Recent Releases of COBREXA
COBREXA - v2.9.0
COBREXA v2.9.0
Merged pull requests: - minor wording fixes in ecfba tutorial (#91) (@exaexa) - add a bit of documentation about missing kcats (#94) (@exaexa) - fix nfilled and add costfilled in gapfillingconstraints (#97) (@exaexa) - medium optimizations (#98) (@exaexa)
Closed issues: - Feature request: allowing NaN values in kcat entries for enzyme-constrained models (#93)
- Julia
Published by github-actions[bot] 8 months ago
COBREXA - v2.5.0
COBREXA v2.5.0
Merged pull requests: - small cleaning (#79) (@exaexa) - add an explicit warning about what happens if people gapfill pseudoreactions (#80) (@exaexa) - Generalize enzymes (#82) (@stelmo)
Closed issues: - Gap filling produces nonempty result when filling a model that is already feasible (#78)
- Julia
Published by github-actions[bot] about 1 year ago
COBREXA - v2.2.2
COBREXA v2.2.2
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)
- Julia
Published by github-actions[bot] over 1 year ago
COBREXA - v2.2.0
COBREXA v2.2.0
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)
- Julia
Published by github-actions[bot] over 1 year ago
COBREXA - 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 fluxbalanceconstraints (#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)
- Julia
Published by github-actions[bot] over 1 year ago