Merge branch 'main' into retry-ci

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

@@ -1,4 +1,4 @@
-name: Build-and-deploy-mac
+name: Mac Release
 run-name: ${{ github.actor }} is building a MAC release for NWB GUIDE
 
 on:

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

@@ -1,4 +1,4 @@
-name: Build-and-deploy-win
+name: Windows Release
 run-name: ${{ github.actor }} is building a Windows release for NWB GUIDE
 
 on:

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

@@ -1,4 +1,4 @@
-name: PyFlask build and distributable tests
+name: Build Tests — Flask
 on:
   schedule:
     - cron: "0 16 * * *"  # Daily at noon EST

.github/workflows/testing-external.yml

@@ -0,0 +1,93 @@
+name: Dev Tests (Live Services)
+on:
+  schedule:
+    - cron: "0 16 * * *"  # Daily at noon EST
+  pull_request:
+
+concurrency:  # Cancel previous workflows on the same pull request
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  CACHE_NUMBER: 2  # increase to reset cache manually
+
+jobs:
+  testing:
+    name: Dev tests with live services on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        include:
+          - os: ubuntu-latest
+            label: environments/environment-Linux.yml
+
+          - os: macos-latest
+            label: environments/environment-Mac.yml
+
+          - os: windows-latest
+            label: environments/environment-Windows.yml
+
+
+    steps:
+      - uses: actions/checkout@v3
+      - run: git fetch --prune --unshallow --tags
+
+      # see https://github.com/conda-incubator/setup-miniconda#caching-environments
+      - name: Setup Mambaforge
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          activate-environment: nwb-guide
+          use-mamba: true
+
+      - name: Set cache date
+        id: get-date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Cache Conda env
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.CONDA }}/envs
+          key: conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
+        id: cache
+
+      - if: steps.cache.outputs.cache-hit != 'true'
+        name: Create and activate environment
+        run: mamba env update -n nwb-guide -f ${{ matrix.label }}
+
+      - name: Use Node.js 18
+        uses: actions/setup-node@v3
+        with:
+          node-version: 18
+
+      - name: Install GUIDE
+        run: npm ci
+
+      - name: Create env file
+        run: |
+          touch .env
+          echo DANDI_STAGING_API_KEY=${{ secrets.DANDI_STAGING_API_KEY }} >> .env
+
+      - if: matrix.os != 'ubuntu-latest'
+        name: Run tests
+        run: npm run coverage:app
+
+      - if: matrix.os == 'ubuntu-latest'
+        name: Run tests with xvfb
+        run: xvfb-run --auto-servernum --server-args="-screen 0 1280x960x24" -- npm run coverage:app
+
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        with:
+          fail_ci_if_error: true

.github/workflows/testing.yml

@@ -1,4 +1,4 @@
-name: Back-end Tests
+name: Dev Tests
 on:
   schedule:
     - cron: "0 16 * * *"  # Daily at noon EST
@@ -13,7 +13,7 @@ env:
 
 jobs:
   testing:
-    name: Back-end tests on ${{ matrix.os }}
+    name: Dev tests on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -74,12 +74,6 @@ jobs:
       - name: Install GUIDE
         run: npm ci
 
-
-      - name: Create env file
-        run: |
-          touch .env
-          echo DANDI_STAGING_API_KEY=${{ secrets.DANDI_STAGING_API_KEY }} >> .env
-
       - if: matrix.os != 'ubuntu-latest'
         name: Run tests
         uses: nick-fields/retry@v3

README.md

@@ -1,17 +1,28 @@
 <p align="center">
   <img src="src/renderer/assets/img/logo-guide-draft-transparent-tight.png" width="250" alt="NeuroConv logo"/>
   <h3 align="center">NWB Graphical User Interface for Data Entry</h3>
+  <p align="center">
+    <a href="https://github.com/NeurodataWithoutBorders/nwb-guide/actions/workflows/testing.yml"><img src="https://github.com/NeurodataWithoutBorders/nwb-guide/actions/workflows/testing.yml/badge.svg" alt="Full Tests"></a>
+    <a href="https://github.com/NeurodataWithoutBorders/nwb-guide/actions/workflows/testing-external.yml"><img src="https://github.com/NeurodataWithoutBorders/nwb-guide/actions/workflows/testing-external.yml/badge.svg" alt="Full Tests with External Dependencies"></a>
+      <a href="https://github.com/neurodatawithoutborders/nwb-guide/actions/workflows/pyflask-build-and-dist-tests.yml"><img src="https://github.com/NeurodataWithoutBorders/nwb-guide/actions/workflows/pyflask-build-and-dist-tests.yml/badge.svg" alt="Build and Distributable Tests"></a>
+    <a href="https://codecov.io/github/NeurodataWithoutBorders/nwb-guide?branch=main"><img src="https://codecov.io/github/NeurodataWithoutBorders/nwb-guide/coverage.svg?branch=main" alt="codecov"></a>
+    <a href="https://nwb-guide.readthedocs.io/en/latest/"><img src="https://readthedocs.org/projects/nwb-guide/badge/?version=latest" alt="Documentation"></a>
+      <a href="https://github.com/catalystneuro/nwb-guide/blob/main/LICENSE"><img src="https://img.shields.io/badge/license-MIT-yellow.svg" alt="License: MIT"></a>
+  </p>
+  <p align="center">
+     <a href="https://github.com/NeurodataWithoutBorders/nwb-guide/actions/workflows/Build-and-deploy-mac.yml"><img src="https://github.com/NeurodataWithoutBorders/nwb-guide/actions/workflows/Build-and-deploy-mac.yml/badge.svg" alt="Mac Build"></a>
+    <a href="https://github.com/NeurodataWithoutBorders/nwb-guide/actions/workflows/Build-and-deploy-win.yml"><img src="https://github.com/NeurodataWithoutBorders/nwb-guide/actions/workflows/Build-and-deploy-win.yml/badge.svg" alt="Windows Build"></a>
+  </p>
+  <p align="center">
+    <a href="https://github.com/psf/black"><img alt="Python code style: black" src="https://img.shields.io/badge/python_code_style-black-000000.svg"></a>
+    <a href="https://github.com/prettier/prettier"><img alt="JavaScript code style: prettier" src="https://img.shields.io/badge/javascript_code_style-prettier-ff69b4.svg?style=flat"></a>
+  </p>
+  <p align="center">
+      <a href="https://join.slack.com/t/nwb-users/shared_invite/enQtNzMwOTcwNzQ2MDM5LWMyZDUwODJjYjM3MzMzYzZiNDk4ZTU3ZjQ3MmMxMmY5MDUyNzc0ZDI5ZjViYmJjYTQ5NjljOGFjZmMwOGIwZmQ"><img src="https://img.shields.io/badge/chat-Slack-lightblue?style=flat&logo=slack" alt="NWB Slack"></a>
+  </p>
 </p>
 
-
 NWB GUIDE is a desktop app that provides a no-code user interface for converting neurophysiology data to NWB.
 
-<p align="center">
-  <a href="https://www.youtube.com/watch?v=z-rk2wi5BDc" target="_blank">
-  <img src="docs/assets/guide-video-image.png" alt="Watch the video" width="500" />
-  </a>
-</p>
-
-
 ## Installation
 See the installation instructions in our [documentation](https://nwb-guide.readthedocs.io/en/latest/installation.html).

docs/developer_guide.rst

@@ -24,7 +24,6 @@ Start by cloning the repository
 Install Python Dependencies
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-
 Install the appropriate Python dependencies for your operating system.
 
 **Windows**
@@ -51,15 +50,19 @@ Install the appropriate Python dependencies for your operating system.
 
     conda env create -f ./environments/environment-Linux.yml
 
+
+Activate the Python Environment
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
 Before starting NWB GUIDE, you'll need to ensure that the Python environment is activated.
 
 .. code-block:: bash
 
     conda activate nwb-guide
 
 
-Installing JavaScript Dependencies
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Install JavaScript Dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Next, install all JavaScript dependencies based on the `package-lock.json` file.
 
@@ -78,7 +81,6 @@ You can now run the following command to start the application using Electron.
     npm start
 
 
-
 Repo Structure
 --------------
 1. **src/renderer/src** - Contains all the source code for the frontend

docs/installation.rst

@@ -5,22 +5,27 @@ Installation
 Windows
 -------
 
-Download and run the `NWB-GUIDE-Setup-vX.Y.Z.exe <https://github.com/NeurodataWithoutBorders/nwb-guide/releases/latest/download/NWB-GUIDE-x64.exe>`_ file and follow all instruction prompts.
+Download and run `NWB-GUIDE-x64.exe <https://github.com/NeurodataWithoutBorders/nwb-guide/releases/latest/download/NWB-GUIDE-x64.exe>`_ and follow all instruction prompts.
 
 MacOS - Intel
 -------------
 
-Download the `NWB-GUIDE-vX.Y.Z.dmg <https://github.com/NeurodataWithoutBorders/nwb-guide/releases/latest/download/NWB-GUIDE-x64.dmg>`_ file, which should prompt you to move it into your 'Applications' folder in order to run.
+Download `NWB-GUIDE-x64.dmg <https://github.com/NeurodataWithoutBorders/nwb-guide/releases/latest/download/NWB-GUIDE-x64.dmg>`_, which should prompt you to move it into your 'Applications' folder in order to run.
 
 MacOS - Apple Silicon
 ---------------------
 
-Download the `NWB-GUIDE-vX.Y.Z-arm64.dmg <https://github.com/NeurodataWithoutBorders/nwb-guide/releases/latest/download/NWB-GUIDE-arm64.dmg>`_ file, which should prompt you to move it into your 'Applications' folder in order to run.
+Download `NWB-GUIDE-arm64.dmg <https://github.com/NeurodataWithoutBorders/nwb-guide/releases/latest/download/NWB-GUIDE-arm64.dmg>`_, which should prompt you to move it into your 'Applications' folder in order to run.
 
 .. note::
    Some data formats can have issues using this build of the application. If you encounter errors when using a particular interface, try following the advanced :ref:`Developer Installation instructions<developer_installation>` instructions.
 
-Ubuntu
-------
+Linux
+-----
 
-Please clone the :linux-fix:`linux-fix <>` branch of the NWB GUIDE and follow the :ref:`Developer Installation instructions<developer_installation>` on this documentation after the "Clone the Repo" step.
+Please clone the :linux-fix:`linux-fix <>` branch of the NWB GUIDE and follow the :ref:`Developer Installation instructions<developer_installation>` after the "Clone the Repo" step.
+
+.. code-block:: bash
+
+   git clone --branch linux-fix https://github.com/NeurodataWithoutBorders/nwb-guide
+   cd nwb-guide

src/renderer/src/stories/InfoBox.js

@@ -1,5 +1,6 @@
 import { LitElement, css, html } from "lit";
 import { Chevron } from "./Chevron";
+import { unsafeHTML } from "lit/directives/unsafe-html.js";
 
 export class InfoBox extends LitElement {
     static get styles() {
@@ -120,7 +121,9 @@ export class InfoBox extends LitElement {
                 ${new Chevron({ direction: "right" })}
             </div>
             <div class="guided--info-container">
-                <span class="guided--help-text">${this.content}</span>
+                <span class="guided--help-text"
+                    >${typeof this.content === "string" ? unsafeHTML(this.content) : this.content}</span
+                >
             </div>
         `;
     }

src/renderer/src/stories/JSONSchemaForm.js

@@ -464,7 +464,6 @@ export class JSONSchemaForm extends LitElement {
 
         // if (!isValid && allErrors.length && nMissingRequired === allErrors.length) message = `${nMissingRequired} required inputs are not defined.`;
 
-        console.log(allErrors);
         // Check if all inputs are valid
         if (flaggedInputs.length) {
             flaggedInputs[0].focus();

src/renderer/src/stories/Search.js

@@ -256,23 +256,37 @@ export class Search extends LitElement {
 
     #sortedCategories = [];
 
+    getTokens = (input) =>
+        input
+            .replaceAll(/[^\w\s]/g, "")
+            .split(" ")
+            .map((token) => token.trim().toLowerCase())
+            .filter((token) => token);
+
     #populate = (input = this.value ?? "") => {
         const toShow = [];
 
-        // Check if the input value matches the label
-        this.#options.forEach(({ option, label }, i) => {
-            if (label.toLowerCase().includes(input.toLowerCase()) && !toShow.includes(i)) toShow.push(i);
-        });
+        const inputTokens = this.getTokens(input);
 
-        // Check if the input value matches any of the keywords
-        this.#options.forEach(({ option, keywords = [], structuredKeywords = {} }, i) => {
-            [...keywords, ...Object.values(structuredKeywords).flat()].forEach((keyword) => {
-                if (keyword.toLowerCase().includes(input.toLowerCase()) && !toShow.includes(i)) toShow.push(i);
-            });
+        // Check if the input value matches the label or any of the keywords
+        this.#options.forEach(({ label, keywords, structuredKeywords }, i) => {
+            const labelTokens = this.getTokens(label);
+            const allKeywords = [...keywords, ...Object.values(structuredKeywords).flat()];
+            const allKeywordTokens = allKeywords.map((keyword) => this.getTokens(keyword)).flat();
+            const allTokens = [...labelTokens, ...allKeywordTokens];
+
+            const result = inputTokens.reduce((acc, token) => {
+                for (let subtoken of allTokens) {
+                    if (subtoken.startsWith(token) && !toShow.includes(i)) return (acc += 1);
+                }
+                return acc;
+            }, 0);
+
+            if (result === inputTokens.length) toShow.push(i);
         });
 
         this.#options.forEach(({ option }, i) => {
-            if (toShow.includes(i)) {
+            if (toShow.includes(i) || !inputTokens.length) {
                 option.removeAttribute("hidden");
             } else {
                 option.setAttribute("hidden", "");
@@ -285,7 +299,7 @@ export class Search extends LitElement {
             else element.removeAttribute("hidden");
         });
 
-        this.setAttribute("active", !!toShow.length);
+        this.setAttribute("active", !!toShow.length || !inputTokens.length);
         this.setAttribute("interacted", true);
     };
 

src/renderer/src/stories/pages/guided-mode/GuidedStart.js

@@ -104,8 +104,7 @@ export class GuidedStartPage extends Page {
                                 Although not required to use the GUIDE, you can learn more about the NWB conversion
                                 process in the
                                 <a href="https://neuroconv.readthedocs.io/en/main" target="_blank"
-                                    >neuroconv documentation page</a
-                                >
+                                    >neuroconv documentation page</a>.
                             `,
                         })}
                     </div>

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

@@ -84,7 +84,6 @@ export class GuidedMetadataPage extends ManagedPage {
     }
 
     beforeSave = () => {
-        console.log(this.localState.results, this.info.globalState.results);
         merge(this.localState.results, this.info.globalState.results);
     };
 
@@ -195,22 +194,21 @@ export class GuidedMetadataPage extends ManagedPage {
             // Set most Ophys tables to have minItems / maxItems equal (i.e. no editing possible)
             drillSchemaProperties(
                 resolvedSchema,
-                (path, schema, target, isPatternProperties) => {
+                (path, schema, target, isPatternProperties, parentSchema) => {
                     if (path[0] === "Ophys") {
                         const name = path.slice(-1)[0];
 
-                        if (isPatternProperties) {
-                            schema.minItems = schema.maxItems = Object.values(resolveFromPath(path, results)).length;
-                            return;
-                        }
+                        if (isPatternProperties)
+                            return (schema.minItems = schema.maxItems =
+                                Object.values(resolveFromPath(path, results)).length);
 
                         if (schema.type === "array") {
-                            if (
-                                name !== "Device" &&
-                                target &&
-                                name in target // Skip unresolved deep in pattern properties
-                            ) {
-                                schema.minItems = schema.maxItems = target[name].length;
+                            if (name !== "Device" && target) {
+                                if (name in target)
+                                    schema.minItems = schema.maxItems = target[name].length; // Skip unresolved deep in pattern properties)
+                                // Remove Ophys requirements if left initially undefined
+                                else if (parentSchema.required.includes(name))
+                                    parentSchema.required = parentSchema.required.filter((n) => n !== name);
                             }
                         }
                     }