lint

nwb_linkml/src/nwb_linkml/adapters/adapter.py

@@ -5,8 +5,8 @@ Base class for adapters
 import sys
 from abc import abstractmethod
 from dataclasses import dataclass, field
-from typing import Any, Generator, List, Literal, Optional, Tuple, Type, TypeVar, Union, overload
 from logging import Logger
+from typing import Any, Generator, List, Literal, Optional, Tuple, Type, TypeVar, Union, overload
 
 from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.linkml_model import (
@@ -104,6 +104,7 @@ class Adapter(BaseModel):
 
     @property
     def logger(self) -> Logger:
+        """A logger with the name of the adapter class! See :class:`.config`"""
         if self._logger is None:
             self._logger = init_logger(self.__class__.__name__)
         return self._logger

nwb_linkml/src/nwb_linkml/config.py

@@ -2,9 +2,9 @@
 Manage the operation of nwb_linkml from environmental variables
 """
 
-from typing import Optional, Literal
 import tempfile
 from pathlib import Path
+from typing import Literal, Optional
 
 from pydantic import (
     BaseModel,

nwb_linkml/src/nwb_linkml/includes/hdmf.py

@@ -577,6 +577,9 @@ class TimeSeriesReferenceVectorDataMixin(VectorDataMixin):
 
     @model_validator(mode="after")
     def ensure_equal_length(self) -> "TimeSeriesReferenceVectorDataMixin":
+        """
+        Each of the three indexing columns must be the same length to work!
+        """
         assert len(self.idx_start) == len(self.timeseries) == len(self.count), (
             f"Columns have differing lengths: idx: {len(self.idx_start)}, count: {len(self.count)},"
             f" timeseries: {len(self.timeseries)}"

nwb_linkml/tests/test_includes/conftest.py

@@ -4,22 +4,22 @@ import numpy as np
 import pytest
 
 from nwb_linkml.models import (
-    ElectricalSeries,
-    ExtracellularEphysElectrodes,
     Device,
-    ElectrodeGroup,
     DynamicTableRegion,
-    Units,
+    ElectricalSeries,
+    ElectrodeGroup,
+    ExtracellularEphysElectrodes,
     IntracellularElectrode,
     IntracellularElectrodesTable,
+    IntracellularRecordingsTable,
     IntracellularResponsesTable,
     IntracellularStimuliTable,
-    IntracellularRecordingsTable,
+    TimeSeriesReferenceVectorData,
+    Units,
     VoltageClampSeries,
     VoltageClampSeriesData,
     VoltageClampStimulusSeries,
     VoltageClampStimulusSeriesData,
-    TimeSeriesReferenceVectorData,
 )
 
 

nwb_linkml/tests/test_includes/test_hdmf.py

@@ -9,6 +9,7 @@ from nwb_linkml.models.pydantic.core.v2_7_0.namespace import (
     VectorIndex,
     VoltageClampStimulusSeries,
 )
+
 from .conftest import _ragged_array