v0.9.4

What's Changed

• Solution for pytfa.relax_dgo (sympy) by @embt in #48
• optlang GLPK interface does not handle tolerance anymore by @psalvy in #49
• Dev by @psalvy in #52

New Contributors

• @embt made their first contribution in #48

Full Changelog: 0.9.3...0.9.4

v0.9.3

859b38f - FIX: actual newer pypi version (Pierre Salvy)
393ccea - FIX: newer pypi version (Pierre Salvy)
2d426b5 - FIX: Equilibrator update + reqs for building Dockerfile (Pierre Salvy)
b8437c0 - FIX: metabolite thermo data was not recovered upon serialization (Pierre Salvy)
1e2e1e3 - MNT: removing warnings from deprecated usage of logger.warn (Pierre Salvy)
e51ca07 - MRG: Github (Pierre Salvy)
cdc661a - MRG: Bump to 0.9.2 (Pierre Salvy)
2ffb0c0 - VER: Bump to 0.9.2 (Pierre Salvy)
6f90e40 - FIX: count thermo items (Pierre Salvy)
478554e - MNT: Gurobi 9.0.1 install scripts (Pierre Salvy)
8103a43 - Allow saving of imported mat files as json (#42) (Daniel F Hernandez)
f1467b2 - Name correction (#41) (Daniel F Hernandez)
f48cfaa - MRG: merge from github (Pierre Salvy)
440f1e1 - LNT: cleanup var call in chebyshev.py (Pierre Salvy)
9de062e - ENH: Moved linearization tools from etfl to here (Pierre Salvy)
d373175 - Feat equilibrator thermodata (#38) (Jorge Carrasco)
58a0b86 - LIC: Create CLAI (Pierre Salvy)
af978e6 - FIX: two issues in chebyshev script were fixed (#37) (OmidOftadeh)
686a6a2 - Fixing a couple of minor bugs and added new variable class (#35) (RémiDhum)
f2acd48 - FIX: Compartments with more than one letter in their symbol werre assigned to None in metabolites (Pierre Salvy)
3e6c973 - MNT: various fixes for warnings and documentation (Pierre Salvy)
aa8a7fb - Chebyshev refactoring, to allow several centers and scaling factors. Also, if no variables w.r.t consider the center are provided, all of them will be summed (Pierre Salvy)
9724094 - Update LICENSE.txt (realLCSB)

v0.9.1

• FIX: wrong Python version test
• TST: optlang errors on cons.change_expr for python 3.5
• FIX: incorrect constraint replacement handling on Python 3.5
• ENH: Gurobi 8.1.1 scripts
• REQ: adding networkx for RedGEM and TQDM for cuter outputs
• MNT: corner cases
• FIX: In dict serialization, dynamic variable and constraint update (#31)
• FIX: handle obj serialization case where no objective is set, or coefficients are not native floats
• DOC: proper acknowledgements for the metaclass property technique
• ENH/FIX: GenericConstraint and GenericVariable are now abstract base classes. Also added a metaclass to enforce the setting of prefixes - any var class or cons class without a prefix will now throw an error. This should address the issues with constraint names colliding with metabolites or variable names colliding with reactions when people forget to set their prefixes.
• FIX: scaling_factor was not passed on variable reconstruction from dict form
• ENH: Adding objective serialization
• FIX: if no seed ID is present, then pass
• FIX: Tentative fix for #30
• DOC: better docstrings

RedGEM

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:

• Fixed variables/constraint removal
• Faster relaxation
• Repaired autodocumentation
• 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

0.8.1

• FIX: Catch None type in formulas

• MNT: Correctly attributed .bashrc file authorship, and commented out the deprected variable GREP_OPTIONS='--color=auto'

• ENH: Big cleanup, renaming the model._update function to model._push_queue, better relaxation with in_place option and queueing of the constraints

• TST: tests for relaxation

• FIX: try block for making the folder if it does not exist

• MNT: Adding chmod in dockerfile for gurobi install, and tqdm as requirement to have better UI

• ENH: Function to find big coefficients in solver matrix

• ENH: Adding support for scaling factors in variables and a tad faster relaxation

• FIX: missing dep tqdm in requirements.txt

• FIX: missing dep tqdm in setup.py

• ENH: hook is now an attribute of the var/cons

• change_expr method added to constraints

• FIX: change_expr of a constraint

• MNT: doc gitignore to ignore build files

• ENH: relaxation uses constraint.change_expr method

• ENH: Chebyshev center computation

• ENH: Improved solver parameters (Gurobi) for relaxation

• MNT: solution.f deprecated in cobra, changed to solution. objective_value

• ENH: Chebyshev center accepts forced inclusion of constraints

• ENH: Update doc version

• FIX: forgot to add the config module

• ENH: Faster constraint evaluation

• MNT: Removing Py 3.4 support and adding 3.7

• FIX: change dist for Py3.7 support

• ENH: Adjusted for ETFL

Cleanup and Speed update

• FIX: Catch None type in formulas

• MNT: Correctly attributed .bashrc file authorship, and commented out the deprected variable GREP_OPTIONS='--color=auto'

• ENH: Big cleanup, renaming the model._update function to model._push_queue, better relaxation with in_place option and queueing of the constraints

• TST: tests for relaxation

• FIX: try block for making the folder if it does not exist

• MNT: Adding chmod in dockerfile for gurobi install, and tqdm as requirement to have better UI

• ENH: Function to find big coefficients in solver matrix

• ENH: Adding support for scaling factors in variables and a tad faster relaxation

• FIX: missing dep tqdm in requirements.txt

• FIX: missing dep tqdm in setup.py

• ENH: hook is now an attribute of the var/cons

• change_expr method added to constraints

• FIX: change_expr of a constraint

• MNT: doc gitignore to ignore build files

• ENH: relaxation uses constraint.change_expr method

• ENH: Chebyshev center computation

• ENH: Improved solver parameters (Gurobi) for relaxation

• MNT: solution.f deprecated in cobra, changed to solution. objective_value

• ENH: Chebyshev center accepts forced inclusion of constraints

• ENH: Update doc version

• FIX: forgot to add the config module

VER: 0.7.1-b2

Added fix on mat file writing/reading

0.7.1-b1

Merge pull request #14 from EPFL-LCSB/dev

VER: v.0.7.1-b1

Bug fixes

Paper pre release 0.7.0-b2

Merge pull request #13 from EPFL-LCSB/dev

VER: Bump to 0.7.0-b2

Pypi fix

Fixed setup.py for pypi release