Support NeuroConv 0.6.5

- Bump neuroconv version from 0.6.1 to 0.6.5 in all environment files
- Update NWBMetaDataEncoder imports to use private _NWBMetaDataEncoder
- Add spikeinterface to PyInstaller modules_to_collect for lazy imports
- Pin pandas < 3.0 to avoid Arrow backend read-only array issue

Closes #960

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: bendichter

environments/environment-Linux.yml

@@ -15,7 +15,8 @@ dependencies:
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
       - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
-      - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.6.1
+      - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.6.5
+      - pandas < 3.0 # pandas 3.0 uses Arrow backend by default, returning read-only arrays that break spikeinterface Phy extractor
       - neo == 0.14.1 # 0.14.2 is not compatible with neuroconv < 0.7.5
       - scikit-learn == 1.4.0 # Tutorial data generation
       - tqdm_publisher >= 0.0.1 # Progress bars

environments/environment-MAC-apple-silicon.yml

@@ -23,7 +23,8 @@ dependencies:
       - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
       # NOTE: the NeuroConv wheel on PyPI includes sonpy which is not compatible with arm64, so build and install
       # NeuroConv from GitHub, which will remove the sonpy dependency when building from Mac arm64
-      - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.6.1
+      - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.6.5
+      - pandas < 3.0 # pandas 3.0 uses Arrow backend by default, returning read-only arrays that break spikeinterface Phy extractor
       - neo == 0.14.1 # 0.14.2 is not compatible with neuroconv < 0.7.5
       - scikit-learn == 1.4.0 # Tutorial data generation
       - tqdm_publisher >= 0.0.1 # Progress bars

environments/environment-MAC-intel.yml

@@ -18,7 +18,8 @@ dependencies:
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
       - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
-      - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.6.1
+      - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.6.5
+      - pandas < 3.0 # pandas 3.0 uses Arrow backend by default, returning read-only arrays that break spikeinterface Phy extractor
       - neo == 0.14.1 # 0.14.2 is not compatible with neuroconv < 0.7.5
       - scikit-learn == 1.4.0 # Tutorial data generation
       - tqdm_publisher >= 0.0.1 # Progress bars

environments/environment-Windows.yml

@@ -18,7 +18,8 @@ dependencies:
       - flask-cors === 3.0.10
       - flask_restx == 1.1.0
       - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
-      - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.6.1
+      - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.6.5
+      - pandas < 3.0 # pandas 3.0 uses Arrow backend by default, returning read-only arrays that break spikeinterface Phy extractor
       - neo == 0.14.1 # 0.14.2 is not compatible with neuroconv < 0.7.5
       - scikit-learn == 1.4.0 # Tutorial data generation
       - tqdm_publisher >= 0.0.1 # Progress bars

nwb-guide.spec

@@ -46,6 +46,7 @@ modules_to_collect = [
     'ScanImageTiffReader',
     'deprecated',
     'probeinterface',
+    'spikeinterface',
 ]
 for module_name in modules_to_collect:
     collection = collect_all(module_name)

src/pyflask/manageNeuroconv/manage_neuroconv.py

@@ -205,7 +205,7 @@ def coerce_schema_compliance_recursive(obj, schema):
 
 def autocomplete_format_string(info: dict) -> str:
     from neuroconv.tools.path_expansion import construct_path_template
-    from neuroconv.utils.json_schema import NWBMetaDataEncoder
+    from neuroconv.utils.json_schema import _NWBMetaDataEncoder as NWBMetaDataEncoder
 
     base_directory = info["base_directory"]
     filesystem_entry_path = info["path"]
@@ -240,7 +240,7 @@ def autocomplete_format_string(info: dict) -> str:
 def locate_data(info: dict) -> dict:
     """Locate data from the specifies directories using fstrings."""
     from neuroconv.tools import LocalPathExpander
-    from neuroconv.utils.json_schema import NWBMetaDataEncoder
+    from neuroconv.utils.json_schema import _NWBMetaDataEncoder as NWBMetaDataEncoder
 
     expander = LocalPathExpander()
 
@@ -431,7 +431,7 @@ def map_interfaces(callback, converter, to_match: Union["BaseDataInterface", Non
 
 def get_metadata_schema(source_data: Dict[str, dict], interfaces: dict) -> Dict[str, dict]:
     """Function used to fetch the metadata schema from a CustomNWBConverter instantiated from the source_data."""
-    from neuroconv.utils import NWBMetaDataEncoder
+    from neuroconv.utils import _NWBMetaDataEncoder as NWBMetaDataEncoder
 
     resolved_source_data = replace_none_with_nan(
         source_data, resolve_references(get_custom_converter(interfaces).get_source_schema())
@@ -1842,7 +1842,7 @@ def get_unit_table_json(interface) -> List[Dict[str, Any]]:
     A convenience function for collecting and organizing the property values of the underlying sorting extractor.
     """
 
-    from neuroconv.utils import NWBMetaDataEncoder
+    from neuroconv.utils import _NWBMetaDataEncoder as NWBMetaDataEncoder
 
     sorting = interface.sorting_extractor
 
@@ -1943,7 +1943,7 @@ def get_electrode_table_json(interface) -> List[Dict[str, Any]]:
     A convenience function for collecting and organizing the property values of the underlying recording extractor.
     """
 
-    from neuroconv.utils import NWBMetaDataEncoder
+    from neuroconv.utils import _NWBMetaDataEncoder as NWBMetaDataEncoder
 
     recording = interface.recording_extractor