**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)