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 .
  • v1.0.6   ## 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   **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)
    Release v1.0.0