Solution for pytfa.relax_dgo (sympy) #48
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VER: 0.9 - RedGEM is Here! Thanks to a lot of work from @PtichapronRouge and @Redlinkk This release includes (finally!) a Python implementation of our redGEM[1] and lumpGEM[2] papers for systematic genome-scale metabolic model reduction. The code is still in development, so any feedback is welcome :) This version also features: * Repaired autodocumentation * Faster relaxation * Lots of code cleanup * Minor fixes [1] Ataman, Meric, et al. "redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models." PLoS computational biology 13.7 (2017): e1005444. https://doi.org/10.1371/journal.pcbi.1005444 [2] Ataman, Meric, and Vassily Hatzimanikatis. "lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites." PLoS computational biology 13.7 (2017): e1005513. https://doi.org/10.1371/journal.pcbi.1005513
Dev: Hotfix v 0.9.0-b1
* MNT: Pypi details * MNT: Adding veriable creation logs * FIX: typo * FIX: Issue EPFL-LCSB#28, incorrect variable referencing * TST: adding tests for some of the analysis functions * FIX: more fixes from EPFL-LCSB#28 * FIX: fixed transport reaction function * TST: Better tests, with a smaller model for I/O * TST/FIX: relative<- absolute paths for small_model resources * FIX: typo in paths to small_model resources for tests * VER: Bump v0.9.0-b2
VER: release v0.9.1
) Thank you @remidhum * FIX: fixed the apply_directionality function solution.raw dataframe index does not contain the fwd and bwd use variables. * ENH: added new binary variable class This class is usefull to deal with inactive reactions in a model. * ENH: deal with models without an objective function Objective function is set to Zero (symbol("0") does not work!) if there is no defined objective function * OOPS: change proper function ... * FIX: fixed the failing test As suggested, I added a check to determine what object type is passed. * MNT: solution object type testing improved
Thank you for this correction :) Since I copied this from Google scholar, maybe check that they got your name right! Cheers, Pierre
* Allow saving of imported mat files as json When importing .mat models, the membranePot type is numpy's int16. The change makes it a standard int so that it can be saved as json. * convert to float
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solution to issue #47