Fix tests for Sphinx 8.1, remove Python 3.9 support (#178)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Philipp A. <[email protected]>

Author: pre-commit-ci[bot]

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
         with:
@@ -31,11 +31,11 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: pip
+      - uses: hynek/setup-cached-uv@v2
+        with:
+          cache-dependency-path: pyproject.toml
       - name: dependencies
-        run: |
-          pip install --upgrade pip wheel
-          pip install .[test,typehints,myst] coverage-rich 'anyconfig[toml] >=0.14'
+        run: uv pip install --system .[test,typehints,myst] coverage-rich 'anyconfig[toml] >=0.14'
       - name: tests
         run: coverage run -m pytest --verbose --color=yes
       - name: show coverage

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: trailing-whitespace
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.7.0
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
@@ -17,7 +17,7 @@ repos:
           - [email protected]
           - [email protected]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.12.1
     hooks:
       - id: mypy
         additional_dependencies:

.readthedocs.yml

@@ -1,8 +1,8 @@
 version: 2
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.11"
+    python: "3.12"
 python:
   install:
     - method: pip

pyproject.toml

@@ -17,10 +17,9 @@ classifiers = [
     'Framework :: Sphinx :: Extension',
     'Typing :: Typed',
 ]
-requires-python = '>=3.9'
+requires-python = '>=3.10'
 dependencies = [
     'sphinx>=7.0',
-    'get-annotations; python_version < "3.10"',
 ]
 
 [project.optional-dependencies]
@@ -30,6 +29,7 @@ test = [
     'coverage',
     'legacy-api-wrap',
     'defusedxml',  # sphinx[test] would also pull in cython
+    'sphinx>=8.1.0' # https://github.com/sphinx-doc/sphinx/pull/12743
 ]
 doc = [
     'scanpydoc[typehints,myst,theme]',

src/scanpydoc/elegant_typehints/_formatting.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import sys
 import inspect
 from types import GenericAlias
 from typing import TYPE_CHECKING, Any, cast, get_args, get_origin
@@ -15,12 +14,6 @@
     from sphinx.config import Config
 
 
-if sys.version_info >= (3, 10):
-    from types import UnionType
-else:  # pragma: no cover
-    UnionType = None
-
-
 def typehints_formatter(annotation: type[Any], config: Config) -> str | None:
     """Generate reStructuredText containing links to the types.
 
@@ -43,7 +36,7 @@ def typehints_formatter(annotation: type[Any], config: Config) -> str | None:
 
     tilde = "" if config.typehints_fully_qualified else "~"
 
-    if isinstance(annotation, (GenericAlias, _GenericAlias)):
+    if isinstance(annotation, GenericAlias | _GenericAlias):
         args = get_args(annotation)
         annotation = cast(type[Any], get_origin(annotation))
     else:

src/scanpydoc/elegant_typehints/_return_tuple.py

@@ -1,8 +1,8 @@
 from __future__ import annotations
 
 import re
-import sys
 import inspect
+from types import UnionType
 from typing import TYPE_CHECKING, Union, get_args, get_origin, get_type_hints
 from typing import Tuple as t_Tuple  # noqa: UP035
 from logging import getLogger
@@ -19,12 +19,7 @@
     from sphinx.ext.autodoc import Options
 
 
-if sys.version_info > (3, 10):
-    from types import UnionType
-
-    UNION_TYPES = {Union, UnionType}
-else:  # pragma: no cover
-    UNION_TYPES = {Union}
+UNION_TYPES = {Union, UnionType}
 
 
 __all__ = ["process_docstring", "_parse_returns_section", "setup"]
@@ -77,7 +72,7 @@ def process_docstring(  # noqa: PLR0913
 
     idxs_ret_names = _get_idxs_ret_names(lines)
     if len(idxs_ret_names) == len(ret_types):
-        for l, rt in zip(idxs_ret_names, ret_types):
+        for l, rt in zip(idxs_ret_names, ret_types, strict=False):
             typ = format_annotation(rt, app.config)
             if (line := lines[l]).lstrip() in {":returns: :", ":return: :", ":"}:
                 transformed = f"{line[:-1]}{typ}"

src/scanpydoc/rtd_github_links/__init__.py

@@ -118,10 +118,7 @@ def _infer_vars(config: Config) -> tuple[str, PurePosixPath]:
 
 
 def _get_annotations(obj: _SourceObjectType) -> dict[str, Any]:
-    if sys.version_info > (3, 10):
-        from inspect import get_annotations
-    else:  # pragma: no cover
-        from get_annotations import get_annotations
+    from inspect import get_annotations
 
     try:
         return get_annotations(obj)  # type: ignore[no-any-return,arg-type,unused-ignore]
@@ -159,7 +156,7 @@ def _get_obj_module(qualname: str) -> tuple[Any, ModuleType]:
                     raise e from None
         if isinstance(thing, ModuleType):  # pragma: no cover
             mod = thing
-        elif is_dataclass(obj) or isinstance(thing, (GenericAlias, _GenericAlias)):
+        elif is_dataclass(obj) or isinstance(thing, GenericAlias | _GenericAlias):
             obj = thing
         else:
             obj = thing

src/scanpydoc/testing.py

@@ -0,0 +1,24 @@
+"""Testing utilities."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, Protocol
+
+
+if TYPE_CHECKING:
+    from typing import Any
+
+    from sphinx.testing.util import SphinxTestApp
+
+
+class MakeApp(Protocol):
+    """Create a SphinxTestApp instance."""
+
+    def __call__(  # noqa: D102
+        self,
+        builder: str = "html",
+        /,
+        *,
+        exception_on_warning: bool = False,
+        **conf: Any,  # noqa: ANN401
+    ) -> SphinxTestApp: ...

tests/conftest.py

@@ -18,16 +18,29 @@
     from pathlib import Path
     from collections.abc import Callable, Generator
 
-    from sphinx.application import Sphinx
+    from sphinx.testing.util import SphinxTestApp
+
+    from scanpydoc.testing import MakeApp
 
 
 @pytest.fixture
-def make_app_setup(
-    make_app: Callable[..., Sphinx], tmp_path: Path
-) -> Callable[..., Sphinx]:
-    def make_app_setup(builder: str = "html", /, **conf: Any) -> Sphinx:  # noqa: ANN401
+def make_app_setup(make_app: type[SphinxTestApp], tmp_path: Path) -> MakeApp:
+    def make_app_setup(
+        builder: str = "html",
+        /,
+        *,
+        exception_on_warning: bool = False,
+        **conf: Any,  # noqa: ANN401
+    ) -> SphinxTestApp:
         (tmp_path / "conf.py").write_text("")
-        return make_app(buildername=builder, srcdir=tmp_path, confoverrides=conf)
+        conf.setdefault("suppress_warnings", []).append("app.add_node")
+        return make_app(
+            buildername=builder,
+            srcdir=tmp_path,
+            confoverrides=conf,
+            warningiserror=exception_on_warning,
+            exception_on_warning=exception_on_warning,
+        )
 
     return make_app_setup
 

tests/test_base.py

@@ -11,17 +11,17 @@
 
 
 if TYPE_CHECKING:
-    from collections.abc import Callable
-
     import pytest
     from sphinx.application import Sphinx
 
+    from scanpydoc.testing import MakeApp
+
 
 DEPRECATED = frozenset({"scanpydoc.autosummary_generate_imported"})
 
 
 def test_all_get_installed(
-    monkeypatch: pytest.MonkeyPatch, make_app_setup: Callable[..., Sphinx]
+    monkeypatch: pytest.MonkeyPatch, make_app_setup: MakeApp
 ) -> None:
     setups_seen: set[str] = set()
     setups_called: dict[str, Sphinx] = {}

tests/test_definition_list_typed_field.py

@@ -11,13 +11,13 @@
 
 
 if TYPE_CHECKING:
-    from collections.abc import Callable
-
     from sphinx.application import Sphinx
 
+    from scanpydoc.testing import MakeApp
+
 
 @pytest.fixture
-def app(make_app_setup: Callable[..., Sphinx]) -> Sphinx:
+def app(make_app_setup: MakeApp) -> Sphinx:
     app = make_app_setup()
     app.setup_extension("scanpydoc.definition_list_typed_field")
     return app
@@ -41,7 +41,7 @@ def app(make_app_setup: Callable[..., Sphinx]) -> Sphinx:
 """
 
 
-def test_apps_separate(app: Sphinx, make_app_setup: Callable[..., Sphinx]) -> None:
+def test_apps_separate(app: Sphinx, make_app_setup: MakeApp) -> None:
     app_no_setup = make_app_setup()
     assert app is not app_no_setup
     assert "scanpydoc.definition_list_typed_field" in app.extensions
@@ -97,11 +97,12 @@ def test_convert_params(
     assert isinstance(cyr := term[2], nodes.classifier)
     assert len(cyr) == len(conv_types), cyr.children
     assert all(
-        isinstance(cyr_part, conv_type) for cyr_part, conv_type in zip(cyr, conv_types)
+        isinstance(cyr_part, conv_type)
+        for cyr_part, conv_type in zip(cyr, conv_types, strict=True)
     )
 
 
-def test_load_error(make_app_setup: Callable[..., Sphinx]) -> None:
+def test_load_error(make_app_setup: MakeApp) -> None:
     with pytest.raises(RuntimeError, match=r"Please load sphinx\.ext\.napoleon before"):
         make_app_setup(
             extensions=["scanpydoc.definition_list_typed_field", "sphinx.ext.napoleon"]

tests/test_elegant_typehints.py

@@ -3,19 +3,9 @@
 from __future__ import annotations
 
 import re
-import sys
 import inspect
 from io import StringIO
-from typing import (
-    TYPE_CHECKING,
-    Any,
-    Union,
-    AnyStr,
-    NoReturn,
-    Optional,
-    cast,
-    get_origin,
-)
+from typing import TYPE_CHECKING, Any, AnyStr, NoReturn, cast, get_origin
 from pathlib import Path
 from operator import attrgetter
 from collections.abc import Mapping, Callable
@@ -31,6 +21,8 @@
 
     from sphinx.application import Sphinx
 
+    from scanpydoc.testing import MakeApp
+
     class ProcessDoc(Protocol):  # noqa: D101
         def __call__(  # noqa: D102
             self, fn: Callable[..., Any], *, run_napoleon: bool = False
@@ -60,7 +52,7 @@ class Gen(Generic[T]): pass
 
 
 @pytest.fixture
-def app(make_app_setup: Callable[..., Sphinx]) -> Sphinx:
+def app(make_app_setup: MakeApp) -> Sphinx:
     return make_app_setup(
         master_doc="index",
         extensions=[
@@ -256,8 +248,8 @@ def fn_test(m: object) -> None:  # pragma: no cover
         AnyStr,
         NoReturn,
         Callable[[int], None],
-        Union[int, str],
-        Union[int, str, None],
+        int | str,
+        int | str | None,
     ],
     ids=lambda p: str(p).replace("typing.", ""),
 )
@@ -274,7 +266,6 @@ def test_typing_classes(app: Sphinx, annotation: type) -> None:
     assert output is None or output.startswith(f":py:data:`typing.{name}")
 
 
-@pytest.mark.skipif(sys.version_info < (3, 10), reason="requires Python 3.10+")
 def test_union_type(app: Sphinx) -> None:
     union = eval("int | str")  # noqa: S307
     assert typehints_formatter(union, app.config) is None
@@ -389,15 +380,15 @@ class B:
     ("return_ann", "foo_rendered"),
     [
         pytest.param(tuple[str, int], ":py:class:`str`", id="tuple"),
-        pytest.param(Optional[tuple[str, int]], ":py:class:`str`", id="tuple | None"),
+        pytest.param(tuple[str, int] | None, ":py:class:`str`", id="tuple | None"),
         pytest.param(
             tuple[Mapping[str, float], int],
             r":py:class:`~collections.abc.Mapping`\ \["
             ":py:class:`str`, :py:class:`float`"
             "]",
             id="complex",
         ),
-        pytest.param(Optional[int], None, id="int | None"),
+        pytest.param(int | None, None, id="int | None"),
     ],
 )
 def test_return_tuple(
@@ -472,14 +463,14 @@ def fn() -> tuple[int, str]:  # pragma: no cover
     assert res[2].startswith(":rtype: :sphinx_autodoc_typehints_type:")
 
 
-def test_load_without_sat(make_app_setup: Callable[..., Sphinx]) -> None:
+def test_load_without_sat(make_app_setup: MakeApp) -> None:
     make_app_setup(
         master_doc="index",
         extensions=["sphinx.ext.autodoc", "scanpydoc.elegant_typehints"],
     )
 
 
-def test_load_error(make_app_setup: Callable[..., Sphinx]) -> None:
+def test_load_error(make_app_setup: MakeApp) -> None:
     with pytest.raises(
         RuntimeError,
         match=r"`scanpydoc.elegant_typehints` requires `sphinx.ext.autodoc`",