v0.6 New features and examples

What's Changed

• Package clean-up by @reykboerner in #124
• test: add more covariance tests by @oameye in #127
• fix: set default verbose=false by @oameye in #128
• docs: add gMAM meierstein as example by @oameye in #66
• docs: add sgMAM example by @oameye in #131
• feat: MAM result struct by @oameye in #133
• feat: rewrite gMAM with optimization callback by @oameye in #134
• style: rm stale dependencies by @oameye in #136
• feat: Rewrite MAM by @oameye in #135
• style: pretty print MLP by @oameye in #137
• docs: improve docs on LDT by @oameye in #138
• docs: add docstring for MaximumLikelihoodPath struct by @oameye in #139
• remove equilib by @oameye in #140
• refactor transitions by @oameye in #141
• feat: string method by @oameye in #142
• style: rename MLP and use StateSpaceSet by @oameye in #146
• make MinimumActionPath non-mutable by @oameye in #147
• feat: make the string method compatiable with StateSpaceSet by @oameye in #148
• feat: add SgMAM StateSpaceSet method by @oameye in #153
• feat: make transitions reproduceable by @oameye in #154
• feat: EnsembleStatistics by @oameye in #155
• feat: add error messages for LDT by @oameye in #157
• feat: Transition Path Theory by @oameye in #159
• build: enable cache in documentation CI by @oameye in #160
• style: refactor tpt by @oameye in #161
• CompatHelper: bump compat for LinearSolve to 3, (keep existing compat) by @github-actions in #166
• CompatHelper: bump compat for IntervalArithmetic to 0.22, (keep existing compat) by @github-actions in #129
• build: fix downgrade CI by @oameye in #168
• CompatHelper: bump compat for Interpolations to 0.16, (keep existing compat) by @github-actions in #169

Full Changelog: v0.5...v0.6

v0.5 Streamlined source code

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 CoupledSDEs re-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

What's Changed

• Stochsystem overhaul by @oameye in #76

This release replaces the StochSystem struct of all previous versions 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: v0.2.1...v0.3.0

`v0.2.1` Freeze before v0.3 overhaul

This freezes the latest running version of the package before breaking changes coming with the v0.3.0 overhaul, where the StochSystem struct will be replaced by the new struct CoupledSDEs.

For more info, view the changelog.

v0.2.0 Compatibility upgrade to DynamicalSystems v3

This version brings our package up-to-date with the v3 release of DynamicalSystems.jl, includes some changes in system definitions and function names, and features a new function to switch from a StochSystem in state space to a StochSystem in pathspace describing a stochastic bridge.

For more details, see the changelog.

v0.1.1 Feature freeze before v0.2.0

Last version compatible with DynamicalSystems v2 before upgrading dependencies to DynamicalSystems v3 and adding breaking changes to the system type definitions.

Changelog: https://github.com/reykboerner/CriticalTransitions.jl/blob/main/CHANGELOG.md

v0.1.0 First beta release

Full Changelog: https://github.com/reykboerner/CriticalTransitions.jl/blob/main/CHANGELOG.md