[pre-commit.ci] auto fixes from pre-commit.com hooks

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catalystneuro · Aug 26, 2024 · 6f23542 · 6f23542
1 parent 8356ca5
commit 6f23542
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Showing 7 changed files with 40 additions and 34 deletions.
diff --git a/README.md b/README.md
@@ -88,7 +88,7 @@ classDiagram
 
     class MultiChannelMicroscopyVolume {
         <<NWBDataInterface>>
-        
+
         --------------------------------------
         attributes
         --------------------------------------
@@ -104,14 +104,14 @@ classDiagram
         --> unit : text
         excitation_light_paths : ExcitationLightPath, excitation_light_paths
         emission_light_paths : EmissionLightPath, emission_light_paths
-        
+
         --------------------------------------
         links
         --------------------------------------
         imaging_space : VolumetricImageSpace
         microscope : Microscope
     }
-    
+
     class ImagingSpace{
         <<NWBContainer>>
 

diff --git a/requirements-min.txt b/requirements-min.txt
@@ -1,2 +1,2 @@
 pynwb
-ndx-ophys-devices git+https://github.com/catalystneuro/ndx-ophys-devices.git@create_specs
+ndx-ophys-devices git+https://github.com/catalystneuro/ndx-ophys-devices.git@create_specs
diff --git a/src/pynwb/ndx_microscopy/__init__.py b/src/pynwb/ndx_microscopy/__init__.py
@@ -19,12 +19,8 @@
     __spec_path = __location_of_this_file.parent.parent.parent / "spec" / f"{extension_name}.namespace.yaml"
 
 load_namespaces(str(__spec_path))
-from ndx_ophys_devices import (
-    OpticalFilter,
-    ExcitationSource,
-    Indicator,
-    Photodetector,
-)
+from ndx_ophys_devices import ExcitationSource, Indicator, OpticalFilter, Photodetector
+
 Microscope = get_class("Microscope", extension_name)
 ExcitationLightPath = get_class("ExcitationLightPath", extension_name)
 EmissionLightPath = get_class("EmissionLightPath", extension_name)

diff --git a/src/pynwb/ndx_microscopy/testing/__init__.py b/src/pynwb/ndx_microscopy/testing/__init__.py
@@ -1,7 +1,7 @@
 from ._mock import (
-    mock_Microscope,
-    mock_ExcitationLightPath,
     mock_EmissionLightPath,
+    mock_ExcitationLightPath,
+    mock_Microscope,
     mock_MicroscopyPlaneSegmentation,
     mock_MicroscopySegmentations,
     mock_MultiChannelMicroscopyVolume,

diff --git a/src/pynwb/ndx_microscopy/testing/_mock.py b/src/pynwb/ndx_microscopy/testing/_mock.py
@@ -3,22 +3,17 @@
 
 import numpy as np
 import pynwb.base
-from pynwb.testing.mock.utils import name_generator
-
-import ndx_microscopy
-
-from ndx_ophys_devices import (
-    OpticalFilter,
-    ExcitationSource,
-    Indicator,
-    Photodetector,
-)
+from ndx_ophys_devices import ExcitationSource, Indicator, OpticalFilter, Photodetector
 from ndx_ophys_devices.testing import (
+    mock_ExcitationSource,
     mock_Indicator,
-    mock_Photodetector,
     mock_OpticalFilter,
-    mock_ExcitationSource,
+    mock_Photodetector,
 )
+from pynwb.testing.mock.utils import name_generator
+
+import ndx_microscopy
+
 
 def mock_Microscope(
     *,

diff --git a/src/pynwb/tests/test_constructors.py b/src/pynwb/tests/test_constructors.py
@@ -4,9 +4,9 @@
 
 import pynwb
 from ndx_microscopy.testing import (
-    mock_Microscope,
-    mock_ExcitationLightPath,
     mock_EmissionLightPath,
+    mock_ExcitationLightPath,
+    mock_Microscope,
     mock_MicroscopyPlaneSegmentation,
     mock_MicroscopySegmentations,
     mock_MultiChannelMicroscopyVolume,
@@ -68,7 +68,10 @@ def test_constructor_planar_microscopy_series():
     emission_light_path = mock_EmissionLightPath()
 
     mock_PlanarMicroscopySeries(
-        microscope=microscope, excitation_light_path=excitation_light_path, imaging_space=imaging_space, emission_light_path=emission_light_path
+        microscope=microscope,
+        excitation_light_path=excitation_light_path,
+        imaging_space=imaging_space,
+        emission_light_path=emission_light_path,
     )
 
 
@@ -79,7 +82,10 @@ def test_constructor_variable_depth_microscopy_series():
     emission_light_path = mock_EmissionLightPath()
 
     mock_VariableDepthMicroscopySeries(
-        microscope=microscope, excitation_light_path=excitation_light_path, imaging_space=imaging_space, emission_light_path=emission_light_path
+        microscope=microscope,
+        excitation_light_path=excitation_light_path,
+        imaging_space=imaging_space,
+        emission_light_path=emission_light_path,
     )
 
 
@@ -90,7 +96,10 @@ def test_constructor_volumetric_microscopy_series():
     emission_light_path = mock_EmissionLightPath()
 
     mock_VolumetricMicroscopySeries(
-        microscope=microscope, excitation_light_path=excitation_light_path, imaging_space=imaging_space, emission_light_path=emission_light_path
+        microscope=microscope,
+        excitation_light_path=excitation_light_path,
+        imaging_space=imaging_space,
+        emission_light_path=emission_light_path,
     )
 
 
@@ -101,7 +110,9 @@ def test_constructor_multi_channel_microscopy_volume():
     emission_light_paths = [mock_EmissionLightPath()]
 
     excitation_light_paths_used_by_volume = pynwb.base.VectorData(
-        name="excitation_light_paths", description="Light sources used by this MultiChannelVolume.", data=excitation_light_paths
+        name="excitation_light_paths",
+        description="Light sources used by this MultiChannelVolume.",
+        data=excitation_light_paths,
     )
     emission_light_paths_used_by_volume = pynwb.base.VectorData(
         name="emission_light_paths",
@@ -126,7 +137,9 @@ def test_constructor_variable_depth_multi_channel_microscopy_volume():
     emission_light_paths = [mock_EmissionLightPath()]
 
     excitation_light_paths_used_by_volume = pynwb.base.VectorData(
-        name="excitation_light_paths", description="Light sources used by this MultiChannelVolume.", data=excitation_light_paths
+        name="excitation_light_paths",
+        description="Light sources used by this MultiChannelVolume.",
+        data=excitation_light_paths,
     )
     emission_light_paths_used_by_volume = pynwb.base.VectorData(
         name="emission_light_paths",

diff --git a/src/pynwb/tests/test_roundtrip.py b/src/pynwb/tests/test_roundtrip.py
@@ -6,9 +6,9 @@
 
 import pynwb
 from ndx_microscopy.testing import (
-    mock_Microscope,
-    mock_ExcitationLightPath,
     mock_EmissionLightPath,
+    mock_ExcitationLightPath,
+    mock_Microscope,
     mock_MicroscopyPlaneSegmentation,
     mock_MicroscopySegmentations,
     mock_MultiChannelMicroscopyVolume,
@@ -199,7 +199,9 @@ def test_roundtrip(self):
         # TODO: It might be more convenient in Python to have a custom constructor that takes in a list of
         # light sources and optical channels and does the VectorData wrapping internally
         excitation_light_paths_used_by_volume = pynwb.base.VectorData(
-            name="excitation_light_paths", description="Light sources used by this MultiChannelVolume.", data=excitation_light_paths
+            name="excitation_light_paths",
+            description="Light sources used by this MultiChannelVolume.",
+            data=excitation_light_paths,
         )
         emission_light_paths_used_by_volume = pynwb.base.VectorData(
             name="emission_light_paths",