Add pytest to deps and CI

austinorr commented 2 months ago

This PR adds pytest to the optional project dependencies, and should get automated tests passing in CI (partially, there's another PR coming that fixes the packaging/install so that the cli works again).

austinorr commented 1 month ago

@PaulDudaRESPEC please review. This PR brings test coverage for all code in the project up to 70%. The failing last cli test looks like an additional packaging detail regarding the data files, but tests pass!

austinorr commented 1 month ago

@PaulDudaRESPEC also, as of this PR you have the option to adopt a policy of having all PRs be required to pass the test suite (which will grow and change) in order for you to approve and merge. Your review will have to include a check to ensure the PR didn’t somehow make the test easier, haha.

should you adopt such a policy, and I think you should, let’s begin with this PR and hold it until I fix the data package bug. I think I know the fix.

austinorr commented 1 month ago

@PaulDudaRESPEC This PR completes the following:

[x] support pandas v1.5-2.0
- [x] cleared as many warnings and errors as possible on both versions.
- [ ] TODO: in readUCI.py df = df.apply(pd.to_numeric, errors='ignore') 'ignore' is deprecated. implementing fix to use 'raise' or 'coerce' may require some refactoring. I tested 'coerce' but it breaks things.
[x] CI test support for pandas 1.5-2.0
[x] parallel CI for lint, pytest suite, install + command line invocation.
[ ] TODO: find much shorter command line test case
[x] support python 3.9+, each with CI test for test suite and install.
[x] run coverage on recommended python (3.11). This is ready to integrate with coverage trackers like codecov or smokeshow

respec / HSPsquared

Add pytest to deps and CI #156