Releases | Open Source Science

Catalyst v15.0.8

Merged pull requests: - Uncap SciMLBase for 15.0.8 (#1275) (@isaacsas)

- Julia
Published by github-actions[bot] 9 months ago

Catalyst v15.0.7

Merged pull requests: - Add finite state projection example (#1269) (@TorkelE) - Update missing test symbolic indexing of solutions (#1270) (@TorkelE) - bump SciMLBase for 15.0.7 (#1273) (@isaacsas)

Closed issues: - plot_network not working with example from docs (#1271)

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Published by github-actions[bot] 9 months ago

Catalyst - v15.0.6

Catalyst v15.0.6

Diff since v15.0.5

Merged pull requests: - Add example of how to compute nullclines using bifurcation kit (#1194) (@TorkelE) - Update documenter version (#1265) (@TorkelE) - bump deps for 15.0.6 (#1268) (@isaacsas)

Closed issues: - Enable interpolation of functional variable (but not its argument). (#1208) - ContinuousCallback not handled correctly (#1262)

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Published by github-actions[bot] 9 months ago

Catalyst - v15.0.5

Catalyst v15.0.5

Diff since v15.0.4

Merged pull requests: - Fix ocasional hybrid test failure (#1255) (@TorkelE) - RemoveDiscreteProblems in tests (#1257) (@TorkelE) - bump versions (#1258) (@isaacsas) - Test release 15.0.5 attempt 2 (#1260) (@isaacsas)

Closed issues: - HC doc examples failing (#1170)

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Published by github-actions[bot] 10 months ago

Catalyst - v15.0.4

Catalyst v15.0.4

Diff since v15.0.3

Merged pull requests: - test: fix parameter initialization test (#1251) (@AayushSabharwal)

Closed issues: - update HH example to just use the DSL (#991)

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Published by github-actions[bot] 10 months ago

Catalyst - v15.0.3

Catalyst v15.0.3

Diff since v15.0.2

Merged pull requests: - remove unpacksys (#1247) (@isaacsas) - Fix indexing deprecation warning (#1248) (@isaacsas) - test: make test robust to ordering of unknowns (#1249) (@AayushSabharwal) - Update constraint tutorial (#1252) (@isaacsas) - bump projects (#1253) (@isaacsas) - release 15.0.3 (#1254) (@isaacsas)

Closed issues: - no longer assume that prob.p is the correct parameters for a problem lacking callbacks and DAEs (#1087) - Interface for specifying what mathematical level to resolve a reaction at (#1112) - Nonnegative rates in jumps (#1225)

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Published by github-actions[bot] 10 months ago

Catalyst - v15.0.2

Catalyst v15.0.2

Diff since v15.0.1

Merged pull requests: - test: broken test is now fixed (#1244) (@AayushSabharwal) - Release 15.0.2 proj bumps (#1245) (@isaacsas)

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Published by github-actions[bot] 10 months ago

Catalyst - v15.0.1

Catalyst v15.0.1

Diff since v15.0.0

Merged pull requests: - Support Jump-ODE models (#1121) (@isaacsas) - Improve expression parser function (#1230) (@TorkelE) - Error when having differentials w.r.t. species (#1237) (@TorkelE) - DSL inference FAQ section (#1238) (@TorkelE) - Remove remove_conserved warning from nonlinear solve doc page (#1239) (@TorkelE) - Enables DSL interpolation of a function name only (#1240) (@TorkelE) - Add PEtab.jl to the docs (#1241) (@sebapersson) - Some doc update post v15 (#1242) (@isaacsas) - CompatHelper: add new compat entry for EnumX at version 1, (keep existing compat) (#1243) (@github-actions[bot])

Closed issues: - Drop Graphviz and requires (#512) - Future addition to Bifurcation diagram tutorial (#741) - valid ways to write equations using the DSL (#1044) - Reenable StructuralIdentifiability tests and tutorial once fixed (#1068) - Cases where a single symbol can explicitly be declared as different things (#1173) - Positive domain enforcement (again, but new area of relevance) (#1195)

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Published by github-actions[bot] 10 months ago

Catalyst - 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) - collectvars 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 @noinfer 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 networkproperties.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]) - networkanalysis 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 plotcomplexes (#1135) - Time can't have units in systems generated by DSL (#1141) - Creation of a ReactionSystem from a reaction involving compounds and onlyuse_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)

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Published by github-actions[bot] 10 months ago

Catalyst - v14.4.1

Catalyst v14.4.1

Diff since v14.4.0

Merged pull requests: - CompatHelper: bump compat for DynamicQuantities to 1, (keep existing compat) (#1031) (@github-actions[bot]) - Fix tests (#1038) (@isaacsas) - update periodic event tutorial (#1039) (@isaacsas) - Update latexifyrecipes.jl (#1040) (@isaacsas) - expanding equations when passed to `@reactionnetwork` (#1041) (@vyudu) - Remove double completion (#1046) (@ChrisRackauckas)

Closed issues: - VariableRateJump Problems (#636) - missing new line in Latexify display after last equation in sytstems with reactions an equations (#927) - Unrechable code in latexify code (#972) - DSL issues with equations (#1022) - @equations not seeing parameters defined outside the @reaction_network macro (#1042)

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Published by github-actions[bot] over 1 year ago

Catalyst - v14.4.0

Catalyst v14.4.0

Diff since v14.3.2

Merged pull requests: - CompatHelper: bump compat for DynamicPolynomials to 0.6, (keep existing compat) (#961) (@github-actions[bot]) - CompatHelper: bump compat for Symbolics to 6, (keep existing compat) (#1016) (@github-actions[bot]) - cleanup DSL generated expression for readability (#1024) (@isaacsas) - Update docs Project.toml (#1030) (@isaacsas)

Closed issues: - Display issues for vector variables/parameters in Latexify (#932) - test for units currently broken (#1035)

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Published by github-actions[bot] over 1 year ago

Catalyst - v14.3.2

Catalyst v14.3.2

Diff since v14.3.1

Merged pull requests: - arguments -> sorted_arguments updates (#1021) (@TorkelE) - Metadata dispatch fix (#1026) (@isaacsas)

Closed issues: - supporting SBML efforts (#312)

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Published by github-actions[bot] over 1 year ago

Catalyst - v14.3.1

Catalyst v14.3.1

Diff since v14.3.0

Merged pull requests: - cleanup reaction getmetadata function and fix error mesg bug (#1019) (@isaacsas) - fix math descript typos (#1020) (@isaacsas)

Closed issues: - dangling line in reaction metadata function (#1018)

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Published by github-actions[bot] over 1 year ago

Catalyst - v14.3.0

Catalyst v14.3.0

Diff since v14.2.0

Merged pull requests: - variable rate jump support (#1015) (@isaacsas)

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Published by github-actions[bot] over 1 year ago

Catalyst - v14.2.0

Catalyst v14.2.0

Diff since v14.1.0

Merged pull requests: - Deficiency one and concnetration robustness (#964) (@vyudu) - Revert SDE change (#979) (@TorkelE) - Latexify fix and add SciMLBase dep for controlling release compat (#1001) (@isaacsas) - Long jump plotting fix (#1006) (@isaacsas) - Uncap SciMLBase (#1007) (@ChrisRackauckas) - test: remove unnecessarily specific parameter type annotations (#1010) (@AayushSabharwal) - add jump auto-alg support (#1013) (@isaacsas) - misc updates (#1014) (@isaacsas)

Closed issues: - Fix long doc build time for single figure in intro to Catalyst (#994) - uncap SciMLBase from 2.44 (#1005) - Bug in function generation with Catalyst.jl v14 (#1009)

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Published by github-actions[bot] over 1 year ago

Catalyst - 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)

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Published by github-actions[bot] over 1 year ago

Catalyst - 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)

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Published by github-actions[bot] over 1 year ago

Catalyst - 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 catalystapi.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 `@combinatoricratelawsto 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) - Addconservedquantitymetadata (#853) (@TorkelE) - Addnonreactionfunction (#854) (@TorkelE) - Addgetvariablesdispatch forReaction(#855) (@TorkelE) - UpdateReactionconstructor (#856) (@TorkelE) - SerialiseReactionSystemto file. (#857) (@TorkelE) - Renamereactionparams` 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 testnetworks.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 settingtinNonlinearSystemcreation (#777) - Thecompletefield is aNum? (#782) -@registerambiguity (#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) -@unpackdoes 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 inHomotopyContinuationdocs tutorial (#860) - Removeusing 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)

- Julia
Published by github-actions[bot] over 1 year ago

Catalyst - 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)

- Julia
Published by github-actions[bot] over 2 years ago

Catalyst - 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)

- Julia
Published by github-actions[bot] over 2 years ago

Catalyst - v13.4.1

Catalyst v13.4.1

Diff since v13.4.0

Merged pull requests: - fix hh docs (#669) (@isaacsas)

- Julia
Published by github-actions[bot] over 2 years ago

Catalyst - 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)

- Julia
Published by github-actions[bot] over 2 years ago

Catalyst - 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])

- Julia
Published by github-actions[bot] almost 3 years ago

Catalyst - 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)

- Julia
Published by github-actions[bot] almost 3 years ago

Catalyst - v13.2.0

Catalyst v13.2.0

Diff since v13.1.0

Merged pull requests: - allow array variables in DSL (#630) (@isaacsas)

- Julia
Published by github-actions[bot] almost 3 years ago

Catalyst - v13.1.0

Catalyst v13.1.0

Diff since v13.0.0

Closed issues: - Tutorials to add (#222) - Allowing units via the DSL (#382) - Add back BifurcationKit tutorial (#604) - add @variables to the DSL (#615) - Allow setting independent variables in the DSL (#624)

Merged pull requests: - Dynamic doc index (#621) (@isaacsas) - Tests remake (#622) (@TorkelE) - Variables in DSL (#623) (@isaacsas) - Finalise test remake (#626) (@TorkelE) - Doc updates (#627) (@isaacsas) - Reorder symbols at beginning of home readme (#628) (@TorkelE)

- Julia
Published by github-actions[bot] almost 3 years ago

Catalyst - v13.0.0

Catalyst v13.0.0

Diff since v12.3.2

Closed issues: - @addreactions macro issue (#249) - TODO per discussion of 11/25 (#280) - Create new model without declaring parameters (#333) - steady-state of reaction system (#389) - disallow repeated substrates or products in reactions (#516) - consider ordering Reaction components (#547) - Distinguishing species from normal variables and handling non-rx equations (#569) - drop addreactions! (#573) - Change Docoument outline (#581) - Enable symbolic manipulation of u0 and p vector (#582) - drop mutating system extenders (#583) - Catalyst 13 TODO (#584) - Variable rate constants in programatically constructed ReactionSystems (#586) - Parse error when defining reaction network in Jupyter notebook (#595) - Forbidden symbols check in DSL no longer working (#597) - Parameter optimization tutorial outdated (#603)

Merged pull requests: - Redo dsl syntax (#572) (@TorkelE) - add and use metadata for species (#585) (@isaacsas) - Fix array printing (#587) (@isaacsas) - Starting documentation reordering (#588) (@TorkelE) - Add form option to latexify (#589) (@TorkelE) - Add advanced simulation tutorial (#591) (@TorkelE) - Various docs fixes (#592) (@TorkelE) - Fix forbidden symbols (#605) (@TorkelE) - Drop mhchem (#609) (@isaacsas) - Update param est tutorial and fix advanced simulation tutorial figures (#611) (@isaacsas) - add back homotopy continuation tutorial (#612) (@isaacsas) - Event tests and continuous event bug fix (#613) (@isaacsas) - constraint and event tutorial with latexify fixes (#614) (@isaacsas) - Disallow repeated reactants and making hashing order independent (#616) (@isaacsas) - tweak event tutorial (#617) (@isaacsas) - doc tweak (#618) (@isaacsas) - fix broken latex from Katex (#619) (@isaacsas)

- Julia
Published by github-actions[bot] almost 3 years ago

Catalyst - v12.3.2

Catalyst v12.3.2

Diff since v12.3.1

Closed issues: - bifurcation analysis support (#81) - Reaction rates with greek letter is followed by a number cause latexify error (#566) - Non-unicode alternative for overriding mass action kinetics (#574) - Unable to remake large network ODEProblem for ensemble calculation (#575)

Merged pull requests: - Remove unnecessary type parameter (#564) (@LilithHafner) - Add tutorial for Catalyst and Julia for users inexperienced with Julia (#565) (@TorkelE) - reproducible docs (#567) (@ArnoStrouwen) - fix local doc builds, use joinpath, and tweak tutorial (#568) (@isaacsas) - [skip ci] doc compat (#570) (@ArnoStrouwen) - [skip ci] doc compats (#577) (@ArnoStrouwen) - Enable => and <= to ignore law of mass action in DSL (#580) (@TorkelE)

- Julia
Published by github-actions[bot] about 3 years ago

Catalyst - v12.3.1

Catalyst v12.3.1

Diff since v12.3.0

Closed issues: - support more general affects (#308) - Matricial ts theory (#555) - Unable to compute sparse jacobian (using SparseDiffTools) for reaction system (UndefVarError: m not defined) (#559) - Unable to plot observables with vars=observed(rn) (#560)

Merged pull requests: - update first few tutorials to be dynamic (#556) (@isaacsas) - allow multivariable states (#557) (@isaacsas) - PDE support doc updates (#561) (@isaacsas) - canonize docs (#562) (@ArnoStrouwen) - add logo (#563) (@ArnoStrouwen)