opencobra/cobratoolbox: The COBRA Toolbox v3.7: Persephone Pipeline Publication Release

What's Changed

• Update workflow to handle none GUI run of the tests by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2566
• Update workflow requirements by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2567
• Update the CI workflow by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2568
• Add completion message to testMultiProductionEnvelope.m by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2569
• Develop by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2570
• Develop by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2572
• Develop by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2573
• update of get corresponding cols by @rmtfleming in https://github.com/opencobra/cobratoolbox/pull/2576
• Bring back the COBRA Toolbox website CI by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2577
• Update pencil icon and clean up documentation by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2579
• Merge master to develop by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2580
• Update performRegressions.m by @CCThinnes in https://github.com/opencobra/cobratoolbox/pull/2585
• Update the COBRA Toolbox website by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2587
• Add the CI a step to update citations on the COBRA Toolbox website by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2588
• Update the template for tutorials page side bar by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2589
• Remove 'ordered' from workflow name by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2590
• Update documentations on the website by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2594
• Enhance documentation for COBRA tutorials by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2596
• Update workflows and website documentations by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2597
• start of dependency analysis by @rmtfleming in https://github.com/opencobra/cobratoolbox/pull/2599
• Resolving QPold method of optimizeWBModel by @faesslerd in https://github.com/opencobra/cobratoolbox/pull/2571
• updated tutorials in ct by @rmtfleming in https://github.com/opencobra/cobratoolbox/pull/2605
• Develop by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2578
• Resolve syntax error that made the QP solution infeasible by @FaizLAB in https://github.com/opencobra/cobratoolbox/pull/2592
• Update Develop branch to master branch by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2598
• Allow for extended species names by @faesslerd in https://github.com/opencobra/cobratoolbox/pull/2600
• Updates to combineHostMicrobiota.m and optimizeWBModel and addition of interrogateWBmodelsQP.m to Persephone by @trjhensen in https://github.com/opencobra/cobratoolbox/pull/2603
• Removed older database file version by @almut-heinken in https://github.com/opencobra/cobratoolbox/pull/2604
• Update website files by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2607
• bugfixes to nutrition toolbox by @bramnap in https://github.com/opencobra/cobratoolbox/pull/2608
• Update submodulesStructure.rst by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2612
• Update parseNCBItaxonomy.m by @bramnap in https://github.com/opencobra/cobratoolbox/pull/2609
• Update documentations for verifymodel and COBRA Model fields table by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2613
• Update tutorial documentation by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2614
• renewed quadLP interface and solvers see testQuadLP by @rmtfleming in https://github.com/opencobra/cobratoolbox/pull/2615
• Develop by @rmtfleming in https://github.com/opencobra/cobratoolbox/pull/2606
• Update testQuadLP test by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2617
• update plotBiomassTestResults by @bramnap in https://github.com/opencobra/cobratoolbox/pull/2616
• Feature/gecko-lift-coupling: limit homogenisation to WBM and fix constraint renaming by @PkiwiBird in https://github.com/opencobra/cobratoolbox/pull/2618
• Add reacting and conserved moieties framework (Rahou et al., JTB 2025) by @hadjar11 in https://github.com/opencobra/cobratoolbox/pull/2622
• updates to DQQ, compare models, moieties tutorial integrated by @rmtfleming in https://github.com/opencobra/cobratoolbox/pull/2623
• Develop by @rmtfleming in https://github.com/opencobra/cobratoolbox/pull/2624
• Revert "Develop" by @rmtfleming in https://github.com/opencobra/cobratoolbox/pull/2625
• Revert "Revert "Develop"" by @rmtfleming in https://github.com/opencobra/cobratoolbox/pull/2626
• update develop with merges by @rmtfleming in https://github.com/opencobra/cobratoolbox/pull/2627
• remove toolbox dependencies on moiety code by @rmtfleming in https://github.com/opencobra/cobratoolbox/pull/2628
• Develop by @rmtfleming in https://github.com/opencobra/cobratoolbox/pull/2629
• findNonBuiltinCalls by @rmtfleming in https://github.com/opencobra/cobratoolbox/pull/2630
• Upgrading server to support QP tests. by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2636
• Debug three failing tests. by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2639
• Back merge to Develop by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2640
• minor bugfixes by @bramnap in https://github.com/opencobra/cobratoolbox/pull/2635
• Develop by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2641
• apply osense when osenseStr is not defined instead of default to max … by @PkiwiBird in https://github.com/opencobra/cobratoolbox/pull/2634
• Feature/gecko relax fba by @PkiwiBird in https://github.com/opencobra/cobratoolbox/pull/2642
• Feature/gecko quadrelax by @PkiwiBird in https://github.com/opencobra/cobratoolbox/pull/2633
• fix(findMIIS): use size(A,1) to get number of rows by @marouenbg in https://github.com/opencobra/cobratoolbox/pull/2645
• FEA: correct hypergeometric test statistics by @marouenbg in https://github.com/opencobra/cobratoolbox/pull/2644
• Develop by @bramnap in https://github.com/opencobra/cobratoolbox/pull/2650
• feat(findBlockedReaction): use L2 min-norm as preprocessing for targeted FVA by @marouenbg in https://github.com/opencobra/cobratoolbox/pull/2646
• Paint4Net Update - Resubmitted by @ruitvrs in https://github.com/opencobra/cobratoolbox/pull/2649
• Apptainer update for Persephone by @TheWileyB in https://github.com/opencobra/cobratoolbox/pull/2653
• replace inf bounds before setting param.maxUB to avoid unbounded solution by @PkiwiBird in https://github.com/opencobra/cobratoolbox/pull/2643
• Persephone pipeline: Clarified output descriptions and new error check by @trjhensen in https://github.com/opencobra/cobratoolbox/pull/2648
• fix(tuneParam): correct csense sizing, safer arg handling, no global solver swap by @marouenbg in https://github.com/opencobra/cobratoolbox/pull/2652
• fix(writePajekNet): directed Pajek output, tolerance filter, robust filtering & checks by @marouenbg in https://github.com/opencobra/cobratoolbox/pull/2651
• Develop by @farid-zare in https://github.com/opencobra/cobratoolbox/pull/2655

New Contributors

• @faesslerd made their first contribution in https://github.com/opencobra/cobratoolbox/pull/2571
• @FaizLAB made their first contribution in https://github.com/opencobra/cobratoolbox/pull/2592
• @PkiwiBird made their first contribution in https://github.com/opencobra/cobratoolbox/pull/2618
• @ruitvrs made their first contribution in https://github.com/opencobra/cobratoolbox/pull/2649

Full Changelog: https://github.com/opencobra/cobratoolbox/compare/v3.6...v3.7