**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)

[Diff since v1.0.0](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.0.0...v1.0.1)

**Closed issues:**
- fluxVariabilityAnalysis doesn't check termination status (#5)
- add travis and github actions (#70)
- FVA does not include optimization problem modifications (#219)
- change suggested solved in README from GLPK to Tulip (#232)
- fix `Edit on Github` button on index.md (#245)
- Register COBREXA.jl (#249)
- add backlink from docs (#250)
- unify contributing.md and howToContribute sections (#253)
- remove Random dependency? (#280)

**Merged pull requests:**
- Fix hit and run sampler (#251) (@stelmo)
- add the abstract screening helper + on-disk externalized models (#254) (@exaexa)
- Revert "change installation to git (temporarily)" (#257) (@laurentheirendt)
- clean up docs badges and acks (#264) (@exaexa)
- switch README to Tulip (#265) (@exaexa)
- add support for travis CI (#268) (@laurentheirendt)
- increase coverage of serialization + fixes (#271) (@exaexa)
- fix banner on 80col terminal (#272) (@exaexa)
- fix a problem in screening (#273) (@exaexa)
- unify contribution guides (#274) (@exaexa)
- Clean up FVA (#275) (@exaexa)
- disable the edit link in docs (#276) (@exaexa)
- Clean up tests (#277) (@exaexa)
- replace index.md link (#278) (@laurentheirendt)
- fix directory in doc deployment (#282) (@laurentheirendt)
- Clean up hit-and-run sampling (#284) (@exaexa)
- docs: improve the contribution edit link (#285) (@exaexa)
- bump to 1.0.1 (#286) (@exaexa)

## COBREXA v1.0.2

[Diff since v1.0.1](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.0.1...v1.0.2)


**Closed issues:**
- speed up testing pipeline (#69)
- Fix samplers and create good tests for them (#82)
- Use normal randoms for generating random directions in samplers (#178)
- Fix `rm!` to actually keep the model consistent (#197)
- Fix docs of reconstructions/CoreModelCoupled (#255)
- overload Base.copy for all models (so that writing model modifiers is easier) (#256)
- Homogenize add/remove functions and add in place versions (#281)
- solver precompilation in tests blocks unnecessarily (#287)
- Improve coverage of src/base/utils/StandardModel.jl (#288)
- Feature to get atomic counts in reactions (#311)
- generalize `get_atom_exchanges` (#317)
- 💄 📝 🚸 Usage pointers (#318)
- 💄 🚸 Result summary function (#323)
- 🩹 `atom_exchange` is not robust to missing formulas (#326)
- 💄  Change order of arguments (#330)

**Merged pull requests:**
- add singularity container (#263) (@laurentheirendt)
- ✨ Basic community model construction functions (#270) (@stelmo)
- Clean up test data handling (#289) (@exaexa)
- Deleted unnecessary dependency (#291) (@stelmo)
- Small fixes (#292) (@exaexa)
- re-add missing directories in ignore (#293) (@laurentheirendt)
- change singularity base img (#295) (@laurentheirendt)
- add tulip to singularity container (#296) (@laurentheirendt)
- ✨ Add `looks_like_xxx` functions to make finding specific reaction/metabolite types easy (#297) (@stelmo)
- 🚚 Rename `add!` and `rm!` functions for `StandardModel` (#298) (@stelmo)
- 🪓 Remove `exchange_reactions` (#299) (@stelmo)
- 🩹 fix docs (#301) (@stelmo)
- 💄 Update pretty printing of models (#302) (@stelmo)
- warmup jump+tulip code to save much time later in testing (#303) (@exaexa)
- 📝 Add emoji references (#304) (@stelmo)
- add shallow copying of StandardModel stuff, useful for writing custom… (#306) (@exaexa)
- Missing functions for CoreModelCoupled (#307) (@laurentheirendt)
- 💄 ⚠️ OSQP (#308) (@stelmo)
- 🩹 ✨ Atoms in reactions and overall flux (#312) (@stelmo)
- backwards compatibility with find_exchange_reactions and pals (#314) (@exaexa)
- clean up exchanges a bit (#316) (@exaexa)
- just reformat everything (#320) (@exaexa)
- Screening cleanup + tutorial (#321) (@exaexa)
- 📝 🚧 Community model construction (#325) (@stelmo)
- 🩹 Make `atom_exchage` robust to metabolites missing formulas (#327) (@stelmo)
- 🚸💄 Added summarize function (#328) (@stelmo)
- make atom_exchange and metabolite_fluxes a bit more generic (#331) (@exaexa)
- fix screening doc build (#332) (@exaexa)
- reformat the community model tutorial (#333) (@exaexa)
- clean up analysis documentation and examples (#334) (@exaexa)
- 💄 Another example (#335) (@stelmo)
- bump version (#336) (@exaexa)

## COBREXA v1.0.3

[Diff since v1.0.2](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.0.2...v1.0.3)


**Closed issues:**
- Overview issue: documentation structure (#137)
- add style guidelines (#163)
- deploy animated history differently (#294)
- 🚸 💄 Informative error message when reaction is not found (#319)
- 🪓 Homogenize `set_bound` and `change_bounds!` and make them generic (#329)
- 💄 📝 🚸 Small improvements (#338)
- Make all oneline function definitions `const` (#356)
- Fix bad references in docs (#370)
- merge or remove `docs/src/unmerged.md` (#374)
- remove trailing whitespace from everywhere (self-reminder) (#375)
- Bad formatting in some docstrings (#381)

**Merged pull requests:**
- CompatHelper: bump compat for "SBML" to "0.5" (#339) (@github-actions[bot])
- SBML-0.5.0 compat (#340) (@exaexa)
- better errors for optimizer mods (#341) (@htpusa)
- don't leak the file object when saving JSON (#342) (@exaexa)
- format #341 + add a tiny simplification (#343) (@exaexa)
- fix only compatible SBML versions (#344) (@exaexa)
- Change `set_bound` to `change_bound` to fit in with `CoreModel` functions (#346) (@stelmo)
- documentation fixes and formatting, ... (#347) (@exaexa)
- resolve and build pkgs in docs (#348) (@laurentheirendt)
- Fix small things (#349) (@stelmo)
- Fix dependency in docs environment (#352) (@laurentheirendt)
- fix for double command - pasting error (#353) (@laurentheirendt)
- deploy animated git history differently (#354) (@laurentheirendt)
- use the raw artifact from the last job via URL (#355) (@laurentheirendt)
- add singularity deployment (#357) (@laurentheirendt)
- Added more tests for community model functions (#359) (@stelmo)
- Custom model tutorial+notebook (#366) (@exaexa)
- autoformat code in master (#367) (@exaexa)
- do not deploy notebook build artifacts to docs (#368) (@exaexa)
- change name of secret (#369) (@laurentheirendt)
- make the comment messages useful (#371) (@exaexa)
- do not define function as (non-const) variables (#372) (@exaexa)
- add some common practices and requirements to CONTRIBUTING.md (#373) (@exaexa)
- minimize the change_bound generator macro (#376) (@exaexa)
- code cleanup before release (#377) (@exaexa)
- formatting report fix: break the line after code quote properly (#378) (@exaexa)
- Fix argument error in community model notebook (#379) (@stelmo)
- bump version to 1.0.3 (#380) (@exaexa)
- final doc fixes for 1.0.3 (#383) (@exaexa)

## COBREXA v1.0.4

[Diff since v1.0.3](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.0.3...v1.0.4)


**Closed issues:**
- establish more elaborate PR and issue templates (#110)
- Make prettyprinting systematic (#154)
- Production envelopes (#267)
- Make model modification functions consistent (#313)
- Tutorials refer to removed functions (#324)
- 🚸Explain FVA better (#345)
- ⚡Conversion to `StandardModel` is slow, speed it up (#350)
- 🚸make `CoreModel` `add_reactions` function more intuitive (#351)
- More running changes (#358)
- 🚸Carefully explain community model construction + pitfalls (#360)
- ✨ Add in place versions of `remove_reaction` and `remove_metabolite` + plural variants for `CoreModel` and `StandardModel` (#362)
- Change `join_with_exchanges` to accept a dictionary of external metabolites instead of two vectors (#365)
- Add latex completion hints for non-ascii characters in docs (#382)
- Banner doesn't display (#390)
- Add optimizer modification to make solvers quiet (#391)
- `StandardModel` does not read in metabolite/reaction/gene names (#392)
- `atom_exchange` does not weight by flux as stated in the doc string of the function (#393)
- Export function to convert reaction equation into a string (#394)
- Simple export of results in JSON (orig: Should we have a function that exports fluxes in a dict for visualization in Escher?) (#397)
- julia-ize the overloading in `change_objective` (#405)
- Change `set_optmodel_bound!` to have kwargs that do not override constraints (#419)
- Implement st-FBA (#423)
- Generalize FBA to include crowding constraints etc. (#436)

**Merged pull requests:**
- some cosmetic README touches, dev doc links (#384) (@exaexa)
- Fix deployment of container images (#386) (@laurentheirendt)
- Use Makie instead of Plots (#387) (@stelmo)
- improve jsonmodel speed + some extra cleanup (#395) (@exaexa)
- compatibility with SBML 0.6 (#398) (@exaexa)
- unsupport `name` field in models (#399) (@exaexa)
- slightly more useful issue/PR templates (#400) (@exaexa)
- simplify trigger mechanism (#401) (@laurentheirendt)
- simplify code by removing unnecessary unicode (#402) (@exaexa)
- display banner consistently at each import (#403) (@exaexa)
- Fix error with screen and `unregister` (#404) (@stelmo)
- implement objective envelopes (aka production envelopes) (#406) (@exaexa)
- document `optimize_objective` (#409) (@exaexa)
- remove optimize_model (it was not used) (#410) (@exaexa)
- Completely remove all JuMP and COBREXA prefixes where possible (#411) (@exaexa)
- clean up `change_objective` (#412) (@exaexa)
- Added `reaction_equation` function and tests (#413) (@stelmo)
- 🪓 some code and streamline utilities for reaction/metabolite balancing (#414) (@stelmo)
- Simple option to silence the JuMP solvers (#415) (@exaexa)
- Update community analysis functions to be more sensible (#416) (@stelmo)
- improve optmodel screening, subsume FVA (#418) (@exaexa)
- Mo tiny fixes (#420) (@stelmo)
- simplify & unsurprise `set_optmodel_bound!` (#421) (@exaexa)
- Add some more explanations for FVA and add `flux_summary` usage to notebook (#424) (@stelmo)
- Add in place `add_reaction!` and `add_reactions!`  (#425) (@stelmo)
- Fix docs (#426) (@stelmo)
- Add `back stoichiometry_string` (#429) (@stelmo)
- bump SBML compat to 0.7.x (#430) (@exaexa)
- Small fix in docstring + function kwarg (#432) (@stelmo)
- start the grand unification of remove_whatever (#433) (@exaexa)
- Update modifications (#438) (@stelmo)
- MMDF cleanup (#440) (@exaexa)
- add an example for objective_envelope (#441) (@exaexa)
- bump version 1.0.4 (#442) (@exaexa)

## COBREXA v1.0.5

[Diff since v1.0.4](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.0.4...v1.0.5)



**Merged pull requests:**
- more efficient building of sparse stoichiometries (#443) (@exaexa)
- Added repostatus badge (#444) (@stelmo)
- CompatHelper: bump compat for "SBML" to "0.8" (#445) (@github-actions[bot])
- improve parametrization of objective_envelope (#447) (@exaexa)
- slightly improve the objective value handling at FVA (#448) (@exaexa)
- correctly forward the `workers` parameter (#449) (@exaexa)
- completely disable JuMP bridge constraints (#450) (@exaexa)
- improve the ability of screening functions to use precompiled code (#451) (@exaexa)
- fix the index in remove_metabolites of CoreModel (#452) (@exaexa)
- bump version to 1.0.5 (#453) (@exaexa)

## COBREXA v1.0.6

[Diff since v1.0.5](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.0.5...v1.0.6)



**Merged pull requests:**
- Revert "completely disable JuMP bridge constraints" (#454) (@exaexa)
- bump version to 1.0.6 (#458) (@exaexa)

## COBREXA v1.1.0

[Diff since v1.0.6](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.0.6...v1.1.0)


**Closed issues:**
- We should eventually use StableRNGs for sampling and all other random number generation. (#84)
- 🚸Explain `serialize_model` better in docs (#361)
- cannot find kernel - binder (#388)
- add Aqua testing (#389)
- Max-min driving force (#422)
- Add MOMENT algorithm (#446)
- Model modifications for `SerializedModel` (#456)
- Add `screen` example to readme (#457)
- The grr parser assigns `[[""]]` to some reactions when it should be `nothing` (#463)
- formatting problem in `flux_variability_summary` (#468)
- Unify the `_dict` and `_vec` function variants with some common reusable code (#474)
- Reorganize docs a bit (#479)
- Add FAQ section in docs (#480)
- Check the cause of test failures with OSQP / MOMA (#485)
- unique links to contributing guide (#490)
- link to `Edit on Github` does not work anymore (#496)
- Rename `API reference` (#497)
- Rename `Detailed tutorial listing` (#499)

**Merged pull requests:**
- Implement max min driving force (#431) (@stelmo)
- Add community functions for `StandardModel` (#435) (@stelmo)
- Add loopless FBA (#437) (@stelmo)
- Add moment algorithm (#455) (@stelmo)
- fix metabolite vector construction ambiguity (#459) (@exaexa)
- add aqua testing (#460) (@exaexa)
- rewrite julia version in notebooks to one compatible with binder (#461) (@exaexa)
- demonstrate screen() in README (#462) (@exaexa)
- Fix some small docstring issues + small readme changes (#464) (@stelmo)
- Modifications unwrap the serialized model (#465) (@exaexa)
- convert the sampling to stable RNGs (#466) (@exaexa)
- fix docs + naming issue (#467) (@stelmo)
- docfixes (#469) (@exaexa)
- remove binder altogether (#470) (@exaexa)
- explain the use of Serialized models better (#471) (@exaexa)
- moma implementation and tests (#472) (@stelmo)
- try to revive binder (#473) (@exaexa)
- remove some of the repeated code, make MOMA more flexible (#475) (@exaexa)
- silence MOMA tests (#476) (@exaexa)
- run tests&docs on develop, trigger gitlab also on new tags (#477) (@exaexa)
- use the gitlab-documenter integration directly (attempt 1) (#481) (@exaexa)
- reflect the workflow change in contrib guide (#482) (@exaexa)
- temporarily increase tolerance on the MOMA test (needs fixup later) (#484) (@exaexa)
- Polish solution for all QP problems (#486) (@stelmo)
- Reorganize the API docs to nice sections (#487) (@exaexa)
- Try to fix gitlab docbuilding deploy (attempt 2) (#488) (@exaexa)
- fix gitlab docs (attempt 3) (#489) (@exaexa)
- Fix contribution docs (#491) (@exaexa)
- Make the GRR parser a bit more robust (#492) (@exaexa)
- Fix the documentation and some small issues  (#493) (@stelmo)
- Polish the notebook/example sections (#494) (@stelmo)
- develop→master (#495) (@exaexa)
- docfixes (#500) (@exaexa)
- reorganize the CI, add a bit of documentation (#501) (@exaexa)
- postpone the external triggers (#502) (@exaexa)
- Mk docfixes 5 (#503) (@exaexa)
- dev→master 20211105 (#504) (@exaexa)
- do not run PR + branch checks together (#505) (@exaexa)
- fix windows compat checks, compat check also BEFORE merging to master (#506) (@exaexa)
- Simplify tests that use OSQP (#507) (@stelmo)
- Develop→master 20211108 (#509) (@exaexa)
- keep Project.toml stuff sorted (#512) (@exaexa)
- [breaking] avoid unnecessary sparsity in lower/upper flux bounds (#513) (@exaexa)
- simplify the _dict and _vec variants of analysis functions (#514) (@exaexa)
- develop→master for 1.1 release (#515) (@exaexa)

## COBREXA v1.2.0

[Diff since v1.1.0](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.1.0...v1.2.0)


**Closed issues:**
- Use `Dictionary.jl` instead of `OrderedCollections.jl` in `StandardModel` (#434)
- Add genes and gene reaction rules to `CoreModel` (#439)
- Fix versioning dropdown in documentation (#498)
- GPU sampler (#524)

**Merged pull requests:**
- Revert "display banner consistently at each import" (#516) (@exaexa)
- Improve `remove_XXX` functions (#517) (@stelmo)
- Extend max-min driving force analysis (#519) (@stelmo)
- Gene-reaction rules for CoreModel and CoreModelCoupled #439 (#521) (@htpusa)
- naming & tests for grr vector function (#522) (@exaexa)
- add the (most relevant) old versions of the docs to gh pages (#523) (@exaexa)
- remove some unnecessarily explicit `Union` types (#525) (@exaexa)
- remove unnecessary documentation deps from the actual package (#526) (@exaexa)
- make sure SBML 0.8.1 doesn't get installed as a dep (#527) (@exaexa)
- fix some wording and make explanation clearer (#529) (@stelmo)
- added `change_objective!` function and tests (#530) (@stelmo)
- use a precise julia compat entry (#532) (@exaexa)
- upgrade julia from 1.5 to 1.7 (#533) (@laurentheirendt)
- remove duplicate function definitions (#534) (@laurentheirendt)
- clean up the change_objective! overloading, add doc (#535) (@exaexa)
- bump up the "history gif" artifact expiration to 3 months (#536) (@exaexa)
- Regular merge develop→master (#537) (@exaexa)
- Added data source for thermodynamic info in tests (#538) (@stelmo)
- bump version 1.1.1 (#539) (@exaexa)
- fix the versioning for compatibility with General (#540) (@exaexa)
- Merge the fixed develop to master (#541) (@exaexa)

## COBREXA v1.2.1

[Diff since v1.2.0](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.2.0...v1.2.1)


**Closed issues:**
- Polishing: add `@__FILE__` and other stuff to macro-generated functions (#508)
- WIP: Miscellaneous fixes (#518)
- Are knockouts potentially confusing? (#520)

**Merged pull requests:**
- CompatHelper: bump compat for "JuMP" to "0.22" (#511) (@github-actions[bot])
- use the keyword arguments in new version of SBML (#544) (@exaexa)
- Revert "Merge pull request #544 from LCSB-BioCore/mk-sbml-091" (#547) (@exaexa)
- Move the changes from #544 to `develop` (#548) (@exaexa)
- CompatHelper checks the `develop` branch (#550) (@exaexa)
- Trigger documentation building on `master` too (#551) (@exaexa)
- explain the multi-gene knockouts better (#553) (@exaexa)
- clean up some leftover unions with Nothing (#555) (@exaexa)
- bemp a small patch release (#556) (@exaexa)
- improve macro-related documentation (#557) (@exaexa)
- Update the dind version in CI (was: fix dind in CI) (#558) (@exaexa)
- Develop → master merge for 1.2.1 (#559) (@exaexa)
- Build docs on PRs to master (to catch doc errors) (#560) (@exaexa)
- COBREXA should be a dep of documentation Project.toml to enforce version checks (#561) (@exaexa)
- postpone JuMP 0.22 compatibility (#562) (@exaexa)

## COBREXA v1.2.2

[Diff since v1.2.1](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.2.1...v1.2.2)


**Closed issues:**
- Problem converting RECON1 to core/standard model (#563)
- Add `name` field to `StandardModel` (#565)
- add CITATION.cff file (#569)

**Merged pull requests:**
- GRR IDs may contain underscores (#564) (@exaexa)
- Add `names` field to genes, metabolites and reaction types. (#566) (@stelmo)
- add SBML name accessors, bump SBML compat (#568) (@exaexa)
- add citation information (#570) (@exaexa)
- bump 1.2.2 (#571) (@exaexa)
- develop → master merge for 1.2.2 (#572) (@exaexa)
- docker&singularity autobuild&autopublish (#573) (@exaexa)
- tulip got fixed, we can bump JuMP dep (#576) (@exaexa)
- fix gource link (#577) (@exaexa)
- second and hopefully final develop → master merge for 1.2.2 (#578) (@exaexa)

## COBREXA v1.2.3

[Diff since v1.2.2](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.2.2...v1.2.3)



**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)

## COBREXA v1.3.0

[Diff since v1.2.3](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.2.3...v1.3.0)


**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)

## COBREXA v1.3.1

[Diff since v1.3.0](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.3.0...v1.3.1)


**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)

## COBREXA v1.4.0

[Diff since v1.3.1](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.3.1...v1.4.0)


**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)

## COBREXA v1.4.1

[Diff since v1.4.0](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.4.0...v1.4.1)


**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)

## COBREXA v1.4.2

[Diff since v1.4.1](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.4.1...v1.4.2)


**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)

## COBREXA v1.4.3

[Diff since v1.4.2](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.4.2...v1.4.3)



**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)

## COBREXA v1.4.4

[Diff since v1.4.3](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.4.3...v1.4.4)


**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)

## COBREXA v1.5.0

[Diff since v1.4.4](https://github.com/LCSB-BioCore/COBREXA.jl/compare/v1.4.4...v1.5.0)


**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)