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BioJulia / BioFmtSpecimens

A collection of bioinformatics file format specimens to test against
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Some mmCIF files (protein structures) #23

Closed jgreener64 closed 6 years ago

jgreener64 commented 6 years ago

I am working on a mmCIF parser for BioStructures.jl, so it would be good to have some mmCIF examples in this repo to test from.

Let me know if this needs anything else!

TransGirlCodes commented 6 years ago

@jgreener64 You could add some invalid files to see if the reader correctly throws if a bad file is provided to your reader, you can do that on this PR if you want or a future one. Once you've decided, I think this can go in.

jgreener64 commented 6 years ago

Yes that's a good idea, have added some.

TransGirlCodes commented 6 years ago

:+1: Awesome, this looks good.

jgreener64 commented 6 years ago

Thanks for the merge. I guess the commit tag for get_bio_fmt_specimens in https://github.com/BioJulia/BioCore.jl/blob/master/src/Testing.jl has to be updated and a new release tagged for BioCore.jl?

This seems a hassle to do every time, could the default argument for get_bio_fmt_specimens just be master?

TransGirlCodes commented 6 years ago

Good idea, I missed that in all the renovations. Rather than pull master blindly we could have it get a latest tag, something like this: https://stackoverflow.com/questions/17414104/git-checkout-latest-tag so then we can start versioning BioFmtSpecimens. I'll implement this, this evening before bed.

jgreener64 commented 6 years ago

Yes that's a good idea.

TransGirlCodes commented 6 years ago

@jgreener64 https://github.com/BioJulia/BioCore.jl/pull/9 has a preview, it can be given a branch / tag / commit, but can by default just figure out the latest tag and use that. It also now has an override to force reinstallation - may be useful in some circumstances.