Improve basic functions #327
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| name: Run pytest | |
| on: | |
| pull_request: | |
| branches: [ main, dev ] | |
| env: | |
| MY_REF: ${{ format('refs/heads/{0}', github.event.pull_request.head.ref) }} | |
| ACTIONS_ALLOW_UNSECURE_COMMANDS: true | |
| PYTHONIOENCODING: utf-8 | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| version: ["3.8", "3.10"] | |
| os: [ubuntu-latest, macos-latest] | |
| steps: | |
| - name: Check if relevant files have changed | |
| uses: actions/github-script@0.9.0 | |
| id: service-changed | |
| with: | |
| result-encoding: string | |
| script: | | |
| const result = await github.pulls.listFiles({ | |
| owner: context.payload.repository.owner.login, | |
| repo: context.payload.repository.name, | |
| pull_number: context.payload.number, | |
| per_page: 100 | |
| }) | |
| const serviceChanged = result.data.filter(f => f.filename.startsWith("proteinflow/")).length > 0 | |
| console.log(serviceChanged) | |
| return serviceChanged | |
| - uses: actions/checkout@v3 | |
| if: ${{ steps.service-changed.outputs.result == 'true' }} | |
| with: | |
| ref: ${{ env.MY_REF }} | |
| fetch-depth: 0 | |
| - name: Install dependencies | |
| if: ${{ steps.service-changed.outputs.result == 'true' }} | |
| run: | | |
| conda update conda -y | |
| conda create --name proteinflow -y python=${{ matrix.version }} | |
| conda install -n proteinflow -c conda-forge -c bioconda mmseqs2 | |
| conda run -n proteinflow python -m pip install torch --extra-index-url https://download.pytorch.org/whl/cpu | |
| conda run -n proteinflow python -m pip install awscli pytest flake8 | |
| conda run -n proteinflow python -m pip install numpy | |
| conda run -n proteinflow python -m pip install "rcsbsearch @ git+https://github.com/sbliven/rcsbsearch@dbdfe3880cc88b0ce57163987db613d579400c8e" | |
| conda run -n proteinflow python -m pip install -e . | |
| - name: Test with pytest | |
| if: ${{ steps.service-changed.outputs.result == 'true' }} | |
| run: | | |
| conda run -n proteinflow pytest tests |