Apply hooks except isort

Author: CBroz1

.pre-commit-config.yaml

@@ -23,12 +23,12 @@ repos:
         args:
           - --line-length=88
 
-  # isort
-  - repo: https://github.com/pycqa/isort
-    rev: 5.11.2
-    hooks:
-      - id: isort
-        description: Sorts imports in an alphabetical order
+  # # isort
+  # - repo: https://github.com/pycqa/isort
+  #   rev: 5.11.2
+  #   hooks:
+  #     - id: isort
+  #       description: Sorts imports in an alphabetical order
 
   # flake8
   - repo: https://github.com/pycqa/flake8

CONTRIBUTING.md

@@ -1,3 +1,3 @@
 # Contribution Guidelines
 
-This project follows the [DataJoint Contribution Guidelines](https://docs.datajoint.io/python/community/02-Contribute.html). Please reference the link for more full details.
+This project follows the [DataJoint Contribution Guidelines](https://docs.datajoint.io/python/community/02-Contribute.html). Please reference the link for more full details.

README.md

@@ -8,5 +8,5 @@ fully functional pipeline.
 
 ![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/diagram_flowchart.svg)
 
-Installation and usage instructions can be found at the 
+Installation and usage instructions can be found at the
 [Element documentation](https://datajoint.com/docs/elements/element-array-ephys).

element_array_ephys/export/nwb/README.md

@@ -52,4 +52,4 @@ which can be called independently:
 
 
     source data -> processing["ecephys"].lfp.electrical_series["ElectricalSeries{insertion_number}"].data
-    source data -> processing["ecephys"].lfp.electrical_series["ElectricalSeries{insertion_number}"].timestamps
+    source data -> processing["ecephys"].lfp.electrical_series["ElectricalSeries{insertion_number}"].timestamps

element_array_ephys/export/nwb/requirements.txt

@@ -1,4 +1,4 @@
 dandi
+neo==0.10.2
 nwb-conversion-tools==0.11.1
 spikeinterface==0.93.0
-neo==0.10.2

element_array_ephys/readers/kilosort.py

@@ -169,8 +169,8 @@ def extract_spike_depths(self):
             spk_feature_ycoord = ycoords[spk_feature_ind]
             # center of mass is sum(coords.*features)/sum(features)
             self._data["spike_depths"] = np.sum(
-                spk_feature_ycoord * pc_features ** 2, axis=1
-            ) / np.sum(pc_features ** 2, axis=1)
+                spk_feature_ycoord * pc_features**2, axis=1
+            ) / np.sum(pc_features**2, axis=1)
         else:
             self._data["spike_depths"] = None
 

requirements.txt

@@ -1,7 +1,7 @@
 datajoint>=0.13
-pyopenephys @ git+https://github.com/datajoint-company/pyopenephys.git
-openpyxl
-pynwb>=2.0.0
 element-interface @ git+https://github.com/datajoint/element-interface.git
+openpyxl
 plotly
+pynwb>=2.0.0
+pyopenephys @ git+https://github.com/datajoint-company/pyopenephys.git
 seaborn