Merge pull request #785 from NeurodataWithoutBorders/enable_isort

Enable isort

.pre-commit-config.yaml

@@ -10,6 +10,10 @@ repos:
     hooks:
     -   id: black
         exclude: ^docs/
+-   repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
 -   repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v4.0.0-alpha.8"
     hooks:

demos/sse/test_sse_display_of_tqdm.py

@@ -1,12 +1,12 @@
-from flask import Flask, render_template, Response
-from typing import List
-import random
 import asyncio
+import os
+import random
+import sys
 import time
-from tqdm import tqdm as base_tqdm
+from typing import List
 
-import sys
-import os
+from flask import Flask, Response, render_template
+from tqdm import tqdm as base_tqdm
 
 SCRIPT_DIR = os.path.dirname(os.path.abspath(os.path.join(__file__, "..", "..", "pyflask")))
 sys.path.append(os.path.dirname(SCRIPT_DIR))

docs/conf.py

@@ -1,15 +1,14 @@
-import sys
 import inspect
-from pathlib import Path
 import json
 import os
+import sys
+from pathlib import Path
 
 sys.path.insert(0, str(Path(__file__).resolve().parents[0]))
 sys.path.insert(0, str(Path(__file__).resolve().parents[1]))
 
 from conf_extlinks import extlinks, intersphinx_mapping  # noqa: E402, F401
 
-
 project = "NWB GUIDE"
 copyright = "2022, CatalystNeuro"  # TODO: how to include NWB?
 author = "Garrett Flynn, Cody Baker, Ryan Ly, Oliver Ruebel, and Ben Dichter"

generateInterfaceSchema.py

@@ -1,6 +1,7 @@
-from pathlib import Path
 import json
-from neuroconv import converters, datainterfaces, NWBConverter
+from pathlib import Path
+
+from neuroconv import NWBConverter, converters, datainterfaces
 
 filepath = Path("guideGlobalMetadata.json")
 generatedJSONSchemaPath = Path("schemas", "json", "generated")

pyflask/apis/__init__.py

@@ -1,3 +1,3 @@
-from .startup import startup_api
-from .neuroconv import neuroconv_api
 from .data import data_api
+from .neuroconv import neuroconv_api
+from .startup import startup_api

pyflask/apis/data.py

@@ -2,10 +2,9 @@
 
 import traceback
 
-from flask_restx import Namespace, Resource, reqparse
-
-from manageNeuroconv import generate_test_data, generate_dataset
 from errorHandlers import notBadRequestException
+from flask_restx import Namespace, Resource, reqparse
+from manageNeuroconv import generate_dataset, generate_test_data
 
 data_api = Namespace("data", description="API route for dataset generation in the NWB GUIDE.")
 

pyflask/apis/neuroconv.py

@@ -2,32 +2,28 @@
 
 import traceback
 
-from flask_restx import Namespace, Resource, reqparse
+from errorHandlers import notBadRequestException
 from flask import Response, request
-
-from manageNeuroconv.info import announcer
-
+from flask_restx import Namespace, Resource, reqparse
 from manageNeuroconv import (
-    get_all_interface_info,
-    get_all_converter_info,
-    locate_data,
     autocomplete_format_string,
-    get_source_schema,
-    get_metadata_schema,
     convert_to_nwb,
-    validate_metadata,
-    listen_to_neuroconv_events,
+    get_all_converter_info,
+    get_all_interface_info,
+    get_interface_alignment,
+    get_metadata_schema,
+    get_source_schema,
+    inspect_multiple_filesystem_objects,
     inspect_nwb_file,
     inspect_nwb_folder,
-    inspect_multiple_filesystem_objects,
-    upload_project_to_dandi,
+    listen_to_neuroconv_events,
+    locate_data,
     upload_folder_to_dandi,
     upload_multiple_filesystem_objects_to_dandi,
-    get_interface_alignment,
+    upload_project_to_dandi,
+    validate_metadata,
 )
-
-from errorHandlers import notBadRequestException
-
+from manageNeuroconv.info import announcer
 
 neuroconv_api = Namespace("neuroconv", description="Neuroconv neuroconv_api for the NWB GUIDE.")
 

pyflask/apis/startup.py

@@ -1,8 +1,7 @@
 """API endpoint definitions for startup operations."""
 
-from flask_restx import Namespace, Resource
-
 from errorHandlers import notBadRequestException
+from flask_restx import Namespace, Resource
 
 startup_api = Namespace("startup", description="API for startup commands related to the NWB GUIDE.")
 

pyflask/app.py

@@ -1,28 +1,29 @@
 """The primary Flask server for the Python backend."""
 
-import sys
 import json
 import multiprocessing
-from os import kill, getpid
-from os.path import isabs
-
-from signal import SIGINT
-from logging import Formatter, DEBUG
+import sys
+from logging import DEBUG, Formatter
 from logging.handlers import RotatingFileHandler
+from os import getpid, kill
+from os.path import isabs
 from pathlib import Path
+from signal import SIGINT
 from urllib.parse import unquote
 
-
 # https://stackoverflow.com/questions/32672596/pyinstaller-loads-script-multiple-times#comment103216434_32677108
 multiprocessing.freeze_support()
 
 
-from flask import Flask, request, send_from_directory, send_file
+from apis import data_api, neuroconv_api, startup_api
+from flask import Flask, request, send_file, send_from_directory
 from flask_cors import CORS
 from flask_restx import Api, Resource
-
-from apis import startup_api, neuroconv_api, data_api
-from manageNeuroconv.info import resource_path, STUB_SAVE_FOLDER_PATH, CONVERSION_SAVE_FOLDER_PATH
+from manageNeuroconv.info import (
+    CONVERSION_SAVE_FOLDER_PATH,
+    STUB_SAVE_FOLDER_PATH,
+    resource_path,
+)
 
 app = Flask(__name__)
 

pyflask/manageNeuroconv/__init__.py

@@ -1,23 +1,21 @@
+from .info import CONVERSION_SAVE_FOLDER_PATH, STUB_SAVE_FOLDER_PATH
 from .manage_neuroconv import (
-    get_all_interface_info,
-    get_all_converter_info,
-    locate_data,
     autocomplete_format_string,
-    get_source_schema,
-    get_metadata_schema,
     convert_to_nwb,
-    validate_metadata,
-    upload_project_to_dandi,
-    upload_folder_to_dandi,
-    upload_multiple_filesystem_objects_to_dandi,
-    listen_to_neuroconv_events,
     generate_dataset,
+    generate_test_data,
+    get_all_converter_info,
+    get_all_interface_info,
+    get_interface_alignment,
+    get_metadata_schema,
+    get_source_schema,
+    inspect_multiple_filesystem_objects,
     inspect_nwb_file,
     inspect_nwb_folder,
-    inspect_multiple_filesystem_objects,
-    get_interface_alignment,
-    generate_test_data,
+    listen_to_neuroconv_events,
+    locate_data,
+    upload_folder_to_dandi,
+    upload_multiple_filesystem_objects_to_dandi,
+    upload_project_to_dandi,
+    validate_metadata,
 )
-
-
-from .info import STUB_SAVE_FOLDER_PATH, CONVERSION_SAVE_FOLDER_PATH

pyflask/manageNeuroconv/info/__init__.py

@@ -1,8 +1,7 @@
+from .sse import announcer, format_sse
 from .urls import (
-    resource_path,
+    CONVERSION_SAVE_FOLDER_PATH,
     GUIDE_ROOT_FOLDER,
     STUB_SAVE_FOLDER_PATH,
-    CONVERSION_SAVE_FOLDER_PATH,
+    resource_path,
 )
-
-from .sse import announcer, format_sse

pyflask/manageNeuroconv/info/sse.py

@@ -1,5 +1,5 @@
-import queue
 import json
+import queue
 
 
 def format_sse(data: str, event=None) -> str:

pyflask/manageNeuroconv/info/urls.py

@@ -1,7 +1,7 @@
-from pathlib import Path
 import json
 import os
 import sys
+from pathlib import Path
 
 
 def resource_path(relative_path):

pyflask/manageNeuroconv/manage_neuroconv.py

@@ -8,11 +8,15 @@
 import re
 from datetime import datetime
 from pathlib import Path
-from shutil import rmtree, copytree
-from typing import Any, Dict, List, Optional
-from typing import Union
+from shutil import copytree, rmtree
+from typing import Any, Dict, List, Optional, Union
 
-from .info import GUIDE_ROOT_FOLDER, STUB_SAVE_FOLDER_PATH, CONVERSION_SAVE_FOLDER_PATH, announcer
+from .info import (
+    CONVERSION_SAVE_FOLDER_PATH,
+    GUIDE_ROOT_FOLDER,
+    STUB_SAVE_FOLDER_PATH,
+    announcer,
+)
 
 EXCLUDED_RECORDING_INTERFACE_PROPERTIES = ["contact_vector", "contact_shapes", "group", "location"]
 
@@ -337,7 +341,7 @@ def get_all_interface_info() -> dict:
 
 # Combine Multiple Interfaces
 def get_custom_converter(interface_class_dict: dict):  # -> NWBConverter:
-    from neuroconv import converters, datainterfaces, NWBConverter
+    from neuroconv import NWBConverter, converters, datainterfaces
 
     class CustomNWBConverter(NWBConverter):
         data_interface_classes = {
@@ -477,8 +481,12 @@ def on_recording_interface(name, recording_interface):
 
         return recording_interface
 
-    from neuroconv.datainterfaces.ecephys.baserecordingextractorinterface import BaseRecordingExtractorInterface
-    from neuroconv.datainterfaces.ecephys.basesortingextractorinterface import BaseSortingExtractorInterface
+    from neuroconv.datainterfaces.ecephys.baserecordingextractorinterface import (
+        BaseRecordingExtractorInterface,
+    )
+    from neuroconv.datainterfaces.ecephys.basesortingextractorinterface import (
+        BaseSortingExtractorInterface,
+    )
 
     # Map recording interfaces to metadata
     map_interfaces(on_recording_interface, converter=converter, to_match=BaseRecordingExtractorInterface)
@@ -605,7 +613,7 @@ def get_check_function(check_function_name: str) -> callable:
 
 def run_check_function(check_function: callable, arg: dict) -> dict:
     """.Function used to run an arbitrary NWB Inspector function."""
-    from nwbinspector.register_checks import InspectorMessage, Importance
+    from nwbinspector.register_checks import Importance, InspectorMessage
 
     output = check_function(arg)
     if isinstance(output, InspectorMessage):
@@ -648,8 +656,8 @@ def validate_nwbfile_metadata(
 
 def validate_metadata(metadata: dict, check_function_name: str) -> dict:
     """Function used to validate data using an arbitrary NWB Inspector function."""
-    from pynwb.file import NWBFile, Subject
     from nwbinspector.nwbinspector import InspectorOutputJSONEncoder
+    from pynwb.file import NWBFile, Subject
 
     check_function = get_check_function(check_function_name)
 
@@ -988,10 +996,10 @@ def _inspect_file_per_job(
     request_id: Optional[str] = None,
 ) -> list:
 
+    import requests
     from nwbinspector import nwbinspector
     from pynwb import NWBHDF5IO
     from tqdm_publisher import TQDMProgressSubscriber
-    import requests
 
     checks = nwbinspector.configure_checks(
         checks=nwbinspector.available_checks,
@@ -1024,6 +1032,7 @@ def _inspect_file_per_job(
 def inspect_all(url, config):
 
     from concurrent.futures import ProcessPoolExecutor, as_completed
+
     from nwbinspector.utils import calculate_number_of_cpu
     from tqdm_publisher import TQDMProgressSubscriber
 
@@ -1085,10 +1094,11 @@ def on_progress_update(message):
 
 
 def inspect_nwb_folder(url, payload) -> dict:
+    from pickle import PicklingError
+
     from nwbinspector import load_config
     from nwbinspector.inspector_tools import format_messages, get_report_header
     from nwbinspector.nwbinspector import InspectorOutputJSONEncoder
-    from pickle import PicklingError
 
     kwargs = dict(
         ignore=[
@@ -1211,7 +1221,7 @@ def generate_test_data(output_path: str):
     """
     import spikeinterface
     from spikeinterface.exporters import export_to_phy
-    from spikeinterface.preprocessing import scale, bandpass_filter, resample
+    from spikeinterface.preprocessing import bandpass_filter, resample, scale
 
     base_path = Path(output_path)
     spikeglx_output_folder = base_path / "spikeglx"

pyflask/tests/conftest.py

@@ -1,5 +1,5 @@
-import pytest
 import app as flask
+import pytest
 
 
 def pytest_addoption(parser):

pyflask/tests/test_generate_tutorial_data.py

@@ -1,6 +1,7 @@
-from utils import post
 from pathlib import Path
 
+from utils import post
+
 
 def test_generate_test_data(client, tmp_path: Path):
     # assert client is None

pyflask/tests/test_neuroconv.py

@@ -1,5 +1,5 @@
 from jsonschema import validate
-from utils import get, post, get_converter_output_schema
+from utils import get, get_converter_output_schema, post
 
 
 def test_get_all_interfaces(client):

pyflask/tests/test_startup.py

@@ -1,4 +1,4 @@
-from utils import get, post, get_converter_output_schema
+from utils import get, get_converter_output_schema, post
 
 
 def test_preload_imports(client):