python_test #682
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| # GitHub Actions workflow for automated testing | |
| # See: https://docs.github.com/en/actions | |
| # | |
| # This workflow runs Python tests on a self-hosted runner | |
| # Jobs are independent to allow partial success/failure reporting | |
| name: Python test | |
| run-name: python_test | |
| on: | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| Preamble: | |
| runs-on: self-hosted | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| steps: | |
| - run: pwd | |
| - run: which python | |
| - run: conda info --envs | |
| - name: Set up repo | |
| uses: actions/checkout@v4 | |
| - run: git status | |
| - run: echo "${{ github.ref }} | ${{ github.repository }} | ${{ github.event.pull_request.title }}" | |
| - name: check labels | |
| run: echo "${{ github.event.pull_request.labels.*.name }}" | |
| - name: Copy files to working-directory | |
| run: cp -r ./* /home/exouser/Desktop/blech_clust | |
| - name: Check files in working-directory | |
| run: ls -R /home/exouser/Desktop/blech_clust | |
| - name: Setup params | |
| run: cp /home/exouser/Desktop/blech_clust/params/_templates/* /home/exouser/Desktop/blech_clust/params | |
| - name: Check params | |
| run: for f in $(find /home/exouser/Desktop/blech_clust/params/ -type f); do echo $f; cat $f; done | |
| Install: | |
| runs-on: self-hosted | |
| needs: Preamble | |
| if: ${{ contains(github.event.pull_request.labels.*.name, 'install') }} | |
| # Only run installation when PR has 'install' label | |
| steps: | |
| - name: Clean install | |
| working-directory: /home/exouser/Desktop/blech_clust | |
| run: | | |
| echo "Running installation for tag ${{ github.ref }}" | |
| make clean | |
| - name: Install dependencies | |
| working-directory: /home/exouser/Desktop/blech_clust | |
| run: | | |
| make base | |
| - name: Install EMG | |
| working-directory: /home/exouser/Desktop/blech_clust | |
| run: | | |
| make emg | |
| - name: Install neuRecommend | |
| working-directory: /home/exouser/Desktop/blech_clust | |
| run: | | |
| make neurec | |
| - name: Install BlechRNN | |
| working-directory: /home/exouser/Desktop/blech_clust | |
| run: | | |
| make blechrnn | |
| - name: Install Prefect | |
| working-directory: /home/exouser/Desktop/blech_clust | |
| run: | | |
| make prefect | |
| - name: Patch dependencies | |
| working-directory: /home/exouser/Desktop/blech_clust | |
| run: | | |
| make patch | |
| Spike-EMG-Install: | |
| runs-on: self-hosted | |
| needs: Install | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| # Test full pipeline with both spike sorting and EMG analysis | |
| if: ${{ contains(github.event.pull_request.labels.*.name, 'install') }} | |
| steps: | |
| - name: Prefect SPIKE then EMG test | |
| shell: bash | |
| working-directory: /home/exouser/Desktop/blech_clust | |
| run: conda run -n blech_clust python pipeline_testing/prefect_pipeline.py --spike-emg 2>&1 | | |
| tee ~/Desktop/blech_clust/github.log; | |
| if grep -q "ERROR" ~/Desktop/blech_clust/github.log; then | |
| echo "ERROR detected by bash"; | |
| ./pipeline_testing/extract_traceback.sh ~/Desktop/blech_clust/github.log; | |
| exit 1; | |
| fi | |
| EMG-Only-Install: | |
| runs-on: self-hosted | |
| needs: Spike-EMG-Install | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| # Test EMG analysis pipeline in isolation | |
| steps: | |
| - name: Prefect EMG only test | |
| shell: bash | |
| working-directory: /home/exouser/Desktop/blech_clust | |
| run: conda run -n blech_clust python pipeline_testing/prefect_pipeline.py -e 2>&1 | | |
| tee ~/Desktop/blech_clust/github.log; | |
| if grep -q "ERROR" ~/Desktop/blech_clust/github.log; then | |
| echo "ERROR detected by bash"; | |
| ./pipeline_testing/extract_traceback.sh ~/Desktop/blech_clust/github.log; | |
| exit 1; | |
| fi | |
| Spike-EMG: | |
| runs-on: self-hosted | |
| needs: Preamble | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| # Test full pipeline with both spike sorting and EMG analysis | |
| if: ${{ !contains(github.event.pull_request.labels.*.name, 'install') }} | |
| steps: | |
| - name: Prefect SPIKE then EMG test | |
| shell: bash | |
| working-directory: /home/exouser/Desktop/blech_clust | |
| run: conda run -n blech_clust python pipeline_testing/prefect_pipeline.py --spike-emg 2>&1 | | |
| tee ~/Desktop/blech_clust/github.log; | |
| if grep -q "ERROR" ~/Desktop/blech_clust/github.log; then | |
| echo "ERROR detected by bash"; | |
| ./pipeline_testing/extract_traceback.sh ~/Desktop/blech_clust/github.log; | |
| exit 1; | |
| fi | |
| EMG-Only: | |
| runs-on: self-hosted | |
| needs: Spike-EMG | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| # Test EMG analysis pipeline in isolation | |
| if: ${{ !contains(github.event.pull_request.labels.*.name, 'install') }} | |
| steps: | |
| - name: Prefect EMG only test | |
| shell: bash | |
| working-directory: /home/exouser/Desktop/blech_clust | |
| run: conda run -n blech_clust python pipeline_testing/prefect_pipeline.py -e 2>&1 | | |
| tee ~/Desktop/blech_clust/github.log; | |
| if grep -q "ERROR" ~/Desktop/blech_clust/github.log; then | |
| echo "ERROR detected by bash"; | |
| ./pipeline_testing/extract_traceback.sh ~/Desktop/blech_clust/github.log; | |
| exit 1; | |
| fi |