INCATools / ontology-access-kit

Ontology Access Kit: A python library and command line application for working with ontologies
https://incatools.github.io/ontology-access-kit/
Apache License 2.0
108 stars 23 forks source link

Can't run tests without LinkML #665

Closed cthoyt closed 3 months ago

cthoyt commented 9 months ago

I installed oak with pip install -e .[tests] but it appears that linkml is a requirement for tests and is not installed. The solution is to add an optional dependency for linkml in the tests group, but I don't know how to do this with poetry.

cmungall commented 7 months ago

I'd recommend using poetry for running the test suite.

Currently the test dependencies (including linkml) are in dev-dependencies. I had assumed this was fairly standard for poetry, but the docs seem to suggest both: https://python-poetry.org/docs/master/managing-dependencies/