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Saturday, December 26, 2020

Bacting: Code coverage, JaCoCo, codecov.io, and API coverage

          A good bit of work to do.      

I have been fan of code coverage. When combined with (unit) testing, it indicates which code of your software has been run and therefore tested. Some 15 years ago, when I worked on making the Chemistry Development Kit code base more stable, I worked on various things: modularization, documentation, (unit) testing. I explored the option in Java. I even extended PMD with CDK-specific unit tests. And my StackOverflow question on JUnit test dependencies still gives me karma points :)

Fast forward to now. Routinely building software has become quite common place as is unit testing. The tools to support this have changed the field. And tools come and go. Travis-CI will became rare for open science projects, but where GitHub replaced SourceForge, GitHub Actions step it.

But I submitted a manuscript to the Journal of Open Source Software, to learn from their submission system (which is open and just plain awesome). One reviewer urged me to test the test coverage of my code and give me a pointer to JaCoCo and codecov.io. I am not sure if the CDK used JaCoCo in the past too, but getting all info on a website was not trivial, tho we got that done. Rajarshi may remember that. but with continuous building and codecov.io it is automatically available on a website. With every commit. Cool!

However, autumn had already started and I had plenty of project work to finish. But it is holiday now, and I could start working on the reviewer comments. It turned out the pointers were enough, and I got codecov.io working for Bacting. Not being tested with a test suite does not mean it is not tested at all. I use Bacting daily, and this use will only grow in the coming year.

That brings me to another reviewer question. How much of the Bioclipse 2 API does Bacting support. Now, that question is a bit tricky. There is the code Bioclipse 2.6 release (doi:10.1186/1471-2105-10-397), but there were a few dozen plugins with many more Bioclipse managers. So, I checked what managers I had locally checked out and created a GitHub Project for this with various columns. And for each manager I have (or want) in Bacting, I created an issue with checkboxes, one for each method to implement. And that looks like this:


I really hope the Maastricht University GitLab will become more user visible in the next year.

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