Development

Testing strategy

Automated unit tests are found in the test directory. These tests check for pipeline or scripts correctness, but do not run dependency programs such as assemblers. They are run automatically as part of the CI pipeline. Once Aviary is setup, tests can be run as below:

pixi run -e dev pytest -v

Integration tests are found in test/test_integration.py. These tests are specific to the Centre for Microbiome Research server setup and check for integration between Aviary and its dependency programs such as assemblers. They are excluded from standard pytest runs and the CI pipeline, but can be run as below:

pixi run -e dev pytest -v --run-expensive --run-qsub

Dependency check

Every push runs .github/workflows/pixi-dependency-check.yml. It re-solves aviary/pixi.lock against the newest packages aviary/pixi.toml allows (installing nothing) and comments the out-of-date packages on the PR the commit belongs to. Pushes without a PR get the report in the job summary only; the re-solved lock is attached to the run as an artifact.