Super duper major update that has just been tagged!
It has been a long time and a lot of hard work, but I can already see it was worth it :')
In the remaining of March I’ll spend time “putting out fires” (as I’m sure something broke that I didn’t foresee), porting the documentation to a DiffEq like style with links to other packages overhead, and making a new logo!
Practically all packages that are part of DynamicalSystems.jl have been overhauled in some way or another. Some have been completely overhauled, like
ComplexityMeasures. Some others have been partially overhauled like
DynamicalSystems.jl was the first library I’ve written and after progressing as a software developer I have learned so much more about good design. I’ve put all this knowledge to good use and decided it was a good point to just do a mass-overhaul on the package.
The packages that compose DynamicalSystems.jl have been split up into more packages, making a more modular library, and also allowing a much smaller dependency tree for users that want only a specific part of the functionality.
The modularization itself did not bring any breaking changes.
This modularization also lead to a documentation overhaul: now every package of the library builds and hosts its own documentation. The DynamicalSystems.jl brings everything together with an overarching tutorial and points to the individual docs.
The main documentation of DynamicalSystems.jl now includes an overarching tutorial and overview, and then “dispatches” to documentations of other packages.
In the near future the documentation will be in the style similar to DiffEqDocs, however, I am still exploring alternative and stable ways to achieve similar results.
Notable breaking changes
trajectoryfunction now returns both the state space set and the time vector. In sort, all code that did
A = trajectory(...)is now broken and should be replaced by
A, tvec = trajectory(...).
There are no longer
diffeqkeyword arguments to downstream functions. All functions such as
lyapunovspectrum, basins_of_attraction, etc. no longer accept the
diffeqkeyword, that used to specify arguments for DifferentialEquations.jl. Instead, the DiffEq solver options are decided during the creation of
CoupledODEs(what was before
The basic dynamical system constructors do not accept a Jacobian. Giving a fourth argument will error. The dedicated
TangentDynamicalSystemshould be used for this.
Some things have been renamed to have a clearer and more specific name. These aren’t breaking changes, only deprecations. From the top of my head, the most important ones are:
Dataset → StateSpaceSet
DiscreteDynamicalSystem → DeterministicIteratedMap
ContinuousDynamicalSystem → CoupledODEs
The special type for 1D discrete dynamical systems has been removed. 1D systems are now represented by a 1D static vector that needs to be reshaped accordingly.
The core library DynamicalSystemsBase.jl has had a complete re-write. This has the following major impacts:
Concept of what is a “dynamical system” is much more general. now
DynamicalSystemdefines a proper, extendable interface. The set of functions that the interface satisfies are listed in
More variants of a dynamical system are offered. Any arbitrary steppable thing, like an agent based model, can become a dynamical system.
Overall much better and rigorous tests.
Now all concrete implementations of
DynamicalSystemcan be iteratively evolved in time via the
step!function. For example,
ContinuousDynamicalSystemis now a light wrapper around
ODEIntegrator. After working with this library for years I realized that the “middle man” of representing a dynamical system (like an ode problem) was not really necessary in downstream functions, since all of them exclusively use an integrator.
Dynamical systems are completely detached from a Jacobian creation, which now is the exclusive task of
TangentDynamicalSystem. As a result all predefined dynamical systems do not include a hand-coded Jacobian; rather the Jacobian needs to be given from
Systemssubmodule to the
Systems submodule has been removed from the DynamicalSystemsBase.jl package and became a new package PredefinedDynamicalSystems.jl. It is untested and it is not recommended to use in any other setting other a demonstrational example. (this was always the case, it’s just that so far we weren’t transparent that nothing there was tested…)
Read more here: DynamicalSystemsBase.jl · DynamicalSystemsBase.jl
ODE solver change
The default integrator used in continuous time Ordinary Differential Equations (what was before called
ContinuousDynamicalSystem and now called
CoupledODEs) is now
Tsit5(). This means that OrdinaryDiffEq.jl is a dependency of DynamicalSystemsBase.jl. It is a better option than the previous
SimpleATsit5(). Additionally, the insane compile and first-use time improvements in latest Julia versions had made the impact of loading OrdinaryDiffEq.jl much smaller.
Package split: StateSpaceSets.jl
It has all functionality surrounding
StateSpaceSet (what was previously known as
Dataset). It therefore detaches the infrastructure for handing numeric data from delay embeddings, and now DelayEmbeddings.jl is a package dedicated to creating and optimizing delay coordinates embeddings.
Package split: FractalDimensions.jl
All functionality related to computing fractal dimensions has been detached from ChaosTools.jl into a new package: FractalDimensions.jl · FractalDimensions.jl
Partial overhaul: RecurrenceAnalysis.jl
RecurrenceAnalysis.jl, now in v2.0, has had its core type (
RecurrenceMatrix) overhauled for better design, more clarity, extendibility, and overall more Julian programming utilizing multiple dispatch and dedicated types to specify options.
Now a subtype of
AbstractRecurrenceType is used to specify how to create a recurrence matrix. More details in the docpage of the package:
New amazing package ComplexityMeasures.jl
This is a complete overhaul and massive enhancement of the previous Entropies.jl and deserves its own announcement post: ComplexityMeasures.jl
New amazing package Attractors.jl
Incredibly exciting stuff that we (@awage @kalelr @Datseris) have been working on for the last year. It features an interface for finding attractors and their basin fractions, as well as a new approach to “continuation”. We are currently writing a paper for this, so the package doesn’t have an announcement yet. Once we have the preprint though, we will write an announcement post for the package and share the pre-print!
For now, feel free to see the docs and give us feedback!!!
Some parts of the library have co-maintainers (Attractors.jl has @awage and @kalelr, ComplexityMeasures.jl and TimeseriesSurrogates.jl have @kahaaga) but this whole ecosystem around DynamicalSystems.jl has become too large and I think I just don’t have the time to maintain it alone anymore. So, I am kindly asking for people with expertise in both NLD and programming to consider coming on board and helping with answering questions, addressing issues, fixing bugs, and testing out the ecosystem. Feel free to contact me via a PM on Slack or here on Discourse!