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Merged
flying-sheep merged 1 commit into from
Mar 7, 2025
Merged

Format TOML with taplo #1898

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4 changes: 4 additions & 0 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
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5 changes: 5 additions & 0 deletions .taplo.toml
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@@ -0,0 +1,5 @@
[formatting]
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@ilan-gold ilan-gold Mar 7, 2025

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why put this toml under a . prefix?

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@flying-sheep flying-sheep Mar 7, 2025

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I think both taplo.toml and .taplo.toml work, but hiding it in file managers makes things a little cleaner. code editors will still display it.

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@flying-sheep flying-sheep Mar 7, 2025

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Ideally, this would happen: tamasfe/taplo#603

array_auto_collapse = false
column_width = 120
compact_arrays = false
indent_string = ' '
22 changes: 11 additions & 11 deletions hatch.toml
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@@ -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}"
Expand All @@ -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" ]
48 changes: 24 additions & 24 deletions pyproject.toml
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@@ -1,6 +1,6 @@
[build-system]
build-backend = "hatchling.build"
requires = ["hatchling", "hatch-vcs"]
requires = [ "hatchling", "hatch-vcs" ]

[project]
name = "anndata"
Expand Down Expand Up @@ -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/"
Expand All @@ -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",
Expand All @@ -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 = [
Expand All @@ -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
Expand Down Expand Up @@ -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]
Expand Down