Add eelpond tests/ directory

dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system

https://dib-lab.github.io/elvers/

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Add eelpond tests/ directory #75

Closed charlesreid1 closed 5 years ago

charlesreid1 commented 5 years ago

This adds individual unit tests for each of eelpond's flags.

Not all of these flag unit tests are implemented yet, but the --dag and --dagfile and --dagpng flags are added/tested, as are the --help and --dry-run flags, to demonstrate how to do it.

This PR will modify PR #73 (Further improvements to DAG handling). I made it a separate pull request so it would be easier to review separately from the changes made in #73.

charlesreid1 commented 5 years ago

This PR is ready to go - I added placeholders for most tests, and may add a few in, but core functionality is done.

To run the tests you can run the command pytest -v from the repository and it will run all the tests. Also added this command to the .travis.yml so you'll see output from pytest in the travis test of this pull request here.

Happy to answer any questions you have and/or discuss over Slack!

ctb commented 5 years ago

Hi @charlesreid1 this looks great thank you!!

Some thoughts (not criticisms!) --

You're making use of class level unittests which I generally discourage because it raises the barrier for entry to new test writers. Not a problem, but an observation!
in particular, module level setup and teardown makes more sense for functional tests IME
we have a substantial body of test experience with command line tests that has made its way into the sourmash_tst_utils codebase in the sourmash project. I think my riposte to this PR will be to drag that infrastructure in here as it seems useful :)