opencobra
Fix FastCC
- [X] fix #1427
- [X] description of feature/fix
- [ ] tests added/passed
- [ ] add an entry to the next release
This brings the method in line with the paper. Still not super fast but it works. Still missing some more tests.
@Midnighter Ah sorry I didn't realise things required checking. So output-wise this fastCC version corresponds to the cobra toolbox (matlab) implementation, and both are congruent with checking for blocked reactions (as in, after removing any things that could not carry flux, no more blocked reactions are detected with other methods (one is MACAW from https://www.biorxiv.org/lookup/doi/10.1101/2024.06.24.600481 ) Code wise it looks correct, however I did not do a line by line comparison. Additionally this is all going by the idea that the Matlab implementation is indeed correct. I will run FVA to make sure that the results corroborate (although I am expecting some reactions with very "bad" stoichiometries to show some deviance).
Some small things in regards to the code (but both of you are my seniors so take them as questions) Edit: I will see if I have time for a full FVA run tomorrow or Tuesday, if that corroborates I think we are good
Thank you for your evaluation @dagl1.
Ah sorry I didn't realise things required checking.
It's not so much that it's strictly required but since most of us work alone rather than pair program, it's always better to have a second pair of eyes.
