Daily Component Tests and Migrations #959
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |