Tags give the ability to mark specific points in history as being important
This project is mirrored from https://github.com/LCSB-BioCore/COBREXA.jl.git. Pull mirroring updated .
  • v1.4.3
    ## 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)
  • v1.4.2
    ## 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)
  • v1.4.1
    ## 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)
  • v1.4.0
    ## 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)
  • v1.3.1
    ## 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)
  • v1.3.0
    ## 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)
  • v1.2.3
    ## 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)
  • v1.2.2
    ## 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)
  • v1.2.1
    ## 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)
  • v1.2.0
    ## 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)
  • v1.1.0
    ## 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)
  • v1.0.6
    ## 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)
  • v1.0.5
    ## 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)
  • v1.0.4
    ## 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)
  • v1.0.3
    ## 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)
  • v1.0.2
    ## 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)
  • v1.0.1
    [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)
  • v1.0.0
    Release 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)