Add all ruff checks we use in anndata (#2761)

docs/api/tools.md

@@ -17,7 +17,7 @@ Any transformation of the data matrix that is not *preprocessing*. In contrast t
    :nosignatures:
    :toctree: ../generated/
 
-   tl.pca
+   pp.pca
    tl.tsne
    tl.umap
    tl.draw_graph

docs/conf.py

@@ -1,11 +1,11 @@
-import os
+from __future__ import annotations
+
 import sys
-from pathlib import Path
 from datetime import datetime
-from typing import Any
+from pathlib import Path
+from typing import TYPE_CHECKING
 
 import matplotlib  # noqa
-from sphinx.application import Sphinx
 from packaging.version import parse as parse_version
 
 # Don’t use tkinter agg when importing scanpy → … → matplotlib
@@ -15,6 +15,9 @@
 sys.path[:0] = [str(HERE.parent), str(HERE / "extensions")]
 import scanpy  # noqa
 
+if TYPE_CHECKING:
+    from sphinx.application import Sphinx
+
 
 # -- General configuration ------------------------------------------------
 

docs/extensions/cite.py

@@ -8,11 +8,11 @@
 from docutils import nodes, utils
 
 if TYPE_CHECKING:
-    from typing import Any
     from collections.abc import Mapping, Sequence
+    from typing import Any
 
-    from sphinx.application import Sphinx
     from docutils.parsers.rst.states import Inliner
+    from sphinx.application import Sphinx
 
 
 def cite_role(

docs/extensions/debug_docstrings.py

@@ -1,10 +1,14 @@
 # Just do the following to see the rst of a function:
-# rm -f _build/doctrees/api/scanpy.<what_you_want>.doctree; DEBUG=1 make html
+# rm ./_build/doctrees/api/generated/scanpy.<what you want>.doctree; DEBUG=1 make html
+from __future__ import annotations
+
 import os
+from typing import TYPE_CHECKING
 
-from sphinx.application import Sphinx
 import sphinx.ext.napoleon
 
+if TYPE_CHECKING:
+    from sphinx.application import Sphinx
 
 _pd_orig = sphinx.ext.napoleon._process_docstring
 

docs/extensions/function_images.py

@@ -1,13 +1,16 @@
 """Images for plot functions"""
+from __future__ import annotations
+
 from pathlib import Path
-from typing import List, Any
+from typing import TYPE_CHECKING, Any
 
-from sphinx.application import Sphinx
-from sphinx.ext.autodoc import Options
+if TYPE_CHECKING:
+    from sphinx.application import Sphinx
+    from sphinx.ext.autodoc import Options
 
 
 def insert_function_images(
-    app: Sphinx, what: str, name: str, obj: Any, options: Options, lines: List[str]
+    app: Sphinx, what: str, name: str, obj: Any, options: Options, lines: list[str]
 ):
     path = app.config.api_dir / f"{name}.png"
     if what != "function" or not path.is_file():

docs/extensions/git_ref.py

@@ -2,12 +2,14 @@
 
 from __future__ import annotations
 
-from functools import lru_cache
-
 import re
 import subprocess
-from sphinx.application import Sphinx
-from sphinx.config import Config
+from functools import lru_cache
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from sphinx.application import Sphinx
+    from sphinx.config import Config
 
 
 def git(*args: str) -> str:

docs/extensions/has_attr_test.py

@@ -1,8 +1,13 @@
+from __future__ import annotations
+
 from inspect import get_annotations
+from typing import TYPE_CHECKING
 
 from jinja2.defaults import DEFAULT_NAMESPACE
 from jinja2.utils import import_string
-from sphinx.application import Sphinx
+
+if TYPE_CHECKING:
+    from sphinx.application import Sphinx
 
 
 def has_member(obj_path: str, attr: str) -> bool:

docs/extensions/param_police.py

@@ -1,8 +1,12 @@
+from __future__ import annotations
+
 import warnings
+from typing import TYPE_CHECKING
 
-from sphinx.application import Sphinx
 from sphinx.ext.napoleon import NumpyDocstring
 
+if TYPE_CHECKING:
+    from sphinx.application import Sphinx
 
 _format_docutils_params_orig = NumpyDocstring._format_docutils_params
 param_warnings = {}

docs/extensions/typed_returns.py

@@ -1,8 +1,13 @@
+from __future__ import annotations
+
 import re
+from typing import TYPE_CHECKING
 
-from sphinx.application import Sphinx
 from sphinx.ext.napoleon import NumpyDocstring
 
+if TYPE_CHECKING:
+    from sphinx.application import Sphinx
+
 
 def process_return(lines):
     for line in lines:

docs/release-notes/1.4.5.md

@@ -20,7 +20,7 @@ Please install `scanpy==1.4.5.post3` instead of `scanpy==1.4.5`.
 - webpage overhaul, ecosystem page, release notes, tutorials overhaul {pr}`960` {pr}`966` {smaller}`A Wolf`
 
 ```{warning}
-- changed default `solver` in {func}`~scanpy.tl.pca` from `auto` to `arpack`
+- changed default `solver` in {func}`~scanpy.pp.pca` from `auto` to `arpack`
 - changed default `use_raw` in {func}`~scanpy.tl.score_genes` from `False` to `None`
 ```
 

pyproject.toml

@@ -106,16 +106,16 @@ test-full = [
     "scanpy[dask-ml]",
 ]
 doc = [
-    "sphinx>=5",
+    "sphinx>=6",
     "sphinx-book-theme>=1.0.1",
     "scanpydoc>=0.9.5",
-    "sphinx-autodoc-typehints",
-    "myst-parser",
-    "myst-nb",
+    "sphinx-autodoc-typehints>=1.23.0",
+    "myst-parser>=2",
+    "myst-nb>=1",
     "sphinx-design",
     "sphinxext-opengraph", # for nice cards when sharing on social
     "sphinx-copybutton",
-    "nbsphinx",
+    "nbsphinx>=0.9",
     "ipython>=7.20",  # for nbsphinx code highlighting
     "matplotlib!=3.6.1",
     # TODO: remove necessity for being able to import doc-linked classes
@@ -177,14 +177,17 @@ source = [".", "**/site-packages"]
 
 [tool.ruff]
 select = [
-    "F",  # Pyflakes
-    "E",  # Pycodestyle errors
-    "W",  # Pycodestyle warnings
+    "E",       # Error detected by Pycodestyle
+    "F",       # Errors detected by Pyflakes
+    "W",       # Warning detected by Pycodestyle
+    "UP",      # pyupgrade
+    "I",       # isort
+    "TCH",     # manage type checking blocks
     "TID251",  # Banned imports
+    "ICN",     # Follow import conventions
+    "PTH",     # Pathlib instead of os.path
 ]
 ignore = [
-    # module imported but unused -> required for Scanpys API
-    "F401",
     # line too long -> we accept long comment lines; black gets rid of long code lines
     "E501",
     # module level import not at top of file -> required to circumvent circular imports for Scanpys API
@@ -197,6 +200,9 @@ ignore = [
 [tool.ruff.per-file-ignores]
 # Do not assign a lambda expression, use a def
 "scanpy/tools/_rank_genes_groups.py" = ["E731"]
+[tool.ruff.isort]
+known-first-party = ["scanpy"]
+required-imports = ["from __future__ import annotations"]
 [tool.ruff.flake8-tidy-imports.banned-api]
 "pytest.importorskip".msg = "Use the “@needs” decorator/mark instead"
 "pandas.api.types.is_categorical_dtype".msg = "Use isinstance(s.dtype, CategoricalDtype) instead"

scanpy/__init__.py

@@ -1,4 +1,5 @@
 """Single-Cell Analysis in Python."""
+from __future__ import annotations
 
 try:  # See https://github.com/maresb/hatch-vcs-footgun-example
     from setuptools_scm import get_version
@@ -20,25 +21,26 @@
 
 # the actual API
 # (start with settings as several tools are using it)
-from ._settings import settings, Verbosity
-from . import tools as tl
-from . import preprocessing as pp
-from . import plotting as pl
-from . import datasets, logging, queries, external, get, metrics, experimental
-
-from anndata import AnnData, concat
 from anndata import (
-    read_h5ad,
+    AnnData,
+    concat,
     read_csv,
     read_excel,
+    read_h5ad,
     read_hdf,
     read_loom,
     read_mtx,
     read_text,
     read_umi_tools,
 )
-from .readwrite import read, read_10x_h5, read_10x_mtx, write, read_visium
+
+from . import datasets, experimental, external, get, logging, metrics, queries
+from . import plotting as pl
+from . import preprocessing as pp
+from . import tools as tl
+from ._settings import Verbosity, settings
 from .neighbors import Neighbors
+from .readwrite import read, read_10x_h5, read_10x_mtx, read_visium, write
 
 set_figure_params = settings.set_figure_params
 
@@ -50,3 +52,36 @@
 
 annotate_doc_types(sys.modules[__name__], "scanpy")
 del sys, annotate_doc_types
+
+__all__ = [
+    "__version__",
+    "AnnData",
+    "concat",
+    "read_csv",
+    "read_excel",
+    "read_h5ad",
+    "read_hdf",
+    "read_loom",
+    "read_mtx",
+    "read_text",
+    "read_umi_tools",
+    "read",
+    "read_10x_h5",
+    "read_10x_mtx",
+    "read_visium",
+    "write",
+    "datasets",
+    "experimental",
+    "external",
+    "get",
+    "logging",
+    "metrics",
+    "queries",
+    "pl",
+    "pp",
+    "tl",
+    "Verbosity",
+    "settings",
+    "Neighbors",
+    "set_figure_params",
+]

scanpy/__main__.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from .cli import console_main
 
 console_main()

scanpy/_compat.py

@@ -2,6 +2,7 @@
 
 from dataclasses import dataclass, field
 from pathlib import Path
+
 from packaging import version
 
 try: