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fraenkel-lab / OmicsIntegrator

This repository is the working directory for the Garnet-Forest bundle of python scripts for analyzing diverse forms of 'omic' data in a network context.
http://fraenkel.mit.edu/omicsintegrator
BSD 2-Clause "Simplified" License
31 stars 21 forks source link

In need of test framework #1

Closed sgosline closed 7 years ago

sgosline commented 9 years ago

We currently have a series of example scripts that could serve as a basis for a test platform. It would be great to see these scripts be called and their results measured to ensure that future modifications to the code base do not alter the ability to perform all features.

agitter commented 9 years ago

I will work on a basic test platform with a student. We'll look into Python's unittest framework first, with the goal of running the test-tgfb-data.py analysis and checking whether the output files match previously saved reference files.

agitter commented 9 years ago

We're moving forward with pytest instead of unittest for testing. We'll submit a pull request with a simple unit test as a proof-of-concept before writing the full end-to-end test.

agitter commented 8 years ago

Use cases to cover in integration tests:

A test case for Forest with protein data only is nearly ready.

agitter commented 8 years ago

The Forest-only test case has been added. We could use this as a model for a Garnet-only or Garnet+Forest test case in the future.

agitter commented 8 years ago

Pull request #14 from @aabaker99 enabled Travis CI continuous integration testing for our Forest unit tests.

agitter commented 7 years ago

Pull request #25 adds a Garnet integration test. There is a lot of room to further improve our testing, but I think we can close this issue once #25 is merged because we'll have end-to-end tests for Garnet and Forest (individually, not run back-to-back).

AmandaKedaigle commented 7 years ago

Agreed, thanks to everyone who worked on these important tests!