**Closed issues:**
- storage of large model (#2)
- i/o of SBML files (#3)
- Expand IO (MAT) (#4)
- Migration to github.com (#6)
- `loadModel` is broken (#12)
- Some SBML formats (level 3?) are not read correctly (#18)
- Wildcard documentation building (#26)
- Name functions consistently with JuMP style? (#32)
- SBMLModel should just be CobraModel  (#36)
- Implement function callbacks to make function modifications uniform and streamlined (#37)
- Automatic file loading (#38)
- `fluxBalanceAnalysisVec` seems to be missing (#39)
- Clean-up downloading of test models (#40)
- change badge links to cobrexa (#41)
- reorganize file contents (#42)
- remove PyCall Dependency (#45)
- clean up error handling and warnings (#47)
- Change CobraModel to FullModel (#54)
- Implement macros for all functions (where appropriate) (#61)
- Regroup tests to files that match src/ (#65)
- add CodeCov (#67)
- trigger test pipelines in external repos (#71)
- Implement knockouts in an efficient way (#72)
- add doc test to pipeline (#74)
- fix badges of CI in readme (#75)
- Add references to methods where possible (#76)
- Explain the need of modifying the sampling defaults in docs (#80)
- replace format check with bot action to fix automagically (#86)
- Ongoing design considerations (#92)
- Homogenize tests (#96)
- Make sure the accessors for MetabolicModel kinda feature-complete (#100)
- Community model + tutorial (#103)
- Bounds should not be sparse vectors, maybe a new data type... (#112)
- Fix the code examples after StandardModel has changed (#117)
- improve readme for beginners (#123)
- generate html files from tutorials automatically (#145)
- Consistent model variable naming (#152)
- File cleanup + housekeeping (#155)
- Making error messages more informative (#160)
- integrate tutorial testing in ci pipeline (#165)
- document internal functions, at least with comments (#179)
- Change `add_reactions!` to accept string ids as inputs (#193)

**Merged pull requests:**
- formatting of license (#1) (@laurentheirendt)
- Community docs (#7) (@laurentheirendt)
- add parallel FVA (#8) (@htpusa)
- Make the banner fit to 80column terminal. (#9) (@exaexa)
- SBML loading (#10) (@exaexa)
- various minor fixes (#11) (@exaexa)
- simplify reader (#13) (@htpusa)
- [WIP] distributed FVA (#15) (@exaexa)
- Writer (#16) (@htpusa)
- clean-up before API changes (#17) (@exaexa)
- remove dup entries in toml (#20) (@laurentheirendt)
- add workflow to contributing guide (#22) (@laurentheirendt)
- Make analysis functions generic and easily extensible (#23) (@exaexa)
- fix docs (#24) (@stelmo)
- simplify the use of `devel` command for contribution guide (#25) (@exaexa)
- parametrize FVA (#27) (@htpusa)
- Add a test for γ-parametrized FVA (#28) (@exaexa)
- Support wildcards in documentation building (#29) (@exaexa)
- WIP: integrate generic interface & cobratools (#30) (@stelmo)
- Docs standardization (#31) (@exaexa)
- add additional FBA output formats (#33) (@exaexa)
- Properly support multiple model types and conversions (#34) (@exaexa)
- fix new-master and cobratools remaining integration issues (#35) (@stelmo)
- reduce size of favicon (#43) (@laurentheirendt)
- fixes for links (#44) (@laurentheirendt)
- fix the nice FBA variants (again) (#46) (@exaexa)
- clean-up downloading of files for testing (#48) (@exaexa)
- Minor package changes (#50) (@laurentheirendt)
- Cherries from PR49 (#51) (@laurentheirendt)
- pause CI gh action (#52) (@laurentheirendt)
- implement callbacks to make problem modification pretty (#53) (@stelmo)
- Move JuliaFormatter to Gitlab CI (#55) (@laurentheirendt)
- add master runs to test and format (#56) (@laurentheirendt)
- add native linux, mac, and windows nodes (#57) (@laurentheirendt)
- Simplifications (#58) (@exaexa)
- Add reaction macro (#59) (@marvinvanaalst)
- Added loopless fba (#60) (@marvinvanaalst)
- remove Conda dep (#62) (@laurentheirendt)
- Add `default_constants` tuple to reduce number of hard coded constants (#63) (@stelmo)
- Generic io interface (#64) (@stelmo)
- Deleted geometric fba (#66) (@stelmo)
- cleaning & recontenting the file structure (#78) (@exaexa)
- Reduce the number of constants (#79) (@exaexa)
- add logos for README (#81) (@exaexa)
- format check returns the failure properly (#83) (@exaexa)
- add codecov and bot for formatting (#85) (@laurentheirendt)
- add automated documentation tests (#87) (@laurentheirendt)
- Small fixes (#88) (@stelmo)
- add docker img for deploy doc stage (#89) (@laurentheirendt)
- The Big Rename of LinearModel to CoreModel (#91) (@exaexa)
- make the abstract interface easily implementable (#95) (@exaexa)
- Prepare accessors for genetic and chemical information (#97) (@exaexa)
- Conversion + genetics and chemical interface for SBML (#99) (@exaexa)
- support n_genes accessor (#101) (@exaexa)
- add annotations (#102) (@exaexa)
- Separated-out JSONModel commits (from elmo) (#104) (@exaexa)
- remove some unneeded dependencies (#107) (@exaexa)
- Implement pretty printing  (#108) (@stelmo)
- Add generic interface for StandardModels (#111) (@stelmo)
- Implement conditional logging switches (#114) (@exaexa)
- MATModel: generic interface + conversions + test (#115) (@exaexa)
- add the forgotten MATModel conversion tests (#118) (@exaexa)
- IO code cleanup (#119) (@exaexa)
- fixed small issues (#120) (@stelmo)
- MetabolicModel→StandardModel conversion (#121) (@stelmo)
- prettyprinting hints & minor fixes (#122) (@exaexa)
- slightly new structure (#124) (@laurentheirendt)
- Add remaining accessors function to MetabolicModel (#125) (@stelmo)
- Add accessors to StandardModel, add tests and doctests (#126) (@stelmo)
- Change defaults of fields in Reaction, Gene and Metabolite to nothing (#127) (@stelmo)
- Add github action with custom docker img (#128) (@laurentheirendt)
- add generic prettyprinting (fixes `ppr(nothing)` bug) (#129) (@exaexa)
- test the prettyprinting correctly (allow some formatting freedom) (#130) (@exaexa)
- Fix JSON code to work with new accessors (#131) (@exaexa)
- add flags to gh action (#132) (@laurentheirendt)
- use precompiled docker img (#133) (@laurentheirendt)
- finalized SBML accessors (#134) (@exaexa)
- avoid uncertainty creep (#135) (@exaexa)
- Steamlined Gene tests (#136) (@stelmo)
- updated readme (#138) (@laurentheirendt)
- Mo tutorial 1 (merge into #139!!) (#140) (@stelmo)
- Added quick start (#141) (@stelmo)
- make MATModel work with the abstract interface (#142) (@exaexa)
- add stage to generate gource history automatically (#143) (@laurentheirendt)
- Simplified example in quick start (#144) (@stelmo)
- add gitattributes file (#146) (@laurentheirendt)
- added tutorial 2 - (merge into #140!!) (#148) (@stelmo)
- fix welcome contributions button (#150) (@laurentheirendt)
- Mva knockout 2 (#151) (@marvinvanaalst)
- Automatic conversion of Jupyter notebooks (#153) (@laurentheirendt)
- Analysis problem modifications: make generic (#156) (@stelmo)
- Instructions for adding solver (#157) (@laurentheirendt)
- support some additional possibilities of MAT file content (#158) (@exaexa)
- Added fba tutorial (merge into #148) (#159) (@stelmo)
- Fix small things in `check_duplicate_annotations` (#161) (@stelmo)
- Fix docs and some functions that use `StandardModel` (#162) (@stelmo)
- Code docstrings and structure finalization (#164) (@exaexa)
- Removal of stuff that won't go to 1.0 + some cleaning (#167) (@exaexa)
- simplify&fix namespace resolution in parallel FVA (#169) (@exaexa)
- Fix small things in stmodel specific functions (#172) (@stelmo)
- add docker container generation (#174) (@laurentheirendt)
- fixed fva tests (checked externally) (#175) (@stelmo)
- Fixed small pfba error (#176) (@stelmo)
- Implement analysis functions for CoreModelCoupled (#177) (@stelmo)
- Export MAX/MIN, squash optimality check, relocate modifications (#180) (@stelmo)
- Fix knockouts (#181) (@stelmo)
- Add Literate.jl (#182) (@laurentheirendt)
- Convert loading notebook to literate file (#183) (@stelmo)
- fix the polymorphism of knockout mod (#184) (@exaexa)
- Literally the basic usage tutorial  (#185) (@stelmo)
- literate structure-up (#186) (@exaexa)
- Basic usage of standardmodel (#187) (@stelmo)
- Normalize variable naming in models (#188) (@exaexa)
- Basic usage of core and coupled models (#189) (@stelmo)
- Document small accessor functions (#190) (@exaexa)
- fix notebooks after master collision (#192) (@exaexa)
- remove notebook converter (#194) (@laurentheirendt)
- Model construction, modification and joining (#195) (@stelmo)
- trigger external repo (#196) (@laurentheirendt)
- skip ci for automatic formatting changes (#198) (@laurentheirendt)
- Housekeeping 🪓 🧟  (#199) (@stelmo)
- Improve how to contribute docs (#200) (@stelmo)
- clean up tutorial 1 (#203) (@exaexa)
- Small cosmetic fixes (#204) (@stelmo)
- debug external trigger (#205) (@laurentheirendt)
- [skip ci] trigger pipeline via API (#206) (@laurentheirendt)
- revert the skip ci for the formatting bot (#207) (@laurentheirendt)
- tutorial2 + notebook2 (#209) (@exaexa)
- Cut example from readme (#210) (@stelmo)
- [skip ci] simplify generating of the doc index (#211) (@exaexa)
- [skip ci] tutorial 3 (#212) (@exaexa)
- Add error message (#213) (@stelmo)
- Improve standardmodel modifications (#214) (@stelmo)
- Add references to analysis functions (#215) (@stelmo)
- change curl command to docker (#218) (@laurentheirendt)
- [skip ci] remove curl output (#220) (@laurentheirendt)
- Add history image to main page of doc (#221) (@laurentheirendt)
- tutorial 4 (#222) (@exaexa)
- move gource asset (#223) (@laurentheirendt)
- fix location (#224) (@laurentheirendt)
- [skip ci] fix assets (#225) (@laurentheirendt)
- new logos (#226) (@laurentheirendt)
- release doc (#227) (@laurentheirendt)
- new banner (#229) (@stelmo)
- Slight improvement to banner (#230) (@stelmo)
- format banner (#231) (@laurentheirendt)
- fix doc deployment (#233) (@laurentheirendt)
- set env for PR/MR (#234) (@laurentheirendt)
- fix syntax for doc deployment (#235) (@laurentheirendt)
- change installation to git (temporarily) (#236) (@exaexa)
- fix issue with travis branch (#237) (@laurentheirendt)
- add tag bot and compathelper (#238) (@laurentheirendt)
- technical changes for doc deployment (#239) (@laurentheirendt)
- bump version for release (#240) (@laurentheirendt)
- Small fixes to the docs (#241) (@stelmo)
- cleanup of dependencies (#242) (@exaexa)
- use a gray filter for all console text (#243) (@exaexa)
- remove devurl (#244) (@laurentheirendt)
- fix nb viewer link (#246) (@laurentheirendt)
- fix nb viewer - second round (#247) (@laurentheirendt)
- fix nb viewer (#248) (@laurentheirendt)

COBREXA v1.0.0

Closed issues:

  • storage of large model (#2)
  • i/o of SBML files (#3)
  • Expand IO (MAT) (#4)
  • Migration to github.com (#6)
  • loadModel is broken (#12)
  • Some SBML formats (level 3?) are not read correctly (#18)
  • Wildcard documentation building (#26)
  • Name functions consistently with JuMP style? (#32)
  • SBMLModel should just be CobraModel (#36)
  • Implement function callbacks to make function modifications uniform and streamlined (#37)
  • Automatic file loading (#38)
  • fluxBalanceAnalysisVec seems to be missing (#39)
  • Clean-up downloading of test models (#40)
  • change badge links to cobrexa (#41)
  • reorganize file contents (#42)
  • remove PyCall Dependency (#45)
  • clean up error handling and warnings (#47)
  • Change CobraModel to FullModel (#54)
  • Implement macros for all functions (where appropriate) (#61)
  • Regroup tests to files that match src/ (#65)
  • add CodeCov (#67)
  • trigger test pipelines in external repos (#71)
  • Implement knockouts in an efficient way (#72)
  • add doc test to pipeline (#74)
  • fix badges of CI in readme (#75)
  • Add references to methods where possible (#76)
  • Explain the need of modifying the sampling defaults in docs (#80)
  • replace format check with bot action to fix automagically (#86)
  • Ongoing design considerations (#92)
  • Homogenize tests (#96)
  • Make sure the accessors for MetabolicModel kinda feature-complete (#100)
  • Community model + tutorial (#103)
  • Bounds should not be sparse vectors, maybe a new data type... (#112)
  • Fix the code examples after StandardModel has changed (#117)
  • improve readme for beginners (#123)
  • generate html files from tutorials automatically (#145)
  • Consistent model variable naming (#152)
  • File cleanup + housekeeping (#155)
  • Making error messages more informative (#160)
  • integrate tutorial testing in ci pipeline (#165)
  • document internal functions, at least with comments (#179)
  • Change add_reactions! to accept string ids as inputs (#193)

Merged pull requests:

  • formatting of license (#1) (@laurentheirendt)
  • Community docs (#7) (@laurentheirendt)
  • add parallel FVA (#8) (@htpusa)
  • Make the banner fit to 80column terminal. (#9) (@exaexa)
  • SBML loading (#10) (@exaexa)
  • various minor fixes (#11) (@exaexa)
  • simplify reader (#13) (@htpusa)
  • [WIP] distributed FVA (#15) (@exaexa)
  • Writer (#16) (@htpusa)
  • clean-up before API changes (#17) (@exaexa)
  • remove dup entries in toml (#20) (@laurentheirendt)
  • add workflow to contributing guide (#22) (@laurentheirendt)
  • Make analysis functions generic and easily extensible (#23) (@exaexa)
  • fix docs (#24) (@stelmo)
  • simplify the use of devel command for contribution guide (#25) (@exaexa)
  • parametrize FVA (#27) (@htpusa)
  • Add a test for γ-parametrized FVA (#28) (@exaexa)
  • Support wildcards in documentation building (#29) (@exaexa)
  • WIP: integrate generic interface & cobratools (#30) (@stelmo)
  • Docs standardization (#31) (@exaexa)
  • add additional FBA output formats (#33) (@exaexa)
  • Properly support multiple model types and conversions (#34) (@exaexa)
  • fix new-master and cobratools remaining integration issues (#35) (@stelmo)
  • reduce size of favicon (#43) (@laurentheirendt)
  • fixes for links (#44) (@laurentheirendt)
  • fix the nice FBA variants (again) (#46) (@exaexa)
  • clean-up downloading of files for testing (#48) (@exaexa)
  • Minor package changes (#50) (@laurentheirendt)
  • Cherries from PR49 (#51) (@laurentheirendt)
  • pause CI gh action (#52) (@laurentheirendt)
  • implement callbacks to make problem modification pretty (#53) (@stelmo)
  • Move JuliaFormatter to Gitlab CI (#55) (@laurentheirendt)
  • add master runs to test and format (#56) (@laurentheirendt)
  • add native linux, mac, and windows nodes (#57) (@laurentheirendt)
  • Simplifications (#58) (@exaexa)
  • Add reaction macro (#59) (@marvinvanaalst)
  • Added loopless fba (#60) (@marvinvanaalst)
  • remove Conda dep (#62) (@laurentheirendt)
  • Add default_constants tuple to reduce number of hard coded constants (#63) (@stelmo)
  • Generic io interface (#64) (@stelmo)
  • Deleted geometric fba (#66) (@stelmo)
  • cleaning & recontenting the file structure (#78) (@exaexa)
  • Reduce the number of constants (#79) (@exaexa)
  • add logos for README (#81) (@exaexa)
  • format check returns the failure properly (#83) (@exaexa)
  • add codecov and bot for formatting (#85) (@laurentheirendt)
  • add automated documentation tests (#87) (@laurentheirendt)
  • Small fixes (#88) (@stelmo)
  • add docker img for deploy doc stage (#89) (@laurentheirendt)
  • The Big Rename of LinearModel to CoreModel (#91) (@exaexa)
  • make the abstract interface easily implementable (#95) (@exaexa)
  • Prepare accessors for genetic and chemical information (#97) (@exaexa)
  • Conversion + genetics and chemical interface for SBML (#99) (@exaexa)
  • support n_genes accessor (#101) (@exaexa)
  • add annotations (#102) (@exaexa)
  • Separated-out JSONModel commits (from elmo) (#104) (@exaexa)
  • remove some unneeded dependencies (#107) (@exaexa)
  • Implement pretty printing (#108) (@stelmo)
  • Add generic interface for StandardModels (#111) (@stelmo)
  • Implement conditional logging switches (#114) (@exaexa)
  • MATModel: generic interface + conversions + test (#115) (@exaexa)
  • add the forgotten MATModel conversion tests (#118) (@exaexa)
  • IO code cleanup (#119) (@exaexa)
  • fixed small issues (#120) (@stelmo)
  • MetabolicModel→StandardModel conversion (#121) (@stelmo)
  • prettyprinting hints & minor fixes (#122) (@exaexa)
  • slightly new structure (#124) (@laurentheirendt)
  • Add remaining accessors function to MetabolicModel (#125) (@stelmo)
  • Add accessors to StandardModel, add tests and doctests (#126) (@stelmo)
  • Change defaults of fields in Reaction, Gene and Metabolite to nothing (#127) (@stelmo)
  • Add github action with custom docker img (#128) (@laurentheirendt)
  • add generic prettyprinting (fixes ppr(nothing) bug) (#129) (@exaexa)
  • test the prettyprinting correctly (allow some formatting freedom) (#130) (@exaexa)
  • Fix JSON code to work with new accessors (#131) (@exaexa)
  • add flags to gh action (#132) (@laurentheirendt)
  • use precompiled docker img (#133) (@laurentheirendt)
  • finalized SBML accessors (#134) (@exaexa)
  • avoid uncertainty creep (#135) (@exaexa)
  • Steamlined Gene tests (#136) (@stelmo)
  • updated readme (#138) (@laurentheirendt)
  • Mo tutorial 1 (merge into #139!!) (#140) (@stelmo)
  • Added quick start (#141) (@stelmo)
  • make MATModel work with the abstract interface (#142) (@exaexa)
  • add stage to generate gource history automatically (#143) (@laurentheirendt)
  • Simplified example in quick start (#144) (@stelmo)
  • add gitattributes file (#146) (@laurentheirendt)
  • added tutorial 2 - (merge into #140!!) (#148) (@stelmo)
  • fix welcome contributions button (#150) (@laurentheirendt)
  • Mva knockout 2 (#151) (@marvinvanaalst)
  • Automatic conversion of Jupyter notebooks (#153) (@laurentheirendt)
  • Analysis problem modifications: make generic (#156) (@stelmo)
  • Instructions for adding solver (#157) (@laurentheirendt)
  • support some additional possibilities of MAT file content (#158) (@exaexa)
  • Added fba tutorial (merge into #148) (#159) (@stelmo)
  • Fix small things in check_duplicate_annotations (#161) (@stelmo)
  • Fix docs and some functions that use StandardModel (#162) (@stelmo)
  • Code docstrings and structure finalization (#164) (@exaexa)
  • Removal of stuff that won't go to 1.0 + some cleaning (#167) (@exaexa)
  • simplify&fix namespace resolution in parallel FVA (#169) (@exaexa)
  • Fix small things in stmodel specific functions (#172) (@stelmo)
  • add docker container generation (#174) (@laurentheirendt)
  • fixed fva tests (checked externally) (#175) (@stelmo)
  • Fixed small pfba error (#176) (@stelmo)
  • Implement analysis functions for CoreModelCoupled (#177) (@stelmo)
  • Export MAX/MIN, squash optimality check, relocate modifications (#180) (@stelmo)
  • Fix knockouts (#181) (@stelmo)
  • Add Literate.jl (#182) (@laurentheirendt)
  • Convert loading notebook to literate file (#183) (@stelmo)
  • fix the polymorphism of knockout mod (#184) (@exaexa)
  • Literally the basic usage tutorial (#185) (@stelmo)
  • literate structure-up (#186) (@exaexa)
  • Basic usage of standardmodel (#187) (@stelmo)
  • Normalize variable naming in models (#188) (@exaexa)
  • Basic usage of core and coupled models (#189) (@stelmo)
  • Document small accessor functions (#190) (@exaexa)
  • fix notebooks after master collision (#192) (@exaexa)
  • remove notebook converter (#194) (@laurentheirendt)
  • Model construction, modification and joining (#195) (@stelmo)
  • trigger external repo (#196) (@laurentheirendt)
  • skip ci for automatic formatting changes (#198) (@laurentheirendt)
  • Housekeeping 🪓 🧟 (#199) (@stelmo)
  • Improve how to contribute docs (#200) (@stelmo)
  • clean up tutorial 1 (#203) (@exaexa)
  • Small cosmetic fixes (#204) (@stelmo)
  • debug external trigger (#205) (@laurentheirendt)
  • [skip ci] trigger pipeline via API (#206) (@laurentheirendt)
  • revert the skip ci for the formatting bot (#207) (@laurentheirendt)
  • tutorial2 + notebook2 (#209) (@exaexa)
  • Cut example from readme (#210) (@stelmo)
  • [skip ci] simplify generating of the doc index (#211) (@exaexa)
  • [skip ci] tutorial 3 (#212) (@exaexa)
  • Add error message (#213) (@stelmo)
  • Improve standardmodel modifications (#214) (@stelmo)
  • Add references to analysis functions (#215) (@stelmo)
  • change curl command to docker (#218) (@laurentheirendt)
  • [skip ci] remove curl output (#220) (@laurentheirendt)
  • Add history image to main page of doc (#221) (@laurentheirendt)
  • tutorial 4 (#222) (@exaexa)
  • move gource asset (#223) (@laurentheirendt)
  • fix location (#224) (@laurentheirendt)
  • [skip ci] fix assets (#225) (@laurentheirendt)
  • new logos (#226) (@laurentheirendt)
  • release doc (#227) (@laurentheirendt)
  • new banner (#229) (@stelmo)
  • Slight improvement to banner (#230) (@stelmo)
  • format banner (#231) (@laurentheirendt)
  • fix doc deployment (#233) (@laurentheirendt)
  • set env for PR/MR (#234) (@laurentheirendt)
  • fix syntax for doc deployment (#235) (@laurentheirendt)
  • change installation to git (temporarily) (#236) (@exaexa)
  • fix issue with travis branch (#237) (@laurentheirendt)
  • add tag bot and compathelper (#238) (@laurentheirendt)
  • technical changes for doc deployment (#239) (@laurentheirendt)
  • bump version for release (#240) (@laurentheirendt)
  • Small fixes to the docs (#241) (@stelmo)
  • cleanup of dependencies (#242) (@exaexa)
  • use a gray filter for all console text (#243) (@exaexa)
  • remove devurl (#244) (@laurentheirendt)
  • fix nb viewer link (#246) (@laurentheirendt)
  • fix nb viewer - second round (#247) (@laurentheirendt)
  • fix nb viewer (#248) (@laurentheirendt)