Merge remote-tracking branch 'refs/remotes/origin/conversion_test' in…

…to conversion_test

src/ibl_to_nwb/_scripts/convert_brainwide_map_processed_only_local_testing.py

@@ -3,24 +3,21 @@
 os.environ["JUPYTER_PLATFORM_DIRS"] = "1"  # Annoying
 
 import os
-
 from pathlib import Path
 from shutil import rmtree
+
 from one.api import ONE
 
-from ibl_to_nwb.converters import BrainwideMapConverter, IblSpikeGlxConverter
+from ibl_to_nwb.converters import BrainwideMapConverter
 from ibl_to_nwb.datainterfaces import (
     BrainwideMapTrialsInterface,
-)
-from ibl_to_nwb.datainterfaces import (
     IblPoseEstimationInterface,
     IblSortingInterface,
     LickInterface,
     PupilTrackingInterface,
     RoiMotionEnergyInterface,
     WheelInterface,
 )
-
 from ibl_to_nwb.testing._consistency_checks import check_written_nwbfile_for_consistency
 
 base_path = Path.home() / "ibl_scratch"  # local directory
@@ -65,12 +62,16 @@
 pupil_tracking_files = session_one.list_datasets(eid=session, filename="*features*")
 for pupil_tracking_file in pupil_tracking_files:
     camera_name = pupil_tracking_file.replace("alf/_ibl_", "").replace(".features.pqt", "")
-    data_interfaces.append(PupilTrackingInterface(one=session_one, session=session, camera_name=camera_name, revision=revision))
+    data_interfaces.append(
+        PupilTrackingInterface(one=session_one, session=session, camera_name=camera_name, revision=revision)
+    )
 
 roi_motion_energy_files = session_one.list_datasets(eid=session, filename="*ROIMotionEnergy.npy*")
 for roi_motion_energy_file in roi_motion_energy_files:
     camera_name = roi_motion_energy_file.replace("alf/", "").replace(".ROIMotionEnergy.npy", "")
-    data_interfaces.append(RoiMotionEnergyInterface(one=session_one, session=session, camera_name=camera_name, revision=revision))
+    data_interfaces.append(
+        RoiMotionEnergyInterface(one=session_one, session=session, camera_name=camera_name, revision=revision)
+    )
 
 if session_one.list_datasets(eid=session, collection="alf", filename="licks*"):
     data_interfaces.append(LickInterface(one=session_one, session=session, revision=revision))

src/ibl_to_nwb/_scripts/convert_brainwide_map_raw_only_local_testing.py

@@ -1,6 +1,8 @@
 # %%
 from pathlib import Path
+
 from one.api import ONE
+
 from ibl_to_nwb.converters import BrainwideMapConverter, IblSpikeGlxConverter
 from ibl_to_nwb.datainterfaces import RawVideoInterface
 
@@ -15,7 +17,7 @@
 nwbfiles_folder_path.mkdir(exist_ok=True)
 
 # Initialize IBL (ONE) client to download processed data for this session
-one_cache_folder_path =  base_path / 'ibl_conversion' / eid / 'cache'
+one_cache_folder_path = base_path / "ibl_conversion" / eid / "cache"
 one = ONE(
     base_url="https://openalyx.internationalbrainlab.org",
     password="international",
@@ -27,7 +29,7 @@
 
 # %% ephys
 session_folder = one.eid2path(eid)
-spikeglx_source_folder_path = session_folder / 'raw_ephys_data'
+spikeglx_source_folder_path = session_folder / "raw_ephys_data"
 
 # Specify the path to the SpikeGLX files on the server but use ONE API for timestamps
 spikeglx_subconverter = IblSpikeGlxConverter(folder_path=spikeglx_source_folder_path, one=one, eid=eid)

src/ibl_to_nwb/_scripts/download_data.py

@@ -1,5 +1,6 @@
 # %%
 from pathlib import Path
+
 from one.api import ONE
 
 # %%

src/ibl_to_nwb/converters/_ibl_spikeglx_converter.py

@@ -1,9 +1,9 @@
+import numpy as np
+from brainbox.io.one import EphysSessionLoader, SpikeSortingLoader
 from neuroconv.converters import SpikeGLXConverterPipe
 from one.api import ONE
 from pydantic import DirectoryPath
 from pynwb import NWBFile
-import numpy as np
-from brainbox.io.one import SpikeSortingLoader, EphysSessionLoader
 
 
 class IblSpikeGlxConverter(SpikeGLXConverterPipe):

src/ibl_to_nwb/datainterfaces/_ibl_sorting_extractor.py

@@ -28,7 +28,7 @@ def __init__(self, session: str, cache_folder: Optional[DirectoryPath] = None, r
             silent=True,
             cache_dir=cache_folder,
         )
-        if revision is None: # latest
+        if revision is None:  # latest
             revision = one.list_revisions(session)[-1]
 
         atlas = AllenAtlas()

src/ibl_to_nwb/datainterfaces/_pose_estimation.py

@@ -1,4 +1,3 @@
-from datetime import datetime
 from typing import Optional
 
 import numpy as np

src/ibl_to_nwb/datainterfaces/_pupil_tracking.py

@@ -29,7 +29,9 @@ def get_metadata(self) -> dict:
     def add_to_nwbfile(self, nwbfile, metadata: dict):
         left_or_right = self.camera_name[:5].rstrip("C")
 
-        camera_data = self.one.load_object(id=self.session, obj=self.camera_name, collection="alf", revision=self.revision)
+        camera_data = self.one.load_object(
+            id=self.session, obj=self.camera_name, collection="alf", revision=self.revision
+        )
 
         pupil_time_series = list()
         for ibl_key in ["pupilDiameter_raw", "pupilDiameter_smooth"]:

src/ibl_to_nwb/testing/_consistency_checks.py

@@ -1,11 +1,11 @@
 from pathlib import Path
 
 import numpy as np
+from brainbox.io.one import SpikeSortingLoader
 from numpy.testing import assert_array_equal, assert_array_less
 from one.api import ONE
 from pandas.testing import assert_frame_equal
 from pynwb import NWBHDF5IO, NWBFile
-from brainbox.io.one import SpikeSortingLoader
 
 
 def check_written_nwbfile_for_consistency(*, one: ONE, nwbfile_path: Path):