Catch all warnings

.github/workflows/ci.yml

@@ -9,7 +9,6 @@ on:
 
 env:
   PYTEST_ADDOPTS: "-v --color=yes -n auto --internet-tests --junitxml=test-data/test-results.xml"
-  PYTHONTRACEMALLOC: "20"
   FORCE_COLOR: "1"
   MPLBACKEND: agg
   UV_CONSTRAINT: ci/constraints.txt

tests/test_get.py

@@ -407,12 +407,11 @@ def test_repeated_index_vals(dim, transform, func):
 )
 def shared_key_adata(request):
     kind = request.param
-    with pytest.warns(ImplicitModificationWarning):
-        adata = sc.AnnData(
-            np.arange(50).reshape((5, 10)),
-            obs=pd.DataFrame(np.zeros((5, 1)), columns=["var_id"]),
-            var=pd.DataFrame(index=["var_id"] + [f"gene_{i}" for i in range(1, 10)]),
-        )
+    adata = sc.AnnData(
+        np.arange(50).reshape((5, 10)),
+        obs=dict(var_id=np.zeros(5)),
+        var=pd.DataFrame(index=["var_id"] + [f"gene_{i}" for i in range(1, 10)]),
+    )
     if kind == "obs_df":
         return (
             adata,

tests/test_logging.py

@@ -82,14 +82,17 @@ def test_logfile(tmp_path: Path, caplog: pytest.LogCaptureFixture):
 
     p = tmp_path / "test.log"
     s.logpath = p
-    assert s.logpath == p
-    assert s.logfile.name == str(p)
-    log.hint("test2")
-    log.debug("invisible")
-    assert s.logpath.read_text() == "--> test2\n"
-
-    # setting a logfile removes all handlers
-    assert not caplog.records
+    try:
+        assert s.logpath == p
+        assert s.logfile.name == str(p)
+        log.hint("test2")
+        log.debug("invisible")
+        assert s.logpath.read_text() == "--> test2\n"
+
+        # setting a logfile removes all handlers
+        assert not caplog.records
+    finally:
+        s.logfile.close()  # TODO: make this unnecessary
 
 
 def test_timing(monkeypatch, capsys: pytest.CaptureFixture):

tests/test_qc_metrics.py

@@ -199,19 +199,14 @@ def adata_mito() -> AnnData:
 
 
 @pytest.mark.parametrize("cls", ARRAY_TYPES_MEM)
-def test_qc_metrics_format(cls, adata_mito: AnnData) -> None:
-    sc.pp.calculate_qc_metrics(adata_mito, qc_vars=["mito"], inplace=True)
-    adata = AnnData(X=cls(adata_mito.X), var=adata_mito.var.copy())
-    sc.pp.calculate_qc_metrics(adata, qc_vars=["mito"], inplace=True)
-    assert np.allclose(adata.obs, adata_mito.obs)
-    for col in adata.var:  # np.allclose doesn't like mix of types
-        assert np.allclose(adata.var[col], adata_mito.var[col])
-
-
-def test_qc_metrics_format_str_qc_vars(adata_mito: AnnData) -> None:
-    sc.pp.calculate_qc_metrics(adata_mito, qc_vars="mito", inplace=True)
-    adata = AnnData(X=adata_mito.X, var=adata_mito.var.copy())
-    sc.pp.calculate_qc_metrics(adata, qc_vars="mito", inplace=True)
+@pytest.mark.parametrize("qc_var_param", ["mito", ["mito"]], ids=["str", "list"])
+def test_qc_metrics_format(
+    cls, adata_mito: AnnData, qc_var_param: list[str] | str
+) -> None:
+    var = adata_mito.var.copy()
+    sc.pp.calculate_qc_metrics(adata_mito, qc_vars=qc_var_param, inplace=True)
+    adata = AnnData(X=cls(adata_mito.X), var=var)
+    sc.pp.calculate_qc_metrics(adata, qc_vars=qc_var_param, inplace=True)
     assert np.allclose(adata.obs, adata_mito.obs)
     for col in adata.var:  # np.allclose doesn't like mix of types
         assert np.allclose(adata.var[col], adata_mito.var[col])