Add microGalaxy lab #339
Workflow file for this run
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| name: Run tests | |
| # This GitHub Actions workflow is designed to automate testing for the project. | |
| # It triggers under two conditions: | |
| # 1. Pull requests targeting the main branch, ensuring that internal changes | |
| # are validated before merging. | |
| # 2. Pushes to the dev branch, allowing for continuous integration | |
| # as changes are made directly to the development branch. | |
| # | |
| # The workflow consists of three main jobs: | |
| # - **test-tools**: Runs tests for tools extracted from the repository. | |
| # - **test-tutorials**: Runs tests for community tutorials. | |
| # - **test-workflows**: Runs tests for workflow scripts. | |
| # | |
| # Each job includes the following steps: | |
| # - Checkout the repository code. | |
| # - Set up the Python environment using the specified version. | |
| # - Install required dependencies. | |
| # - Execute scripts for extraction and filtering of tools, tutorials, or workflows. | |
| # | |
| # This ensures that the code remains reliable and functional as new changes are introduced. | |
| on: | |
| pull_request: | |
| branches: | |
| - main # Trigger on pull requests targeting the main branch | |
| push: | |
| branches: | |
| - dev # Trigger on pushes to the dev branch | |
| jobs: | |
| test-tools: | |
| runs-on: ubuntu-20.04 | |
| # This job runs tests for tools. | |
| # It checks for internal pull requests targeting the main branch, | |
| # as well as pushes to the dev branch. | |
| # The workflow performs the following steps: | |
| # 1. Checkout the repository code. | |
| # 2. Set up Python environment using the specified version. | |
| # 3. Install required Python packages. | |
| # 4. Extract tools using a provided script. | |
| # 5. Filter community tools using a provided script. | |
| # 6. Format tools into an interactive table and generate a word cloud. | |
| if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev' | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| environment: fetch-tools | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install requirements | |
| run: python -m pip install -r requirements.txt | |
| - name: Tool extraction | |
| run: | | |
| bash sources/bin/extract_all_tools.sh test | |
| env: | |
| GITHUB_API_KEY: ${{ secrets.GH_API_TOKEN }} | |
| - name: Tool filter | |
| run: | | |
| bash sources/bin/get_community_tools.sh test | |
| - name: Create interactive table and wordcloud | |
| run: | | |
| bash sources/bin/format_tools.sh test | |
| test-tutorials: | |
| runs-on: ubuntu-20.04 | |
| # This job runs tests for tutorials. | |
| # Similar to the tools job, it checks for internal pull requests | |
| # to the main branch and pushes to the dev branch. | |
| # The workflow performs the following steps: | |
| # 1. Checkout the repository code. | |
| # 2. Set up Python environment using the specified version. | |
| # 3. Install required Python packages. | |
| # 4. Extract tutorials using a provided script. | |
| # 5. Filter community tutorials using a provided script. | |
| if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev' | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install requirements | |
| run: python -m pip install -r requirements.txt | |
| - name: Tutorial extraction | |
| run: | | |
| bash sources/bin/extract_all_tutorials.sh test | |
| env: | |
| PLAUSIBLE_API_KEY: ${{ secrets.PLAUSIBLE_API_TOKEN }} | |
| - name: Tutorial filtering | |
| run: | | |
| bash sources/bin/get_community_tutorials.sh test | |
| test-workflows: | |
| runs-on: ubuntu-20.04 | |
| # This job runs tests for workflows. | |
| # It performs the same checks as the other jobs, ensuring | |
| # quality for workflow scripts. | |
| if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev' | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install requirements | |
| run: python -m pip install -r requirements.txt | |
| - name: Workflow extraction | |
| run: | | |
| bash sources/bin/extract_all_workflows.sh test | |
| - name: Workflow filtering | |
| run: | | |
| bash sources/bin/get_community_workflows.sh test |