v14.0.0
·
304 commits
to master
since this release
Catalyst 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
andD
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 forReaction
(#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
not0.0
indiff_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
inNonlinearSystem
creation (#777) - The
complete
field is aNum
? (#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)