panaroo-CI #162
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| name: panaroo-CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - devel | |
| pull_request: | |
| branches: | |
| - master | |
| - devel | |
| schedule: | |
| - cron: '1 1 1 * *' | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install cd-hit | |
| sudo apt-get install mafft | |
| wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar | |
| tar -xvf mash-Linux64-v2.2.tar | |
| sudo cp ./mash-Linux64-v2.2/mash /usr/bin/mash | |
| python --version | |
| pip install -U pip | |
| pip install -U pytest | |
| wget https://github.com/gtonkinhill/panaroo_test_data/releases/download/v0.0.2/travis_test_data.zip | |
| unzip travis_test_data.zip | |
| - name: Install | |
| run: pip install . | |
| - name: Validation Tests | |
| run: pytest -W ignore -q --datafolder="${{ github.workspace }}/travis_test_data/" | |