Daily Component Tests and Migrations #479
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| name: Daily Component Tests and Migrations | |
| on: | |
| schedule: | |
| - cron: "0 9 * * *" | |
| jobs: | |
| build: | |
| name: Daily Component Tests (Python ${{ matrix.python-version }}) | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.7] | |
| fail-fast: false | |
| steps: | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: 'latest' | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge,bioconda | |
| activate-environment: anvio_env | |
| - name: "Set up the conda environment" | |
| shell: bash -l {0} | |
| run: | | |
| conda info -a | |
| conda install -y "mamba >=0.24.0" | |
| mamba env create -f ../.conda/environment.yaml | |
| - uses: actions/checkout@v2 | |
| - name: "Install anvi'o from the codebase" | |
| shell: bash -l {0} | |
| run: | | |
| pip install . | |
| - name: "Run component tests for general metagenomics tasks" | |
| shell: bash -l {0} | |
| run: | | |
| anvi-self-test --suite metagenomics-full --no-interactive | |
| - name: "Run component tests for metabolism framework" | |
| shell: bash -l {0} | |
| run: | | |
| anvi-self-test --suite metabolism --no-interactive | |
| # the following causes our actions to fail due to space limitations :/ | |
| # please do not uncomment this until we have a solution. | |
| #- name: "Migrate ancient anvi'o databases" | |
| # shell: bash -l {0} | |
| # run: | | |
| # anvi-self-test --suite database-migrations |