Make some methods private (#1050)

Co-authored-by: Cody Baker <[email protected]>

CHANGELOG.md

@@ -1,6 +1,7 @@
 # Upcoming
 
 ### Deprecations
+* The following classes and objects are now private `NWBMetaDataEncoder`, `NWBMetaDataEncoder`, `check_if_imaging_fits_into_memory`, `NoDatesSafeLoader` [PR #1050](https://github.com/catalystneuro/neuroconv/pull/1050)
 
 ### Features
 

src/neuroconv/basedatainterface.py

@@ -19,7 +19,7 @@
 )
 from .tools.nwb_helpers._metadata_and_file_helpers import _resolve_backend
 from .utils import (
-    NWBMetaDataEncoder,
+    _NWBMetaDataEncoder,
     get_json_schema_from_method_signature,
     load_dict_from_file,
 )
@@ -63,7 +63,7 @@ def get_metadata(self) -> DeepDict:
 
     def validate_metadata(self, metadata: dict, append_mode: bool = False) -> None:
         """Validate the metadata against the schema."""
-        encoder = NWBMetaDataEncoder()
+        encoder = _NWBMetaDataEncoder()
         # The encoder produces a serialized object, so we deserialized it for comparison
 
         serialized_metadata = encoder.encode(metadata)

src/neuroconv/datainterfaces/behavior/neuralynx/neuralynx_nvt_interface.py

@@ -8,7 +8,7 @@
 
 from .nvt_utils import read_data, read_header
 from ....basetemporalalignmentinterface import BaseTemporalAlignmentInterface
-from ....utils import DeepDict, NWBMetaDataEncoder, get_base_schema
+from ....utils import DeepDict, _NWBMetaDataEncoder, get_base_schema
 from ....utils.path import infer_path
 
 
@@ -136,7 +136,7 @@ def add_to_nwbfile(
                 unit="pixels",
                 conversion=1.0,
                 timestamps=self.get_timestamps(),
-                description=f"Pixel x and y coordinates from the .nvt file with header data: {json.dumps(self.header, cls=NWBMetaDataEncoder)}",
+                description=f"Pixel x and y coordinates from the .nvt file with header data: {json.dumps(self.header, cls=_NWBMetaDataEncoder)}",
             )
 
             nwbfile.add_acquisition(Position([spatial_series], name="NvtPosition"))
@@ -151,7 +151,7 @@ def add_to_nwbfile(
                         unit="degrees",
                         conversion=1.0,
                         timestamps=spatial_series if add_position else self.get_timestamps(),
-                        description=f"Angle from the .nvt file with header data: {json.dumps(self.header, cls=NWBMetaDataEncoder)}",
+                        description=f"Angle from the .nvt file with header data: {json.dumps(self.header, cls=_NWBMetaDataEncoder)}",
                     ),
                     name="NvtCompassDirection",
                 )

src/neuroconv/datainterfaces/ecephys/mearec/mearecdatainterface.py

@@ -3,7 +3,7 @@
 from pydantic import FilePath
 
 from ..baserecordingextractorinterface import BaseRecordingExtractorInterface
-from ....utils.json_schema import NWBMetaDataEncoder
+from ....utils.json_schema import _NWBMetaDataEncoder
 
 
 class MEArecRecordingInterface(BaseRecordingExtractorInterface):
@@ -61,7 +61,7 @@ def get_metadata(self) -> dict:
         for unneeded_key in ["fs", "dtype"]:
             recording_metadata.pop(unneeded_key)
         metadata["Ecephys"].update(
-            {self.es_key: dict(name=self.es_key, description=json.dumps(recording_metadata, cls=NWBMetaDataEncoder))}
+            {self.es_key: dict(name=self.es_key, description=json.dumps(recording_metadata, cls=_NWBMetaDataEncoder))}
         )
 
         return metadata

src/neuroconv/nwbconverter.py

@@ -29,7 +29,7 @@
     unroot_schema,
 )
 from .utils.dict import DeepDict
-from .utils.json_schema import NWBMetaDataEncoder, NWBSourceDataEncoder
+from .utils.json_schema import _NWBMetaDataEncoder, _NWBSourceDataEncoder
 
 
 class NWBConverter:
@@ -63,7 +63,7 @@ def validate_source(cls, source_data: dict[str, dict], verbose: bool = True):
 
     def _validate_source_data(self, source_data: dict[str, dict], verbose: bool = True):
 
-        encoder = NWBSourceDataEncoder()
+        encoder = _NWBSourceDataEncoder()
         # The encoder produces a serialized object, so we deserialized it for comparison
 
         serialized_source_data = encoder.encode(source_data)
@@ -104,7 +104,7 @@ def get_metadata(self) -> DeepDict:
 
     def validate_metadata(self, metadata: dict[str, dict], append_mode: bool = False):
         """Validate metadata against Converter metadata_schema."""
-        encoder = NWBMetaDataEncoder()
+        encoder = _NWBMetaDataEncoder()
         # The encoder produces a serialized object, so we deserialized it for comparison
         serialized_metadata = encoder.encode(metadata)
         decoded_metadata = json.loads(serialized_metadata)

src/neuroconv/tools/roiextractors/__init__.py

@@ -1,5 +1,5 @@
 from .roiextractors import (
-    check_if_imaging_fits_into_memory,
+    _check_if_imaging_fits_into_memory,
     get_nwb_imaging_metadata,
     get_nwb_segmentation_metadata,
     add_background_fluorescence_traces,

src/neuroconv/tools/roiextractors/roiextractors.py

@@ -558,7 +558,7 @@ def add_photon_series_to_nwbfile(
     return nwbfile
 
 
-def check_if_imaging_fits_into_memory(imaging: ImagingExtractor) -> None:
+def _check_if_imaging_fits_into_memory(imaging: ImagingExtractor) -> None:
     """
     Raise an error if the full traces of an imaging extractor are larger than available memory.
 
@@ -625,7 +625,7 @@ def data_generator(imaging):
     iterator_options = dict() if iterator_options is None else iterator_options
 
     if iterator_type is None:
-        check_if_imaging_fits_into_memory(imaging=imaging)
+        _check_if_imaging_fits_into_memory(imaging=imaging)
         return imaging.get_video().transpose((0, 2, 1))
 
     if iterator_type == "v1":

src/neuroconv/tools/testing/data_interface_mixins.py

@@ -33,7 +33,7 @@
     configure_backend,
     get_default_backend_configuration,
 )
-from neuroconv.utils import NWBMetaDataEncoder
+from neuroconv.utils import _NWBMetaDataEncoder
 
 
 class DataInterfaceTestMixin:
@@ -98,7 +98,7 @@ def check_metadata(self):
         if "session_start_time" not in metadata["NWBFile"]:
             metadata["NWBFile"].update(session_start_time=datetime.now().astimezone())
         # handle json encoding of datetimes and other tricky types
-        metadata_for_validation = json.loads(json.dumps(metadata, cls=NWBMetaDataEncoder))
+        metadata_for_validation = json.loads(json.dumps(metadata, cls=_NWBMetaDataEncoder))
         validate(metadata_for_validation, schema)
         self.check_extracted_metadata(metadata)
 

src/neuroconv/utils/__init__.py

@@ -7,7 +7,7 @@
     load_dict_from_file,
 )
 from .json_schema import (
-    NWBMetaDataEncoder,
+    _NWBMetaDataEncoder,
     fill_defaults,
     get_base_schema,
     get_metadata_schema_for_icephys,

src/neuroconv/utils/dict.py

@@ -12,7 +12,7 @@
 from pydantic import FilePath
 
 
-class NoDatesSafeLoader(yaml.SafeLoader):
+class _NoDatesSafeLoader(yaml.SafeLoader):
     """Custom override of yaml Loader class for datetime considerations."""
 
     @classmethod
@@ -33,7 +33,7 @@ def remove_implicit_resolver(cls, tag_to_remove):
             ]
 
 
-NoDatesSafeLoader.remove_implicit_resolver("tag:yaml.org,2002:timestamp")
+_NoDatesSafeLoader.remove_implicit_resolver("tag:yaml.org,2002:timestamp")
 
 
 def load_dict_from_file(file_path: FilePath) -> dict:
@@ -44,7 +44,7 @@ def load_dict_from_file(file_path: FilePath) -> dict:
 
     if file_path.suffix in (".yml", ".yaml"):
         with open(file=file_path, mode="r") as stream:
-            dictionary = yaml.load(stream=stream, Loader=NoDatesSafeLoader)
+            dictionary = yaml.load(stream=stream, Loader=_NoDatesSafeLoader)
     elif file_path.suffix == ".json":
         with open(file=file_path, mode="r") as fp:
             dictionary = json.load(fp=fp)

src/neuroconv/utils/json_schema.py

@@ -16,7 +16,7 @@
 from pynwb.icephys import IntracellularElectrode
 
 
-class NWBMetaDataEncoder(json.JSONEncoder):
+class _NWBMetaDataEncoder(json.JSONEncoder):
     """
     Custom JSON encoder for NWB metadata.
 
@@ -43,7 +43,7 @@ def default(self, obj):
         return super().default(obj)
 
 
-class NWBSourceDataEncoder(NWBMetaDataEncoder):
+class _NWBSourceDataEncoder(_NWBMetaDataEncoder):
     """
     Custom JSON encoder for data interface source data (i.e. kwargs).
 
@@ -350,7 +350,7 @@ def get_metadata_schema_for_icephys():
 
 def validate_metadata(metadata: dict[str, dict], schema: dict[str, dict], verbose: bool = False):
     """Validate metadata against a schema."""
-    encoder = NWBMetaDataEncoder()
+    encoder = _NWBMetaDataEncoder()
     # The encoder produces a serialized object, so we deserialized it for comparison
 
     serialized_metadata = encoder.encode(metadata)

tests/test_minimal/test_tools/test_expand_paths.py

@@ -9,7 +9,7 @@
 from neuroconv.tools import LocalPathExpander
 from neuroconv.tools.path_expansion import construct_path_template
 from neuroconv.tools.testing import generate_path_expander_demo_ibl
-from neuroconv.utils import NWBMetaDataEncoder
+from neuroconv.utils import _NWBMetaDataEncoder
 
 
 def create_test_directories_and_files(
@@ -409,7 +409,7 @@ def test_expand_paths_ibl(tmpdir):
             ),
         ),
     )
-    path_expansion_results = json.loads(json.dumps(path_expansion_results, cls=NWBMetaDataEncoder))
+    path_expansion_results = json.loads(json.dumps(path_expansion_results, cls=_NWBMetaDataEncoder))
 
     # build expected output from file
     expected_file_path = Path(__file__).parent / "expand_paths_ibl_expected.json"

tests/test_minimal/test_utils/test_json_schema_utils.py

@@ -6,7 +6,7 @@
 from pynwb.ophys import ImagingPlane, TwoPhotonSeries
 
 from neuroconv.utils import (
-    NWBMetaDataEncoder,
+    _NWBMetaDataEncoder,
     dict_deep_update,
     fill_defaults,
     get_schema_from_hdmf_class,
@@ -204,5 +204,5 @@ def test_get_schema_from_TwoPhotonSeries_array_type():
 
 def test_np_array_encoding():
     np_array = np.array([1, 2, 3])
-    encoded = json.dumps(np_array, cls=NWBMetaDataEncoder)
+    encoded = json.dumps(np_array, cls=_NWBMetaDataEncoder)
     assert encoded == "[1, 2, 3]"

tests/test_ophys/test_tools_roiextractors.py

@@ -27,14 +27,14 @@
 
 from neuroconv.tools.nwb_helpers import get_module
 from neuroconv.tools.roiextractors import (
+    _check_if_imaging_fits_into_memory,
     add_devices_to_nwbfile,
     add_fluorescence_traces_to_nwbfile,
     add_image_segmentation_to_nwbfile,
     add_imaging_plane_to_nwbfile,
     add_photon_series_to_nwbfile,
     add_plane_segmentation_to_nwbfile,
     add_summary_images_to_nwbfile,
-    check_if_imaging_fits_into_memory,
 )
 from neuroconv.tools.roiextractors.imagingextractordatachunkiterator import (
     ImagingExtractorDataChunkIterator,
@@ -1539,7 +1539,7 @@ def test_non_iterative_write_assertion(self):
         reg_expression = "Memory error, full TwoPhotonSeries data is (.*?) are available! Please use iterator_type='v2'"
 
         with self.assertRaisesRegex(MemoryError, reg_expression):
-            check_if_imaging_fits_into_memory(imaging=mock_imaging)
+            _check_if_imaging_fits_into_memory(imaging=mock_imaging)
 
     def test_non_iterative_two_photon(self):
         """Test adding two photon series with using DataChunkIterator as iterator type."""