Merge branch 'main' into fix_chunks

iohub/ngff/nodes.py

@@ -193,7 +193,7 @@ def __delitem__(self, key):
 
     def __contains__(self, key):
         key = normalize_storage_path(key)
-        return key in self._member_names
+        return key.lower() in [name.lower() for name in self._member_names]
 
     def __iter__(self):
         yield from self._member_names

tests/ngff/test_ngff.py

@@ -681,17 +681,18 @@ def test_position_scale(channels_and_random_5d):
         assert dataset.scale == scale
 
 
+@pytest.mark.skip(reason="https://github.com/czbiohub-sf/iohub/issues/255")
 def test_combine_fovs_to_hcs():
     fovs = {}
     fov_paths = ("A/1/0", "B/1/0", "H/12/9")
-    for path in fov_paths:
-        with open_ome_zarr(hcs_ref) as hcs_store:
+    with open_ome_zarr(hcs_ref) as hcs_store:
+        for path in fov_paths:
             fovs[path] = hcs_store["B/03/0"]
     with TemporaryDirectory() as temp_dir:
         store_path = os.path.join(temp_dir, "combined.zarr")
-        combined_plate = Plate.from_positions(store_path, fovs)
+        Plate.from_positions(store_path, fovs).close()
         # read data with an external reader
-        ext_reader = Reader(parse_url(combined_plate.zgroup.store.path))
+        ext_reader = Reader(parse_url(store_path))
         node = list(ext_reader())[0]
         plate_meta = node.metadata["metadata"]["plate"]
         assert len(plate_meta["rows"]) == 3

tests/ngff/test_ngff_utils.py

@@ -501,7 +501,7 @@ def test_create_empty_plate(plate_setup, extra_channels):
     setup=apply_transform_czyx_setup(),
     constant=st.integers(min_value=1, max_value=5),
 )
-@settings(max_examples=5, deadline=1200)
+@settings(max_examples=5, deadline=None)
 def test_apply_transform_to_zyx_and_save(setup, constant):
     (
         position_keys,
@@ -565,7 +565,7 @@ def test_apply_transform_to_zyx_and_save(setup, constant):
     constant=st.integers(min_value=1, max_value=3),
     num_processes=st.integers(min_value=1, max_value=3),
 )
-@settings(max_examples=3, deadline=2000)
+@settings(max_examples=3, deadline=None)
 def test_process_single_position(setup, constant, num_processes):
     # def test_process_single_position(setup, constant, num_processes):
     (