pin last packages #182
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| 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=13.3.0=py312h8e83189_0 cupy-core=13.3.0=py312h53955ab_0 libgcc=14.1 numpy=2.1.1 c-ares=1.33.1 libnghttp2=1.58.0 libsqlite=3.46.1 sqlite=3.46.1 conda=24.9.1 cuda-version=11.8 curl unzip | |
| python -m pip install markupsafe==2.1.5 distlib==0.3.8 coverage==7.6.1 mkdocs-material==9.5.39 pillow==10.4.0 pyparsing==3.1.4 virtualenv==20.26.6 ruff==0.6.9 pre-commit==4.0.0 | |
| 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 |