AlphaX cross-projects tests #6
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| name: AlphaX cross-projects tests | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| alphabase_ref: | |
| description: "alphabase version: version of alphabase to use. Can be a commit hash, branch name or 'latest' for the latest release." | |
| default: latest | |
| alphatims_ref: | |
| description: "alphatims version" | |
| default: latest | |
| alpharaw_ref: | |
| description: "alpharaw version" | |
| default: development # TODO: change to latest once properly tagged release is out | |
| alphaviz_ref: | |
| description: "alphaviz version" | |
| default: latest | |
| alphapeptdeep_ref: | |
| description: "alphapeptdeep version" | |
| default: latest | |
| directlfq_ref: | |
| description: "alphatims version" | |
| default: latest | |
| alphadia_ref: | |
| description: "alphadia version" | |
| default: latest | |
| jobs: | |
| build_image: | |
| runs-on: AlphaDIA | |
| steps: | |
| - name: Print input parameters | |
| run: echo "${{ toJSON(github.event.inputs) }}" | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| # # avoid "no space left on device" error | |
| # # https://github.com/actions/runner-images/issues/2840#issuecomment-790492173 | |
| # - name: cleanup | |
| # run: | | |
| # sudo rm -rf /usr/share/dotnet | |
| # sudo rm -rf /opt/ghc | |
| # sudo rm -rf "/usr/local/share/boost" | |
| # sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Build and export | |
| uses: docker/build-push-action@v6 | |
| with: | |
| tags: alphax:latest | |
| context: ./alphatesting | |
| outputs: type=docker,dest=/tmp/alphax.tar | |
| # cache-from: type=gha | |
| # cache-to: type=gha,mode=max | |
| no-cache: True | |
| build-args: | | |
| ALPHABASE_REF=${{ inputs.alphabase_ref }} | |
| ALPHATIMS_REF=${{ inputs.alphatims_ref }} | |
| ALPHARAW_REF=${{ inputs.alpharaw_ref }} | |
| ALPHAVIZ_REF=${{ inputs.alphaviz_ref }} | |
| ALPHAPEPTDEEP_REF=${{ inputs.alphapeptdeep_ref }} | |
| DIRECTLFQ_REF=${{ inputs.directlfq_ref }} | |
| ALPHADIA_REF=${{ inputs.alphadia_ref }} | |
| - name: Upload artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: alphax | |
| path: /tmp/alphax.tar | |
| alphabase_tests: | |
| runs-on: AlphaDIA | |
| needs: [ build_image ] | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: alphax | |
| path: /tmp | |
| - name: Load image | |
| run: | | |
| docker load --input /tmp/alphax.tar | |
| docker image ls -a | |
| - name: Print pip freeze | |
| run: | | |
| docker run alphax bash -c "pip freeze" | |
| - name: alphabase tests | |
| id: alphabase_tests | |
| run: | | |
| docker run alphax bash -c "cd alphabase/tests && chmod +x run_tests.sh && ./run_tests.sh" | |
| alpharaw_tests: | |
| runs-on: AlphaDIA | |
| needs: [ build_image ] | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: alphax | |
| path: /tmp | |
| - name: Load image | |
| run: | | |
| docker load --input /tmp/alphax.tar | |
| docker image ls -a | |
| - name: Print pip freeze | |
| run: | | |
| docker run alphax bash -c "pip freeze" | |
| - name: alpharaw tests | |
| id: alpharaw_tests | |
| run: | | |
| docker run alphax bash -c "cd alpharaw/tests && ls && python -m download_test_data && chmod +x run_tests.sh && ./run_tests.sh" | |
| alphaviz_tests: | |
| runs-on: AlphaDIA | |
| needs: [ build_image ] | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: alphax | |
| path: /tmp | |
| - name: Load image | |
| run: | | |
| docker load --input /tmp/alphax.tar | |
| docker image ls -a | |
| - name: Print pip freeze | |
| run: | | |
| docker run alphax bash -c "pip freeze" | |
| - name: alphaviz tests | |
| id: alphaviz_tests | |
| run: | | |
| docker run alphax bash -c "cd alphaviz/tests && ls && python -m pytest test_io.py && python -m pytest test_preprocessing.py" | |
| alphapeptdeep_tests: | |
| runs-on: AlphaDIA | |
| needs: [ build_image ] | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: alphax | |
| path: /tmp | |
| - name: Load image | |
| run: | | |
| docker load --input /tmp/alphax.tar | |
| docker image ls -a | |
| - name: Print pip freeze | |
| run: | | |
| docker run alphax bash -c "pip freeze" | |
| - name: alphapeptdeep tests | |
| id: alphapeptdeep_tests | |
| run: | | |
| docker run alphax bash -c "cd alphapeptdeep/tests && chmod +x run_tests.sh && ./run_tests.sh" | |
| alphadia_tests: | |
| runs-on: AlphaDIA | |
| needs: [ build_image ] | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: alphax | |
| path: /tmp | |
| - name: Load image | |
| run: | | |
| docker load --input /tmp/alphax.tar | |
| docker image ls -a | |
| - name: Print pip freeze | |
| run: | | |
| docker run alphax bash -c "pip freeze" | |
| - name: alphadia unit tests ('not slow') | |
| id: alphadia_unit_tests | |
| run: | | |
| docker run alphax bash -c "cd alphadia/tests && python -m pytest -k 'not slow'" | |
| - name: alphadia unit tests ('slow') | |
| id: alphadia_slow_unit_tests | |
| run: | | |
| docker run alphax bash -c "cd alphadia/tests && python -m pytest -k 'slow'" | |
| - name: alphadia e2e test 'basic' | |
| id: alphadia_e2e_tests | |
| run: | | |
| TEST_CASE_NAME=basic | |
| docker run alphax bash -c "cd alphadia/tests/e2e_tests \ | |
| && python prepare_test_data.py $TEST_CASE_NAME \ | |
| && alphadia --config $TEST_CASE_NAME/config.yaml" |