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Improve test coverage - currently 49.5% in bio-java core #944
Description
Test coverage is little low - covering more code would enable
- more confident refactoring. In a code-base with contributions over a long period of time there are cases where new language features can replace existing code in perhaps a more reliable way, but without tests it's sometimes hard to be sure
- greater confidence in the existing functionality
- self-documentation of methods
- identifying obsolete or unused code which could perhaps be scheduled for removal or marked deprecated?
Like covid vaccination rates 100% is unachievable but 50% is a bit on the low side, especially for a library project.
Making sure all public methods are invoked in test code would be a start, and it could be incremental.
I'll attach a PR adding some tests for some utility methods which identified 1 bug to get the ball rolling...
Activity
josemduarte commentedon Jul 26, 2021
Thanks @richarda23 . Totally agree, this has been an eternal pending issue for this project. More test coverage is badly needed.
One curiosity. How did you measure coverage?
I actually setup SonarCloud for biojava sometime ago (which does coverage too), but I'm not sure if that's accessible to everyone.
richarda23 commentedon Jul 30, 2021
For this, I just manually ran EclEmma which is an Eclipse plugin (I'm not sure if it's actually maintained any longer), but I expect most tools give similar information.
Merge pull request #951 from richarda23/crc64checksumtest
Merge pull request #957 from richarda23/core-utils-tests-part2
richarda23 commentedon Nov 17, 2021
Latest values are 75% class, 56% method, 58% line - so some improvement. Will try to add more tests to at least touch uncovered non-trivial classes
josemduarte commentedon Nov 17, 2021
That's great news. Thanks @richarda23 . FYI I did set up Sonarqube cloud in CI. But I think test coverage reporting is somehow not working.
Anyway if you are interested the Sonarqube reports are available here: https://sonarcloud.io/organizations/biojava/projects . Let me know if you can't access that and I'll see how to add accounts.
richarda23 commentedon Nov 19, 2021
Thanks Jose, I can see Sonarqube results fine. I'm tackling some classes now in biojava-core o.b.n.core.sequence package (ChromosomeSequence, ExonSequence etc) as some of these aren't covered by tests.
I've come across quite a few issues with some of the classes that I would consider bugs, for example:
What would you advise? I can raise a PR with the tests I've written, with those failing ones marked @disabled for discussion, or raise what I think are issues.
josemduarte commentedon Nov 19, 2021
That sounds like a good plan @richarda23 . Let's start a discussion based on a PR.
Merge pull request #998 from richarda23/#944-testcoverage
Merge pull request biojava#951 from richarda23/crc64checksumtest
Merge pull request biojava#957 from richarda23/core-utils-tests-part2
Merge pull request biojava#998 from richarda23/biojava#944-testcoverage