Merge branch 'main' into linux-dev

.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/_static/css/custom.css

@@ -0,0 +1,33 @@
+/* Improve spacing */
+.version-switcher__container.dropdown {
+    margin-left: 10px;
+}
+
+button.btn.version-switcher__button {
+    margin-bottom: 0px;
+}
+
+/* Show on hover */
+.version-switcher__container.dropdown:hover .dropdown-menu {
+    display: block;
+    left: 0;
+    margin-top: var(--bs-dropdown-spacer);
+    top: 100%;
+}
+
+.dropdown-menu.show {
+    display: none;
+}
+
+/* Remove underline and borders */
+button.btn.version-switcher__button:hover {
+    text-decoration: none;
+}
+
+.version-switcher__menu a.list-group-item {
+    border: none !important;
+}
+
+.version-switcher__menu a.list-group-item:hover {
+    text-decoration: none !important;
+}

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"
@@ -45,9 +44,9 @@
 ]
 
 # These paths are either relative to html_static_path or fully qualified paths (eg. https://...)
-# html_css_files = [
-#     "css/custom.css",
-# ]
+html_css_files = [
+    "css/custom.css",
+]
 
 linkcheck_anchors = False
 
@@ -85,6 +84,7 @@
 version_match = os.environ.get("READTHEDOCS_VERSION")
 with open("../package.json") as f:
     release = json.load(f)["version"]
+
 # If READTHEDOCS_VERSION doesn't exist, we're not on RTD
 # If it is an integer, we're in a PR build and the version isn't correct.
 # If it's "latest" → change to "dev" (that's what we want the switcher to call it)
@@ -144,3 +144,6 @@ def _correct_signatures(app, what, name, obj, options, signature, return_annotat
 
 def setup(app):  # This makes the data-interfaces signatures display on the docs/api, they don't otherwise
     app.connect("autodoc-process-signature", _correct_signatures)
+
+    # Add custom CSS
+    app.add_css_file("css/custom.css")

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")

guide_testing_suite.yml

@@ -24,10 +24,19 @@ pipelines:
     PhySortingInterface:
       folder_path: ephy_testing_data/phy/phy_example_0
 
+
   SpikeGLX_v1_SingleProbe_AP:
     SpikeGLXRecordingInterface:
       file_path: ephy_testing_data/spikeglx/Noise4Sam_g0/Noise4Sam_g0_imec0/Noise4Sam_g0_t0.imec0.ap.bin
 
+
+  SpikeGLXConverter-Phy:
+    SpikeGLXConverterPipe:
+      folder_path: ephy_testing_data/spikeglx/Noise4Sam_g0
+    PhySortingInterface:
+      folder_path: ephy_testing_data/phy/phy_example_0
+
+
   Suite2P_SinglePlane_SingleChannel:
     metadata:
       NWBFile:

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):