Backport PR #1298 on branch 0.10.x (Fix test compatibility with Pytest 8)

anndata/tests/test_io_warnings.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import re
 import warnings
 from importlib.util import find_spec
 from pathlib import Path
@@ -14,10 +15,26 @@
 def test_old_format_warning_thrown():
     import scanpy as sc
 
-    with pytest.warns(ad._warnings.OldFormatWarning):
-        pth = Path(sc.datasets.__file__).parent / "10x_pbmc68k_reduced.h5ad"
+    pth = Path(sc.datasets.__file__).parent / "10x_pbmc68k_reduced.h5ad"
+    # TODO: with Pytest 8, all this can be a
+    #       `with pytest.warns(...), pytest.warns(...):`
+    with warnings.catch_warnings(record=True) as record:
+        warnings.simplefilter("always", ad.OldFormatWarning)
+        warnings.simplefilter("always", FutureWarning)
         ad.read_h5ad(pth)
 
+    assert any(issubclass(w.category, ad.OldFormatWarning) for w in record), [
+        w.message for w in record if not issubclass(w.category, FutureWarning)
+    ]
+    assert any(
+        issubclass(w.category, FutureWarning)
+        and re.match(
+            r"Moving element from \.uns\['neighbors']\['distances'] to \.obsp\['distances']\.",
+            str(w.message),
+        )
+        for w in record
+    ), [w.message for w in record if not issubclass(w.category, ad.OldFormatWarning)]
+
 
 def test_old_format_warning_not_thrown(tmp_path):
     pth = tmp_path / "current.h5ad"

conftest.py

@@ -18,11 +18,14 @@
     from pathlib import Path
 
 
-doctest_marker = pytest.mark.usefixtures("doctest_env")
+@pytest.fixture(autouse=True)
+def _suppress_env_for_doctests(request: pytest.FixtureRequest) -> None:
+    if isinstance(request.node, pytest.DoctestItem):
+        request.getfixturevalue("_doctest_env")
 
 
-@pytest.fixture
-def doctest_env(
+@pytest.fixture()
+def _doctest_env(
     request: pytest.FixtureRequest, cache: pytest.Cache, tmp_path: Path
 ) -> Generator[None, None, None]:
     from scanpy import settings
@@ -44,7 +47,7 @@ def doctest_env(
 
 
 def pytest_itemcollected(item: pytest.Item) -> None:
-    """Define behavior of pytest.mark.gpu and doctests."""
+    """Define behavior of pytest.mark.gpu."""
     from importlib.util import find_spec
 
     is_gpu = len([mark for mark in item.iter_markers(name="gpu")]) > 0
@@ -53,9 +56,6 @@ def pytest_itemcollected(item: pytest.Item) -> None:
             pytest.mark.skipif(not find_spec("cupy"), reason="Cupy not installed.")
         )
 
-    if isinstance(item, pytest.DoctestItem):
-        item.add_marker(doctest_marker)
-
 
 def pytest_addoption(parser: pytest.Parser) -> None:
     """Hook to register custom CLI options and config values"""

pyproject.toml

@@ -81,7 +81,7 @@ doc = [
 ]
 test = [
     "loompy>=3.0.5",
-    "pytest >=6.0, !=8.0.0rc1", # https://github.com/pytest-dev/pytest/issues/11759
+    "pytest >=6.0",
     "pytest-cov>=2.10",
     "zarr",
     "matplotlib",