fix: zarr loading and rename numpy_folder -> binary

Author: alejoe91

src/spikeinterface/core/loading.py

@@ -292,23 +292,17 @@ def _load_object_from_zarr(folder_or_url, object_type, **kwargs):
     elif object_type == "Recording":
         from .zarrextractors import read_zarr_recording
 
-        storage_options = kwargs.get("storage_options", None)
-        load_compression_ratio = kwargs.get("load_compression_ratio", False)
-        recording = read_zarr_recording(
-            folder_or_url, storage_options=storage_options, load_compression_ratio=load_compression_ratio
-        )
+        recording = read_zarr_recording(folder_or_url, **kwargs)
         return recording
     elif object_type == "Sorting":
         from .zarrextractors import read_zarr_sorting
 
-        storage_options = kwargs.get("storage_options", None)
-        sorting = read_zarr_sorting(folder_or_url, storage_options=storage_options)
+        sorting = read_zarr_sorting(folder_or_url, **kwargs)
         return sorting
     elif object_type == "Recording|Sorting":
         # This case shoudl deprecated soon because the read_zarr is ultra ambiguous
         # just testing if the zarr contains unit_ids or channel_ids but many object also contains it (see template)!!!!
         from .zarrextractors import read_zarr
 
-        storage_options = kwargs.get("storage_options", None)
-        rec_or_sorting = read_zarr(folder_or_url, storage_options=storage_options)
+        rec_or_sorting = read_zarr(folder_or_url, **kwargs)
         return rec_or_sorting

src/spikeinterface/core/tests/test_basesorting.py

@@ -78,7 +78,7 @@ def test_BaseSorting(create_cache_folder):
     # cache new format : numpy_folder
     folder = cache_folder / "simple_sorting_numpy_folder"
     sorting.set_property("test", np.ones(len(sorting.unit_ids)))
-    sorting.save(folder=folder, format="numpy_folder")
+    sorting.save(folder=folder, format="binary")
     sorting2 = BaseExtractor.load(folder)
     assert isinstance(sorting2, NumpyFolderSorting)
 
@@ -143,7 +143,7 @@ def test_BaseSorting(create_cache_folder):
 
     # test save to zarr
     # compressor = get_default_zarr_compressor()
-    sorting_zarr = sorting.save(format="zarr", folder=cache_folder / "sorting")
+    sorting_zarr = sorting.save(format="zarr", folder=cache_folder / "sorting.zarr")
     sorting_zarr_loaded = load(cache_folder / "sorting.zarr")
     # annotations is False because Zarr adds compression ratios
     check_sortings_equal(sorting, sorting_zarr, check_annotations=False, check_properties=True)

src/spikeinterface/core/tests/test_loading.py

@@ -102,7 +102,7 @@ def test_load_binary_recording(generate_recording_sorting, tmp_path, output_form
     check_recordings_equal(rec, rec_loaded)
 
 
-@pytest.mark.parametrize("output_format", ["numpy_folder", "zarr"])
+@pytest.mark.parametrize("output_format", ["binary", "zarr"])
 def test_load_binary_sorting(generate_recording_sorting, tmp_path, output_format):
     _, sort = generate_recording_sorting
     _ = sort.save(folder=tmp_path / "test_sorting", format=output_format, overwrite=True)

src/spikeinterface/core/tests/test_zarrextractors.py

@@ -60,13 +60,13 @@ def test_ZarrSortingExtractor(tmp_path):
     np_sorting = generate_sorting()
 
     # store in root standard normal way
-    folder = tmp_path / "zarr_sorting"
+    folder = tmp_path / "zarr_sorting.zarr"
     ZarrSortingExtractor.write_sorting(np_sorting, folder)
     sorting = ZarrSortingExtractor(folder)
     sorting = load(sorting.to_dict())
 
     # store the sorting in a sub group (for instance SortingResult)
-    folder = tmp_path / "zarr_sorting_sub_group"
+    folder = tmp_path / "zarr_sorting_sub_group.zarr"
     zarr_root = zarr.open(folder, mode="w")
     zarr_sorting_group = zarr_root.create_group("sorting")
     add_sorting_to_zarr_group(sorting, zarr_sorting_group)

src/spikeinterface/core/zarrextractors.py

@@ -495,6 +495,7 @@ def write_sorting(
         zarr_root = zarr.open(str(folder_path), mode="w", storage_options=storage_options)
         zarr_root.attrs["zarr_class_info"] = retrieve_importing_provenance(ZarrSortingExtractor)
         add_sorting_to_zarr_group(sorting, zarr_root, **kwargs)
+        return ZarrSortingExtractor(folder_path, storage_options=storage_options)
 
 
 read_zarr_recording = define_function_from_class(source_class=ZarrRecordingExtractor, name="read_zarr_recording")