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@github-actions github-actions released this 12 Jul 01:08
· 304 commits to master since this release
v14.0.0
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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 upcoming) PRs (#710)
  • Implement equations in DSL planning (#717)
  • New Julia user tutorial should start with creating an empty environment (#722)
  • Conversion to non-linear system does not handle presence of differential equations: (#727)
  • For conservation law parameters, add to their meta data that they are conservation law parameters (#729)
  • Add check for whenever systems are time dependent, and use for steady state related functions (#731)
  • Functionality for converting non-MA jumps to MA jumps (#747)
  • Add function for balancing all reactions in a reaction system (#753)
  • Symbolic remaking of jump problem errors (#758)
  • Enable setting t in NonlinearSystem creation (#777)
  • The complete field is a Num? (#782)
  • @register ambiguity (#788)
  • Warning message when using parametric stoichiometries (#795)
  • Miscomputation when using a stoichiometric coefficient != 1 (#802)
  • Weird inconsistency for Jump simulations declared with/without Catalyst (#803)
  • @unpack does not work on observables (#811)
  • v14 tests broken (#824)
  • incorrect Float64 assumptions in diff_to_zero (#825)
  • don't use internal Symbolics.jl functions (#826)
  • Fix test deprecation warnings (#827)
  • Catalyst precompilation will stop at ModelingToolkit precompilation (#858)
  • Typo in HomotopyContinuation docs tutorial (#860)
  • Remove using DifferentialEquations from the docs (#872)
  • type of parameters not always preserved with symbolic indexing (#939)
  • link errors in doc builds (#941)
  • unit problems in tests (#945)
  • Error with vector arguments (#954)

Contributors

ChrisRackauckas, isaacsas, and 7 other contributors
Assets 2
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