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VER: 0.9 - RedGEM is Here!#26

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realLCSB merged 180 commits intomasterEPFL-LCSB/pytfa:masterfrom devEPFL-LCSB/pytfa:devCopy head branch name to clipboardMay 13, 2019

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Commits

Commits on Jun 5, 2018

• FIX: Catch None type in formulas

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• Merge pull request #18 from weilandtd/read_matfiles

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Commits on Jun 29, 2018

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

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• Merge branch 'dev' of https://github.com/EPFL-LCSB/pytfa into dev

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Commits on Aug 3, 2018

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

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• TST: tests for relaxation

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Commits on Aug 6, 2018

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

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Commits on Aug 23, 2018

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

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• ENH: Function to find big coefficients in solver matrix

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Commits on Oct 30, 2018

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

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Commits on Oct 31, 2018

• FIX: missing dep tqdm in requirements.txt

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• FIX: missing dep tqdm in setup.py

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Commits on Nov 7, 2018

• Added line to .gitignore and changed rights to docker/run

  

  Benjamin Mouscadet

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• ENH : Created lumpGEM class and initializer

  

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• ENH : Added binary variables and carbon intake related constraints

  

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• DOC : Addition of documentation in lumgem/lumpgem.py

  

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Commits on Nov 8, 2018

• FIX : corrected syntax error and logic error in lumpgem/lumpgem.py

  

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• FIX : corrected syntax error and logic error in lumpgem/lumpgem.py

  

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• ENH : Started to deal with applying thermo constraints

  

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Commits on Nov 27, 2018

• FIX : fixed minor suntax errors. Added TODO flags

  

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• ENH : BBB now user-defined. Improved loading of core/ncore

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Commits on Nov 29, 2018

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

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• change_expr method added to constraints

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• FIX: change_expr of a constraint

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• MNT: doc gitignore to ignore build files

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• ENH: relaxation uses constraint.change_expr method

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• ENH: Chebyshev center computation

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Commits on Dec 12, 2018

• Added docker/temp in gitignore

  

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• ENH : Added growth rate constraints

  

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• ENH : Applied thermodynamic constraints to core reactions

  

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Commits on Jan 22, 2019

• ENH: Improved solver parameters (Gurobi) for relaxation

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

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• ENH: Chebyshev center accepts forced inclusion of constraints

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• ENH: Update doc version

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• FIX: forgot to add the config module

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Commits on Feb 4, 2019

• REF : reorganizing lumpgem structure, added clarity

  

  Benjamin Mouscadet

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• FIX : fixed binary variables creation

  

  Benjamin Mouscadet

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• ENH : added function to load GEM, based on path suffix

  

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• FIX : removed erroneous line

  

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Commits on Feb 7, 2019

• ENH: Faster constraint evaluation

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Commits on Feb 13, 2019

• Added __init_py to enable import

  

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• ENH : Added function to generate lumped biomass reaction

  

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• Added a function which generates the objective function

  

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• ENH : proper generation of binary variables and flux constraints

  

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Commits on Feb 20, 2019

• MNT : Improved perfs, using symbol_sum instead of np.sum

  

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Commits on Feb 21, 2019

• ENH : Added function to generate lumped reactions

  

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• FIX : corrected wrong use of BinaryVariable

  

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• ENH : Finalized management of core subsystems

  

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• GUI : added comments and doc

  

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• FIX : removed redundant instruction

  

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• FIX : added forgotten variable declaration

  

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Commits on Feb 22, 2019

• MNT: Removing Py 3.4 support and adding 3.7

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• FIX: change dist for Py3.7 support

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Commits on Mar 25, 2019

• FIX : corrected multiple problems with constraints

  

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Commits on Mar 26, 2019

• ENH: Add first implementation of redgem

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• DOC: Add breadth_first_search_paths_length_d docstring

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• DOC: Add is_node_allowed docstring

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• DOC: Add retrieve_all_paths docstring

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• DOC: Add retrieve_intermediate_metabolites_and_reactions docstring

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Commits on Mar 28, 2019

• ENH: Adjusted for ETFL

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Commits on Mar 29, 2019

• Merge branch 'master' into dev

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Commits on Apr 2, 2019

• DOC: Add find_min_distance_between_subsystems docstring

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• DOC: Add is_node_allowed_extracellular docstring

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• DOC: Add breadth_search_extracellular_system_paths docstring

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• DOC: Add retrieve_intermediate_extracellular_metabolites_and_reactions docstring

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• DOC: Add run_between_all_subsystems docstring

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• DOC: Add run_extracellular_system docstring

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• DOC: Add extract_sub_network docstring

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• DOC: Add run docstring

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Commits on Apr 3, 2019

• REF : changed activation_vars creation

  

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• ENH : added sinks creation

  

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Commits on Apr 5, 2019

• ENH : improve sinks management

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• ENH : added lumps creation, sinks taken into account

  

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Commits on Apr 17, 2019

• FIX : sign error in sinks

  

  Benjamin Mouscadet

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• Merge branch 'lumpgem' into dev

  

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Commits on Apr 18, 2019

• REF: Change class name from redgem to network_expansion

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Commits on Apr 24, 2019

• FIX: COBRA changed the location of the sampling functions

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• REF : removed temporary model to compute lump

  

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• REF : TFA model must be passed as argument, is not built by lumpgem

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• DOC : added DOCSTRING

  

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• DOC : generated last missing DOCSTRINGs

  

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• FIX : removed mcore list, was useless

  

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• ENH : added timeout for optimization

  

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• ENH : added the sink to the lumped reaction

  

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• FIX : changed the default timeout limit

  

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• FIX : corrected wrong parameter name in DOCSTRING

  

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• Merge branch 'lumpgem' into dev

  

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• Merge branch 'redgem_master' into dev

  

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• Merge branch 'redgem_master' into dev

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• Revert "REF: Change class name from redgem to network_expansion"

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Commits on Apr 25, 2019

• FIX: LFS hook reset

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• Merge branch 'dev' of https://c4science.ch/source/pytfa into dev

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Commits on Apr 26, 2019

• DOC: Autodoc repaired

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• Merge branch 'dev' of https://github.com/EPFL-LCSB/pytfa into dev

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• MRG: Doc

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Commits on May 1, 2019

• REF : Moved lumpgem code into redgem folmder, with NetworkExpansion

  

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• ENH : Added return to run method in NetworkExpansion class

  

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• REF : removed deepcopy of the gem in the NetworkExpansion class

  

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• ENH : added redgem class - wrapper of the NetworkExpansion and Lumpgem

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• ENH : added automatic extraction of inorganics

  

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• MNT: Clean up network_expansion

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• MNT: Remove duplicate code

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• FIX: Remove unused imports

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• FIX: Multiple fix

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• REF: Update parameters for network expansion

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• FIX: Remove unused parameter

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• FIX: Remove unused attributes

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• Revert "FIX: Remove unused attributes"

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• FIX: Remove unused attributes in network_expansion

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• FIX: Remove unused attributes in network_expansion

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• REF: Change subsystem_names to core_subsystems

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• REF: Change params order and default value for redgem

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• FIX: Fix wrong function call

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• ENH: Add test script

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• ENH: added yaml parameters file for redgem

  

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• FIX: corrected wrong model use

  

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• FIX: typo in extracellular_systems and extract_inorganics method

  

  Benjamin Mouscadet

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• FIX: fixed parameter name in yaml file

  

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• FIX: Sanitize user input

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Commits on May 2, 2019

• REF: Use tuple for cofactor_pairs

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• REF: Better name for parameter

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• FIX: Use gem instead of reduced gem for lumpgem

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• FIX: Remove unused parameters in test script

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• ENH: Combine results to create final network

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• ENH: added exceptions when solver status is infeasible

  

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• ENH: added tolerance choice in yaml parameter file

  

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• FIX: Run lumping before expansion because expansion modifies the gem

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• FIX: Fix typo

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Commits on May 3, 2019

• FIX: Init HRSampler in GeneralizedHRSampler

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• ENH : added default value to timeout when not set in yaml parameters

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• FIX: typo

  

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• FIX: sanitize input in yaml parameters file

  

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• FIX: corrected sum that was leading to MemoryError in Cobra

  

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• ENH: added force_solve parameter, to ignore "infeasible" solver status

  

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• FIX: corrected attribute name

  

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• ENH: modified id of lumps reactions

  

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Commits on May 6, 2019

• TST: More robust paths

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• TST: more realistic N/D parameters, and corrected cofactor pairs ids

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• WIP: cleanup round

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• Merge pull request #25 from remidhum/dev

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• Merge commit '05142bc' into redgem_merge

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• WIP: merge lumpgem fixes

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• WIP: Cleanup and Merge.

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Commits on May 7, 2019

• MNT: Remove old comments

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• ENH: debugging scripts

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• FIX: Lumping after intra subsystem expansion, adding exchange reactions after lump addition, Inorganics correction (find_inorganics was previously finding organics)

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• Merge branch 'redgem_merge' of https://c4science.ch/source/pytfa into redgem_merge

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Commits on May 8, 2019

• MNT: moving subclass discovery function from ETFL

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• ENH: working test_redgem. Changed the constraint formulation, added a trim of fluxes below solver sensitivity

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• REF: moving around functions

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• ENH: Logger in redgem

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• FIX: decreased log level of timeit, for less clutter

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• Merge branch 'dev' into redgem_merge

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• FIX: decreased log level of thermo constraints/variables not created, for less clutter

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• Merge branch 'dev' into redgem_merge

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• ENH: Transports are considered independently, cute progress bar

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• BUG: FVA blocked reaction detection not working

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Commits on May 9, 2019

• ENH: rounding the stoichiometric coeffs according to solver accuracy

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• ENH: Added a YAML flag for removing blocked reactions, fixed the procedure by using pyTFA VA instead of cobra's, prepared the code for other lumping methods

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• WIP: Find all lumps of minimal length + p

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Commits on May 10, 2019

• ENH: Capacity to calculate lumps of min length + p

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• REF/ENH : Cleaned up redgem init and replaced carbon uptake YAML argument by medium override definition

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• Merge branch 'dev' of https://github.com/EPFL-LCSB/pytfa into dev

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• VER: BUMP version 0.9

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• TST: Detects if TRAVIS CI env, to spend less time on lumps in redgem test

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• FIX: typo

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• FIX: initial biomass trim was infeasible

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• ENH: redgem tutorial

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• FIX: Reducing even more the bio_rxn as GLPK seems to struggle on Travis

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• FIX: Typo

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• FIX: Typo - I should sleep more

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• FIX: Cannot figure out if optimization is too long or if the test does not know it is being run on Travis

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• ENH: better redgem tutorial

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• TST: Looks like it is a computational power limitation. Allowing the test to skip while working on a solution

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• Merge branch 'master' into dev

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Commits on May 13, 2019

• MNT: Downgrade warnings to debug for metabolites with missing IDs

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• TST: Easier test case for CI

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• FIX: the lumping was iterating on metabolites rather than reactans. Adding a home-made function for reaction summing to try to avoid gpr eval memory issues

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• REF: changed the lump handling, removed all pointers to objetc belonging to models in favor of a lightweight dict_based method.

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• ENH: allows the user to choose which constraint method to use to calculate lumps

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