Remaining warnings

.azure-pipelines.yml

@@ -63,12 +63,13 @@ jobs:
         condition: and(eq(variables['RUN_COVERAGE'], 'yes'), eq(variables['PRERELEASE_DEPENDENCIES'], 'no'))
 
       # TODO: fix all the exceptions here
-      # replacing “:Trying to modify attribute” and “:Transforming to str index”
+      # replacing “:Setting element”, “:Trying to modify attribute” and “:Transforming to str index”
       # with “::anndata._warnings.ImplicitModificationWarning” breaks,
       # because we’re neither using editable installs nor a src/ layout
       - script: >
           pytest
           -W error
+          -W 'default:Setting element:UserWarning'
           -W 'default:Trying to modify attribute:UserWarning'
           -W 'default:Transforming to str index:UserWarning'
           -W 'default:Observation names are not unique. To make them unique:UserWarning'

anndata/tests/test_layers.py

@@ -6,6 +6,7 @@
 import numpy as np
 import pandas as pd
 import pytest
+from numba.core.errors import NumbaDeprecationWarning
 
 from anndata import AnnData, read_h5ad, read_loom
 from anndata.tests.helpers import gen_typed_df_t2_size
@@ -78,7 +79,10 @@ def test_readwrite(backing_h5ad):
 def test_readwrite_loom(tmp_path):
     loom_path = tmp_path / "test.loom"
     adata = AnnData(X=X, layers=dict(L=L.copy()))
-    adata.write_loom(loom_path)
+
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore", NumbaDeprecationWarning)
+        adata.write_loom(loom_path)
     adata_read = read_loom(loom_path, X_name="")
 
     assert adata.layers.keys() == adata_read.layers.keys()