[pytest]
# ignore biopython's deprecation warnings about alphabet that are outside of our control
filterwarnings =
    ignore::PendingDeprecationWarning:Bio.Alphabet
    ignore:Coverage disabled

addopts =
    # do not capture any output---necessary for interactive breakpoints
    -s

    # report any tests that are skipped, xfailed, or xpassed
    -rsxX

    # report local variables with every stack trace
    -l

    # output verbosity
    # show individual test names
    -vv

    # run any doctests found in .py modules
    --doctest-modules

    # calculate test coverage for the `augur` module
    --cov=augur

    # add html coverage report generation
    --cov-report=html

    # output short traceback
    --tb=short

testpaths =
    augur/
    tests/
