Add tests, minor refactors - Githubissues

JudeWells / chainsaw

MIT License

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Add tests, minor refactors #1

Closed sillitoe closed 1 year ago

sillitoe commented 1 year ago

Adds unit / e2e tests and makes the code a bit more portable / testable

allow stride path to be specified with ENV
adds end-to-end tests (running in isolated tmp dir)
add some unit tests (and a couple of minor refactors to make unit tests easier)
parses results into PredictionResult class (uses pydantic to catch errors)
adjusts the output format (1 record per line)
adds GitHub actions to automatically check tests (pushes to main and PR)
fix: silent error on renum_pdb_file when running in different directory

Notes:

bumps the version of all libraries to latest - pandas, numpy, etc (required when using more recent pythons)