restore public status of NWBMetaDataEncoder encoder (#1142)

CHANGELOG.md

@@ -6,6 +6,7 @@
 
 ## Bug Fixes
 * datetime objects now can be validated as conversion options [#1139](https://github.com/catalystneuro/neuroconv/pull/1126)
+* Make `NWBMetaDataEncoder` public again [PR #1142](https://github.com/catalystneuro/neuroconv/pull/1142)
 * Fix a bug where data in `DeepLabCutInterface` failed to write when `ndx-pose` was not imported. [#1144](https://github.com/catalystneuro/neuroconv/pull/1144)
 * `SpikeGLXConverterPipe` converter now accepts multi-probe structures with multi-trigger and does not assume a specific folder structure [#1150](https://github.com/catalystneuro/neuroconv/pull/1150)
 

docs/api/utils.rst

@@ -8,6 +8,8 @@ Dictionaries
 JSON Schema
 -----------
 .. automodule:: neuroconv.utils.json_schema
+    :members:
+    :exclude-members: NWBMetaDataEncoder
 
 Common Reused Types
 -------------------

src/neuroconv/basedatainterface.py

@@ -19,12 +19,11 @@
 )
 from .tools.nwb_helpers._metadata_and_file_helpers import _resolve_backend
 from .utils import (
-    _NWBMetaDataEncoder,
     get_json_schema_from_method_signature,
     load_dict_from_file,
 )
 from .utils.dict import DeepDict
-from .utils.json_schema import _NWBSourceDataEncoder
+from .utils.json_schema import _NWBMetaDataEncoder, _NWBSourceDataEncoder
 
 
 class BaseDataInterface(ABC):

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

@@ -8,7 +8,8 @@
 
 from .nvt_utils import read_data, read_header
 from ....basetemporalalignmentinterface import BaseTemporalAlignmentInterface
-from ....utils import DeepDict, _NWBMetaDataEncoder, get_base_schema
+from ....utils import DeepDict, get_base_schema
+from ....utils.json_schema import _NWBMetaDataEncoder
 from ....utils.path import infer_path
 
 

src/neuroconv/tools/nwb_helpers/_metadata_and_file_helpers.py

@@ -8,7 +8,6 @@
 from datetime import datetime
 from pathlib import Path
 from typing import Literal, Optional
-from warnings import warn
 
 from hdmf_zarr import NWBZarrIO
 from pydantic import FilePath
@@ -26,7 +25,7 @@ def get_module(nwbfile: NWBFile, name: str, description: str = None):
     """Check if processing module exists. If not, create it. Then return module."""
     if name in nwbfile.processing:
         if description is not None and nwbfile.processing[name].description != description:
-            warn(
+            warnings.warn(
                 "Custom description given to get_module does not match existing module description! "
                 "Ignoring custom description."
             )
@@ -157,7 +156,7 @@ def _attempt_cleanup_of_existing_nwbfile(nwbfile_path: Path) -> None:
     # Windows in particular can encounter errors at this step
     except PermissionError:  # pragma: no cover
         message = f"Unable to remove NWB file located at {nwbfile_path.absolute()}! Please remove it manually."
-        warn(message=message, stacklevel=2)
+        warnings.warn(message=message, stacklevel=2)
 
 
 @contextmanager

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.json_schema import _NWBMetaDataEncoder
 
 
 class DataInterfaceTestMixin:

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/json_schema.py

@@ -16,13 +16,8 @@
 from pynwb.icephys import IntracellularElectrode
 
 
-class _NWBMetaDataEncoder(json.JSONEncoder):
-    """
-    Custom JSON encoder for NWB metadata.
-
-    This encoder extends the default JSONEncoder class and provides custom serialization
-    for certain data types commonly used in NWB metadata.
-    """
+class _GenericNeuroconvEncoder(json.JSONEncoder):
+    """Generic JSON encoder for NeuroConv data."""
 
     def default(self, obj):
         """
@@ -36,45 +31,38 @@ def default(self, obj):
         if isinstance(obj, np.generic):
             return obj.item()
 
+        # Numpy arrays should be converted to lists
         if isinstance(obj, np.ndarray):
             return obj.tolist()
 
+        # Over-write behaviors for Paths
+        if isinstance(obj, Path):
+            return str(obj)
+
         # The base-class handles it
         return super().default(obj)
 
 
-class _NWBSourceDataEncoder(_NWBMetaDataEncoder):
+class _NWBMetaDataEncoder(_GenericNeuroconvEncoder):
     """
-    Custom JSON encoder for data interface source data (i.e. kwargs).
-
-    This encoder extends the default JSONEncoder class and provides custom serialization
-    for certain data types commonly used in interface source data.
+    Custom JSON encoder for NWB metadata.
     """
 
-    def default(self, obj):
 
-        # Over-write behaviors for Paths
-        if isinstance(obj, Path):
-            return str(obj)
-
-        return super().default(obj)
+class _NWBSourceDataEncoder(_GenericNeuroconvEncoder):
+    """
+    Custom JSON encoder for data interface source data (i.e. kwargs).
+    """
 
 
-class _NWBConversionOptionsEncoder(_NWBMetaDataEncoder):
+class _NWBConversionOptionsEncoder(_GenericNeuroconvEncoder):
     """
     Custom JSON encoder for conversion options of the data interfaces and converters (i.e. kwargs).
-
-    This encoder extends the default JSONEncoder class and provides custom serialization
-    for certain data types commonly used in interface source data.
     """
 
-    def default(self, obj):
-
-        # Over-write behaviors for Paths
-        if isinstance(obj, Path):
-            return str(obj)
 
-        return super().default(obj)
+# This is used in the Guide so we will keep it public.
+NWBMetaDataEncoder = _NWBMetaDataEncoder
 
 
 def get_base_schema(

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.json_schema import _NWBMetaDataEncoder
 
 
 def create_test_directories_and_files(

tests/test_minimal/test_utils/test_json_schema_utils.py

@@ -6,12 +6,12 @@
 from pynwb.ophys import ImagingPlane, TwoPhotonSeries
 
 from neuroconv.utils import (
-    _NWBMetaDataEncoder,
     dict_deep_update,
     fill_defaults,
     get_schema_from_hdmf_class,
     load_dict_from_file,
 )
+from neuroconv.utils.json_schema import _NWBMetaDataEncoder
 
 
 def compare_dicts(a: dict, b: dict):