Daily Component Tests and Migrations #968
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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 |