## 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)