Merge pull request #196 from phac-nml/dev/columns #323
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| name: Integration Tests | |
| on: | |
| pull_request: # Run on all pull requests | |
| push: | |
| branches: # Run on any push to master and development | |
| - master | |
| - development | |
| schedule: # Run weekly on master and development | |
| - cron: 0 2 * * 0 | |
| branches: master | |
| - cron: 0 2 * * 0 | |
| branches: development | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| env: | |
| DATABASE_COMMITS: '--resfinder-commit fa32d9a3cf0c12ec70ca4e90c45c0d590ee810bd --pointfinder-commit 8c694b9f336153e6d618b897b3b4930961521eb8 --plasmidfinder-commit 1a443a19a1142aa1018ef62f0bdbfd871b79eab6' | |
| strategy: | |
| fail-fast: False | |
| matrix: | |
| include: | |
| - python-version: "3.9" | |
| other-packages: "mlst numpy pandas" | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Setup Conda with Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| activate-environment: staramr-env | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install conda packages | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| conda config --add channels defaults | |
| conda config --add channels conda-forge | |
| conda config --add channels bioconda | |
| conda install -n base conda-libmamba-solver | |
| conda config --set solver libmamba | |
| conda install Cython blast git perl-list-moreutils ${{ matrix.other-packages }} -y | |
| - name: Setup python packages | |
| shell: bash -l {0} | |
| run: | | |
| python --version | |
| python setup.py -q install | |
| - name: Build database | |
| shell: bash -l {0} | |
| run: staramr db build --dir staramr/databases/data ${{ env.DATABASE_COMMITS }} | |
| - name: Run Tests | |
| shell: bash -l {0} | |
| run: python setup.py test |