Apply black, ruff, isort

docs/source/conf.py

@@ -45,9 +45,10 @@
 #  CUSTOM CONFIGURATIONS ADDED BY THE NWB TOOL FOR GENERATING FORMAT DOCS
 ###########################################################################
 
-import sphinx_rtd_theme  # noqa: E402
 import textwrap  # noqa: E402
 
+import sphinx_rtd_theme  # noqa: E402
+
 # -- Options for intersphinx  ---------------------------------------------
 intersphinx_mapping.update({
     'core': ('https://nwb-schema.readthedocs.io/en/latest/', None),
@@ -61,8 +62,8 @@
 
 def run_doc_autogen(_):
     # Execute the autogeneration of Sphinx format docs from the YAML sources
-    import sys
     import os
+    import sys
     conf_file_dir = os.path.dirname(os.path.abspath(__file__))
     sys.path.append(conf_file_dir)  # Need so that generate format docs can find the conf_doc_autogen file
     from conf_doc_autogen import spec_output_dir

docs/source/conf_doc_autogen.py

@@ -81,6 +81,7 @@
 # Default type map to be used. This is the type map where dependent namespaces are stored. In the case of
 # NWB this is spec_default_type_map = pynwb.get_type_map()
 import pynwb  # noqa: E402
+
 spec_default_type_map = pynwb.get_type_map()
 
 # Default specification classes for groups datasets and namespaces. In the case of NWB these are the NWB-specfic

src/pynwb/ndx_extracellular_channels/__init__.py

@@ -1,5 +1,6 @@
 import os
-from pynwb import load_namespaces, get_class
+
+from pynwb import get_class, load_namespaces
 
 try:
     from importlib.resources import files

src/pynwb/ndx_extracellular_channels/io.py

@@ -1,8 +1,10 @@
 from __future__ import annotations  # postpone type hint evaluation
+
+import warnings
+from typing import TYPE_CHECKING, List, Union
+
 import ndx_extracellular_channels
 import numpy as np
-from typing import Union, List, TYPE_CHECKING
-import warnings
 
 if TYPE_CHECKING:
     import probeinterface
@@ -83,7 +85,8 @@ def to_probeinterface(ndx_probe: ndx_extracellular_channels.Probe) -> probeinter
         probeinterface.Probe.device_channel_indices
     ndx_extracellular_channels.Probe.probe_model.contacts_table["shank_id"] -> probeinterface.Probe.shank_ids
     ndx_extracellular_channels.Probe.probe_model.contacts_table["plane_axes"] -> probeinterface.Probe.contact_plane_axes
-    ndx_extracellular_channels.Probe.probe_model.contacts_table["radius_in_um"] -> probeinterface.Probe.contact_shapes["radius"]
+    ndx_extracellular_channels.Probe.probe_model.contacts_table["radius_in_um"] ->
+        probeinterface.Probe.contact_shapes["radius"]
 
 
     Parameters

src/pynwb/tests/test_classes.py

@@ -1,18 +1,18 @@
 """Unit and integration tests for the ndx_extracellular_channels types."""
 
-from hdmf.common import DynamicTableRegion
 import numpy as np
-from pynwb import NWBFile
-from pynwb.testing import TestCase, NWBH5IOFlexMixin
-
+from hdmf.common import DynamicTableRegion
 from ndx_extracellular_channels import (
-    ProbeInsertion,
-    ContactsTable,
-    ProbeModel,
-    Probe,
     ChannelsTable,
+    ContactsTable,
     ExtracellularSeries,
+    Probe,
+    ProbeInsertion,
+    ProbeModel,
 )
+from pynwb.testing import NWBH5IOFlexMixin, TestCase
+
+from pynwb import NWBFile
 
 
 class TestContactsTable(TestCase):

src/pynwb/tests/test_example_usage_all.py

@@ -1,18 +1,19 @@
 import datetime
-from hdmf.common import DynamicTableRegion
-import numpy as np
-from pynwb import NWBFile, NWBHDF5IO
 import uuid
 
+import numpy as np
+from hdmf.common import DynamicTableRegion
 from ndx_extracellular_channels import (
-    ProbeInsertion,
-    ContactsTable,
-    ProbeModel,
-    Probe,
     ChannelsTable,
+    ContactsTable,
     ExtracellularSeries,
+    Probe,
+    ProbeInsertion,
+    ProbeModel,
 )
 
+from pynwb import NWBHDF5IO, NWBFile
+
 
 def test_all_classes():
 

src/pynwb/tests/test_example_usage_probeinterface.py

@@ -1,10 +1,12 @@
 import datetime
+import uuid
+
 import ndx_extracellular_channels
 import numpy as np
 import numpy.testing as npt
 import probeinterface
+
 import pynwb
-import uuid
 
 
 def test_from_probeinterface():
@@ -158,7 +160,7 @@ def test_from_probeinterface():
         npt.assert_array_equal(nwbfile.devices["renamed_probe3"].probe_model.contacts_table["shape"].data[:], "circle")
         npt.assert_array_equal(
             nwbfile.devices["renamed_probe3"].probe_model.contacts_table["radius_in_um"].data[:],
-            probe3.to_numpy()["radius"]
+            probe3.to_numpy()["radius"],
         )
 
 

src/spec/create_extension_spec.py

@@ -1,14 +1,7 @@
 # -*- coding: utf-8 -*-
 import os.path
 
-from pynwb.spec import (
-    NWBNamespaceBuilder,
-    export_spec,
-    NWBGroupSpec,
-    NWBAttributeSpec,
-    NWBDatasetSpec,
-    NWBLinkSpec,
-)
+from pynwb.spec import NWBAttributeSpec, NWBDatasetSpec, NWBGroupSpec, NWBLinkSpec, NWBNamespaceBuilder, export_spec
 
 
 def main():