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jayjaybillings / fire

Repository for the Fire framework
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Refactor the flux map construction code #10

Open jayjaybillings opened 7 years ago

jayjaybillings commented 7 years ago

The ReactionNetwork::buildFluxMaps() operation needs to be refactored. It is based on the original routine from FERN. It is all sorts of mangled and tangled.

jayjaybillings commented 7 years ago

This should include enhancing the test code, which right now can't be that thorough because of the lack of design of the original code in FERN. All of the flux maps are currently just a bunch of big arrays that cannot be easily checked without writing a test that will just need to be rewritten. That is, the tests would only be about self-consistency and not correctness.