Format (#187)

.pre-commit-config.yaml

@@ -9,7 +9,12 @@ repos:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: "2.2.1"
     hooks:
-      - id: prettier
+      - id: pyproject-fmt
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v0.4.0
+    hooks:
+      - id: biome-format
+        additional_dependencies: ["@biomejs/[email protected]"]

.vscode/launch.json

@@ -3,7 +3,7 @@
     "configurations": [
         {
             "name": "Python: Debug Tests",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${file}",
             "purpose": ["debug-test"],

.vscode/settings.json

@@ -1,4 +1,8 @@
 {
+    "[json][jsonc]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "biomejs.biome",
+    },
     "[python]": {
         "editor.formatOnSave": true,
         "editor.defaultFormatter": "charliermarsh.ruff",

biome.jsonc

@@ -0,0 +1,21 @@
+{
+    "$schema": "https://biomejs.dev/schemas/1.8.3/schema.json",
+    "formatter": {
+        "indentStyle": "space",
+        "indentWidth": 4,
+    },
+    "overrides": [
+        {
+            "include": ["./.vscode/*.json", "**/*.jsonc"],
+            "json": {
+                "formatter": {
+                    "trailingCommas": "all",
+                },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}

pyproject.toml

@@ -1,104 +1,106 @@
+[build-system]
+build-backend = "hatchling.build"
+requires = [ "hatch-vcs", "hatchling" ]
+
 [project]
-name = 'anndata2ri'
+name = "anndata2ri"
+readme = "README.rst"
 authors = [
-    { name = 'Philipp A.', email = '[email protected]' },
+    { name = "Philipp A.", email = "[email protected]" },
 ]
-readme = 'README.rst'
+requires-python = ">=3.9"
 classifiers = [
-    'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
-    'Development Status :: 4 - Beta',
-    'Intended Audience :: Developers',
-    'Intended Audience :: Science/Research',
-    'Programming Language :: Python :: 3',
-    'Programming Language :: R',
-    'Topic :: Scientific/Engineering :: Bio-Informatics',
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: R",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
-urls.'Documentation' = 'https://icb-anndata2ri.readthedocs-hosted.com/'
-urls.'Source Code' = 'https://github.com/theislab/anndata2ri'
-urls.'Issue Tracker' = 'https://github.com/theislab/anndata2ri/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc'
-dynamic = ['version']
-requires-python = '>= 3.9'
+dynamic = [ "version" ]
 dependencies = [
-    'rpy2 >= 3.5.2',  # first with get_conversion
-    'tzlocal',  # for pandas2ri
-    'anndata',
+    "anndata",
+    "rpy2>=3.5.2", # first with get_conversion
+    "tzlocal",     # for pandas2ri
 ]
 
-[project.optional-dependencies]
-dev = ['pre-commit', 'setuptools-scm']
-test = [
-    'pytest',
-    'pytest-faulthandler',
-    'pygments',
-    'scanpy',
+optional-dependencies.dev = [ "pre-commit", "setuptools-scm" ]
+optional-dependencies.doc = [
+    "lxml",                       # For scraping the R link info
+    "scanpydoc[theme,typehints]",
+    "sphinx>=3",
 ]
-doc = [
-    'sphinx>=3.0',
-    'scanpydoc[theme,typehints]',
-    'lxml',  # For scraping the R link info
+optional-dependencies.test = [
+    "pygments",
+    "pytest",
+    "pytest-faulthandler",
+    "scanpy",
 ]
+urls.'Documentation' = "https://icb-anndata2ri.readthedocs-hosted.com/"
+urls.'Issue Tracker' = "https://github.com/theislab/anndata2ri/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc"
+urls.'Source Code' = "https://github.com/theislab/anndata2ri"
 
 [tool.hatch.version]
-source = 'vcs'
-raw-options = { local_scheme = 'no-local-version' }  # be able to publish dev version
+source = "vcs"
+raw-options = { local_scheme = "no-local-version" } # be able to publish dev version
 
 [tool.hatch.build.hooks.vcs]
-version-file = 'src/anndata2ri/_version.py'
+version-file = "src/anndata2ri/_version.py"
 
 [tool.hatch.envs.default]
-installer = 'uv'
+installer = "uv"
 
 [tool.hatch.envs.docs]
-features = ['doc']
+features = [ "doc" ]
 [tool.hatch.envs.docs.scripts]
-build = 'sphinx-build -M html docs docs/_build'
+build = "sphinx-build -M html docs docs/_build"
 
 [tool.hatch.envs.hatch-test]
-features = ['test']
-
-[tool.pytest.ini_options]
-addopts = [
-    '--import-mode=importlib',
-    '-panndata2ri.test_utils',
-    '-Werror',
-]
+features = [ "test" ]
 
 [tool.ruff]
 line-length = 120
-[tool.ruff.lint]
-select = ['ALL']
-ignore = [
-    'Q', # handled by formatter
-    'ANN101', # self type doesn’t need to be annotated
-    'C408', # dict() calls are nice
-    'COM812', # trailing commas handled by black
-    'D203', # prefer 0 to 1 blank line before class members
-    'D213', # prefer docstring summary on first line
-    'FIX002', # “TODO” comments
-    'PLR0913', # having many (kw)args is fine
-    'S101', # asserts are fine
+format.quote-style = "single"
+lint.select = [ "ALL" ]
+lint.ignore = [
+    "ANN101",  # self type doesn’t need to be annotated
+    "C408",    # dict() calls are nice
+    "COM812",  # trailing commas handled by black
+    "D203",    # prefer 0 to 1 blank line before class members
+    "D213",    # prefer docstring summary on first line
+    "FIX002",  # “TODO” comments
+    "PLR0913", # having many (kw)args is fine
+    "Q",       # handled by formatter
+    "S101",    # asserts are fine
 ]
-allowed-confusables = ['’', '×']
-[tool.ruff.lint.per-file-ignores]
-'**/*.ipynb' = [
-    'T201',  # Allow print in notebooks
-    'F821',  # `%%R -o` means that ruff doesn’t understand which variables exist
+lint.per-file-ignores.'**/*.ipynb' = [
+    "F821", # `%%R -o` means that ruff doesn’t understand which variables exist
+    "T201", # Allow print in notebooks
 ]
-'src/**/*.py' = ['PT']  # No Pytest checks
-'docs/**/*.py' = ['INP001']  # No __init__.py in docs
-'tests/**/*.py' = [
-    'INP001', # No __init__.py in tests
-    'D100', # test modules don’t need docstrings
-    'D103', # tests don’t need docstrings
-    'PD901', # “df” is a fine var name in tests
-    'PLR2004', # magic numbers are fine in tests
+lint.per-file-ignores.'docs/**/*.py' = [ "INP001" ] # No __init__.py in docs
+lint.per-file-ignores.'src/**/*.py' = [ "PT" ] # No Pytest checks
+lint.per-file-ignores.'tests/**/*.py' = [
+    "D100",    # test modules don’t need docstrings
+    "D103",    # tests don’t need docstrings
+    "INP001",  # No __init__.py in tests
+    "PD901",   # “df” is a fine var name in tests
+    "PLR2004", # magic numbers are fine in tests
 ]
-[tool.ruff.lint.isort]
-known-first-party = ['anndata2ri']
-lines-after-imports = 2
-[tool.ruff.format]
-quote-style = 'single'
+lint.allowed-confusables = [ "×", "’" ]
+lint.isort.known-first-party = [ "anndata2ri" ]
+lint.isort.lines-after-imports = 2
 
-[build-system]
-requires = ['hatchling', 'hatch-vcs']
-build-backend = 'hatchling.build'
+[tool.pyproject-fmt]
+indent = 4
+
+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+    "-panndata2ri.test_utils",
+    "-Werror",
+]