fix typeguard/CI errors in tests/test_soma_sparse_nd_array.py

single-cell-data · Oct 12, 2022 · fdef919 · fdef919
1 parent 74ee1dc
commit fdef919
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Showing 3 changed files with 20 additions and 9 deletions.
diff --git a/apis/python/tests/__init__.py b/apis/python/tests/__init__.py
@@ -1,17 +1,20 @@
 import pyarrow as pa
 from typeguard.importhook import TypeguardFinder, install_import_hook
 
+
 class CustomFinder(TypeguardFinder):
     """
     As noted in apis/python/src/tiledbsoma/query_condition.py we intentionally
     suppress ``mypy`` there. However we need this extra step to also suppress
     ``typeguard`` there.
     """
+
     def should_instrument(self, module_name: str):
-        if module_name == 'tiledbsoma.query_condition':
+        if module_name == "tiledbsoma.query_condition":
             return False
         return True
 
+
 install_import_hook("tiledbsoma", cls=CustomFinder)
 
 """Types supported in a SOMA*NdArray """

diff --git a/apis/python/tests/test_soma_dense_nd_array.py b/apis/python/tests/test_soma_dense_nd_array.py
@@ -1,4 +1,4 @@
-from typing import Tuple
+from typing import List, Tuple, Union
 
 import numpy as np
 import pyarrow as pa
@@ -21,7 +21,7 @@ def test_soma_dense_nd_array_ok_no_storage():
 )
 @pytest.mark.parametrize("element_type", NDARRAY_ARROW_TYPES_SUPPORTED)
 def test_soma_dense_nd_array_create_ok(
-    tmp_path, shape: Tuple[int, ...], element_type: pa.DataType
+    tmp_path, shape: Union[Tuple[int, ...], List], element_type: pa.DataType
 ):
     """
     Test all cases we expect "create" to succeed.

diff --git a/apis/python/tests/test_soma_sparse_nd_array.py b/apis/python/tests/test_soma_sparse_nd_array.py
@@ -1,4 +1,4 @@
-from typing import Optional, Tuple, Union
+from typing import List, Optional, Tuple, Union
 
 import numpy as np
 import pyarrow as pa
@@ -24,7 +24,7 @@ def test_soma_sparse_nd_array_ok_no_storage():
 )
 @pytest.mark.parametrize("element_type", NDARRAY_ARROW_TYPES_SUPPORTED)
 def test_soma_sparse_nd_array_create_ok(
-    tmp_path, shape: Tuple[int, ...], element_type: pa.DataType
+    tmp_path, shape: Union[Tuple[int, ...], List[int]], element_type: pa.DataType
 ):
     """
     Test all cases we expect "create" to succeed.
@@ -250,7 +250,7 @@ def test_soma_sparse_nd_array_read_write_sparse_tensor(
     assert a.shape == shape
 
     # make a random sample in the desired format
-    data = create_random_tensor(format, shape, np.float64)
+    data = create_random_tensor(format, shape, np.dtype(np.float64))
     a.write_sparse_tensor(data)
     del a
 
@@ -271,7 +271,7 @@ def test_soma_sparse_nd_array_read_write_table(
     assert a.shape == shape
 
     # make a random sample in the desired format
-    data = create_random_tensor("table", shape, np.float32)
+    data = create_random_tensor("table", shape, np.dtype(np.float32))
     a.write_table(data)
     del a
 
@@ -282,7 +282,15 @@ def test_soma_sparse_nd_array_read_write_table(
     assert tables_are_same_value(data, t)
 
 
-@pytest.mark.parametrize("dtype", [np.float32, np.float64, np.int32, np.int64])
+@pytest.mark.parametrize(
+    "dtype",
+    [
+        np.dtype(np.float32),
+        np.dtype(np.float64),
+        np.dtype(np.int32),
+        np.dtype(np.int64),
+    ],
+)
 @pytest.mark.parametrize("shape", [(1,), (23, 14), (35, 3, 2), (8, 4, 2, 30)])
 def test_soma_sparse_nd_array_read_as_pandas(
     tmp_path, dtype: np.dtype, shape: Tuple[int, ...]
@@ -378,7 +386,7 @@ def test_soma_sparse_nd_array_nnz(tmp_path):
         assert a.nnz == 0
 
     t: pa.SparseCOOTensor = create_random_tensor(
-        "coo", a.shape, pa.int32().to_pandas_dtype(), 0.1
+        "coo", a.shape, np.dtype(pa.int32().to_pandas_dtype()), 0.1
     )
     a.write_sparse_tensor(t)
     with pytest.raises(NotImplementedError):