diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6a933b9..0ca4eaa 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ repos: - id: end-of-file-fixer - id: trailing-whitespace - repo: https://github.com/psf/black - rev: 23.12.1 + rev: 24.1.1 hooks: - id: black exclude: ^docs/ diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/basedattainterface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/basedattainterface.py index 40a5035..f446f66 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/basedattainterface.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/basedattainterface.py @@ -1,4 +1,5 @@ """Primary class for handling metadata non-specific to any other DataInterfaces.""" + from pathlib import Path import pandas as pd diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/basevideointerface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/basevideointerface.py index 41066ea..a446775 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/basevideointerface.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/basevideointerface.py @@ -1,4 +1,5 @@ """Base class for converting raw video data.""" + from pathlib import Path import numpy as np diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/behavioralsyllableinterface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/behavioralsyllableinterface.py index 920922d..792372b 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/behavioralsyllableinterface.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/behavioralsyllableinterface.py @@ -1,4 +1,5 @@ """Primary class for converting experiment-specific behavior.""" + import numpy as np import pandas as pd from pynwb import NWBFile diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/convert_dataset.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/convert_dataset.py index 57c89e0..6fb4e79 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/convert_dataset.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/convert_dataset.py @@ -1,4 +1,5 @@ """Convert the entire dataset.""" + import json from pathlib import Path from typing import Union diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/convert_session.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/convert_session.py index 893e376..4002ee6 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/convert_session.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/convert_session.py @@ -1,4 +1,5 @@ """Primary script to run to convert an entire session for of data using the NWBConverter.""" + import shutil import traceback from pathlib import Path diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/depthvideointerface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/depthvideointerface.py index 0ba01d7..b752735 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/depthvideointerface.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/depthvideointerface.py @@ -1,4 +1,5 @@ """Primary class for converting raw depth video data.""" + from pynwb import NWBFile from .basevideointerface import BaseVideoInterface diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/fiberphotometryinterface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/fiberphotometryinterface.py index b1c73ae..719262b 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/fiberphotometryinterface.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/fiberphotometryinterface.py @@ -1,4 +1,5 @@ """Primary class for converting fiber photometry data (dLight fluorescence).""" + from typing import Union import pandas as pd diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/irvideointerface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/irvideointerface.py index 10d58fb..f6ef0e9 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/irvideointerface.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/irvideointerface.py @@ -1,4 +1,5 @@ """Primary class for converting raw ir video data.""" + from pynwb import NWBFile from .basevideointerface import BaseVideoInterface diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/moseqextractinterface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/moseqextractinterface.py index 0004478..d1a7ca0 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/moseqextractinterface.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/moseqextractinterface.py @@ -1,4 +1,5 @@ """Primary class for converting MoSeq Extraction data.""" + from pynwb import NWBFile import h5py import numpy as np diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/nwbconverter.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/nwbconverter.py index 7760b9a..6c3ce29 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/nwbconverter.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/nwbconverter.py @@ -1,4 +1,5 @@ """Primary NWBConverter class for this dataset.""" + from neuroconv import NWBConverter from .fiberphotometryinterface import FiberPhotometryInterface from .optogeneticinterface import OptogeneticInterface diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/optogeneticinterface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/optogeneticinterface.py index cc8c150..a213b27 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/optogeneticinterface.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/optogeneticinterface.py @@ -1,4 +1,5 @@ """Primary class for converting fiber photometry data (dLight fluorescence).""" + # Standard Scientific Python import pandas as pd import numpy as np diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/rawfiberphotometryinterface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/rawfiberphotometryinterface.py index d21ec47..96f4a27 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/rawfiberphotometryinterface.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/rawfiberphotometryinterface.py @@ -1,4 +1,5 @@ """Primary class for converting Raw fiber photometry data (dLight fluorescence) from the TDT system.""" + from pathlib import Path from typing import Union diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_HEK/convert_session.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_HEK/convert_session.py index 3757bbf..03233d1 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_HEK/convert_session.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_HEK/convert_session.py @@ -1,4 +1,5 @@ """Primary script to run to convert an entire session for of data using the NWBConverter.""" + from pathlib import Path from typing import Union from neuroconv.utils import dict_deep_update, load_dict_from_file diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_HEK/hekinterface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_HEK/hekinterface.py index 5d5d6e7..352d3ca 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_HEK/hekinterface.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_HEK/hekinterface.py @@ -1,4 +1,5 @@ """Primary class for converting in-vitro photometry data.""" + from typing import Literal, Optional import numpy as np from pynwb import NWBFile diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_HEK/nwbconverter.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_HEK/nwbconverter.py index 3b7e091..546faf0 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_HEK/nwbconverter.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_HEK/nwbconverter.py @@ -1,4 +1,5 @@ """Primary NWBConverter class for this dataset.""" + from neuroconv import NWBConverter from .hekinterface import HEKInterface diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/convert_session.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/convert_session.py index bd11a22..4a8b7a1 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/convert_session.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/convert_session.py @@ -1,4 +1,5 @@ """Primary script to run to convert an entire session for of data using the NWBConverter.""" + # Standard Library from pathlib import Path import shutil diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/fiberphotometryinterface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/fiberphotometryinterface.py index 1e0878c..d0c4076 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/fiberphotometryinterface.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/fiberphotometryinterface.py @@ -1,4 +1,5 @@ """Primary class for converting fiber photometry data (dLight fluorescence).""" + # Standard Scientific Python import numpy as np import joblib diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/irvideointerface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/irvideointerface.py index c0fb761..52b9158 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/irvideointerface.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/irvideointerface.py @@ -1,4 +1,5 @@ """Base class for converting raw video data.""" + from pynwb import NWBFile import numpy as np from pathlib import Path diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/keypointinterface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/keypointinterface.py index dfececb..e03c8d2 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/keypointinterface.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/keypointinterface.py @@ -1,4 +1,5 @@ """Primary class for converting experiment-specific behavior.""" + import numpy as np from pynwb import NWBFile from pynwb.image import RGBImage, Images diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/nwbconverter.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/nwbconverter.py index e71a71a..7e16966 100644 --- a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/nwbconverter.py +++ b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/nwbconverter.py @@ -1,4 +1,5 @@ """Primary NWBConverter class for this dataset.""" + from neuroconv import NWBConverter from .fiberphotometryinterface import FiberPhotometryInterface from .irvideointerface import IRVideoInterface