Merge branch 'main' into debug_mac_dist

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.9.1
     hooks:
     -   id: black
         exclude: ^docs/

docs/format_support.rst

@@ -0,0 +1,7 @@
+Ecosystem Format Support
+=======================================
+The following is a live record of all the supported formats in the NWB GUIDE and underlying ecosystem.
+
+.. raw:: html
+
+    <iframe style="width: 100%; height: 50vh; border: none;" src="https://catalystneuro.github.io/format-support-table/"></iframe>

docs/index.rst

@@ -19,3 +19,4 @@ The resulting files are fully compliant with the best practices expected of the
    :maxdepth: 2
 
    developer_guide
+   format_support

environments/environment-Windows.yml

@@ -21,28 +21,3 @@ dependencies:
       - pytest == 7.2.2
       - pytest-cov == 4.1.0
       - email-validator == 2.0.0
-
-# name: nwb-guide
-# channels:
-#   - conda-forge
-#   - defaults
-# dependencies:
-#   - python = 3.9.18
-#   - PyInstaller = 5.13.0
-#   - nodejs = 18.16.1
-#   - numcodecs = 0.11.0  # not sure if this is needed
-#   - pywin32 = 303  # not sure if this is needed
-#   # install these from conda-forge so that dependent packages get included in the distributable
-#   - jsonschema = 4.18.0  # installs jsonschema-specifications
-#   - pydantic[email] = 2.0.2  # installs email-validator
-#   - pip
-#   - pip:
-#       - chardet == 5.1.0
-#       - configparser == 6.0.0
-#       - flask == 2.3.2
-#       - flask-cors == 4.0.0
-#       - flask_restx == 1.1.0
-#       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
-#       - hdmf >= 3.7.0
-#       - pytest == 7.4.0
-#       - pytest-cov == 4.1.0

pyflask/apis/startup.py

@@ -1,6 +1,8 @@
 """API endpoint definitions for startup operations."""
 from flask_restx import Namespace, Resource
 
+from errorHandlers import notBadRequestException
+
 startup_api = Namespace("startup", description="API for startup commands related to the NWB GUIDE.")
 
 parser = startup_api.parser()
@@ -19,3 +21,25 @@ class Echo(Resource):
     def get(self):
         args = parser.parse_args()
         return args["arg"]
+
+
+@startup_api.route("/preload-imports")
+class PreloadImports(Resource):
+    """
+    Preload various imports on startup instead of waiting for them later on.
+
+    Python caches all modules that have been imported at least once in the same kernel,
+    even if their namespace is not always exposed to a given scope. This means that later imports
+    simply expose the cached namespaces to their scope instead of retriggering the entire import.
+    """
+
+    @startup_api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def get(self):
+        try:
+            import neuroconv
+
+            return True
+        except Exception as exception:
+            if notBadRequestException(exception=exception):
+                startup_api.abort(500, str(exception))
+            raise exception

pyflask/tests/test_neuroconv.py

@@ -2,9 +2,8 @@
 from utils import get, post, get_converter_output_schema
 
 
-# --------------------- Tests ---------------------
-# Accesses the dictionary of all interfaces and their metadata
 def test_get_all_interfaces(client):
+    """Accesses the dictionary of all interfaces and their metadata."""
     validate(
         get("neuroconv", client),
         schema={
@@ -23,14 +22,14 @@ def test_get_all_interfaces(client):
     )
 
 
-# Test single interface schema request
 def test_single_schema_request(client):
+    """Test single interface schema request."""
     interfaces = {"myname": "SpikeGLXRecordingInterface"}
     validate(post("neuroconv/schema", interfaces, client), schema=get_converter_output_schema(interfaces))
 
 
-# Uses the NWBConverter Class to combine multiple interfaces
 def test_multiple_schema_request(client):
+    """Uses the NWBConverter Class to combine multiple interfaces."""
     interfaces = {"myname": "SpikeGLXRecordingInterface", "myphyinterface": "PhySortingInterface"}
     data = post("/neuroconv/schema", interfaces, client)
     validate(data, schema=get_converter_output_schema(interfaces))

pyflask/tests/test_startup.py

@@ -0,0 +1,7 @@
+from utils import get, post, get_converter_output_schema
+
+
+def test_preload_imports(client):
+    """Verify that the preload import endpoint returned good status."""
+    result = get("startup/preload-imports", client)
+    assert result == True

src/renderer/src/index.ts

@@ -94,18 +94,22 @@ async function checkInternetConnection() {
     return hasInternet
 };
 
-// Check if the Pysoda server is live
+// Check if the Flask server is live
 const serverIsLiveStartup = async () => {
   const echoResponse = await fetch(`${baseUrl}/startup/echo?arg=server ready`).then(res => res.json()).catch(e => e)
   return echoResponse === "server ready" ? true : false;
 };
 
+// Preload Flask imports for faster on-demand operations
+const preloadFlaskImports = async () => await fetch(`${baseUrl}/startup/preload-imports`).then(res => res.json()).catch(e => e)
+
 let openPythonStatusNotyf: undefined | any;
 
 async function pythonServerOpened() {
 
   // Confirm requests are actually received by the server
   const isLive = await serverIsLiveStartup()
+  if (isLive) await preloadFlaskImports() // initiate preload of Flask imports
   if (!isLive) return pythonServerClosed()
 
   // Update server status and throw a notification

src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js

@@ -75,9 +75,9 @@ export class GuidedStructurePage extends Page {
     };
 
     async updated() {
-        const selected = this.info.globalState.interfaces;
+        const { interfaces = {} } = this.info.globalState;
 
-        if (Object.keys(selected).length > 0) this.list.emptyMessage = "Loading valid interfaces...";
+        if (Object.keys(interfaces).length > 0) this.list.emptyMessage = "Loading valid interfaces...";
 
         this.search.options = await fetch(`${baseUrl}/neuroconv`)
             .then((res) => res.json())
@@ -93,7 +93,7 @@ export class GuidedStructurePage extends Page {
             )
             .catch((e) => console.error(e));
 
-        for (const [key, name] of Object.entries(selected || {})) {
+        for (const [key, name] of Object.entries(interfaces)) {
             let found = this.search.options?.find((o) => o.value === name);
 
             // If not found, spoof based on the key and names provided previously