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Changelog for CriticalTransitions.jl

v0.5.0

Package clean-up

This release brings a streamlined source code, with unused and deprecated code removed, dependencies reduced, and a unified style of displaying progress meters.

Changed functions

  • intervals_to_box is now part of the ChaosToolsExt extension and is loaded only when using ChaosTools
  • The keyword argument showprogress changed to show_progress in several functions for consistency
  • In min_action_method, the keyword argument Stol is now called action_tol

Deprecations

  • Functions make_h5 and make_jld2 have been removed
  • Dependencies HDF5, JLD2, and ProgressBars have been removed
  • Dependency IntervalArithmetic is now only a dependency of some extensions

Full changelog here.

v0.4.0

New CoupledSDEs design

This release upgrades CriticalTransitions.jl to be compatible with the re-design of CoupledSDEs, which has now been integrated in DynamicalSystemsBase.jl v3.11.

Since we have updated the syntax of defining a CoupledSDEs system, this is a breaking change.

Changed functions

  • CoupledSDEs is now constructed with different args and kwargs
  • fw_action, geometric_action and om_action now normalize the covariance matrix when computing the action functional
  • noise_strength is not a function anymore but a kwarg for CoupledSDEs and other functions
  • om_action now requires noise_strength as input argument
  • relax was renamed to deterministic_orbit
  • trajectory has been added to replace simulate

Deprecations

  • add_noise_strength, idfunc and idfunc! are no longer needed and have been removed
  • the function noise_strength(::CoupledSDEs) has been removed
  • simulate has been removed

Full changelog here.

v0.3.0

Major overhaul introducing CoupledSDEs

This release replaces the StochSystem struct with the new CoupledSDEs struct to define a stochastic dynamical system. To see how the new version works, check out the documentation.

The update is a breaking change for almost all functions, because the interface is now built around CoupledSDEs. The benefit is that the package now integrates much more seamlessly with DynamicalSystems.jl and DifferentialEquations.jl. To use the package with the old StochSystem struct, choose version v0.2.1 or lower.

Full changelog here

v0.2.1

Freeze before major overhaul v0.3.0

Fixes

  • bug fixes in the following functions:
    • min_action_method
    • geometric_min_action_method
    • StochSystem(::CouplesODEs)
    • fhn_pathspace_sampling

Enhancements

  • expanded output of transitions function

Additions

  • tests for various functions
  • dev functions basboundary, bisect_to_edge2, langevinmcmc_not_every_step

Deprecations

  • to_cds function (still exists but will raise deprecation warning)

Since v0.2.0, we also joined JuliaDynamics with this package, such that the code is now hosted at https://github.com/JuliaDynamics/CriticalTransitions.jl, and improved the documentation.

v0.2.0

Compatibility upgrade to DynamicalSystems v3

BREAKING changes

  • changed StochSystem.dim to StochSystem.u
  • changed keyword arguments in basins and bisect_to_edge functions
  • removed tocds function (replaced by CoupledODEs)
  • renamed functions:
    • mam -> min_action_method
    • gmam -> geometric_min_action_method
    • FitzHughNagumo -> fitzhugh_nagumo
    • FitzHughNagumo! -> fitzhugh_nagumo!

New functions

  • stochastic_bridge
  • CoupledODEs(sys::StochSystem, ...)
  • StochSystem(ode::CoupledODEs, ...)

First prototype of a RateSystem.

v0.1.1

Feature freeze before v0.2.0

This version is compatible with v2 of DynamicalSystems.jl (specifically DynamicalSystems v2.3.2). The next release (v0.2.0) will include some breaking changes in the system type definitions and upgrade its dependencies to DynamicalSystems v3.

New functionality since previous release

  • Large deviation theory: fw_action, om_action, geometric_action, action, mam and gmam
  • Langevin MCMC sampling in pathspace: langevinmcmc
  • Edge tracking algorithm: edgetracking
  • Basins of attraction: basins, basinboundary
  • additional convenience functions added

New predefined systems

  • Ocean models: stommel, cessi, rooth_smooth
  • Population dynamics: originaltruscottbrindley, modifiedtruscottbrindley, rivals

Tested main functions on the FitzHugh-Nagumo model by running test/functest.jl.

v0.1.0

First release! 🎉

Tested for out-of-place system function FitzHughNagumo with WhiteGauss noise

Current functionality

Introduced the StochSystem type with the following methods:

  • equilib - get equilibrium starting from initial condition
  • fixedpoints - get fixedpoints of system as in DynamicalSystems.jl
  • relax - simulate deterministic dynamics from initial condition
  • simulate - simulate stochastic dynamics from initial condition
  • transition - simulate transition sample from state 1 to state 2
  • transitions - simulate an ensemble of transition samples from state 1 to 2
  • tocds - convert StochSystem to ContinuousDynamicalSystem of DynamicalSystems.jl

Added convenience functions make_jld2, sys_string, sys_info, idfunc, idfunc!.

Systems

  • FitzHughNagumo, FitzHughNagumo!