Need test coverage of Sims and Groups. about mdsynthesis HOT 12 CLOSED

Thoughts on using the MDAnalysisTests package for testing real PSF/DCDs?

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Good idea, since it saves us having to package our own. I'll add MDAnalysisTests as a dependency for the tests on Travis. Will add this to the docs as well.

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Hey David, is this still open?

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It is. I've been hammering on #16 and #8 over the past few weeks (see 8d11c58 on the member_aggs branch; required some overhauls, and still working on it), so haven't spent much time on improving this one.

The Container API has enough tests for now, but neither Sim nor Group have tests for their unique components (universes and selections; members). If you're interested in adding some, I'd suggest working from here. This is one of the issues holding back a first release, so any help would certainly speed things along!

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Ok I'll have a go, I had a read of the current tests, pytest looks very cool to use!

Have you looked at including coverage in your CI? It took me maybe 5 lines and 1 website signup to get it working on MDAnalysis

richardjgowers/mdanalysis@9fb0869

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Ok I'll have a go, I had a read of the current tests, pytest looks very cool to use!

Thanks! Yeah, its implementation of fixtures takes a little getting used to, but it makes writing tests for large varieties of inputs, including permutations, a bit less painful. The tests for data storage and retrieval are a good example.

I'm trying out codecov for test coverage. Just updated the development branch with the appropriate includes in .travis.yml. In addition to coverage, I also added pep8 checks to the test execution line, and this spat out a whole slew of violations. cracks knuckles

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The good news is that we so far have 42% test coverage according to pytest. Once we have coverage of Sim- and Group-specific elements, this will probably rise to over 70%.

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Make that 47% test coverage after I removed some old unused code. Beyond code coverage, however, we'll also need stress tests of file locking mechanisms for both state files and data. The tricky part with those is that they'll require tests using multiprocessing, and I'm not sure if/how that's done with pytest. It's a separate issue (#22), however.

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We're now up to 62% test coverage. I merged the major changes I made to how Group works underneath the hood into master, and along with this were some changes to both the Sim and Group state file schema. As such, old Sim and Group state files won't work anymore; I worked a bit on building a conversion script, but I wasn't sure it was worth the time. In the future, changes to schema will only occur across major releases, and we'll have code built into these Containers to handle updating their schema internally based on stored version numbers.

There's still Sim.selections to test, along with the features of Bundle (new!). I'll be working to close the gaps in the coming days.

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I think the easiest jump in coverage looks like core/aggregators, so I'll make some for them.

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Moving this to 0.5.1; quite a bit of progress has been made, and the gaps will be filled in there.

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This is pretty well done. There may be some cracks yet, but they're not really hiding out in Sims and Groups.

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