Merge pull request #101 from usegalaxy-eu/pandas-df #256
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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 |