v1.5.1

COBREXA v1.5.1

Diff since v1.5.0

Merged pull requests:

• make the semantics cut (#776) (@exaexa)
• fix sparsevec (#783) (@exaexa)

v1.5.0

COBREXA v1.5.0

Diff since v1.4.4

Closed issues:

• Model type overlay that describes the genetic manipulation (#552)
• max_min_driving_force and moment should be a ModelWrapper (#614)
• JSON model format incompatible with escher (#758)

Merged pull requests:

• pFBA pipe (#747) (@stelmo)
• Add test for multiple capacity enzyme bounds (#748) (@stelmo)
• Add another convenience constructor for enzyme constrained models (#749) (@stelmo)
• Add model annotation details (#750) (@stelmo)
• port GRR parsing to 2.0, avoid DNF complexity explosions (#752) (@exaexa)
• remove and clean up GeneAssociations alias (#753) (@exaexa)
• Remove unnecessary docstrings (#754) (@stelmo)
• Fix model accessor bugs (#755) (@stelmo)
• Return enzyme concentrations in useful units (#757) (@stelmo)
• Make kwargs for convenience enzyme constrained consistent (#759) (@stelmo)
• Add plural to change_bounds and add change_constraints (#760) (@stelmo)
• Fix and extend reconstruction functions and pipes for objectmodel (#762) (@stelmo)
• Result wrapper (#763) (@exaexa)
• Fix cFBA implementation (#764) (@stelmo)
• Add basic show for ModelWithResult (#766) (@stelmo)
• split wrappers off to a separate module (#767) (@exaexa)
• unify L2-like QP handling (#769) (@exaexa)
• Make kwarg plural (#770) (@stelmo)
• Rename GeneAssociation file (#771) (@stelmo)
• Extend simplified enzyme model to include multiple capacity constraints (#772) (@stelmo)
• implement wrappy pFBA using the normal L2 wrappers (#773) (@exaexa)
• Fix EqualGrowthCommunityModel accessors (#774) (@stelmo)
• implement expression-limited fluxes (E-Flux like algorihm) (#777) (@exaexa)
• fixed merge of #777 (#778) (@exaexa)
• Develop → master merge for 1.5.0 (#779) (@exaexa)
• fix filename (#781) (@exaexa)

v1.4.4

COBREXA v1.4.4

Diff since v1.4.3

Closed issues:

• Incorrect gene reaction rule parsing (#711)

Merged pull requests:

• Turn MMDF analysis into a wrapper (#699) (@stelmo)
• Add convenience macro that loads all the functions in modules (#716) (@stelmo)
• Implement a variant of Constrained Allocation Flux Balance Analysis (#717) (@stelmo)
• Delete reaction overloads (#718) (@stelmo)
• Rename GeckoModel to EnzymeConstrainedModel (#719) (@stelmo)
• Rename SMomentModel to SimplifiedEnzymeConstrainedModel (#720) (@stelmo)
• Rename reaction_gene_association to reaction_gene_associations (#721) (@stelmo)
• Replace uses of :reverse with :backward to be consistent (#722) (@stelmo)
• Rename file (#723) (@stelmo)
• Add accessors for enzyme associated data (#724) (@stelmo)
• Remove crowding (obsolete via SMOMENT) (#725) (@stelmo)
• remove obsolete print_banner() from the SIF container (#727) (@exaexa)
• LICENSE file type was not markdown (#728) (@exaexa)
• CompatHelper: bump compat for SBML to 1, (keep existing compat) (#729) (@github-actions[bot])
• remove a config from local CI (#730) (@exaexa)
• add an actual GPA/GRR to DNF parser (#731) (@exaexa)
• Fix test bugs in new parser (#732) (@stelmo)
• GPA ordering fix (#733) (@exaexa)
• fix GRA compat once more (and hopefully the last time) (#734) (@exaexa)
• extensible variable semantics (#735) (@exaexa)
• Q-opt support (#736) (@exaexa)
• version bump for 1.4.4 (#737) (@exaexa)
• Develop → master merge for 1.4.4 (#738) (@exaexa)
• Add more reconstruction functions to ObjectModel (#739) (@stelmo)
• Remove switching argument for reaction constructors (#740) (@stelmo)
• Remove double s from enzyme semantics (#741) (@stelmo)
• Add some more semantics to EnzymeConstrainedModel (#742) (@stelmo)
• Add balance accessor to community model (#743) (@stelmo)
• clean up SBML unit-error throwing (#744) (@exaexa)
• Homogenize bound kwargs (#746) (@stelmo)

v1.4.3

COBREXA v1.4.3

Diff since v1.4.2

Merged pull requests:

• freeze SBML dictionary ordering (#706) (@exaexa)
• bump hotfix release 1.4.3 (#707) (@exaexa)
• Develop → master merge for 1.4.3 (#708) (@exaexa)

v1.4.2

COBREXA v1.4.2

Diff since v1.4.1

Closed issues:

• Consistent argument/kwarg naming (#623)
• Add stoichiometry to gene reaction rules (#655)
• Organize everything into submodules (#663)
• .mat model not loading (#691)

Merged pull requests:

• Use smaller organized namespaces. (#674) (@exaexa)
• switch tests julia from 1.7 to 1.8 (#680) (@exaexa)
• Delete moment algorithm modification (#686) (@stelmo)
• Rename MetabolicModel to AbstractMetabolicModel (#687) (@stelmo)
• Add ext option (#688) (@josePereiro)
• Update gene associations (#689) (@stelmo)
• Indent submodule definitions (#690) (@exaexa)
• fix loading of matlab version of yeast GEM (#692) (@exaexa)
• sync julia version with artenolis (#693) (@exaexa)
• Extend community model (#696) (@stelmo)
• Remove @add_reactions (#697) (@stelmo)
• use a softer failure when unit annotations are missing in SBML (#701) (@exaexa)
• use the latest recommended Julia CI on master+develop for generating … (#702) (@exaexa)
• Release 1.4.2 (#703) (@exaexa)
• Develop → master merge for v1.4.2 (#704) (@exaexa)
• upgrade julia version on ci and set mac path (#705) (@laurentheirendt)

v1.4.1

COBREXA v1.4.1

Diff since v1.4.0

Closed issues:

• generate FROG reports (models reproducibility) (#609)
• pFBA does not fail gracefully (#625)
• Gapfilling not giving any solutions (#653)
• Drop OSQP and use Clarabel instead for QPs (#666)

Merged pull requests:

• remove lots of lb/ub shortcuts from API (#637) (@exaexa)
• Remove the banner (#649) (@stelmo)
• Add some constructors (#654) (@stelmo)
• hotfix: bump CompatHelper version to work with 1.8 (#656) (@exaexa)
• Update compathelper CI script (#658) (@exaexa)
• Fix pFBA issue with return type nothing (#659) (@stelmo)
• Finally add DocStringExtensions 🥳 (#661) (@stelmo)
• add an explanation of what happens when you gapfill a feasible model (#662) (@exaexa)
• Add SBO terms (#667) (@stelmo)
• use Clarabel instd of OSQP (#669) (@exaexa)
• CompatHelper: bump compat for SBML to 1, (keep existing compat) (#670) (@github-actions[bot])
• Make the SBML annotations work just like with JSON models (#676) (@exaexa)
• docs: reflect the solver change in Project.toml (#677) (@exaexa)
• fix docbuild: JuMP MIN_SENSE and MAX_SENSE disappeared (#679) (@exaexa)
• remove polish parameter specific to osqp (#681) (@exaexa)
• Develop → master merge for v1.4.1 (#682) (@exaexa)
• backmerge master changes to develop to resolve merge conflicts (#683) (@exaexa)

v1.4.0

COBREXA v1.4.0

Diff since v1.3.1

Closed issues:

• Prettyprinting should not hide any information (#77)
• change the auto-formatting mechanism (#322)
• Switch to ReadableRegex (#601)
• Progress meter for long running ops (#626)
• fast mmap()able model type (#641)

Merged pull requests:

• Fix small error with gapfill modifications (#622) (@stelmo)
• fix example formatting in add_moment_constraints (#624) (@exaexa)
• sampling improvements (#627) (@exaexa)
• docs reorganization (#628) (@exaexa)
• Add examples (#631) (@stelmo)
• allow hyphens in gene names in GRRs (#634) (@exaexa)
• Merge autoformatter improvements from SBML.jl (#635) (@exaexa)
• make reaction_atom_balance have generic MetabolicModel as type (#636) (@HettieC)
• support SBML writing (#639) (@exaexa)
• HDF5 model storage and fast memory mapping support (#642) (@exaexa)
• Adds more details to mmdf and gecko (#643) (@stelmo)
• extend the autoformatting priveleges a bit (#644) (@exaexa)
• unify the reference section with the rest of the docs (#645) (@exaexa)
• Small docs fixes (#646) (@stelmo)
• Add better links (#647) (@stelmo)
• version bump for 1.4 (#650) (@exaexa)
• Develop → master merge for 1.4 (#651) (@exaexa)

v1.3.1

COBREXA v1.3.1

Diff since v1.3.0

Closed issues:

• generate and deploy docker & singularity containers (#68)
• Implement GECKO (#574)
• Implement sMOMENT (#575)
• fix import of yeast GEM models (#600)
• use asyncmap instead of map to collect information from workers (#603)

Merged pull requests:

• switch to asyncmap for fetching results from multiple workers (#610) (@exaexa)
• load more metadata from models (#611) (@exaexa)
• Update mods to handle gecko model (#612) (@stelmo)
• Check format using github actions, implement the /format command (#615) (@exaexa)
• Explain reactions better (#616) (@exaexa)
• Add a gap filling algorithm (#617) (@stelmo)
• clean up the gapfilling code (#618) (@exaexa)
• bemp version 1.3.1 (#619) (@exaexa)
• Develop→master for 1.3.1 (#620) (@exaexa)
• fix documentation issues and warnings (#621) (@exaexa)

v1.3.0

COBREXA v1.3.0

Diff since v1.2.3

Closed issues:

• Moment modification deletes ATPM bounds (#542)

Merged pull requests:

• banner again! (#585) (@exaexa)
• Implement GECKO and SMOMENT (#586) (@stelmo)
• CompatHelper: bump compat for "JuMP" to "0.23" (#587) (@github-actions[bot])
• prepare a macro for inheriting the accessors for model data (#588) (@exaexa)
• Fixing typos (#589) (@htpusa)
• Fix argument forwarding in find_biomass_reaction_ids (#590) (@exaexa)
• CompatHelper: bump compat for "DistributedData" to "0.2" (#593) (@github-actions[bot])
• CompatHelper: bump compat for "JuMP" to "1" (#594) (@github-actions[bot])
• Add deprecation warning (#595) (@stelmo)
• Systematic model wrappers (#597) (@exaexa)
• make stoichiometries easily extensible to encompass more complicated analyses (#598) (@exaexa)
• Add some accessors for MATModel (#602) (@stelmo)
• "minor" fixes for enzyme-constrained models (#604) (@exaexa)
• Small fixes to enzyme PR (#605) (@stelmo)
• Small fixes (#606) (@stelmo)
• Bump version 1.3.0 (#607) (@stelmo)
• develop -> master for v1.3.0 (#608) (@stelmo)

v1.2.3

COBREXA v1.2.3

Diff since v1.2.2

Merged pull requests:

• Fix small error (#579) (@stelmo)
• prevent more directional typos (#580) (@exaexa)
• fix pretty reaction builders (#581) (@exaexa)
• docker build from gitlab (#582) (@exaexa)
• bump version 1.2.3 (#583) (@exaexa)
• Develop → master merge for 1.2.3 (#584) (@exaexa)