v2.3.1

COBREXA v2.3.1

Diff since v2.3.0

Merged pull requests:

• add a few packages to the docker (#75) (@exaexa)
• use a parallel reduction for isozyme_amount_variables (#76) (@exaexa)

v2.3.0

COBREXA v2.3.0

Diff since v2.2.2

Merged pull requests:

• implement gapfilling (#74) (@exaexa)

Closed issues:

• check if docker containers are tagged properly on releases (#46)
• Gap-filling / knock-in support (#73)

v2.2.2

COBREXA v2.2.2

Diff since v2.2.1

Merged pull requests:

• trigger CI on tags instd of releases (seems more reliable) (#47) (@exaexa)
• document ecFVA (#68) (@exaexa)
• document cyclefreeflux (#69) (@exaexa)
• refer to the @edit macro (#70) (@exaexa)
• bump v2.2.2 (#71) (@exaexa)

Closed issues:

• Feature: CycleFreeFluxes (#29)
• Docs: Refer to the possibility to use @edit in julia session to see what the code does (#52)
• MAT model not loading (#66)
• Feature: enzyme constrained FVA function (#67)

v2.2.1

COBREXA v2.2.1

Diff since v2.2.0

Merged pull requests:

• stabilize the FBC interface (#65) (@exaexa)

v2.2.0

COBREXA v2.2.0

Diff since v2.1.0

Merged pull requests:

• Fix warning box in mmdf section (#56) (@stelmo)
• document why people should use cobrexa (#59) (@exaexa)
• try switching the tutorials from glpk to highs, see what happens (#60) (@exaexa)
• improve the type&conversion handling around IO (#63) (@exaexa)

Closed issues:

• Switch all documentation over from GLPK to HiGHs (#57)
• Documentation request: Comparisons to cobrapy, COBRA.jl, RAVEN etc (#58)
• Saving StandardModel makes a model in wrong format (#62)

v2.1.0

COBREXA v2.1.0

Diff since v2.0.2

Merged pull requests:

• allow direct CTs in cFBA (#51) (@exaexa)
• implement bounds removal (helpful for sign splitting) (#54) (@exaexa)
• fix README a lil bit (#55) (@exaexa)

v2.0.2

COBREXA v2.0.2

Diff since v2.0.1

Merged pull requests:

• allow easier default bounds for community building (#50) (@exaexa)
• fix sign-splitting of unbounded values (#53) (@exaexa)

v2.0.1

COBREXA v2.0.1

Diff since v2.0.0

Merged pull requests:

• remove doc generation from a file that no longer exists (#44) (@exaexa)
• fix a corner case in community builder (#48) (@exaexa)
• dodge julia 1.10 coverage issues (#49) (@exaexa)

v2.0.0

COBREXA v2.0.0

Merged pull requests:

• backmerge the old master branch to keep history intact (#1) (@exaexa)
• separate the frontend functions from frontend-style builders and builders (#2) (@exaexa)
• fix doc paths (#3) (@exaexa)
• link everything to the docs (#4) (@exaexa)
• Small frontend cleaning things (#6) (@exaexa)
• Move log_concentration_constraints (#7) (@stelmo)
• Small changes to MMDF (#9) (@stelmo)
• Small fixes to unsigned (#10) (@stelmo)
• Functionalize constraint builder for enzymes (#11) (@stelmo)
• Implement SMoment (#12) (@stelmo)
• test&fix stuff (#15) (@exaexa)
• implement sampling (#16) (@exaexa)
• add some docstrings (#17) (@exaexa)
• add some docs (#18) (@exaexa)
• minor doc fixes (#19) (@exaexa)
• fix readme a bit (#21) (@exaexa)
• CompatHelper: bump compat for ConstraintTrees to 1, (keep existing compat) (#22) (@github-actions[bot])
• do not imply that shallow copying is supported (#23) (@exaexa)
• add the docker-building action (#24) (@exaexa)
• fix docker icon (ghcr gogogo) (#25) (@exaexa)
• update github things (#26) (@exaexa)
• fix performance of stoichiometry conversion in flux_balance_constraints (#27) (@exaexa)
• use the efficient JuMP substitutes, clean up the bounds transcription (#28) (@exaexa)
• source fixes from #20 (#30) (@exaexa)
• doc fixes from #20 (#31) (@exaexa)
• maintenance merge of the remainder of doc fixes (#33) (@exaexa)
• add the leftover misc tests (#34) (@exaexa)
• add notes about forwarding the project configuration (#36) (@exaexa)
• finalize the examples (#37) (@exaexa)
• efficiency: switch the larger sums to CT's pairwise sum (#39) (@exaexa)
• CompatHelper: bump compat for AbstractFBCModels to 0.3, (keep existing compat) (#40) (@github-actions[bot])
• add support for loading the coupling bounds from FBC (#41) (@exaexa)
• remove obsolete data loading from tests, add cph to misc.jl (#42) (@exaexa)
• hotpatch: this is no longer TODO (#43) (@exaexa)

Closed issues:

• sums should use the pairwise reduce (#38)