Merge branch 'main' into inspect-progress-bars

.github/workflows/Build-and-deploy-mac.yml

@@ -1,5 +1,6 @@
 name: Mac Release
 run-name: ${{ github.actor }} is building a MAC release for NWB GUIDE
+# NOTE: even though the runner is an arm64 mac, both x64 and arm64 releases will be made
 
 on:
   workflow_dispatch:
@@ -22,7 +23,7 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: nwb-guide
-          environment-file: environments/environment-MAC.yml
+          environment-file: environments/environment-MAC-arm64.yml
           auto-activate-base: false
 
       - uses: actions/setup-node@v3

.github/workflows/pyflask-build-and-dist-tests.yml

@@ -32,8 +32,13 @@ jobs:
           #   prefix: /usr/share/miniconda3/envs/nwb-guide
 
           - python-version: "3.9"
-            os: macos-latest
-            label: environments/environment-Mac.yml
+            os: macos-latest  # Mac arm64 runner
+            label: environments/environment-MAC-arm64.yml
+            prefix: /Users/runner/miniconda3/envs/nwb-guide
+
+          - python-version: "3.9"
+            os: macos-13  # Mac x64 runner
+            label: environments/environment-MAC.yml
             prefix: /Users/runner/miniconda3/envs/nwb-guide
 
           - python-version: "3.9"
@@ -45,6 +50,9 @@ jobs:
       - uses: actions/checkout@v4
       - run: git fetch --prune --unshallow --tags
 
+      - name: Printout architecture
+        run: uname -m
+
       # see https://github.com/conda-incubator/setup-miniconda#caching-environments
       - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v3
@@ -81,7 +89,7 @@ jobs:
       - run: npm ci --verbose
 
       # fix for macos build
-      - if: matrix.os == 'macos-latest'
+      - if: matrix.os == 'macos-latest' || matrix.os == 'macos-13'
         run: rm -f /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
 
       - name: Build PyFlask distribution

.github/workflows/testing-live-services.yml

@@ -27,8 +27,11 @@ jobs:
           - os: ubuntu-latest
             label: environments/environment-Linux.yml
 
-          - os: macos-latest
-            label: environments/environment-Mac.yml
+          - os: macos-latest  # Mac arm64 runner
+            label: environments/environment-MAC-arm64.yml
+
+          - os: macos-13  # Mac x64 runner
+            label: environments/environment-MAC.yml
 
           - os: windows-latest
             label: environments/environment-Windows.yml

.github/workflows/testing.yml

@@ -27,8 +27,11 @@ jobs:
           - os: ubuntu-latest
             label: environments/environment-Linux.yml
 
-          - os: macos-latest
-            label: environments/environment-Mac.yml
+          - os: macos-latest  # Mac arm64 runner
+            label: environments/environment-MAC-arm64.yml
+
+          - os: macos-13  # Mac x64 runner
+            label: environments/environment-MAC.yml
 
           - os: windows-latest
             label: environments/environment-Windows.yml

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 24.4.0
+    rev: 24.4.2
     hooks:
     -   id: black
         exclude: ^docs/

docs/index.rst

@@ -1,5 +1,5 @@
-Welcome to the NWB GUIDE documentation!
-=======================================
+NWB GUIDE documentation
+=======================
 |
 
 .. image:: ../src/renderer/assets/img/logo-guide-draft-transparent-tight.png
@@ -13,7 +13,7 @@ Welcome to the NWB GUIDE documentation!
 The **NWB Graphical User Interface for Data Entry (GUIDE)** is an Electron-based application designed to help you navigate
 the complex process of converting data from common proprietary formats into the :nwb-overview:`Neurodata Without Borders (NWB) <>` standard.
 
-The resulting files are fully compliant with the best practices expected of the :dandi-archive:`Distributed Archives for Neurophysiology Data Integration (DANDI) <>`.
+The resulting files are fully compliant with the best practices expected by the :dandi-archive:`Distributed Archives for Neurophysiology Data Integration (DANDI) <>`.
 
 .. toctree::
    :maxdepth: 2

docs/tutorials/dataset.rst

@@ -1,5 +1,5 @@
-Dataset Generation
-==================
+Example Dataset Generation
+==========================
 
 Our tutorials focus on converting extracellular electrophysiology data in the SpikeGLX and Phy formats.
 To get you started as quickly as possible, we’ve created a way to generate this Neuropixel-like dataset at the click of a button!

src/renderer/src/pages.js

@@ -144,6 +144,7 @@ const pages = {
                 title: "Conversion Review",
                 label: "Review conversion",
                 section: sections[2],
+                sync: ["conversion"],
             }),
 
             upload: new GuidedUploadPage({

src/renderer/src/progress/index.js

@@ -182,13 +182,13 @@ export const get = (name) => {
     );
 };
 
-export function resume(name) {
+export async function resume(name) {
     const global = this ? this.load(name) : get(name);
 
     let commandToResume = global["page-before-exit"] || "//details";
     updateURLParams({ project: name });
 
-    if (this) this.onTransition(commandToResume);
+    if (this) await this.onTransition(commandToResume);
 
     return commandToResume;
 }

src/renderer/src/stories/Dashboard.js

@@ -242,7 +242,7 @@ export class Dashboard extends LitElement {
 
         this.page.set(toPass, false);
 
-        this.page.checkSyncState().then(() => {
+        this.page.checkSyncState().then(async () => {
             const projectName = info.globalState?.project?.name;
 
             this.subSidebar.header = projectName
@@ -264,8 +264,8 @@ export class Dashboard extends LitElement {
                 });
 
                 // Skip right over the page if configured as such
-                if (previous && previous.info.previous === this.page) this.page.onTransition(-1);
-                else this.page.onTransition(1);
+                if (previous && previous.info.previous === this.page) await this.page.onTransition(-1);
+                else await this.page.onTransition(1);
             }
         });
     }
@@ -328,13 +328,13 @@ export class Dashboard extends LitElement {
             if (typeof transition === "number") {
                 const info = this.page.info;
                 const sign = Math.sign(transition);
-                if (sign === 1) return this.setAttribute("activePage", info.next.info.id);
-                else if (sign === -1) return this.setAttribute("activePage", (info.previous ?? info.parent).info.id); // Default to back in time
+                if (sign === 1) transition = info.next.info.id;
+                else if (sign === -1) transition = (info.previous ?? info.parent).info.id; // Default to back in time
             }
 
             this.setAttribute("activePage", transition);
 
-            return await promise;
+            return promise;
         };
 
         this.main.updatePages = () => {

src/renderer/src/stories/pages/FormPage.js

@@ -63,7 +63,7 @@ export class GuidedFormPage extends Page {
         onNext: async () => {
             await this.save(); // Save in case validation fails
             await this.form.validate(); // Validate the results of the form
-            this.to(1);
+            return this.to(1);
         },
     };
 

src/renderer/src/stories/pages/Page.js

@@ -1,7 +1,7 @@
 import { LitElement, html } from "lit";
 import { runConversion } from "./guided-mode/options/utils.js";
 import { get, save } from "../../progress/index.js";
-import { dismissNotification, notify } from "../../dependencies/globals.js";
+import { dismissNotification, isStorybook, notify } from "../../dependencies/globals.js";
 import { randomizeElements, mapSessions, merge } from "./utils.js";
 
 import { resolveMetadata } from "./guided-mode/data/utils.js";
@@ -134,9 +134,10 @@ export class Page extends LitElement {
 
         // Indicate conversion has run successfully
         const { desyncedData } = this.info.globalState;
+        if (!desyncedData) this.info.globalState.desyncedData = {};
+
         if (desyncedData) {
-            delete desyncedData[key];
-            if (Object.keys(desyncedData).length === 0) delete this.info.globalState.desyncedData;
+            desyncedData[key] = false;
             await this.save({}, false);
         }
     }
@@ -233,18 +234,18 @@ export class Page extends LitElement {
 
     checkSyncState = async (info = this.info, sync = info.sync) => {
         if (!sync) return;
+        if (isStorybook) return;
 
         const { desyncedData } = info.globalState;
-        if (desyncedData) {
-            return Promise.all(
-                sync.map((k) => {
-                    if (desyncedData[k]) {
-                        if (k === "conversion") return this.convert();
-                        else if (k === "preview") return this.convert({ preview: true });
-                    }
-                })
-            );
-        }
+
+        return Promise.all(
+            sync.map((k) => {
+                if (desyncedData?.[k] !== false) {
+                    if (k === "conversion") return this.convert();
+                    else if (k === "preview") return this.convert({ preview: true });
+                }
+            })
+        );
     };
 
     updateSections = () => {

tests/e2e/e2e.test.ts

@@ -144,17 +144,8 @@ describe('E2E Test', () => {
 
         }, { upload_to_dandi: true })
 
-        await toNextPage('structure') // Save data without a popup
         await to('//conversion')
-
-        // Do not prompt to save
-        await evaluate(() => {
-          const dashboard = document.querySelector('nwb-dashboard')
-          const page = dashboard.page
-          page.unsavedUpdates = false
-        })
-
-        await to('//upload') // NOTE: It would be nice to avoid having to re-run the conversion...
+        await to('//upload')
 
       })
 

tests/e2e/workflow.ts

@@ -1,4 +1,4 @@
-import { describe, test } from "vitest"
+import { describe, expect, test } from "vitest"
 
 import { sleep } from '../puppeteer'
 
@@ -429,21 +429,30 @@ export default async function runWorkflow(name, workflow, identifier) {
 
   test('Review NWB Inspector output', async () => {
 
-    await takeScreenshot(join(identifier, 'inspect-page'), 5000) // Finish file inspection and allow full load of Neurosift page
+    await takeScreenshot(join(identifier, 'inspect-page'), 5000) // Allow for the completion of file validation
     await toNextPage('preview')
 
   })
 
   test('Review Neurosift visualization', async () => {
-    await takeScreenshot(join(identifier, 'preview-page'), 1000) // Finish loading Neurosift
+    await takeScreenshot(join(identifier, 'preview-page'), 1000) // Allow full load of Neurosift page
     await toNextPage('conversion')
   })
 
   test('View the conversion results', async () => {
+    await takeScreenshot(join(identifier, 'conversion-results-page'), 1000)
+
+    const conversionCompleted = await evaluate(() => {
+      const dashboard = document.querySelector('nwb-dashboard')
+      const page = dashboard.page
+      return !!page.info.globalState.conversion
+    })
 
-    await takeScreenshot(join(identifier, 'conversion-results-page'), 300)
     if (workflow.upload_to_dandi) await toNextPage('upload')
     else await toNextPage('')
+
+    expect(conversionCompleted).toBe(true)
+
   })