Add missing typing to NWBConverter backend and backend options (#1160)

CHANGELOG.md

@@ -31,7 +31,7 @@
 * Use pytest format for dandi tests to avoid window permission error on teardown [PR #1151](https://github.com/catalystneuro/neuroconv/pull/1151)
 * Added many docstrings for public functions [PR #1063](https://github.com/catalystneuro/neuroconv/pull/1063)
 * Clean up with warnings and deprecations in the testing framework [PR #1158](https://github.com/catalystneuro/neuroconv/pull/1158)
-
+* Enhance the typing of the signature on the `NWBConverter` by adding zarr as a literal option on the backend and backend configuration [PR #1160](https://github.com/catalystneuro/neuroconv/pull/1160)
 
 # v0.6.5 (November 1, 2024)
 

docs/conversion_examples_gallery/fiberphotometry/tdt_fp.rst

@@ -207,15 +207,13 @@ Convert TDT Fiber Photometry data to NWB using
     >>> LOCAL_PATH = Path(".") # Path to neuroconv
     >>> editable_metadata_path = LOCAL_PATH / "tests" / "test_on_data" / "ophys" / "fiber_photometry_metadata.yaml"
 
-    >>> interface = TDTFiberPhotometryInterface(folder_path=folder_path, verbose=True)
-    Source data is valid!
+    >>> interface = TDTFiberPhotometryInterface(folder_path=folder_path, verbose=False)
     >>> metadata = interface.get_metadata()
     >>> metadata["NWBFile"]["session_start_time"] = datetime.now(tz=ZoneInfo("US/Pacific"))
     >>> editable_metadata = load_dict_from_file(editable_metadata_path)
     >>> metadata = dict_deep_update(metadata, editable_metadata)
 
     >>> # Choose a path for saving the nwb file and run the conversion
-    >>> nwbfile_path = LOCAL_PATH / "example_tdtfp.nwb"
+    >>> nwbfile_path =  f"{path_to_save_nwbfile}"
     >>> # t1 and t2 are optional arguments to specify the start and end times for the conversion
     >>> interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata, t1=0.0, t2=1.0)
-    NWB file saved at example_tdtfp.nwb!

src/neuroconv/nwbconverter.py

@@ -204,11 +204,8 @@ def run_conversion(
         nwbfile: Optional[NWBFile] = None,
         metadata: Optional[dict] = None,
         overwrite: bool = False,
-        # TODO: when all H5DataIO prewraps are gone, introduce Zarr safely
-        # backend: Union[Literal["hdf5", "zarr"]],
-        # backend_configuration: Optional[Union[HDF5BackendConfiguration, ZarrBackendConfiguration]] = None,
-        backend: Optional[Literal["hdf5"]] = None,
-        backend_configuration: Optional[HDF5BackendConfiguration] = None,
+        backend: Optional[Literal["hdf5", "zarr"]] = None,
+        backend_configuration: Optional[Union[HDF5BackendConfiguration, ZarrBackendConfiguration]] = None,
         conversion_options: Optional[dict] = None,
     ) -> None:
         """
@@ -226,11 +223,11 @@ def run_conversion(
         overwrite : bool, default: False
             Whether to overwrite the NWBFile if one exists at the nwbfile_path.
             The default is False (append mode).
-        backend : "hdf5", optional
+        backend : {"hdf5", "zarr"}, optional
             The type of backend to use when writing the file.
             If a `backend_configuration` is not specified, the default type will be "hdf5".
             If a `backend_configuration` is specified, then the type will be auto-detected.
-        backend_configuration : HDF5BackendConfiguration, optional
+        backend_configuration : HDF5BackendConfiguration or ZarrBackendConfiguration, optional
             The configuration model to use when configuring the datasets for this backend.
             To customize, call the `.get_default_backend_configuration(...)` method, modify the returned
             BackendConfiguration object, and pass that instead.

tests/test_on_data/ophys/test_miniscope_converter.py

@@ -159,8 +159,8 @@ def assertNWBFileStructure(self, nwbfile_path: str):
             nwbfile = io.read()
 
             self.assertEqual(
-                nwbfile.session_start_time,
-                datetime(2021, 10, 7, 15, 3, 28, 635).astimezone(),
+                nwbfile.session_start_time.replace(tzinfo=None),
+                datetime(2021, 10, 7, 15, 3, 28, 635),
             )
 
             self.assertIn(self.device_name, nwbfile.devices)