tutorial-tests.yml

name: Test Tutorial
# following example: https://securitylab.github.com/research/github-actions-preventing-pwn-requests/
on:
  push:
    branches:
      - main
      - test_tutorial
    tags:
      - "[0-9]+.[0-9]+.[0-9]+"
  schedule:
    # Weekly on saturday 23:59
    - cron: "59 23 * * 6"


jobs:
  test-tutorial:
    runs-on: [self-hosted, linux, x64, gpu]
    container:
      image: continuumio/miniconda3
      options: --runtime=nvidia --gpus all --oom-kill-disable
    defaults:
      run:
        working-directory: ./docs/tutorials
    steps:
      - name: Pull code
        uses: actions/checkout@v4
      - name: Install dependencies, code, and list everything
        working-directory: ./
        run: |
          conda install -y -c conda-forge python=3 cupy cuda-version=11.8 curl unzip
          python -m pip install coverage mdextractor #mdextractor is new and might need to be replaced later
          python -m pip install .[all]
          conda list
      - name: Grab files needed for tests
        run: |
          mkdir dataset
          mkdir templates
          mkdir results_80S
          mkdir results_60S
          cd templates
          cp ../data/6qzp_60S.mrc .
          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
          cd ../dataset
          curl -L -O -J -H "X-Dataverse-key:${{ secrets.DATAVERSE_API_TOKEN }}" https://dataverse.nl/api/access/datafiles/384731,384724,384706,384718
          unzip dataverse_files.zip
          # this inflates into a 'tutorial' folder, moving everything out
          mv tutorial/* .
      - name: Set TQDM_MININTERVAL
        run: echo "TQDM_MININTERVAL=10" >> "$GITHUB_ENV"
      - name: see ENV and nvidia-smi
        run: |
          env
          nvidia-smi
      - 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 -u $(which pytom_create_template.py) -i templates/emd_2938.map -o templates/80S.mrc --input-voxel 1.1 --output-voxel 13.79 --center --invert -b 60 --log debug
          # python -u tests/test_tutorial.py