Apply isort

Author: CBroz1

.pre-commit-config.yaml

@@ -23,12 +23,13 @@ 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
+        args: ["--profile", "black"]
+        description: Sorts imports in an alphabetical order
 
   # flake8
   - repo: https://github.com/pycqa/flake8

element_array_ephys/__init__.py

@@ -1,6 +1,8 @@
-import datajoint as dj
 import logging
 import os
+
+import datajoint as dj
+
 from . import ephys_acute as ephys
 
 __all__ = ["ephys", "get_logger"]

element_array_ephys/ephys_acute.py

@@ -1,17 +1,17 @@
-import datajoint as dj
+import gc
+import importlib
+import inspect
 import pathlib
 import re
-import numpy as np
-import inspect
-import importlib
-import gc
 from decimal import Decimal
-import pandas as pd
 
-from element_interface.utils import find_root_directory, find_full_path, dict_to_uuid
+import datajoint as dj
+import numpy as np
+import pandas as pd
+from element_interface.utils import dict_to_uuid, find_full_path, find_root_directory
 
-from .readers import spikeglx, kilosort, openephys
-from . import probe, get_logger, ephys_report
+from . import ephys_report, get_logger, probe
+from .readers import kilosort, openephys, spikeglx
 
 log = get_logger(__name__)
 

element_array_ephys/ephys_chronic.py

@@ -1,16 +1,16 @@
-import datajoint as dj
-import pathlib
-import numpy as np
-import inspect
-import importlib
 import gc
+import importlib
+import inspect
+import pathlib
 from decimal import Decimal
-import pandas as pd
 
-from element_interface.utils import find_root_directory, find_full_path, dict_to_uuid
+import datajoint as dj
+import numpy as np
+import pandas as pd
+from element_interface.utils import dict_to_uuid, find_full_path, find_root_directory
 
-from .readers import spikeglx, kilosort, openephys
-from . import probe, get_logger, ephys_report
+from . import ephys_report, get_logger, probe
+from .readers import kilosort, openephys, spikeglx
 
 log = get_logger(__name__)
 

element_array_ephys/ephys_no_curation.py

@@ -1,17 +1,18 @@
-import datajoint as dj
+import gc
+import importlib
+import inspect
 import pathlib
 import re
-import numpy as np
-import inspect
-import importlib
-import gc
 from decimal import Decimal
+
+import datajoint as dj
+import numpy as np
 import pandas as pd
+from element_interface.utils import dict_to_uuid, find_full_path, find_root_directory
 
-from element_interface.utils import find_root_directory, find_full_path, dict_to_uuid
-from .readers import spikeglx, kilosort, openephys
-from element_array_ephys import probe, get_logger, ephys_report
+from element_array_ephys import ephys_report, get_logger, probe
 
+from .readers import kilosort, openephys, spikeglx
 
 log = get_logger(__name__)
 

element_array_ephys/ephys_precluster.py

@@ -1,14 +1,14 @@
-import datajoint as dj
+import importlib
+import inspect
 import re
+
+import datajoint as dj
 import numpy as np
-import inspect
-import importlib
 import pandas as pd
+from element_interface.utils import dict_to_uuid, find_full_path, find_root_directory
 
-from element_interface.utils import find_root_directory, find_full_path, dict_to_uuid
-
-from .readers import spikeglx, kilosort, openephys
-from . import probe, ephys_report
+from . import ephys_report, probe
+from .readers import kilosort, openephys, spikeglx
 
 schema = dj.schema()
 

element_array_ephys/export/nwb/nwb.py

@@ -1,9 +1,11 @@
-import os
 import decimal
 import json
+import os
+import warnings
+
+import datajoint as dj
 import numpy as np
 import pynwb
-import datajoint as dj
 from element_interface.utils import find_full_path
 from hdmf.backends.hdf5 import H5DataIO
 from hdmf.data_utils import GenericDataChunkIterator
@@ -13,10 +15,9 @@
 )
 from spikeinterface import extractors
 from tqdm import tqdm
-import warnings
-from ... import probe
-from ... import ephys_no_curation as ephys
 
+from ... import ephys_no_curation as ephys
+from ... import probe
 
 ephys_mode = os.getenv("EPHYS_MODE", dj.config["custom"].get("ephys_mode", "acute"))
 if ephys_mode != "no-curation":

element_array_ephys/plotting/widget.py

@@ -1,12 +1,14 @@
+import pathlib
 from modulefinder import Module
+
 import ipywidgets as widgets
-import pathlib
-from IPython.display import display
-from .. import ephys_report
-import plotly.graph_objs as go
 import plotly.express as px
+import plotly.graph_objs as go
+from IPython.display import display
 from skimage import io
 
+from .. import ephys_report
+
 
 def main(ephys: Module) -> widgets:
 

element_array_ephys/readers/kilosort.py

@@ -1,10 +1,12 @@
-from os import path
-from datetime import datetime
+import logging
 import pathlib
-import pandas as pd
-import numpy as np
 import re
-import logging
+from datetime import datetime
+from os import path
+
+import numpy as np
+import pandas as pd
+
 from .utils import convert_to_number
 
 log = logging.getLogger(__name__)

element_array_ephys/readers/kilosort_triggering.py

@@ -1,25 +1,24 @@
-import subprocess
-import shutil
-import sys
-import pathlib
-import json
-import re
 import inspect
+import json
 import os
-import scipy.io
-import numpy as np
+import pathlib
+import re
+import shutil
+import subprocess
+import sys
 from datetime import datetime, timedelta
 
+import numpy as np
+import scipy.io
 from element_interface.utils import dict_to_uuid
 
-
 # import the spike sorting packages
 try:
-    from ecephys_spike_sorting.scripts.create_input_json import createInputJson
-    from ecephys_spike_sorting.scripts.helpers import SpikeGLX_utils
     from ecephys_spike_sorting.modules.kilosort_helper.__main__ import (
         get_noise_channels,
     )
+    from ecephys_spike_sorting.scripts.create_input_json import createInputJson
+    from ecephys_spike_sorting.scripts.helpers import SpikeGLX_utils
 except Exception as e:
     print(f'Error in loading "ecephys_spike_sorting" package - {str(e)}')