guide-notebooks-ec2.yml

name: Guide Notebooks Regression - EC2
run-name: ${{ github.ref_name }} - Guide Notebooks Regression - EC2
on: [push]
jobs:
  start-runner:
    name: Start self-hosted EC2 runner
    runs-on: ubuntu-latest
    outputs:
      label: ${{ steps.start-ec2-runner.outputs.label }}
      ec2-instance-id: ${{ steps.start-ec2-runner.outputs.ec2-instance-id }}
    steps:
      - name: Configure AWS credentials
        uses: aws-actions/configure-aws-credentials@v1
        with:
          aws-access-key-id: ${{ secrets.AWS_KEY_ID }}
          aws-secret-access-key: ${{ secrets.AWS_KEY_SECRET }}
          aws-region: ${{ vars.AWS_REGION }}
      - name: Start EC2 runner
        id: start-ec2-runner
        uses: machulav/ec2-github-runner@v2
        with:
          mode: start
          github-token: ${{ secrets.GH_TOKEN }}
          ec2-image-id: ${{ vars.AWS_IMAGE_ID }}
          ec2-instance-type: ${{ vars.AWS_INSTANCE_TYPE }}
          subnet-id: ${{ vars.AWS_SUBNET }}
          security-group-id: ${{ vars.AWS_SECURITY_GROUP }}

  guide_notebooks_regression_ec2:
    needs: start-runner # required to start the main job when the runner is ready
    runs-on: ${{ needs.start-runner.outputs.label }} # run the job on the newly created runner
    steps:
      - name: clone
        uses: actions/checkout@v3
      - name: install
        run: |
          set -xe
          cd ${{ github.workspace }}
          source /opt/tensorflow/bin/activate
          export LD_LIBRARY_PATH=opt/amazon/efa/lib:/opt/amazon/openmpi/lib:/usr/local/cuda/efa/lib:/usr/local/cuda/lib:/usr/local/cuda:/usr/local/cuda/lib64:/usr/local/cuda/extras/CUPTI/lib64:/usr/local/cuda/targets/x86_64-linux/lib:/usr/local/lib:/usr/lib
          echo $LD_LIBRARY_PATH
          pip install matplotlib nilearn
          pip install -U tensorflow
          pip install -e .
          nobrainer info
      - name: run
        run: |
          set -xe
          cd ${{ github.workspace }}
          git clone https://github.com/neuronets/nobrainer-book.git
          cd nobrainer-book

          # if there is a matching book branch, switch to it
          if [ $(git ls-remote --heads https://github.com/neuronets/nobrainer-book.git ${{ github.ref_name }} | wc -l) -ne 0 ]; then
            echo "Checking out branch ${{ github.ref_name }}"
            git checkout ${{ github.ref_name }};
          else
            echo "No matching branch found, sticking with the default"
          fi

          cd ${{ github.workspace }}
          export LD_LIBRARY_PATH=opt/amazon/efa/lib:/opt/amazon/openmpi/lib:/usr/local/cuda/efa/lib:/usr/local/cuda/lib:/usr/local/cuda:/usr/local/cuda/lib64:/usr/local/cuda/extras/CUPTI/lib64:/usr/local/cuda/targets/x86_64-linux/lib:/usr/local/lib:/usr/lib
          source /opt/tensorflow/bin/activate
          for notebook_script in $(ls nobrainer-book/docs/nobrainer-guides/scripts/*.py); do
            echo "running ${notebook_script}"
            python ${notebook_script}
          done

  stop-runner:
    name: Stop self-hosted EC2 runner
    needs:
      - start-runner # required to get output from the start-runner job
      - guide_notebooks_regression_ec2 # required to wait when the main job is done
    runs-on: ubuntu-latest
    if: ${{ always() }} # required to stop the runner even if the error happened in the previous jobs
    steps:
      - name: Configure AWS credentials
        uses: aws-actions/configure-aws-credentials@v1
        with:
          aws-access-key-id: ${{ secrets.AWS_KEY_ID }}
          aws-secret-access-key: ${{ secrets.AWS_KEY_SECRET }}
          aws-region: ${{ vars.AWS_REGION }}
      - name: Stop EC2 runner
        uses: machulav/ec2-github-runner@v2
        with:
          mode: stop
          github-token: ${{ secrets.GH_TOKEN }}
          label: ${{ needs.start-runner.outputs.label }}
          ec2-instance-id: ${{ needs.start-runner.outputs.ec2-instance-id }}