New python tests #11
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| name: Python workflow Tests | ||
| on: | ||
| push: | ||
| paths: | ||
| - biobb_wf_ligand_parameterization/python/workflow.env.yml | ||
| workflow_dispatch: | ||
| jobs: | ||
| detect-files: | ||
| name: Detect Changed Files | ||
| runs-on: self-hosted | ||
| outputs: | ||
| changed_files: ${{ steps.detect_changes.outputs.changed_files }} | ||
| steps: | ||
| - name: Checkout code | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| fetch-depth: 0 | ||
| - name: Detect changed files | ||
| id: detect_changes | ||
| run: | | ||
| git diff --name-only ${{ github.event.before }} ${{ github.sha }} > changed_files.txt | ||
| # echo "::set-output name=changed_files::$(cat changed_files.txt)" | ||
| changed_files=$(cat changed_files.txt) | ||
| echo "changed_files=$changed_files" >> $GITHUB_ENV | ||
| shell: bash | ||
| run-jobs: | ||
| needs: detect-files | ||
| runs-on: self-hosted | ||
| # strategy: | ||
| # matrix: | ||
| # include: | ||
| # - file: 'biobb_wf_ligand_parameterization/python/workflow.env.yml' | ||
| # job: 'biobb_wf_ligand_parameterization' | ||
| # wf_name: 'biobb_wf_ligand_parameterization' | ||
| # # - file: 'path/to/another/file.yml' | ||
| # # job: 'another_job' | ||
| # # wf_name: 'another_workflow' | ||
| steps: | ||
| # - name: Checkout code | ||
| # uses: actions/checkout@v3 | ||
| # - name: Run conditional job | ||
| # if: contains(needs.detect-files.outputs.changed_files, matrix.file) | ||
| # uses: ./.github/workflows/common-python.yaml | ||
| # with: | ||
| # wf_name: ${{ matrix.wf_name }} | ||
| - name: Check out repository code | ||
| if: contains(needs.detect-files.outputs.changed_files, 'biobb_wf_amber_md_setup/python/workflow.env.yml') | ||
| uses: actions/checkout@v4 | ||
| # - run: echo "Repository -> ${{ github.repository }}" | ||
| # - run: echo "Branch -> ${{ github.ref }}" | ||
| # - run: echo "Trigger event -> ${{ github.event_name }}" | ||
| # - run: echo "Runner OS -> ${{ runner.os }}" | ||
| # - name: List files in the repository | ||
| # run: | | ||
| # ls ${{ github.workspace }} | ||
| - name: Remove all micromamba installations | ||
| if: contains(needs.detect-files.outputs.changed_files, 'biobb_wf_amber_md_setup/python/workflow.env.yml') | ||
| run: | | ||
| rm -rf $HOME/.bash_profile $HOME/.conda $HOME/micromamba $HOME/micromamba-bin 2>/dev/null | ||
| touch $HOME/.bash_profile | ||
| - name: setup-micromamba | ||
| if: contains(needs.detect-files.outputs.changed_files, 'biobb_wf_amber_md_setup/python/workflow.env.yml') | ||
| uses: mamba-org/[email protected] | ||
| with: | ||
| generate-run-shell: true | ||
| micromamba-version: '2.0.2-2' | ||
| post-cleanup: 'all' | ||
| init-shell: bash | ||
| environment-file: biobb_wf_ligand_parameterization/python/workflow.env.yml | ||
| create-args: >- | ||
| pytest | ||
| # - name: List installed package versions | ||
| # shell: bash -l {0} | ||
| # run: micromamba list | ||
| - name: Run tests | ||
| if: contains(needs.detect-files.outputs.changed_files, 'biobb_wf_amber_md_setup/python/workflow.env.yml') | ||
| shell: bash -l {0} | ||
| run: | | ||
| export PYTHONPATH=.:./biobb_common:$PYTHONPATH | ||
| cd biobb_wf_ligand_parameterization/tests/python | ||
| # Production one | ||
| pytest biobb_wf_ligand_parameterization.py --config ../../python/workflow.yml --remove | ||
