CICD updates - Githubissues

maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data

http://snakepipes.readthedocs.io

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CICD updates #906

Closed WardDeb closed 1 year ago

WardDeb commented 1 year ago

Some proposed changes to the CI tests.

snakemake 7.18.2 capped in envCI yaml (previously snakemake 6.x was pulled in, which != version in the latest releases)
include graphviz in envCI yaml ( 'dot' is not available on gh action runners, not sure why this doesn't cause issues in test_dag.sh )
strict channel priorities w/ new setup-micromamba (@adRn-s )

and the initiation of pytests for testing the workflows

tests exitcodes
tests number of jobs (rather then linecount #901), hopefully this will be more versatile across snakemake versions
test data is created as a fixture, omitting the need for the files in .ci_stuff