planemo still requires samtools #402
Workflow file for this run
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| name: Test | |
| on: [push, pull_request] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| check_versions_matches: | |
| name: Check deeptools version matches galaxy tools | |
| runs-on: ubuntu-latest | |
| if: github.base_ref == 'master' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Check path | |
| run: find /home/runner/work/deepTools/deepTools -name "pyproject.toml" | |
| - name: Get Version of Deeptools | |
| run: echo "deeptools_version=$(grep "version" /home/runner/work/deepTools/deepTools/pyproject.toml | awk '{print substr($NF, 2, length($NF) - 2)}')" >> $GITHUB_ENV | |
| - name: Get Version of Galaxy tools | |
| run: echo "galaxy_deeptools_version=$(grep "token.*TOOL_VERSION" /home/runner/work/deepTools/deepTools/galaxy/wrapper/deepTools_macros.xml | awk -F '>|<' '{print $3}')" >> $GITHUB_ENV | |
| - name: Versions | |
| run: | | |
| echo deeptools version=${deeptools_version} | |
| echo deeptools version in galaxy=${galaxy_deeptools_version} | |
| - name: Fail PR if versions not matching | |
| run: | | |
| if [ -z $galaxy_deeptools_version ]; then | |
| echo "galaxy_deeptools_version not defined change the github action" | |
| exit 1 | |
| fi | |
| if [ -z $deeptools_version ]; then | |
| echo "deeptools_version not defined change the github action" | |
| exit 1 | |
| fi | |
| if [ "$galaxy_deeptools_version" != "$deeptools_version" ]; then | |
| echo "versions do not match" | |
| exit 1 | |
| fi | |
| build-linux: | |
| name: Test on Linux | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: mamba-org/setup-micromamba@main | |
| with: | |
| environment-file: .github/test_and_build.yml | |
| cache-downloads: true | |
| environment-name: test_and_build | |
| - name: pip install | |
| run: | | |
| micromamba activate test_and_build | |
| pip install . | |
| - name: PEP8 | |
| run: | | |
| micromamba activate test_and_build | |
| flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E722,W504,W605 | |
| - name: Test deepTools | |
| run: | | |
| micromamba activate test_and_build | |
| pytest -v | |
| - name: make an artifact | |
| run: | | |
| micromamba activate test_and_build | |
| rm -f dist/* | |
| python -m build | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: "distfiles" | |
| path: "dist" | |
| test-wheels: | |
| name: test wheel | |
| runs-on: ubuntu-latest | |
| needs: build-linux | |
| strategy: | |
| matrix: | |
| python-version: ['3.8','3.9','3.10', '3.11', '3.12'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: "distfiles" | |
| path: ~/dist/ | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: install wheel | |
| run: | | |
| pip install ~/dist/*whl | |
| deeptools -h | |
| - name: pytest | |
| run: | | |
| pip install pytest | |
| pytest -v | |
| build-osx: | |
| name: Test on OSX | |
| runs-on: macOS-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: mamba-org/setup-micromamba@main | |
| with: | |
| environment-file: .github/test_and_build.yml | |
| cache-downloads: true | |
| environment-name: test_and_build | |
| - name: pip install | |
| run: | | |
| micromamba activate test_and_build | |
| pip install . | |
| - name: Test deepTools | |
| run: | | |
| micromamba activate test_and_build | |
| pytest -v |