Tags: SciML/Catalyst.jl
Tags
[Diff since v14.4.0](v14.4.0...v14.4.1) **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 latexify_recipes.jl (#1040) (@isaacsas) - expanding equations when passed to `@reaction_network` (#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)
[Diff since v14.3.2](v14.3.2...v14.4.0) **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)
[Diff since v14.1.0](v14.1.0...v14.2.0) **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)
[Diff since v14.0.1](v14.0.1...v14.1.0) **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)
[Diff since v14.0.0](v14.0.0...v14.0.1) **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)
[Diff since v13.5.1](v13.5.1...v14.0.0) **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 `Reactions`s (#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)
PreviousNext