Daily Component Tests and Migrations #956
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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: ["3.10"] | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: 'latest' | |
| auto-update-conda: true | |
| activate-environment: anvio_env | |
| environment-file: .conda/environment.yaml | |
| python-version: ${{ matrix.python-version }} | |
| - name: "Install Bioconductor qvalue package for R" | |
| shell: bash -l {0} | |
| run: | | |
| Rscript -e 'install.packages("BiocManager", repos="https://cran.rstudio.com"); BiocManager::install("qvalue")' | |
| - name: "Conda environment summary" | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| - uses: actions/checkout@v4 | |
| - name: "Install anvi'o from the codebase" | |
| shell: bash -l {0} | |
| run: | | |
| pip install . | |
| - name: "Set Anvi'o interactive directory path" | |
| shell: bash -l {0} | |
| run: | | |
| interactive_dir=$(python -c "import site; print(site.getsitepackages()[0] + '/anvio/data/interactive')") | |
| echo "interactive_dir_path=$interactive_dir" >> $GITHUB_ENV | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: 18 | |
| - name: "Install npm dependencies for Anvi'o interactive interfaces" | |
| shell: bash -l {0} | |
| run: | | |
| cd ${{ env.interactive_dir_path }} | |
| npm install | |
| cd - | |
| - name: "Run component tests" | |
| shell: bash -l {0} | |
| run: | | |
| anvi-self-test --suite metagenomics-full --no-interactive | |
| anvi-self-test --suite pangenomics --no-interactive | |
| anvi-self-test --suite inversions --no-interactive | |
| # the following steps cause our actions to fail on GitHub runners | |
| # due to space limitations :/ please do not uncomment this until we | |
| # have a solution for this :/ | |
| #- name: "Run component tests for metabolism framework" | |
| # shell: bash -l {0} | |
| # run: | | |
| # anvi-self-test --suite metabolism --no-interactive | |
| #- name: "Migrate ancient anvi'o databases" | |
| # shell: bash -l {0} | |
| # run: | | |
| # anvi-self-test --suite database-migrations |