_version.py", "**/test_*.py" ]
 [tool.coverage.xml]
 output = "test-data/coverage.xml"
 [tool.coverage.paths]
-source = ["./src", "**/site-packages"]
+source = [ "./src", "**/site-packages" ]
 
 [tool.coverage.report]
 exclude_also = [
@@ -147,21 +147,21 @@ filterwarnings_when_strict = [
     "default:(Observation|Variable) names are not unique. To make them unique:UserWarning",
     "default::scipy.sparse.SparseEfficiencyWarning",
     "default::dask.array.core.PerformanceWarning",
-    "default:anndata will no longer support zarr v2:DeprecationWarning"
+    "default:anndata will no longer support zarr v2:DeprecationWarning",
 ]
 python_files = "test_*.py"
 testpaths = [
-    "anndata", # docstrings (module name due to --pyargs)
-    "./tests", # unit tests
-    "./ci/scripts", # CI script tests
+    "anndata",                  # docstrings (module name due to --pyargs)
+    "./tests",                  # unit tests
+    "./ci/scripts",             # CI script tests
     "./docs/concatenation.rst", # further doctests
 ]
 # For some reason this effects how logging is shown when tests are run
 xfail_strict = true
-markers = ["gpu: mark test to run on GPU"]
+markers = [ "gpu: mark test to run on GPU" ]
 
 [tool.ruff]
-src = ["src"]
+src = [ "src" ]
 
 [tool.ruff.format]
 docstring-code-format = true
@@ -197,17 +197,17 @@ ignore = [
 ]
 [tool.ruff.lint.per-file-ignores]
 # E721 comparing types, but we specifically are checking that we aren't getting subtypes (views)
-"tests/test_readwrite.py" = ["E721"]
+"tests/test_readwrite.py" = [ "E721" ]
 [tool.ruff.lint.isort]
-known-first-party = ["anndata"]
-required-imports = ["from __future__ import annotations"]
+known-first-party = [ "anndata" ]
+required-imports = [ "from __future__ import annotations" ]
 [tool.ruff.lint.flake8-tidy-imports.banned-api]
 "subprocess.call".msg = "Use `subprocess.run([…])` instead"
 "subprocess.check_call".msg = "Use `subprocess.run([…], check=True)` instead"
 "subprocess.check_output".msg = "Use `subprocess.run([…], check=True, capture_output=True)` instead"
 "legacy_api_wrap.legacy_api".msg = "Use anndata.compat.old_positionals instead"
 [tool.ruff.lint.flake8-type-checking]
-exempt-modules = []
+exempt-modules = [  ]
 strict = true
 
 [tool.codespell]