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Update to DynamicalSystems.jl v3 (#299)
* get_state -> current_state * remove all files form include until update * `lyapunov` ported to v3.0 :) * finish lyapunov from data AND add new test file for lyapunovs * move code to TantentDynamicalSystem * delete all old useless stuff * lyapunovspectrum code works (add tests) * lyapunovspectrum tests pass * fully finish local growth rates * fully finish gali and its tests * polish and reorganize expansion entropy * hopefully update expansion entropy * add linreg (used by other unctions) * rename test files * update test suite * update testchaos01 * use readme as module docs * generalize orbit diagram * add progress meter in OD * finish OD for all systems! * rename * renames * upodate broomhead king * update tests * finish `fixedpoints` * finish estimate period * update periodicorbits * add preliminary doc files * copy docs over from DynamicalSystems.jl * remove delayembeddings from deps * finish lyapunovs docpage * finish orbitdiagram docs * fix yin algorithm * finish periodicity docs * finish updating chaos detection * finish chaostools.jl docs * hell yeah all tests pass * add error if distance isn't what its supposed to be * up changelog * update docstyle * fix docs * update readme * update CI files * all sysstems go * add delay embeddings to test suite * also add statistics * use a seed for the test,,...? * use simpler docbuild
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‎.github/ISSUE_TEMPLATE/bug_report.md

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If the code is **runnable**, it will help us identify the problem faster.
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**Agents.jl version**
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**Package versions**
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Please provide the version you use (you can do `Pkg.status("Agents")`.
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Please provide the versions of packages you use. To do this, run the code:
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```julia
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import Pkg
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Pkg.status([
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"Package1", "Package2"]; # etc.
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mode = PKGMODE_MANIFEST
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)
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```
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Please also include the Julia version you run.

‎.github/ISSUE_TEMPLATE/feature_request.md

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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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**Describe the feature you'd like to have**
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Cite scientific papers related to the feature/algorithm**
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**If possible, sketch out an implementation strategy**

‎.github/dependabot.yml

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version: 2
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updates:
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# Maintain dependencies for GitHub Actions
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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# Check for updates to GitHub Actions every week
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interval: "weekly"

‎.github/workflows/TagBot.yml

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lookback:
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default: 3
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permissions:
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actions: read
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checks: read
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contents: write
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deployments: read
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issues: read
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discussions: read
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packages: read
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pages: read
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pull-requests: read
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repository-projects: read
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security-events: read
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statuses: read
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jobs:
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‎.github/workflows/ci.yml

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pull_request:
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- main
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- '**' # matches every branch
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push:
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- main
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matrix:
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version:
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os: [ubuntu-latest]
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os: [ubuntu-latest] # adjust according to need, e.g. os: [ubuntu-latest] if testing only on linux
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arch:
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- x64
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steps:
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# Cancel ongoing CI test runs if pushing to branch again before the previous tests
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# have finished
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- name: Cancel ongoing test runs for previous commits
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uses: styfle/cancel-workflow-action@0.6.0
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uses: styfle/cancel-workflow-action@0.11.0
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with:
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access_token: ${{ github.token }}
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# Do tests
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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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- uses: julia-actions/setup-julia@v1
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with:
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version: ${{ matrix.version }}
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arch: ${{ matrix.arch }}
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- uses: actions/cache@v2
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- uses: actions/cache@v3
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env:
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${{ runner.os }}-test-${{ env.cache-name }}-
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${{ runner.os }}-test-
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${{ runner.os }}-
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- uses: julia-actions/julia-buildpkg@latest
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- uses: julia-actions/julia-runtest@latest
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- uses: julia-actions/julia-buildpkg@v1
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- uses: julia-actions/julia-runtest@v1
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- uses: julia-actions/julia-processcoverage@v1
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- uses: codecov/codecov-action@v3
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with:
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file: lcov.info

‎.github/workflows/doccleanup.yml

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name: Doc Preview Cleanup
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on:
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pull_request:
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types: [closed]
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jobs:
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doc-preview-cleanup:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout gh-pages branch
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uses: actions/checkout@v3
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with:
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ref: gh-pages
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- name: Delete preview and history
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run: |
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git config user.name "Documenter.jl"
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git config user.email "[email protected]"
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git rm -rf "previews/PR$PRNUM"
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git commit -m "delete preview"
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git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
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env:
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PRNUM: ${{ github.event.number }}
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- name: Push changes
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run: |
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git push --force origin gh-pages-new:gh-pages

‎.github/workflows/documentation.yml

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name: Documentation
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branches:
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- main
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tags: '*'
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pull_request:
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jobs:
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build:
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permissions:
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contents: write
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: julia-actions/setup-julia@v1
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with:
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version: '1'
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- name: Install dependencies
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run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
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- name: Build and deploy
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
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DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
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run: julia --project=docs/ docs/make.jl

‎.gitignore

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*.jl.mem
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*.css
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*.scss
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*style.jl

‎CHANGELOG.md

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# main
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**The following will become the 3.0 - Major release.**
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# v3.0
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Major release part of the DynamicalSystems.jl v3.
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The DynamicalSystems.jl v3 changelog summarizes the highlights. Here we will list all changes to _this specific package_.
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## Breaking
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- All `diffeq` keywords to all functions have been removed as per update to DynamicalSystems v3.0. Arguments to DifferentialEquations.jl solvers are now given in system construction when making a `CoupledODEs` (previously `ContinuousDynamicalSystem`).
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- The dependency list of ChaosTools.jl has been reduced by half; many things that used to be exported from here are no longer (see refactoring).
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- Low-level call signatures have been adjusted to fit DynamicalSystems.jl v3.0
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## Refactoring/removal
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- All functionality related to attractors and basins of attraction (e.g., `AttractorMapper`, `basins_fractions`) has been moved to a new package Attractors.jl. Notice that functions such as `fixedpoints` and `periodicorbits` stay in ChaosTools.jl because they aren't only about attractors; they also find unstable fixed points and/or periodic orbits.
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- All fractal dimension related functionality has been moved to a new package FractalDimensions.jl. This includes the functionality for finding linear regions and fitting them.
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## Rare events
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- New dedicated folder structure and functionality targeting rare events in ChaosTools.jl. If it becomes extensive, it can be split off to a different package.
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- New dedicated folder structure and functionality targeting rare events in ChaosTools.jl. If it becomes extensive, it can be split off to a new package.
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- Source code for `exit_entry_times` has been completely overhauled and is now
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## Other
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- New method for fractal dimension: `higuchi`
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- Improved the documentation of chaos detection methods overall.
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## Other enhancements
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- `orbitdiagram` is a completely generic function that works for any kind of `DynamicalSystem`. `produce_orbitdiagram` is deprecated as it is now practically useless.
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- ChaosTools.jl now has its own documentation as per DynamicalSystems.jl v3.0.
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- More examples have been placed that also better highlight how to parallelize.
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- Tests have been overhauled and never use predefined systems (which is a really bad practice when it comes to testing)
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* Improved the `AttractorsViaFeaturizing` algorithm by improving the method for finding the optimal radius used in the clustering. This consisted in (i) maximizing the average silhouette values, instead of minimum (slight improvement), (ii) min-max rescaling the features for the clustering (big improvement); (iii) adding an alternative method ,called elbow method, that is faster but worse at clustering.

‎CITATION.bib

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@article{Datseris2018,
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@article{DynamicalSystems.jl-2018,
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doi = {10.21105/joss.00598},
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url = {https://doi.org/10.21105/joss.00598},
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year = {2018},
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title = {DynamicalSystems.jl: A Julia software library for chaos and nonlinear dynamics},
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journal = {Journal of Open Source Software}
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}
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@book{DatserisParlitz2022,
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doi = {10.1007/978-3-030-91032-7},
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url = {https://doi.org/10.1007/978-3-030-91032-7},
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year = {2022},
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publisher = {Springer Nature},
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author = {George Datseris and Ulrich Parlitz},
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title = "Nonlinear dynamics: A concise introduction interlaced with code",
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address = "Cham, Switzerland",
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language = "en",
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}

‎Project.toml

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[deps]
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Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
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Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
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ComplexityMeasures = "ab4b797d-85ee-42ba-b621-05d793b346a2"
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DSP = "717857b8-e6f2-59f4-9121-6e50c889abd2"
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DelayEmbeddings = "5732040d-69e3-5649-938a-b6b4f237613f"
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Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
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Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
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DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4"
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Optim = "429524aa-4258-5aef-a3af-852621145aeb"
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ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
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Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
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Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
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Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
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SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
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StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
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Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
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DynamicalSystemsBase = "3"
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Reexport = "1"
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StatsBase = "0.24.0, 0.32, 0.33"
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julia = "1.5"
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[extras]
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DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
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Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
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LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
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OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
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Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
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Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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[targets]
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test = ["LinearAlgebra", "Test", "OrdinaryDiffEq", "DelimitedFiles", "Downloads", "Random"]
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julia = "1.5"

‎README.md

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![DynamicalSystems.jl logo: The Double Pendulum](https://i.imgur.com/nFQFdB0.gif)
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[![](https://img.shields.io/badge/docs-dev-lightblue.svg)](https://JuliaDynamics.github.io/ChaosTools.jl/dev)
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[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://JuliaDynamics.github.io/ChaosTools.jl/stable)
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[![](https://img.shields.io/badge/DOI-10.1007%2F978--3--030--91032--7-purple)](https://link.springer.com/book/10.1007/978-3-030-91032-7)
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[![CI](https://github.com/JuliaDynamics/ChaosTools.jl/workflows/CI/badge.svg)](https://github.com/JuliaDynamics/ChaosTools.jl/actions?query=workflow%3ACI)
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[![codecov](https://codecov.io/gh/JuliaDynamics/ChaosTools.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/JuliaDynamics/ChaosTools.jl)
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[![Package Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/ChaosTools)](https://pkgs.genieframework.com?packages=ChaosTools)
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Repository containing tools for the exploration of chaos and nonlinear dynamics. It
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is part of the library [DynamicalSystems.jl](https://juliadynamics.github.io/DynamicalSystems.jl/latest/).
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A Julia module that offers various tools for analysing nonlinear dynamics and chaotic behaviour.
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It can be used as a standalone package, or as part of
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[DynamicalSystems.jl](https://juliadynamics.github.io/DynamicalSystems.jl/dev/).
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| **Documentation** | **Tests** | Gitter |
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|:--------:|:-------------------:|:-----:|
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|[![](https://img.shields.io/badge/docs-latest-blue.svg)](https://JuliaDynamics.github.io/DynamicalSystems.jl/dev) | [![CI](https://github.com/juliadynamics/ChaosTools.jl/workflows/CI/badge.svg)](https://github.com/JuliaDynamics/ChaosTools.jl/actions) | [![Gitter](https://img.shields.io/gitter/room/nwjs/nw.js.svg)](https://gitter.im/JuliaDynamics/Lobby)
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To install it, run `import Pkg; Pkg.add("ChaosTools")`.
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The features of ChaosTools.jl are updated and expanded frequently and therefore we
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All further information is provided in the documentation, which you can either find [online](https://juliadynamics.github.io/ChaosTools.jl/dev/) or build locally by running the `docs/make.jl` file.
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_ChaosTools.jl is the jack-of-all-trades package of the DynamicalSystems.jl library: methods that are not extensive enough to be a standalone package are added here. You should see the full DynamicalSystems.jl library for other packages that may contain functionality you are looking for but did not find in ChaosTools.jl._

‎benchmark/default_alg.jl

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