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