Ruff (#112)

.pre-commit-config.yaml

@@ -2,14 +2,14 @@ repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
-  - id: double-quote-string-fixer
   - id: trailing-whitespace
 - repo: https://github.com/psf/black
   rev: 23.3.0
   hooks:
   - id: black
     language_version: python3
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.0.278
   hooks:
-  - id: isort
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]

.vscode/settings.json

@@ -2,9 +2,10 @@
     "[python]": {
         "editor.formatOnSave": true,
         "editor.defaultFormatter": "ms-python.black-formatter",
-        //"editor.codeActionsOnSave": {
-        //    "source.fixAll.ruff": true,
-        //},
+        "editor.codeActionsOnSave": {
+            "source.fixAll.ruff": true,
+            "source.organizeImports.ruff": true,
+        },
     },
     "python.testing.pytestArgs": [],
     "python.testing.unittestEnabled": false,

docs/conf.py

@@ -1,6 +1,8 @@
+"""Sphinx configuration."""
+
 import sys
 from abc import ABC
-from datetime import datetime
+from datetime import datetime, timezone
 from pathlib import Path
 from unittest.mock import MagicMock, patch
 
@@ -11,8 +13,8 @@
     from importlib_metadata import metadata
 
 
-def mock_rpy2():
-    # Can’t use autodoc_mock_imports as we import anndata2ri
+def mock_rpy2() -> None:
+    """Can’t use autodoc_mock_imports as we import anndata2ri."""
     patch('rpy2.situation.get_r_home', lambda: None).start()
     sys.modules['rpy2.rinterface_lib'] = MagicMock()
     submods = ['embedded', 'conversion', 'memorymanagement', 'sexp', 'bufferprotocol', 'callbacks', '_rinterface_capi']
@@ -27,7 +29,7 @@ def mock_rpy2():
     import rpy2.rinterface_lib.sexp
 
     rpy2.rinterface_lib = sys.modules['rpy2.rinterface_lib']
-    rpy2.rinterface._MissingArgType = object
+    rpy2.rinterface._MissingArgType = object  # noqa: SLF001
     rpy2.rinterface.initr_simple = lambda *_, **__: None
 
     assert rpy2.rinterface_lib.sexp is sexp
@@ -48,15 +50,14 @@ def mock_rpy2():
 project = 'anndata2ri'
 meta = metadata(project)
 author = meta['author-email'].split('"')[1]
-copyright = f'{datetime.now():%Y}, {author}.'
+copyright = f'{datetime.now(tz=timezone.utc):%Y}, {author}.'  # noqa: A001
 version = meta['version']
 release = version
 
 # default settings
 templates_path = ['_templates']
 source_suffix = '.rst'
 master_doc = 'index'
-# default_role = '?'
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 pygments_style = 'sphinx'
 

docs/ext/r_links.py

@@ -1,22 +1,34 @@
+"""Sphinx extension for links to R documentation."""
+
+from __future__ import annotations
+
 import logging
-from typing import Tuple
+from typing import TYPE_CHECKING, ClassVar
 
 from docutils import nodes
-from sphinx.application import Sphinx
-from sphinx.environment import BuildEnvironment
 from sphinx.roles import XRefRole
 
 
+if TYPE_CHECKING:
+    from sphinx.application import Sphinx
+    from sphinx.environment import BuildEnvironment
+
+
 class RManRefRole(XRefRole):
-    nodeclass = nodes.reference
+    """R reference role."""
+
+    nodeclass: ClassVar[nodes.Node] = nodes.reference
+    topic_cache: ClassVar[dict[str, dict[str, str]]] = {}
+    """pkg → alias → url"""
 
-    topic_cache = {}
+    cls: bool
 
-    def __init__(self, *a, cls: bool = False, **kw):
+    def __init__(self, *a, cls: bool = False, **kw) -> None:  # noqa: ANN002, ANN003
+        """Set self.cls."""
         super().__init__(*a, **kw)
         self.cls = cls
 
-    def _get_man(self, pkg: str, alias: str):
+    def _get_man(self, pkg: str, alias: str) -> str:
         from urllib.error import HTTPError
 
         pkg_cache = type(self).topic_cache.setdefault(pkg)
@@ -25,14 +37,14 @@ def _get_man(self, pkg: str, alias: str):
                 try:
                     pkg_cache = self._fetch_cache(repo, pkg)
                     break
-                except HTTPError:
+                except HTTPError:  # noqa: PERF203
                     pass
             else:
                 return None
             type(self).topic_cache[pkg] = pkg_cache
         return pkg_cache.get(alias)
 
-    def _fetch_cache(self, repo: str, pkg: str):
+    def _fetch_cache(self, repo: str, pkg: str) -> dict[str, str]:
         from urllib.parse import urljoin
         from urllib.request import urlopen
 
@@ -41,13 +53,18 @@ def _fetch_cache(self, repo: str, pkg: str):
         if repo.startswith('R'):
             url = f'https://stat.ethz.ch/R-manual/{repo}/library/{pkg}/html/00Index.html'
             tr_xpath = '//tr'
-            get = lambda tr: (tr[0][0].text, tr[0][0].attrib['href'])
+
+            def get(tr: html.HtmlElement) -> tuple[str, str]:
+                return tr[0][0].text, tr[0][0].attrib['href']
+
         else:
             url = f'https://rdrr.io/{repo}/{pkg}/api/'
             tr_xpath = "//div[@id='body-content']//tr[./td]"
-            get = lambda tr: (tr[0].text, tr[1][0].attrib['href'])
 
-        with urlopen(url) as con:
+            def get(tr: html.HtmlElement) -> tuple[str, str]:
+                return tr[0].text, tr[1][0].attrib['href']
+
+        with urlopen(url) as con:  # noqa: S310
             txt = con.read().decode(con.headers.get_content_charset())
         doc = html.fromstring(txt)
         cache = {}
@@ -57,8 +74,14 @@ def _fetch_cache(self, repo: str, pkg: str):
         return cache
 
     def process_link(
-        self, env: BuildEnvironment, refnode: nodes.reference, has_explicit_title: bool, title: str, target: str
-    ) -> Tuple[str, str]:
+        self,
+        env: BuildEnvironment,  # noqa: ARG002
+        refnode: nodes.reference,
+        has_explicit_title: bool,  # noqa: ARG002, FBT001
+        title: str,
+        target: str,
+    ) -> tuple[str, str]:
+        """Derive link title and URL from target."""
         qualified = not target.startswith('~')
         if not qualified:
             target = target[1:]
@@ -70,16 +93,11 @@ def process_link(
         url = self._get_man(package, topic)
         refnode['refuri'] = url
         if not url:
-            logging.warning(f'R topic {target} not found.')
+            logging.warning('R topic %s not found.', target)
         return title, url
 
-    # def result_nodes(self, document: nodes.document, env: BuildEnvironment, node: nodes.reference, is_ref: bool):
-    #    target = node.get('reftarget')
-    #    if target:
-    #        node.attributes['refuri'] = target
-    #    return [node], []
-
 
-def setup(app: Sphinx):
+def setup(app: Sphinx) -> None:
+    """Set Sphinx extension up."""
     app.add_role('rman', RManRefRole())
     app.add_role('rcls', RManRefRole(cls=True))

pyproject.toml

@@ -84,11 +84,35 @@ filterwarnings = [
 line-length = 120
 skip-string-normalization = true
 
-[tool.isort]
-profile = 'black'
-line_length = 120
-lines_after_imports = 2
-length_sort_straight = true
+[tool.ruff]
+line-length = 120
+select = ['ALL']
+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
+    'S101', # asserts are fine
+]
+allowed-confusables = ['’', '×']
+[tool.ruff.per-file-ignores]
+'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
+]
+[tool.ruff.isort]
+known-first-party = ['anndata2ri']
+lines-after-imports = 2
+[tool.ruff.flake8-quotes]
+inline-quotes = 'single'
 
 [build-system]
 requires = ['hatchling', 'hatch-vcs']

src/anndata2ri/__init__.py

@@ -1,6 +1,4 @@
-r"""
-Converter between Python’s AnnData and R’s SingleCellExperiment.
-
+r"""Converter between Python’s AnnData and R’s SingleCellExperiment.
 
 ==========================================================  =  ========================================================
 :rcls:`~SingleCellExperiment::SingleCellExperiment`            :class:`~anndata.AnnData`
@@ -14,17 +12,23 @@
 :rman:`~SingleCellExperiment::reducedDim`\ ``(d, 'DM')``    ⇄  ``d.``\ :attr:`~anndata.AnnData.obsm`\ ``['X_diffmap']``
 ==========================================================  =  ========================================================
 """
-__all__ = ['activate', 'deactivate', 'py2rpy', 'rpy2py', 'converter']
+from __future__ import annotations
 
 from pathlib import Path
-from typing import Any
+from typing import TYPE_CHECKING
+
+from . import _py2r, _r2py  # noqa: F401
+from ._conv import activate, converter, deactivate
 
-from rpy2.rinterface import Sexp
 
-from . import py2r, r2py
-from .conv import activate, converter, deactivate
+if TYPE_CHECKING:
+    from anndata import AnnData
+    from pandas import DataFrame
+    from rpy2.rinterface import Sexp
 
 
+__all__ = ['__version__', 'activate', 'deactivate', 'py2rpy', 'rpy2py', 'converter']
+
 HERE = Path(__file__).parent
 
 __author__ = 'Philipp Angerer'
@@ -35,22 +39,25 @@
 except (ImportError, LookupError):
     try:
         from ._version import __version__
-    except ImportError:
-        raise ImportError('Cannot infer version. Make sure to `pip install` the project or install `setuptools-scm`.')
+    except ImportError as e:
+        msg = 'Cannot infer version. Make sure to `pip install` the project or install `setuptools-scm`.'
+        raise ImportError(msg) from e
 
 
-def py2rpy(obj: Any) -> Sexp:
-    """
-    Convert Python objects to R interface objects. Supports:
+def py2rpy(obj: AnnData) -> Sexp:
+    """Convert Python objects to R interface objects.
+
+    Supports:
 
     - :class:`~anndata.AnnData` → :rcls:`~SingleCellExperiment::SingleCellExperiment`
     """
     return converter.py2rpy(obj)
 
 
-def rpy2py(obj: Any) -> Sexp:
-    """
-    Convert R interface objects to Python objects. Supports:
+def rpy2py(obj: Sexp) -> AnnData | DataFrame:
+    """Convert R interface objects to Python objects.
+
+    Supports:
 
     - :rcls:`~SingleCellExperiment::SingleCellExperiment` → :class:`~anndata.AnnData`
     - :rcls:`S4Vectors::DataFrame` → :class:`pandas.DataFrame`

src/anndata2ri/conv.py → src/anndata2ri/_conv.py

@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
 import pandas as pd
 from rpy2.robjects import conversion, numpy2ri, pandas2ri
@@ -8,13 +10,20 @@
 from . import scipy2ri
 
 
+if TYPE_CHECKING:
+    from collections.abc import Callable
+
+    from rpy2.rinterface import Sexp
+    from scipy.sparse import spmatrix
+
+
 original_converter: conversion.Converter | None = None
 converter = conversion.Converter('original anndata conversion')
 
 _mat_converter = numpy2ri.converter + scipy2ri.converter
 
 
-def mat_py2rpy(obj: np.ndarray) -> np.ndarray:
+def mat_py2rpy(obj: np.ndarray | spmatrix | pd.DataFrame) -> Sexp:
     if isinstance(obj, pd.DataFrame):
         numeric_cols = obj.dtypes <= np.number
         if not numeric_cols.all():
@@ -25,7 +34,7 @@ def mat_py2rpy(obj: np.ndarray) -> np.ndarray:
     return _mat_converter.py2rpy(obj)
 
 
-mat_rpy2py = _mat_converter.rpy2py
+mat_rpy2py: Callable[[Sexp], np.ndarray | spmatrix | Sexp] = _mat_converter.rpy2py
 
 
 def full_converter() -> conversion.Converter:
@@ -40,15 +49,16 @@ def full_converter() -> conversion.Converter:
     return new_converter
 
 
-def activate():
-    r"""
-    Activate conversion for :class:`~anndata.AnnData` objects
+def activate() -> None:
+    r"""Activate conversion for supported objects.
+
+    This includes :class:`~anndata.AnnData` objects
     as well as :ref:`numpy:arrays` and :class:`pandas.DataFrame`\ s
     via ``rpy2.robjects.numpy2ri`` and ``rpy2.robjects.pandas2ri``.
 
     Does nothing if this is the active converter.
     """
-    global original_converter
+    global original_converter  # noqa: PLW0603
 
     if original_converter is not None:
         return
@@ -58,9 +68,9 @@ def activate():
     conversion.set_conversion(new_converter)
 
 
-def deactivate():
+def deactivate() -> None:
     """Deactivate the conversion described above if it is active."""
-    global original_converter
+    global original_converter  # noqa: PLW0603
 
     if original_converter is None:
         return

src/anndata2ri/conv_name.py → src/anndata2ri/_conv_name.py

@@ -1,3 +1,6 @@
+from __future__ import annotations
+
+
 dimension_reductions = {
     'pca',
     'dca',