Improved use of GitHub Actions + pandas warning fix #253
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python application | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| version: ["3.8", "3.13"] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install . | |
| - name: Test base functionality tool | |
| run: | | |
| ena-upload-cli --help | |
| - name: Create credentials file | |
| run: | | |
| echo "username: ${{ secrets.ENA_USERNAME }}" >> .secrets.yaml | |
| echo "password: ${{ secrets.ENA_PASSWORD }}" >> .secrets.yml | |
| - name: Test submission in --draft mode | |
| run: | | |
| ena-upload-cli --action add --draft --dev --center ${{ secrets.ENA_CENTER }} --data example_data/ENA_TEST1.R1.fastq.gz example_data/ENA_TEST2.R1.fastq.gz example_data/ENA_TEST2.R2.fastq.gz --checklist ERC000033 --secret .secret.yml --xlsx example_tables/ENA_excel_example_ERC000033.xlsx | |
| - name: Run Python to get temp directory | |
| run: | | |
| echo "TEMP_DIR=$(python -c 'import tempfile; print(tempfile.gettempdir())')" >> $GITHUB_ENV | |
| - uses: actions/upload-artifact@v4 | |
| name: Output XMLs for ${{ matrix.os }} Python ${{ matrix.os }} | |
| with: | |
| name: ena-upload-cli_output_${{ matrix.os }}_python_${{ matrix.version }} | |
| path: ${{ env.TEMP_DIR}}/*.xml |