v15.0.0

Catalyst v15.0.0

Diff since v14.4.1

This is a breaking release, please see the HISTORY.md file for details on breaking changes.

Merged pull requests:

• Detailed balance (#965) (@vyudu)
• Refactor "src/dsl.jl" file (#985) (@TorkelE)
• history.MD update (#1047) (@vyudu)
• Fix DAE tests (#1050) (@TorkelE)
• drop scalarizing (#1052) (@isaacsas)
• Added docs and assets for interactive simulation plotting tutorial (#1053) (@jonathanfischer97)
• Fix broken tests (#1070) (@TorkelE)
• docs: add missing backtick (#1072) (@Mo-Gul)
• disable SI for now (#1074) (@vyudu)
• collect_vars support (#1077) (@isaacsas)
• Update hodgkin huxley example (#1082) (@isaacsas)
• bump optimization libs (#1084) (@isaacsas)
• Fixed doc build error by specifying DISPLAY, other workflow improvements (#1086) (@jonathanfischer97)
• try to update to SciML CI (#1094) (@isaacsas)
• fix tests (#1098) (@isaacsas)
• uncap master (#1100) (@isaacsas)
• BifurcationKit test (#1101) (@vyudu)
• Cap SciMLBase (#1103) (@isaacsas)
• Add compose dispatch and constent handling of scoping to MTK (#1104) (@isaacsas)
• add GLMakie dep (#1106) (@isaacsas)
• Add devdocs (#1108) (@isaacsas)
• CompatHelper: bump compat for NonlinearSolve to 4 for package docs, (keep existing compat) (#1109) (@github-actions[bot])
• switch docs to using OrdinaryDiffEq sublibraries (#1110) (@vyudu)
• fix docstrings (#1111) (@vyudu)
• Try smaller doc collapselevel (#1113) (@isaacsas)
• GraphMakie update (#1115) (@vyudu)
• Update PEtab tutorial (#1119) (@sebapersson)
• updating comments in extension files (#1120) (@vyudu)
• Add @no_infer flag for turning off species/variable/parameter inferring (#1122) (@vyudu)
• Add non-fileld arrow (=>) documentation to DSL docs (#1123) (@TorkelE)
• Fix dsl obs try again (#1124) (@TorkelE)
• Attempt to fix possible multiple PR docs build error (#1125) (@jonathanfischer97)
• Bump codecov/codecov-action from 4 to 5 (#1126) (@dependabot[bot])
• Uncap those bases (#1127) (@isaacsas)
• Drop OrdinaryDiffEq from tests (#1128) (@vyudu)
• @require_declaration docs (#1129) (@vyudu)
• GraphMakie docs update (#1130) (@vyudu)
• @require_declaration docs edits (#1131) (@vyudu)
• Update spatial models for new MTK release (#1133) (@TorkelE)
• Add API functions for the other kinds of matrixes that a CRN ODE system can be factored into (#1134) (@vyudu)
• Update test extensions Project.toml (#1136) (@isaacsas)
• Fix plot_complexes (#1138) (@vyudu)
• Improvements to graph plotting (#1140) (@vyudu)
• Refactoring network analysis docs (#1142) (@vyudu)
• fix: handle bug in remove_denominators (#1143) (@AayushSabharwal)
• Upate devdoc link (#1144) (@TorkelE)
• Fix serialisation tests (#1145) (@TorkelE)
• Reenable spatial tests (#1146) (@TorkelE)
• Add tutorial set-up code (#1147) (@TorkelE)
• Add errors for array species/parameters when submitted to LatticeReactionSystems (#1148) (@TorkelE)
• Update Optimization/parameter fitting tutorial (#1149) (@TorkelE)
• Remove last OrdinaryDiffEq mention (#1150) (@TorkelE)
• MTK tests update (#1153) (@TorkelE)
• Compound fixe (#1154) (@TorkelE)
• Remove glmakie in docs (#1155) (@isaacsas)
• test: added some edge cases in reactionsystem.jl and network_properties.jl (#1158) (@sivasathyaseeelan)
• Create DocsCleanup.yml (#1160) (@andreasnoack)
• Remove old previews (#1162) (@andreasnoack)
• Cap mtk (#1163) (@isaacsas)
• test: added an edge case for LatticeReactionSystem (#1164) (@sivasathyaseeelan)
• try to uncap symbolicutils (#1168) (@isaacsas)
• Try to enable SI on 1.11 (#1169) (@isaacsas)
• CompatHelper: add new compat entry for NetworkLayout at version 0.4 for package docs, (keep existing compat) (#1171) (@github-actions[bot])
• network_analysis cleanup: Updating ratematrix to be more similar to new matrix API functions (#1172) (@vyudu)
• test: added an edge case in ReactionSystem (#1174) (@sivasathyaseeelan)
• Update inference of variables and default differential from @equations macro (#1175) (@TorkelE)
• CompatHelper: bump compat for CairoMakie in [weakdeps] to 0.13, (keep existing compat) (#1176) (@github-actions[bot])
• CompatHelper: bump compat for CairoMakie to 0.13 for package docs, (keep existing compat) (#1177) (@github-actions[bot])
• Fix deprecation warnings in Latexify 0.16.6 (#1179) (@devmotion)
• Add advice on checking built docs to dev documentation (#1180) (@TorkelE)
• CompatHelper: bump compat for LinearSolve to 3 for package docs, (keep existing compat) (#1181) (@github-actions[bot])
• Consider the Danish/Norwegian letter ∅ as the empty set symbol (Ø) (#1184) (@TorkelE)
• Spatial plotting fixes (#1185) (@TorkelE)
• fixes for MTK changes (#1186) (@TorkelE)
• Fix graph defaults, plotting graphs (#1189) (@vyudu)
• Enable functional/time dependent parameters (#1191) (@TorkelE)
• Finish dsl src update (reorder functions) (#1193) (@TorkelE)
• Reenable stability computation docs and tests (#1196) (@TorkelE)
• [WIP] Minor docfixes (#1197) (@TorkelE)
• Add simulation type preservation tests (#1198) (@TorkelE)
• Update README.md with installation instructions (#1200) (@isaacsas)
• Remake for conservation laws update (#1203) (@TorkelE)
• Use MTK's symbol handling (#1205) (@TorkelE)
• Re-enable conservation laws for NonlinearSystems (#1206) (@TorkelE)
• Remove note about structural identifiability removal from history file. (#1207) (@TorkelE)
• Examples of ways to model noise (#1209) (@TorkelE)
• Example: Measuring activation time distribution (#1210) (@TorkelE)
• Add additional Jacobian tests (including sparsity) (#1211) (@TorkelE)
• CompatHelper: bump compat for DataInterpolations to 8 for package docs, (keep existing compat) (#1212) (@github-actions[bot])
• Add catalys version to serialisation function (#1213) (@TorkelE)
• test: fix DelayParentScope test (#1214) (@AayushSabharwal)
• BifurcationKit document update (#1215) (@TorkelE)
• Bifurcationkit periodic orbits example (#1216) (@TorkelE)
• Codim 2 bifurcation example (#1217) (@TorkelE)
• Re-add StructuralIdentifiability in lists on README.md page (#1218) (@TorkelE)
• Throw error when bundling reactions where only the rates differe (#1222) (@TorkelE)
• Add note about OrdinaryDiffEq solver libraries on simulation page (#1223) (@TorkelE)
• Expand Catalyst functions when converting (#1224) (@isaacsas)
• Project.toml housekeeping (#1226) (@TorkelE)
• Update installation instructions (#1228) (@isaacsas)
• Changes from doc readthrough (#1229) (@TorkelE)
• Drop symmap in docs (#1231) (@isaacsas)
• Release 15.0 (#1232) (@isaacsas)
• Disable PEtab doc (#1233) (@TorkelE)

Closed issues:

• Network analysis algorithms (#840)
• Explicitly mark variable-rate reactions (#1033)
• add option to turn off auto-discovery of species / parameters / variables (#1045)
• Extemely slow creation of ODEProblem from ReactionSystem (#1051)
• DSL doesn't allow @species to be assigned default values and metadata when using begin ... end syntax (#1054)
• DSL variables created from observable eqs are not equivalent to normal variables (#1057)
• TODO before V15 (i.e. scalarizing changes) (#1060)
• Catalyst does not work with ModelingToolkit v9.46 (#1075)
• Catalyst StackOverflowError for large Vector{Reaction} (#1080)
• doc builds failing (#1085)
• update CI scripts (#1093)
• drop OrdinaryDiffEq CI (#1096)
• Catalyst V15 todo (#1097)
• add compose(::ReactionSystem, ...) dispatch (#1099)
• Further decompostion of a system of ODEs coming from mass-action chemical reaction networks (#1132)
• Wrong edge labels in plot_complexes (#1135)
• Time can't have units in systems generated by DSL (#1141)
• Creation of a ReactionSystem from a reaction involving compounds and only_use_rate=true (#1151)
• test: Some tests are missing in Catalyst.jl/src/graphs.jl (#1157)
• Recent MTK regression errors (#1161)
• docs: creating DEVELOPMENT.md and MAINTAINERS.md (#1178)
• Missing plots in network graph plotting docs (#1182)
• Change some network graph plotting defaults (#1183)
• The parameter fitting example from the documentation throws an error (#1188)
• Pure jump process solution now has Float64 trajectories? (#1190)
• Cannot recreate circadian model JumpProcess example (#1199)
• Graph(rn) fails to create species nodes when species are defined programmatically (#1201)
• Catalyst V15 TODO version 2 (#1202)
• Consider restricting bundling (with multiple rates but singular reactant parts) (#1219)