ImmutableComputableGraph code improvement + unit tests

broadinstitute / gatk-protected

Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead

BSD 3-Clause "New" or "Revised" License

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ImmutableComputableGraph code improvement + unit tests #1042

Open mbabadi opened 7 years ago

mbabadi commented 7 years ago

reviewed and restricted the access modifiers of all ICG-related classes
got rid of the functionality to hold on to old caches: whenever a cache goes out of date, the reference is immediately made null in the new ICG
completely rewrote ComputableGraphStructure in a functional style
got rid of unused and unnecessary methods
Created an ImmutableComputableGraphUtils and factored out the builder and other common methods
math equality asserts for NDArray
unit tests for ComputableGraphStructure
unit tests for ImmutableComputableGraph
unit tests for ImmutableComputableGraphUtils

mbabadi commented 7 years ago

@samuelklee can you suggest a reviewer? this is smaller than it seems :)

samuelklee commented 7 years ago

@asmirnov239, perhaps you can take a look after you issue the PR for the germline WDL? Otherwise I will take it when I get back, if you don't get to it by then.

asmirnov239 commented 7 years ago

Yes sure! I can review it after I come back Wednesday next week

droazen commented 7 years ago

@mbabadi Migration instructions for this branch: https://github.com/broadinstitute/gatk/wiki/Migrating-branches-from-gatk-protected-to-gatk

mbabadi commented 7 years ago

@asmirnov239 OK, done with the review! :) I addressed all of your comments except for one (concrete example for graph structure). Will move to main repo and merge after the tests pass.