Bypassing Travis because failing on GLPK not sympy anymore. See PR #49 * Dev: Incremental update (#29) * MNT: Pypi details * MNT: Adding veriable creation logs * FIX: typo * FIX: Issue #28, incorrect variable referencing * TST: adding tests for some of the analysis functions * FIX: more fixes from #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: bump to v0.9.1 * Update LICENSE.txt * Fixing a couple of minor bugs and added new variable class (#35) 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 * LIC: Create CLAI * Name correction (#41) 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 (#42) * 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 * VER: Bump to 0.9.2 * MNT: removing warnings from deprecated usage of logger.warn * FIX: metabolite thermo data was not recovered upon serialization * FIX: Equilibrator update + reqs for building Dockerfile * FIX: newer pypi version * FIX: actual newer pypi version * Update README.rst * Update utils.py * Zero import Co-authored-by: realLCSB <31034133+realLCSB@users.noreply.github.com> Co-authored-by: Pierre Salvy <psalvy@users.noreply.github.com> Co-authored-by: Pierre Salvy <pierre.salvy@epfl.ch> Co-authored-by: RémiDhum <rdhumeaux@gmail.com> Co-authored-by: Daniel F Hernandez <dan.fhg@gmail.com>

Commits

Commits on Mar 4, 2021

optlang GLPK interface does not handle tolerance anymore

Solution for pytfa.relax_dgo (sympy) (#48)

FIX: Solver tolerance handling

FIX: model-specific solver

Update lumpgem.py

optlang GLPK interface does not handle tolerance anymore (#49)

Solution for pytfa.relax_dgo (sympy) (#48 )

optlang GLPK interface does not handle tolerance anymore (#49 )