tutorial-tests.yml

name: Test Tutorial
# following example: https://securitylab.github.com/research/github-actions-preventing-pwn-requests/
on:
  workflow_run:
    workflows: ["Unit tests"]
    types:
      - completed

jobs:
  test-tutorial:
    if: >
      github.event.workflow_run.event == 'pull_request' &&
      github.event.workflow_run.conclusion == 'success'
    runs-on: [self-hosted, linux, x64, gpu]
    container:
      image: continuumio/miniconda3
      options: --runtime=nvidia --gpus all
    permissions:
      # Read the action that triggered this one
      actions: read
      # Allow to write check runs
      checks: write
      # Read and update commit statuses
      statuses: write
    steps:
      - name: Pull code
        uses: actions/checkout@v4
        with:
          repository: github.event.workflow_run.head_repository
          ref: github.event.workflow_run.head_sha
      - name: Pull wiki
        uses: actions/checkout@v4
        with:
          # Only check the wiki of the calling repo
          repository: ${{github.repository}}.wiki 
          path: wiki
      - name: Install dependencies, code, and list everything
        run: |
          conda install -y -c conda-forge python=3 cupy cuda-version=11.8
          python -m pip install coverage mdextractor #mdextractor is new and might need to be replaced later
          python -m pip install .[dev]
          conda list
      - name: Grab files needed for tests
        run: |
          mkdir wiki/dataset
          mkdir wiki/templates
          mkdir wiki/results_80S
          mkdir wiki/results_60S
          cd wiki/templates
          cp ../data/6qzp_60S wiki/templates/
          curl https://files.wwpdb.org/pub/emdb/structures/EMD-2938/map/emd_2938.map.gz -o emd_2938.map.gz
          gunzip emd_2938.map.gz
          mv emd_2938.map emd_2938.mrc
          cd ../dataset
          curl -L -O -J -H "X-Dataverse-key:${{ secrets.DATAVERSE_API_TOKEN }}" https://dataverse.nl/api/access/datafiles/384731,384724,384706,384718
          unzip dataverse_files.zip
          mv tutorial/* .
          cd ../
      - name: Run Tutorial test
        run: |
          # Hardcode the conversion line
          for x in dataset/*.mrc; do python -c "import mrcfile; mrc = mrcfile.mmap('$x', 'r+'); mrc.voxel_size = 13.79"; done
          python tests/test_tutorial.py