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develop -> master for v1.3.0#608

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exaexa merged 125 commits intomasterLCSB-BioCore/COBREXA.jl:masterfrom developLCSB-BioCore/COBREXA.jl:developCopy head branch name to clipboardApr 27, 2022

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Commits

Commits on Feb 18, 2022

• Revert "Revert "display banner consistently at each import""

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• add sensible conditions to banner display

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• Merge pull request #585 from LCSB-BioCore/mk-ununbanner

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Commits on Feb 26, 2022

• CompatHelper: bump compat for "JuMP" to "0.23"

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Commits on Mar 7, 2022

• Merge pull request #587 from LCSB-BioCore/compathelper/new_version/2022-02-26-00-18-33-280-879680524

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Commits on Mar 8, 2022

• prepare a macro for inheriting the accessors

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Commits on Mar 11, 2022

• quickstart example should work now, word missing in documentation

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Commits on Mar 13, 2022

• Merge pull request #589 from LCSB-BioCore/tp-typos

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Commits on Mar 16, 2022

• Merge pull request #588 from LCSB-BioCore/mk-generalize-wrappers

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Commits on Mar 17, 2022

• fix argument forwarding in find_biomass_reaction_ids

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• realign one comment

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• Merge pull request #590 from LCSB-BioCore/mk-looks-like-params-semicolon

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Commits on Mar 23, 2022

• CompatHelper: bump compat for "DistributedData" to "0.2"

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• Merge pull request #593 from LCSB-BioCore/compathelper/new_version/2022-03-23-00-22-45-699-2123585176

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Commits on Mar 25, 2022

• CompatHelper: bump compat for "JuMP" to "1"

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• Merge pull request #594 from LCSB-BioCore/compathelper/new_version/2022-03-25-00-19-55-239-2739295806

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Commits on Apr 1, 2022

• add deprecation warning

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• format

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• Merge pull request #595 from LCSB-BioCore/mo-depr-moment

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Commits on Apr 3, 2022

• make the model wrapping a bit more systematic

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• add some forgotten functions to CoreModel and CoreModelCoupled

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• reimagine CoreModelCoupled as a wrapper

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• make the deprecation warning more specific

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• Merge pull request #597 from LCSB-BioCore/mk-systematic-wrappers

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• abstract out a function for converting optimizer solutions to fluxes

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• fixup: flux_vec and flux_dict use solution_flux

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Commits on Apr 4, 2022

• side-commit: remove a bit of a freshly discovered trailing whitespace

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• redo CoreModelCoupled as a more generic CoreCoupling

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• generalize some of the CMC modifications to CoreCoupling

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• fix a blatant inconsistency in logo coloring

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• materialize the reactions-to-flux mapping in accessors

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Commits on Apr 5, 2022

• clean up MetabolicModel

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• fix type of genes(::CoreModel)

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• fix ModelWrapper gene accessors

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• fix gene enumeration in CoreModel

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• adjust flux sampling to new fluxes() vs reactions()

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• flux_variability_analysis now works on fluxes instead of bare reactions

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Commits on Apr 6, 2022

• Merge pull request #598 from LCSB-BioCore/mk-extensible-stoichiometries

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Commits on Apr 8, 2022

• update accessors

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• add gets and update accessors

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• format

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• Merge pull request #602 from LCSB-BioCore/mo-mat-import

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• added gecko and test

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• added smoment and small fixes to gecko

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• format

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• update method signatures

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• make explicit model change

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• fix test

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• reduce bound, unnecessarily high

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• gecko streamlined

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• fixed enzyme constrained problems

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• format

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• added data source

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• obliterate traling whitespace

  

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• add isozyme funct

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• format and fix

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• update kwarg

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• fix another kwarg

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• fix kwargs in tests

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• more kwargs

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• fix has reaction edge case

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• fixup gecko

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Commits on Apr 10, 2022

• add smoment and fixup gecko

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• format

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Commits on Apr 11, 2022

• fix args

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• fix func name

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Commits on Apr 12, 2022

• fix funcs more

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• implement reviews

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• format and fix test

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• get rid of kwargs

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• fix flux_dict error

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• fix the last formatting error

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• clean up trailing blanks

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• optimization sense should be passed to FBA via modifications

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• add an example for flux_dict

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• clean up struct Isozyme

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• clean up solver stuff

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• reimplement sMOMENT as a wrapper around the model

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• mangle accordingly.

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• fix format

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• forgot a file

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• improve guessing of smoment coupling size

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• prepare make_smoment_model for overloading

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• many small smoment fixes that should make it just work

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• someone transposed the matrix for us!

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• document make_smoment_model

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Commits on Apr 13, 2022

• gecko stage 1 (still TODO: the mass fraction coupling)

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• fixup

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• fixups vol 2

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• works partially

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• add gecko.jl (finally!)

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• switch gecko to gene-based mass groups (seems simpler)

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• remove unused code, sprinkle TODOs

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Commits on Apr 14, 2022

• remove the unnecessary reaction coupling from sMOMENT

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• formatting

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• fixup: constructors

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• simplify gecko a bit (remove unnecessary reaction arms)

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• add a shortcut for extracting sMOMENT mass utilization

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• more cleaning

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• please add function types

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Commits on Apr 15, 2022

• regroup enzymatic model utilities, remove bounds-changing functions

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• clean up

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• fix smoment syntax

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Commits on Apr 18, 2022

• Minor docstring fixes

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• fix errors

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Commits on Apr 19, 2022

• fix test kwargs

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• fix more kwargs

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• remove relaxed arms

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• remove relaxed arm test

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• make gecko resemble published version

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• fixed gecko

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• format

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  6a53937

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• format again

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• fix model

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• add more docstrings

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• format again

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Commits on Apr 20, 2022

• implement reviews

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• more comments

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• Merge pull request #605 from LCSB-BioCore/mo-mk-gecko-etc

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• Merge pull request #604 from LCSB-BioCore/mk-gecko-etc

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• Merge pull request #586 from LCSB-BioCore/mo-enzyme-constrained

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Commits on Apr 27, 2022

• small fixes

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• Merge pull request #606 from LCSB-BioCore/mo-small-fixes

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• bump version

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• Merge pull request #607 from LCSB-BioCore/mo-bump

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