From 4c6bba0dcbc2718babcb6d5e50c28332a8bcda56 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 9 Feb 2026 18:33:32 +0000 Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/biomejs/pre-commit: v2.3.10 → v2.3.14](https://github.com/biomejs/pre-commit/compare/v2.3.10...v2.3.14) - [github.com/tox-dev/pyproject-fmt: v2.11.1 → v2.14.2](https://github.com/tox-dev/pyproject-fmt/compare/v2.11.1...v2.14.2) - [github.com/astral-sh/ruff-pre-commit: v0.14.14 → v0.15.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.14...v0.15.0) --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f3021c8..254225f 100644 --- a/.pre-commit-config.yaml +++ b/.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: v2.3.14 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: v2.14.2 hooks: - id: pyproject-fmt - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.14.14 + rev: v0.15.0 hooks: - id: ruff-check types_or: [python, pyi, jupyter] From 91cd98f61bdaa22d23f0843abbe61d42471acbb5 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 9 Feb 2026 18:35:00 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- pyproject.toml | 70 +++++++++++++++++--------------------------------- 1 file changed, 24 insertions(+), 46 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 4e9b520..d75d190 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,7 +28,6 @@ classifiers = [ "Topic :: Scientific/Engineering :: Bio-Informatics", ] dynamic = [ "version" ] - dependencies = [ "anndata>=0.10.8", "h5py", @@ -38,7 +37,6 @@ dependencies = [ # for debug logging (referenced from the issue template) "session-info2", ] - optional-dependencies.io = [ "fsspec", "zarr" ] # https://docs.pypi.org/project_metadata/#project-urls urls.Documentation = "https://mudata.readthedocs.io/" @@ -52,13 +50,11 @@ dev = [ "pre-commit", "twine>=4.0.2", ] - test = [ "coverage>=7.10", "pytest", "zarr", ] - doc = [ "docutils>=0.8,!=0.18.*,!=0.19.*", "ipykernel", @@ -76,51 +72,33 @@ doc = [ "sphinxext-opengraph", ] -[tool.hatch.version] -source = "vcs" - -[tool.hatch.build.hooks.vcs] -version-file = "src/mudata/_version.py" - -[tool.hatch.envs.default] -installer = "uv" -dependency-groups = [ "dev" ] - -[tool.hatch.envs.docs] -dependency-groups = [ "doc" ] -scripts.build = "sphinx-build -M html docs docs/_build {args}" -scripts.open = "python -m webbrowser -t docs/_build/html/index.html" -scripts.clean = "git clean -fdX -- {args:docs}" - -# Test the lowest and highest supported Python versions with normal deps -[[tool.hatch.envs.hatch-test.matrix]] -deps = [ "stable" ] -python = [ "3.11", "3.14" ] - -# Test the newest supported Python version also with pre-release deps -[[tool.hatch.envs.hatch-test.matrix]] -deps = [ "pre" ] -python = [ "3.14" ] - -[tool.hatch.envs.hatch-test] -dependency-groups = [ "dev", "test" ] - -[tool.hatch.envs.hatch-test.overrides] +[tool.hatch] +build.hooks.vcs.version-file = "src/mudata/_version.py" +envs.default.installer = "uv" +envs.default.dependency-groups = [ "dev" ] +envs.docs.dependency-groups = [ "doc" ] +envs.docs.scripts.build = "sphinx-build -M html docs docs/_build {args}" +envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html" +envs.docs.scripts.clean = "git clean -fdX -- {args:docs}" +envs.hatch-test.dependency-groups = [ "dev", "test" ] +envs.hatch-test.matrix = [ + { deps = [ "stable" ], python = [ "3.11", "3.14" ] }, + { deps = [ "pre" ], python = [ "3.14" ] } +] # If the matrix variable `deps` is set to "pre", # set the environment variable `UV_PRERELEASE` to "allow". -matrix.deps.env-vars = [ +envs.hatch-test.overrides.matrix.deps.env-vars = [ { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] }, ] +version.source = "vcs" [tool.ruff] line-length = 120 src = [ "src" ] extend-include = [ "*.ipynb" ] - format.skip-magic-trailing-comma = true format.exclude = [ "*.ipynb" ] format.docstring-code-format = true - lint.select = [ "B", # flake8-bugbear "BLE", # flake8-blind-except @@ -135,11 +113,11 @@ lint.select = [ "W", # Warning detected by Pycodestyle ] lint.ignore = [ - "B008", # Errors from function calls in argument defaults. These are fine when the result is immutable. - "D100", # Missing docstring in public module - "D104", # Missing docstring in public package - "D105", # __magic__ methods are often self-explanatory, allow missing docstrings - "D107", # Missing docstring in __init__ + "B008", # Errors from function calls in argument defaults. These are fine when the result is immutable. + "D100", # Missing docstring in public module + "D104", # Missing docstring in public package + "D105", # __magic__ methods are often self-explanatory, allow missing docstrings + "D107", # Missing docstring in __init__ # Disable one in each pair of mutually incompatible rules "D203", # We don’t want a blank line before a class docstring "D213", # <> We want docstrings to start immediately after the opening triple quote @@ -163,10 +141,10 @@ addopts = [ "--import-mode=importlib", # allow using test files with same name ] -[tool.coverage.run] -source = [ "mudata" ] -patch = [ "subprocess" ] -omit = [ +[tool.coverage] +run.source = [ "mudata" ] +run.patch = [ "subprocess" ] +run.omit = [ "**/test_*.py", ]