Simplify testing #37
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Simplify testing #37
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…toy HPO are fixtures now, create predicate within the test function instead of creating a fixture.
ielis
approved these changes
Sep 11, 2023
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Hi @lnrekerle
looks good, thanks a lot!
While looking at the code, I added a few additional changes.
- I think we can consider the toy HPO and the test cohort as fixtures, right? I turned these two into fixtures.
- In predicate test, the predicates are instantiated instead of using them as fixtures. Thanks to removing the fixtures, we are left with a file with parameterized tests only. I think this structure is easier to read.
- I removed the usage of HPO to get term names when creating the test cohort. We can just hard-code those strings, it's easier to see what's going on.
- I fixed a bug where we were provided the chromosome as an
intinstead of astr(thanks PyCharm & type annotations! :) )
With all this in place, the tests (within package, outside package & doctests) pass.
Please have a look and merge if looks OK.
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Changes to testing so we do not need to access VEP, and there is less being created in the test file itself.