pytest.ini

[pytest]
log_cli = true
# Default (fast) tier: everything except `slow`. The slow tier is the end-to-end VCF
# parsing/annotation and est-sfs comparisons; run the whole suite with `make test-full`.
addopts = -m "not slow" -s
testpaths = testing
filterwarnings =
    # the VCF-Zarr layout requires fixed-length strings, whose zarr-v3 spec is still unstable; not actionable
    ignore::zarr.errors.UnstableSpecificationWarning
markers =
    slow: end-to-end VCF parsing/annotation and est-sfs binary comparisons; excluded from the default fast tier
    very_slow: subset of `slow` whose data/binaries are NOT committed (est-sfs binary, SnpEff/VEP outputs, Papio/human-HGDP/full Betula datasets) and must be produced by an external build or the snakemake pipeline; excluded from the coverage run
    inference: heavier integration tests over committed fixtures
    serial