## 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)
This tag has no release notes.