Containerization of workflow #6
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| name: build containers and run tests | |
| #todo: change this to an on_pullrequest trigger only to main branch | |
| on: | |
| pull_request: | |
| branches: | |
| - '*' | |
| jobs: | |
| Setup_and_build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| environment-file: env.yml | |
| init-shell: bash | |
| - name: Install local python package | |
| run: | | |
| pip install . --no-deps | |
| shell: micromamba-shell {0} | |
| - name: build containers | |
| run: | | |
| python containers/build_containers.py | |
| env: | |
| TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| shell: micromamba-shell {0} | |
| - name: zip built containers | |
| run: | | |
| cd ./containers/ | |
| tar -czvf containers.tar.gz builtcontainers.json $(find . -type f -name "*.tar" -printf '%f ') | |
| - name: Upload container artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: built_containers | |
| path: ./containers/containers.tar.gz | |
| Test: | |
| runs-on: ubuntu-latest | |
| needs: Setup_and_build | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: built_containers | |
| - name: move artifact | |
| run: | | |
| mv ./containers.tar.gz ./containers/containers.tar.gz | |
| - name: unzip built containers | |
| run: | | |
| cd ./containers/ | |
| tar -xzvf containers.tar.gz | |
| cd .. | |
| - name: Setup Apptainer | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| - name: Setup Mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| environment-file: env.yml | |
| init-shell: bash | |
| - name: Install local python package | |
| run: | | |
| pip install . --no-deps | |
| shell: micromamba-shell {0} | |
| - name: convert containers | |
| run: | | |
| python containers/convert_artifact_containers_for_apptainer.py | |
| - name: download existing containers | |
| run: | | |
| python containers/pull_published_containers.py | |
| shell: micromamba-shell {0} | |
| ## rest of the testing suite here |