nanoporetech / medaka

Sequence correction provided by ONT Research
https://nanoporetech.com
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add GHA for multiple versions of python and tensorflow using Medaka test suite #461

Closed rpetit3 closed 9 months ago

rpetit3 commented 9 months ago

This PR adds a Github Action to test Medaka for multiple versions of Python and Tensorflow. It was written to mimic the setup that is used on GitLab.

After setup, it runs the tests available from make test, which assumes they are sufficient to test whether Medaka is properly functioning with the different versions of Python and Tensorflow

Currently it tests:

Here is an example execution of this action: https://github.com/rpetit3/medaka/actions/runs/6398866670/job/17369898556

cjw85 commented 9 months ago

The release process for medaka involves QA testing steps to determine that the code can be used for both training and inference. The unit tests run by make test do not assert these properties; the furthest they go with respect to tensorflow is to check the model data can be loaded.

We test also on a matrix of linux and macOS devices with x86 and aarch64.

By the time code has makes it to GitHub medaka is considered fully tested. A GitHub action performing a subset of the testing with mutated requirements is not sufficient to ensure the mutated requirements would meet all of our internal testing procedure.