Test Tutorial #16
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| 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 |