test-tutorials.yml

name: Test tutorials

on: [push]

jobs:
  build:

    runs-on: ubuntu-latest

    steps:
      # This cancels any such job that is still running
    - name: Cancel Previous Runs
      uses: styfle/cancel-workflow-action@0.9.1
      with:
        access_token: ${{ github.token }}
    - uses: actions/checkout@v4
    - name: Set up Python 3.10
      uses: actions/setup-python@v5
      with:
        python-version: '3.10'
    - name: Install graphviz
      run: |
        sudo apt-get update -y -qq
        sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
          libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 \
          libxcb-xinerama0 libxcb-xinput0 graphviz graphviz-dev \
          libegl1-mesa libgl1-mesa-dri libxcb-xfixes0-dev mesa-vulkan-drivers \
          libxcb-cursor0
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        python -m pip install pathos pygraphviz neuron cloud-volume k3d scikit-image open3d
        python -m pip install -e .[test-notebook,all]
    - name: Download test data
      run: |
        chmod +x download_test_data.sh
        ./download_test_data.sh
    - name: Download downsampled test transform
      run: |
        mkdir -p -- $HOME/flybrain-data
        curl -o $HOME/flybrain-data/JRC2018F_JRCFIB2018F.h5 https://flyem.mrc-lmb.cam.ac.uk/flyconnectome/misc/JRC2018F_JRCFIB2018F.h5
        curl -o $HOME/flybrain-data/JRC2018F_FAFB.h5 https://flyem.mrc-lmb.cam.ac.uk/flyconnectome/misc/JRC2018F_FAFB.h5
    - name: Run tutorials
      uses: coactions/setup-xvfb@v1
      env:
        NEUPRINT_APPLICATION_CREDENTIALS: ${{ secrets.neuprint }}
        INSECT_BRAIN_DB_USER: ${{ secrets.insect_brain_db_user }}
        INSECT_BRAIN_DB_PASSWORD: ${{ secrets.insect_brain_db_password }}
        CAVE_SECRET: ${{ secrets.cave_secret }}
        NAVIS_PLOT3D_BACKEND: plotly
        QT_QPA_PLATFORM: offscreen
      with:
        run: |
          python -c "import os;print('CPU count:', os.cpu_count())"
          python docs/examples/5_nblast/plot_00_nblast_intro.py
          python -c "import os;from caveclient import CAVEclient;client=CAVEclient();client.auth.save_token(os.getenv('CAVE_SECRET'))"
          python tests/test_tutorials.py