don't configure black (#2701)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Philipp A <flying-sheep@web.de>

docs/conf.py

@@ -9,29 +9,29 @@
 from packaging.version import parse as parse_version
 
 # Don’t use tkinter agg when importing scanpy → … → matplotlib
-matplotlib.use('agg')
+matplotlib.use("agg")
 
 HERE = Path(__file__).parent
-sys.path[:0] = [str(HERE.parent), str(HERE / 'extensions')]
+sys.path[:0] = [str(HERE.parent), str(HERE / "extensions")]
 import scanpy  # noqa
 
 
 # -- General configuration ------------------------------------------------
 
 
 nitpicky = True  # Warn about broken links. This is here for a reason: Do not change.
-needs_sphinx = '4.0'  # Nicer param docs
+needs_sphinx = "4.0"  # Nicer param docs
 suppress_warnings = [
-    'ref.citation',
-    'myst.header',  # https://github.com/executablebooks/MyST-Parser/issues/262
+    "ref.citation",
+    "myst.header",  # https://github.com/executablebooks/MyST-Parser/issues/262
 ]
 
 # General information
-project = 'Scanpy'
-author = 'Scanpy development team'
+project = "Scanpy"
+author = "Scanpy development team"
 repository_url = "https://github.com/scverse/scanpy"
-copyright = f'{datetime.now():%Y}, the Scanpy development team.'
-version = scanpy.__version__.replace('.dirty', '')
+copyright = f"{datetime.now():%Y}, the Scanpy development team."
+version = scanpy.__version__.replace(".dirty", "")
 
 # Bumping the version updates all docs, so don't do that
 if parse_version(version).is_devrelease:
@@ -41,44 +41,44 @@
 release = version
 
 # default settings
-templates_path = ['_templates']
-master_doc = 'index'
-default_role = 'literal'
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
+templates_path = ["_templates"]
+master_doc = "index"
+default_role = "literal"
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
 
 extensions = [
-    'myst_nb',
-    'sphinx_copybutton',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.doctest',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.extlinks',
-    'matplotlib.sphinxext.plot_directive',
-    'sphinx_autodoc_typehints',  # needs to be after napoleon
-    'git_ref',  # needs to be before scanpydoc.rtd_github_links
-    'scanpydoc',  # needs to be before sphinx.ext.linkcode
-    'sphinx.ext.linkcode',
-    'sphinx_design',
-    'sphinxext.opengraph',
-    *[p.stem for p in (HERE / 'extensions').glob('*.py') if p.stem not in {'git_ref'}],
+    "myst_nb",
+    "sphinx_copybutton",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.doctest",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.extlinks",
+    "matplotlib.sphinxext.plot_directive",
+    "sphinx_autodoc_typehints",  # needs to be after napoleon
+    "git_ref",  # needs to be before scanpydoc.rtd_github_links
+    "scanpydoc",  # needs to be before sphinx.ext.linkcode
+    "sphinx.ext.linkcode",
+    "sphinx_design",
+    "sphinxext.opengraph",
+    *[p.stem for p in (HERE / "extensions").glob("*.py") if p.stem not in {"git_ref"}],
 ]
 
 # Generate the API documentation when building
 autosummary_generate = True
-autodoc_member_order = 'bysource'
+autodoc_member_order = "bysource"
 # autodoc_default_flags = ['members']
 napoleon_google_docstring = False
 napoleon_numpy_docstring = True
 napoleon_include_init_with_doc = False
 napoleon_use_rtype = True  # having a separate entry generally helps readability
 napoleon_use_param = True
-napoleon_custom_sections = [('Params', 'Parameters')]
+napoleon_custom_sections = [("Params", "Parameters")]
 todo_include_todos = False
-api_dir = HERE / 'api'  # function_images
+api_dir = HERE / "api"  # function_images
 myst_enable_extensions = [
     "amsmath",
     "colon_fence",
@@ -96,35 +96,35 @@
 ogp_site_url = "https://scanpy.readthedocs.io/en/stable/"
 ogp_image = "https://scanpy.readthedocs.io/en/stable/_static/Scanpy_Logo_BrightFG.svg"
 
-typehints_defaults = 'braces'
+typehints_defaults = "braces"
 
 pygments_style = "default"
 pygments_dark_style = "native"
 
 intersphinx_mapping = dict(
-    anndata=('https://anndata.readthedocs.io/en/stable/', None),
-    bbknn=('https://bbknn.readthedocs.io/en/latest/', None),
-    cuml=('https://docs.rapids.ai/api/cuml/stable/', None),
-    cycler=('https://matplotlib.org/cycler/', None),
-    dask=('https://docs.dask.org/en/stable/', None),
-    dask_ml=('https://ml.dask.org/', None),
-    h5py=('https://docs.h5py.org/en/stable/', None),
-    ipython=('https://ipython.readthedocs.io/en/stable/', None),
-    igraph=('https://python.igraph.org/en/stable/api/', None),
-    leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None),
-    louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None),
-    matplotlib=('https://matplotlib.org/stable/', None),
-    networkx=('https://networkx.org/documentation/stable/', None),
-    numpy=('https://numpy.org/doc/stable/', None),
-    pandas=('https://pandas.pydata.org/pandas-docs/stable/', None),
-    pynndescent=('https://pynndescent.readthedocs.io/en/latest/', None),
-    pytest=('https://docs.pytest.org/en/latest/', None),
-    python=('https://docs.python.org/3', None),
-    rapids_singlecell=('https://rapids-singlecell.readthedocs.io/en/latest/', None),
-    scipy=('https://docs.scipy.org/doc/scipy/', None),
-    seaborn=('https://seaborn.pydata.org/', None),
-    sklearn=('https://scikit-learn.org/stable/', None),
-    tutorials=('https://scanpy-tutorials.readthedocs.io/en/latest/', None),
+    anndata=("https://anndata.readthedocs.io/en/stable/", None),
+    bbknn=("https://bbknn.readthedocs.io/en/latest/", None),
+    cuml=("https://docs.rapids.ai/api/cuml/stable/", None),
+    cycler=("https://matplotlib.org/cycler/", None),
+    dask=("https://docs.dask.org/en/stable/", None),
+    dask_ml=("https://ml.dask.org/", None),
+    h5py=("https://docs.h5py.org/en/stable/", None),
+    ipython=("https://ipython.readthedocs.io/en/stable/", None),
+    igraph=("https://python.igraph.org/en/stable/api/", None),
+    leidenalg=("https://leidenalg.readthedocs.io/en/latest/", None),
+    louvain=("https://louvain-igraph.readthedocs.io/en/latest/", None),
+    matplotlib=("https://matplotlib.org/stable/", None),
+    networkx=("https://networkx.org/documentation/stable/", None),
+    numpy=("https://numpy.org/doc/stable/", None),
+    pandas=("https://pandas.pydata.org/pandas-docs/stable/", None),
+    pynndescent=("https://pynndescent.readthedocs.io/en/latest/", None),
+    pytest=("https://docs.pytest.org/en/latest/", None),
+    python=("https://docs.python.org/3", None),
+    rapids_singlecell=("https://rapids-singlecell.readthedocs.io/en/latest/", None),
+    scipy=("https://docs.scipy.org/doc/scipy/", None),
+    seaborn=("https://seaborn.pydata.org/", None),
+    sklearn=("https://scikit-learn.org/stable/", None),
+    tutorials=("https://scanpy-tutorials.readthedocs.io/en/latest/", None),
 )
 
 
@@ -135,10 +135,10 @@
     "repository_url": repository_url,
     "use_repository_button": True,
 }
-html_static_path = ['_static']
+html_static_path = ["_static"]
 html_css_files = ["css/override.css"]
 html_show_sphinx = False
-html_logo = '_static/img/Scanpy_Logo_BrightFG.svg'
+html_logo = "_static/img/Scanpy_Logo_BrightFG.svg"
 html_title = "scanpy"
 
 
@@ -159,9 +159,9 @@ def setup(app: Sphinx):
 
 # -- Options for other output formats ------------------------------------------
 
-htmlhelp_basename = f'{project}doc'
-doc_title = f'{project} Documentation'
-latex_documents = [(master_doc, f'{project}.tex', doc_title, author, 'manual')]
+htmlhelp_basename = f"{project}doc"
+doc_title = f"{project} Documentation"
+latex_documents = [(master_doc, f"{project}.tex", doc_title, author, "manual")]
 man_pages = [(master_doc, project, doc_title, [author], 1)]
 texinfo_documents = [
     (
@@ -170,8 +170,8 @@ def setup(app: Sphinx):
         doc_title,
         author,
         project,
-        'One line description of project.',
-        'Miscellaneous',
+        "One line description of project.",
+        "Miscellaneous",
     )
 ]
 
@@ -190,18 +190,18 @@ def setup(app: Sphinx):
 
 nitpick_ignore = [
     # Will probably be documented
-    ('py:class', 'scanpy._settings.Verbosity'),
-    ('py:class', 'scanpy.neighbors.OnFlySymMatrix'),
+    ("py:class", "scanpy._settings.Verbosity"),
+    ("py:class", "scanpy.neighbors.OnFlySymMatrix"),
     # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810
-    ('py:class', 'seaborn.ClusterGrid'),
+    ("py:class", "seaborn.ClusterGrid"),
     # Won’t be documented
-    ('py:class', 'scanpy.plotting._utils._AxesSubplot'),
-    ('py:class', 'scanpy._utils.Empty'),
-    ('py:class', 'numpy.random.mtrand.RandomState'),
-    ('py:class', 'scanpy.neighbors._types.KnnTransformerLike'),
+    ("py:class", "scanpy.plotting._utils._AxesSubplot"),
+    ("py:class", "scanpy._utils.Empty"),
+    ("py:class", "numpy.random.mtrand.RandomState"),
+    ("py:class", "scanpy.neighbors._types.KnnTransformerLike"),
     # Will work once scipy 1.8 is released
-    ('py:class', 'scipy.sparse.base.spmatrix'),
-    ('py:class', 'scipy.sparse.csr.csr_matrix'),
+    ("py:class", "scipy.sparse.base.spmatrix"),
+    ("py:class", "scipy.sparse.csr.csr_matrix"),
 ]
 
 # Options for plot examples

docs/extensions/cite.py

@@ -25,9 +25,9 @@ def cite_role(
     content: Sequence[str] = (),
 ) -> tuple[list[nodes.Node], list[nodes.system_message]]:
     key = utils.unescape(text)
-    node = nodes.citation_reference(f'[{key}]_', key)
+    node = nodes.citation_reference(f"[{key}]_", key)
     return [node], []
 
 
 def setup(app: Sphinx):
-    app.add_role('cite', cite_role, override=True)
+    app.add_role("cite", cite_role, override=True)

docs/extensions/debug_docstrings.py

@@ -11,9 +11,9 @@
 
 def pd_new(app, what, name, obj, options, lines):
     _pd_orig(app, what, name, obj, options, lines)
-    print(*lines, sep='\n')
+    print(*lines, sep="\n")
 
 
 def setup(app: Sphinx):
-    if os.environ.get('DEBUG') is not None:
+    if os.environ.get("DEBUG") is not None:
         sphinx.ext.napoleon._process_docstring = pd_new

docs/extensions/function_images.py

@@ -9,17 +9,17 @@
 def insert_function_images(
     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():
+    path = app.config.api_dir / f"{name}.png"
+    if what != "function" or not path.is_file():
         return
     lines[0:0] = [
-        f'.. image:: {path.name}',
-        '   :width: 200',
-        '   :align: right',
-        '',
+        f".. image:: {path.name}",
+        "   :width: 200",
+        "   :align: right",
+        "",
     ]
 
 
 def setup(app: Sphinx):
-    app.add_config_value('api_dir', Path(), 'env')
-    app.connect('autodoc-process-docstring', insert_function_images)
+    app.add_config_value("api_dir", Path(), "env")
+    app.connect("autodoc-process-docstring", insert_function_images)

docs/extensions/git_ref.py

@@ -35,7 +35,7 @@ def get() -> str | None:
 
 
 def set_ref(app: Sphinx, config: Config):
-    app.config['html_theme_options']['repository_branch'] = get() or 'main'
+    app.config["html_theme_options"]["repository_branch"] = get() or "main"
 
 
 def setup(app: Sphinx) -> None:

docs/extensions/param_police.py

@@ -8,9 +8,9 @@
 param_warnings = {}
 
 
-def scanpy_log_param_types(self, fields, field_role='param', type_role='type'):
+def scanpy_log_param_types(self, fields, field_role="param", type_role="type"):
     for _name, _type, _desc in fields:
-        if not _type or not self._obj.__module__.startswith('scanpy'):
+        if not _type or not self._obj.__module__.startswith("scanpy"):
             continue
         w_list = param_warnings.setdefault((self._name, self._obj), [])
         if (_name, _type) not in w_list:
@@ -24,18 +24,18 @@ def show_param_warnings(app, exception):
     for (fname, fun), params in param_warnings.items():
         _, line = inspect.getsourcelines(fun)
         file_name = inspect.getsourcefile(fun)
-        params_str = '\n'.join(f'\t{n}: {t}' for n, t in params)
+        params_str = "\n".join(f"\t{n}: {t}" for n, t in params)
         warnings.warn_explicit(
-            f'\nParameters in `{fname}` have types in docstring.\n'
-            f'Replace them with type annotations.\n{params_str}',
+            f"\nParameters in `{fname}` have types in docstring.\n"
+            f"Replace them with type annotations.\n{params_str}",
             UserWarning,
             file_name,
             line,
         )
     if param_warnings:
-        raise RuntimeError('Encountered text parameter type. Use annotations.')
+        raise RuntimeError("Encountered text parameter type. Use annotations.")
 
 
 def setup(app: Sphinx):
     NumpyDocstring._format_docutils_params = scanpy_log_param_types
-    app.connect('build-finished', show_param_warnings)
+    app.connect("build-finished", show_param_warnings)

docs/extensions/typed_returns.py

@@ -6,7 +6,7 @@
 
 def process_return(lines):
     for line in lines:
-        m = re.fullmatch(r'(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)', line)
+        m = re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line)
         if m:
             # Once this is in scanpydoc, we can use the fancy hover stuff
             yield f'**{m["param"]}** : :class:`~{m["type"]}`'
@@ -16,9 +16,9 @@ def process_return(lines):
 
 def scanpy_parse_returns_section(self, section):
     lines_raw = list(process_return(self._dedent(self._consume_to_next_section())))
-    lines = self._format_block(':returns: ', lines_raw)
+    lines = self._format_block(":returns: ", lines_raw)
     if lines and lines[-1]:
-        lines.append('')
+        lines.append("")
     return lines
 
 

pyproject.toml

@@ -167,9 +167,6 @@ omit = ["*/tests/*"]
 [tool.coverage.paths]
 source = [".", "**/site-packages"]
 
-[tool.black]
-skip-string-normalization = true
-
 [tool.ruff]
 select = [
     "F",  # Pyflakes

scanpy/__init__.py

@@ -45,8 +45,8 @@
 # has to be done at the end, after everything has been imported
 import sys
 
-sys.modules.update({f'{__name__}.{m}': globals()[m] for m in ['tl', 'pp', 'pl']})
+sys.modules.update({f"{__name__}.{m}": globals()[m] for m in ["tl", "pp", "pl"]})
 from ._utils import annotate_doc_types
 
-annotate_doc_types(sys.modules[__name__], 'scanpy')
+annotate_doc_types(sys.modules[__name__], "scanpy")
 del sys, annotate_doc_types

scanpy/_compat.py

@@ -15,15 +15,15 @@ class DaskArray:
         pass
 
 
-__all__ = ['cache', 'DaskArray', 'fullname', 'pkg_metadata', 'pkg_version']
+__all__ = ["cache", "DaskArray", "fullname", "pkg_metadata", "pkg_version"]
 
 
 def fullname(typ: type) -> str:
     module = typ.__module__
     name = typ.__qualname__
-    if module == 'builtins' or module is None:
+    if module == "builtins" or module is None:
         return name
-    return f'{module}.{name}'
+    return f"{module}.{name}"
 
 
 def pkg_metadata(package):