v14.1.0

Catalyst v14.1.0

Diff since v14.0.1

Merged pull requests:

• Documentation page on how to access model properties (#889) (@TorkelE)
• Adding cycles/flux mode calculation (#893) (@vyudu)
• Specialised conservation law section on the network analysis doc page (#903) (@TorkelE)
• Tutorial on periodic events (#946) (@TorkelE)
• Expand tests (#973) (@TorkelE)
• Spatial modelling documentation (#976) (@TorkelE)
• Improve conservation law handling in find_identifiable_functions (#984) (@TorkelE)
• More t is now a parameter test (#989) (@TorkelE)
• Fix spatial sim aniamtions in doc (#993) (@TorkelE)
• update video display strategy (#995) (@TorkelE)
• Api update (#997) (@TorkelE)
• Separate conservation law page (#998) (@TorkelE)
• remove bondgraphs from docs and fix SBMLImporter link (#999) (@isaacsas)

Closed issues:

• Project: Qualitative Analysis (#43)
• Register (#127)
• Proposed notation for delay (#191)
• Reaction expression parser (#330)
• Zero order reactions with arrows that disable mass action (#379)
• Deficiency theorem zero applied to the reaction network (#410)
• alias elimination (#413)
• conservation of energy (#424)
• Gillespie simulations on GPU (#543)
• Separate /test/Project.toml environment file (#578)
• Fix Latexify tests (#610)
• fix formatting failures (#653)
• Problem with extend if things are in a specific order (ERROR: type ReactionSystem has no field gui_metadata) (#658)
• broken doc examples due to new Int -> Float64 conversion (#699)
• Spatial Required updates list (#726)
• Reenable formatter CI when fixed (#754)
• Improve documentation of remove_conserved when creating an ODESystem - and make it default to true? (#773)
• remake doesn't recompute conservation law constants (#807)
• Reorganisations/renamings to the docs (#837)
• List of doc update PRs for doc overhaul (#850)
• show in a tutorial how to do periodic events with jumps (#936)
• Add missing model acces functions to API (and add links to it where functions are mentioned) (#990)

v14.0.1

Catalyst v14.0.1

Diff since v14.0.0

Merged pull requests:

• Strong and terminal linkage classes (#963) (@vyudu)
• Cache incidence matrix (#975) (@vyudu)
• Use !!! warning not !!! warn in docs (#981) (@TorkelE)
• Fix GitHub readme links (#982) (@TorkelE)
• Simulation structure interfacing docs update (#983) (@TorkelE)
• math model description page (#987) (@isaacsas)
• make t a parameter now (#988) (@isaacsas)

Closed issues:

• Catalyst V14 TODO (#775)
• Add equations to the docs (#978)

v14.0.0

Catalyst v14.0.0

Diff since v13.5.1

Merged pull requests:

• Spatial Reaction Network Implementation (#644) (@TorkelE)
• [v14 ready] Improve noise scaling implementation (#678) (@TorkelE)
• Inverse problem doc remake and new petab tutorial (#701) (@TorkelE)
• Bifurcation kit extension (#707) (@TorkelE)
• Create function for expanding e.g. mm expressions, and use for e.g. HomotopyContinuation (#713) (@TorkelE)
• Docs housekeeping (#715) (@TorkelE)
• Tutorial for using optimization to optimize for other stuff than parameter fitting (#719) (@TorkelE)
• Tutorial on how to find system steady states usings NonlinearSolve.jl (#720) (@TorkelE)
• Add tests for NonlinearSolve and NonlinearProblem (#721) (@TorkelE)
• CompatHelper: add new compat entry for SteadyStateDiffEq at version 1 for package docs, (keep existing compat) (#728) (@github-actions[bot])
• Test on 1.9 instead of 1.6 (#733) (@TorkelE)
• [v14 ready] RDME and graph SSAs (#737) (@TorkelE)
• [v14 ready] Updated SciML/Optimiation for non-parameter fitting optimization tutorial (#738) (@TorkelE)
• [v14 ready] New stability computation (#739) (@TorkelE)
• New SciML/Optimization for fitting parameters of ODEs tutorial tutorial (#740) (@TorkelE)
• [v14 ready] Latexify improvement (#742) (@TorkelE)
• [v14 ready] Global Sensitivity analysis tutorial (#744) (@TorkelE)
• Update catalyst_api.md (#745) (@TorkelE)
• [v14 ready] Implement metadata for Reactionss (#749) (@TorkelE)
• [v14 ready] Tutorial for ensuring performance for ODE simulations (#751) (@TorkelE)
• warning fixes (#755) (@isaacsas)
• [WIP] LatticeReactionSystem internal update (#756) (@TorkelE)
• Remove minus sign in ub=1e-2 and unneeded 'as' (#759) (@elbert5770)
• [v14 ready] Tutorial on how to use DynamicalSystems.jl for Catalyst (#764) (@TorkelE)
• [v14 ready] Change basic model examples to library of basic models (#765) (@TorkelE)
• Bump actions/cache from 3 to 4 (#766) (@dependabot[bot])
• Doc updates (#768) (@TorkelE)
• Structuralidentifiabilityextension (#769) (@TorkelE)
• Chemistry functionality docs (#770) (@TorkelE)
• Enable dsl observed (#771) (@TorkelE)
• mention constant species (#772) (@ranocha)
• [v14 ready] Fixes StructuralIdentifiability extension for new SI update (#776) (@TorkelE)
• Bump codecov/codecov-action from 3 to 4 (#779) (@dependabot[bot])
• ci: explicitly specify token for codecov (#780) (@thazhemadam)
• ci: explicitly specify token for codecov (#781) (@thazhemadam)
• Add reaction system metadata (#783) (@TorkelE)
• Handle test errors from MTKv9 update (including ReactionSystem completeness) (#784) (@TorkelE)
• Change states to unknowns (#785) (@TorkelE)
• Use MTK's default t and D throughout repository (#786) (@TorkelE)
• Handle different parameters types (#797) (@TorkelE)
• Handle units (#798) (@TorkelE)
• Noise scaling update (#800) (@TorkelE)
• Equations and events reupload (#801) (@TorkelE)
• Bump julia-actions/setup-julia from 1 to 2 (#804) (@dependabot[bot])
• New indexing and simulation input tests (#805) (@TorkelE)
• Docs restructure (#810) (@TorkelE)
• Simulation introduction docs (#812) (@TorkelE)
• Intro to catalyst new juliausers update (#813) (@TorkelE)
• Dsl docs remake (#817) (@TorkelE)
• Simulation plotting doc (#819) (@TorkelE)
• Monte carlo simulation docs (#820) (@TorkelE)
• Structure interfacing doc (#821) (@TorkelE)
• Complex balancing (#822) (@vyudu)
• Drop mutating API functions and macro (#823) (@isaacsas)
• Add @combinatoric_ratelaws to DSL (#828) (@isaacsas)
• merge Catalyst version 14 into master (#830) (@isaacsas)
• Test restructure and parallelisation (#835) (@TorkelE)
• Source folder restructure (#838) (@TorkelE)
• [Non-urgent - Ready] Doc home update (#842) (@TorkelE)
• [Non-urgent - Ready] GitHub readme update (#843) (@TorkelE)
• Programmatic generative modelling example (#844) (@TorkelE)
• SDE performance tutorial (#845) (@TorkelE)
• Optim param fitting doc (#846) (@TorkelE)
• Visualisation docs (#847) (@TorkelE)
• Nonlinearsolve doc remake (#848) (@TorkelE)
• HC doc update (#849) (@TorkelE)
• Full system balancing (#851) (@TorkelE)
• Add two new reaction metadata (#852) (@TorkelE)
• Add conservedquantity metadata (#853) (@TorkelE)
• Add nonreaction function (#854) (@TorkelE)
• Add get_variables dispatch for Reaction (#855) (@TorkelE)
• Update Reaction constructor (#856) (@TorkelE)
• Serialise ReactionSystem to file. (#857) (@TorkelE)
• Rename reactionparams and similar functions (#859) (@TorkelE)
• v14 doc update (#861) (@TorkelE)
• Api doc proposed changes (#862) (@TorkelE)
• proposed param stoich doc changes (#864) (@TorkelE)
• Proposed compositional modelling doc updates (#865) (@TorkelE)
• Proposed hh model example changes (#867) (@TorkelE)
• change to not depend on equality after seed in stoch tests (#868) (@TorkelE)
• Remove @paraemter lists in test_networks.jl (#870) (@TorkelE)
• Proposed FAq doc updates (#874) (@TorkelE)
• Skip bits that yield weird documenter errors (#875) (@TorkelE)
• CompatHelper: bump compat for OptimizationBBO to 0.2 for package docs, (keep existing compat) (#876) (@github-actions[bot])
• CompatHelper: add new compat entry for JumpProcesses at version 9 for package docs, (keep existing compat) (#877) (@github-actions[bot])
• CompatHelper: add new compat entry for IncompleteLU at version 0.2 for package docs, (keep existing compat) (#879) (@github-actions[bot])
• CompatHelper: add new compat entry for LinearSolve at version 2 for package docs, (keep existing compat) (#880) (@github-actions[bot])
• CompatHelper: add new compat entry for DynamicalSystems at version 3 for package docs, (keep existing compat) (#881) (@github-actions[bot])
• CompatHelper: add new compat entry for CairoMakie at version 0.12 for package docs, (keep existing compat) (#882) (@github-actions[bot])
• CompatHelper: add new compat entry for BenchmarkTools at version 1 for package docs, (keep existing compat) (#883) (@github-actions[bot])
• Doc merge updates (#884) (@TorkelE)
• [WIP] Fix Symbolics related stuff (#887) (@TorkelE)
• Use 0 not 0.0 in diff_2_zero (#892) (@TorkelE)
• CompatHelper: add new compat entry for DynamicPolynomials at version 0.5, (keep existing compat) (#894) (@github-actions[bot])
• add back model visualization doc page (#899) (@TorkelE)
• Documentation of file loading/saving (#902) (@TorkelE)
• Remove DifferentialEquations.jl doc dependency (#904) (@TorkelE)
• Update bifurcationkit doc page (#905) (@TorkelE)
• Expand conservation law tests (#907) (@TorkelE)
• No longer require Julia v1.10.2 in CI/docs (#911) (@TorkelE)
• Revert "Update Reaction constructor" (#912) (@TorkelE)
• Proposed change to index page (#914) (@TorkelE)
• Misc updates to reaction system serialisation function (#915) (@TorkelE)
• [WIP] Formating (#916) (@TorkelE)
• doc updates (#917) (@TorkelE)
• New Reaction inputs update (#918) (@TorkelE)
• Update smol tutorial (#919) (@isaacsas)
• proposed intro to Catlayst changes (#920) (@TorkelE)
• Proposed constraint equations doc changes (#921) (@TorkelE)
• turn off that warnings do not lead to doc failures (#922) (@isaacsas)
• Fix runtest file (#923) (@TorkelE)
• [v14 - Ready] Remove empty cross references (#925) (@TorkelE)
• Ensure all footnote entries are referenced (#926) (@TorkelE)
• [v14 - Ready] Fix deprecated method usage and unnecessary prints while tests run (#928) (@TorkelE)
• [v14 - Ready] Fix bug where expand_registered_functions mutated original reaction system (#929) (@TorkelE)
• [v14 - Ready] Go through broken tests (#930) (@TorkelE)
• ReactionSystem serialisation update (#931) (@TorkelE)
• [v14 - Ready] Fixes latexify tests (#933) (@TorkelE)
• [v14 - Ready] Migration guide and fixes to history file (#934) (@TorkelE)
• Add warning to ReactionSystem field list (#937) (@TorkelE)
• fix jump internals test (#938) (@isaacsas)
• Fix parametric stoich tutorial (#940) (@isaacsas)
• [WIP] Fix remaining doc issues (#943) (@TorkelE)
• fix Catalyst using warning (#944) (@isaacsas)
• Update to general namespace separator (#951) (@ChrisRackauckas)
• [v14] Conservation law warnings (#955) (@TorkelE)
• [v14 - Awaiting Catalyst update] New default prob update tests (#956) (@TorkelE)
• [v14 - Awaiting MTK fix] Tests for vector valued species/parameters (#957) (@TorkelE)
• [v14 - ready] Doc figure display performance update (#958) (@TorkelE)
• [v14 ready] Mark regressed mtk tests as broken (#959) (@TorkelE)
• fix markdown (#966) (@spaette)
• fix typos (#967) (@spaette)
• Fix sdes (#968) (@TorkelE)
• Doc updates (#969) (@TorkelE)
• Simulation introduction doc page update (#970) (@TorkelE)
• Expand reaction system serialisation tests (#971) (@TorkelE)
• Update upstream mtk tests (#974) (@TorkelE)
• doc tweaks for v14 (#977) (@isaacsas)
• doc updates (#980) (@isaacsas)

Closed issues:

• Representing Spatial Reaction Networks (#229)
• update tests to not assume specific orderings of states and parameters (#433)
• writing ReactionSystem to file (#456)
• Enable chain of reactions in macro (#496)
• Support for Spatial Models (#537)
• 'latexify(rn; form=:ode)` not working for documenter (#596)
• Utilise package extensions to add features (#650)
• Spatial modelling integration planning (#659)
• Designating noise scailing parameter in DSL (and maybe as meta data)? (#660)
• Separate inverse problem documentation section, and expanded documentation for these (#672)
• Add "Further reading" sections in documentation (#676)
• Add documentation for chemistry related functionality (#677)
• Enable and document observables (#689)
• Compounds don't support interpolation of variables (#690)
• Enable reaction specific additional data in DSL (#693)
• Adding events macro to reaction network DSL (#694)
• Reduce use of special characters in DSL in documentation (e.g. use "-->" instead of "→") (#696)
• Redo how functions are unfolded in Homotopyc continuation extension (#700)
• Tracker of status of current (and upcomi...

v13.5.1

Catalyst v13.5.1

Diff since v13.5.0

Merged pull requests:

• fix depreciation message typo (#705) (@tstrey)
• General doc update (#706) (@TorkelE)

v13.5.0

Catalyst v13.5.0

Diff since v13.4.1

Merged pull requests:

• Update index.md (#671) (@ElisabethRoesch)
• Bump actions/checkout from 3 to 4 (#673) (@dependabot[bot])
• Documentation of initial conditions that depend on a parameter (#681) (@TorkelE)
• Test cleanup (#682) (@TorkelE)
• Homotopy Continuation extension and remake (#683) (@TorkelE)
• Bump Optimization bound (#688) (@ChrisRackauckas)
• CompatHelper: bump compat for NonlinearSolve to 2 for package docs, (keep existing compat) (#698) (@github-actions[bot])

Closed issues:

• Unable to interpolate parameters when using @parameters within DSL (#692)

v13.4.1

Catalyst v13.4.1

Diff since v13.4.0

Merged pull requests:

• fix hh docs (#669) (@isaacsas)

v13.4.0

Catalyst v13.4.0

Diff since v13.3.0

Closed issues:

• @parameters and @variables are malfunctioning (#646)
• Linear Interpolation as an algebraic function in a reaction network (#647)
• Species' order is not defined by @species (#649)

Merged pull requests:

• Tutorial for (mostly Symbol based) interfacing with problems, integrators, and solutions (#639) (@TorkelE)
• CompatHelper: add new compat entry for OrdinaryDiffEq at version 6 for package docs, (keep existing compat) (#642) (@github-actions[bot])
• CompatHelper: add new compat entry for StochasticDiffEq at version 6 for package docs, (keep existing compat) (#643) (@github-actions[bot])
• finish Hodgkin-Huxley tutorial (#645) (@isaacsas)
• Adds @Compound macro (#651) (@LalitChauhan56)
• adding discrete event to event doc (#652) (@tstrey)
• disable formatter on test files (#654) (@isaacsas)
• Fix namespacing (#666) (@YingboMa)
• Finish balancing PR (#667) (@isaacsas)
• update HISTORY for compounds (#668) (@isaacsas)

v13.3.0

Catalyst v13.3.0

Diff since v13.2.1

Merged pull requests:

• CompatHelper: bump compat for Latexify to 0.16, (keep existing compat) (#640) (@github-actions[bot])
• CompatHelper: bump compat for Latexify to 0.16 for package docs, (keep existing compat) (#641) (@github-actions[bot])

v13.2.1

Catalyst v13.2.1

Diff since v13.2.0

Closed issues:

• xrightleftharpoons not rendered in VSCode (#637)

Merged pull requests:

• enable dependabot for GitHub actions (#631) (@ranocha)
• Bump codecov/codecov-action from 1 to 3 (#632) (@dependabot[bot])
• Bump actions/cache from 1 to 3 (#633) (@dependabot[bot])
• Bump actions/checkout from 1 to 3 (#634) (@dependabot[bot])
• mathjax mhchem workaround (#638) (@isaacsas)

v13.2.0

Catalyst v13.2.0

Diff since v13.1.0

Merged pull requests:

• allow array variables in DSL (#630) (@isaacsas)