Merge branch 'main' into small-fixes

NeurodataWithoutBorders · Feb 27, 2024 · 89935b5 · 89935b5
2 parents 52059a3 + 374ed89
commit 89935b5
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diff --git a/.github/workflows/testing-external.yml b/.github/workflows/testing-external.yml
@@ -0,0 +1,93 @@
+name: External Tests
+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: External tests 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
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -71,12 +71,6 @@ 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
         run: npm run test:coverage

diff --git a/docs/developer_guide.rst b/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

diff --git a/docs/installation.rst b/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