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* remove warnings of untyped parameters * more unused typed paramas * renames for StateSpaceSets.jl v1 * update readme * bump version to 3.0 * folder refactor * better readme * add docs here from DynamicalSystems.jl * state space set reference * update version to 2.6 * finish separated embedding page * finish unified page as well * bump version to 2.7 * update github workflows * fix auto separated embeddding tests * fix autodelay time tests * remove old file * use dedicated test project toml
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| --- | ||
| name: Bug report | ||
| about: Create a report to help us improve | ||
| title: '' | ||
| labels: '' | ||
| assignees: '' | ||
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| --- | ||
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| **Describe the bug** | ||
| A clear and concise description of what the bug is. | ||
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| **Minimal Working Example** | ||
| Please provide a piece of code that leads to the bug you encounter. | ||
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| If the code is **runnable**, it will help us identify the problem faster. | ||
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| **Package versions** | ||
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| Please provide the versions of packages you use. To do this, run the code: | ||
| ```julia | ||
| import Pkg | ||
| Pkg.status([ | ||
| "Package1", "Package2"]; # etc. | ||
| mode = PKGMODE_MANIFEST | ||
| ) | ||
| ``` | ||
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| Please also include the Julia version you run. |
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| --- | ||
| name: Feature request | ||
| about: Suggest an idea for this project | ||
| title: '' | ||
| labels: '' | ||
| assignees: '' | ||
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| **Describe the feature you'd like to have** | ||
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| **Cite scientific papers related to the feature/algorithm** | ||
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| **If possible, sketch out an implementation strategy** |
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| version: 2 | ||
| updates: | ||
| # Maintain dependencies for GitHub Actions | ||
| - package-ecosystem: "github-actions" | ||
| directory: "/" | ||
| schedule: | ||
| # Check for updates to GitHub Actions every week | ||
| interval: "weekly" |
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| name: TagBot | ||
| on: | ||
| schedule: | ||
| - cron: 0 * * * * | ||
| issue_comment: | ||
| types: | ||
| - created | ||
| workflow_dispatch: | ||
| inputs: | ||
| lookback: | ||
| default: 3 | ||
| permissions: | ||
| actions: read | ||
| checks: read | ||
| contents: write | ||
| deployments: read | ||
| issues: read | ||
| discussions: read | ||
| packages: read | ||
| pages: read | ||
| pull-requests: read | ||
| repository-projects: read | ||
| security-events: read | ||
| statuses: read | ||
| jobs: | ||
| TagBot: | ||
| if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot' | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: JuliaRegistries/TagBot@v1 | ||
| with: | ||
| token: ${{ secrets.GITHUB_TOKEN }} | ||
| ssh: ${{ secrets.DOCUMENTER_KEY }} |
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| name: Doc Preview Cleanup | ||
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| on: | ||
| pull_request: | ||
| types: [closed] | ||
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| jobs: | ||
| doc-preview-cleanup: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout gh-pages branch | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| ref: gh-pages | ||
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| - name: Delete preview and history | ||
| run: | | ||
| git config user.name "Documenter.jl" | ||
| git config user.email "[email protected]" | ||
| git rm -rf "previews/PR$PRNUM" | ||
| git commit -m "delete preview" | ||
| git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree}) | ||
| env: | ||
| PRNUM: ${{ github.event.number }} | ||
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| - name: Push changes | ||
| run: | | ||
| git push --force origin gh-pages-new:gh-pages |
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| name: Documentation | ||
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| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| tags: '*' | ||
| pull_request: | ||
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| jobs: | ||
| build: | ||
| permissions: | ||
| contents: write | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: julia-actions/setup-julia@v1 | ||
| with: | ||
| version: '1' | ||
| - name: Install dependencies | ||
| run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()' | ||
| - name: Build and deploy | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token | ||
| DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key | ||
| run: julia --project=docs/ docs/make.jl |
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| Manifest.toml | ||
| *.csv | ||
| docs/build/* | ||
| Manifest.toml | ||
| *.scss | ||
| *.css | ||
| .DS_Store | ||
| *vscode | ||
| *.css | ||
| *.scss | ||
| *style.jl |
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| # DelayEmbeddings.jl | ||
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|  | ||
| [](https://JuliaDynamics.github.io/DelayEmbeddings.jl/dev) | ||
| [](https://JuliaDynamics.github.io/DelayEmbeddings.jl/stable) | ||
| [](https://link.springer.com/book/10.1007/978-3-030-91032-7) | ||
| [](https://github.com/JuliaDynamics/DelayEmbeddings.jl/actions?query=workflow%3ACI) | ||
| [](https://codecov.io/gh/JuliaDynamics/DelayEmbeddings.jl) | ||
| [](https://pkgs.genieframework.com?packages=DelayEmbeddings) | ||
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| | **Documentation** | **Tests** | Gitter | | ||
| |:--------:|:-------------------:|:-----:| | ||
| |[](https://JuliaDynamics.github.io/DynamicalSystems.jl/dev) | [](https://github.com/JuliaDynamics/DelayEmbedding.jl/actions) | [](https://gitter.im/JuliaDynamics/Lobby) | ||
| A Julia package that provides a generic interface for performing delay coordinate embeddings, as well as cutting edge algorithms for creating optimal embeddings given some data. | ||
| It can be used as a standalone package, or as part of | ||
| [DynamicalSystems.jl](https://juliadynamics.github.io/DynamicalSystems.jl/dev/). | ||
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| To install it, run `import Pkg; Pkg.add("DelayEmbeddings")`. | ||
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| Contained here: | ||
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| 1. Defines the `Dataset` structure, which is a wrapper of `Vector{SVector}`, used in **DynamicalSystems.jl**. | ||
| 2. Implements methods for delay coordinates embedding with high performance and many features. | ||
| 3. Algorithms for estimating optimal delay embedding parameters, the delay time and the number of temporal neighbors (generalization of the "embedding dimension"). | ||
| 4. New, _unified_ algorithms for optimal delay embedding. | ||
| All further information is provided in the documentation, which you can either find [online](https://juliadynamics.github.io/DelayEmbeddings.jl/stable/) or build locally by running the `docs/make.jl` file. |
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| Original file line number | Diff line number | Diff line change |
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| [deps] | ||
| CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" | ||
| ChaosTools = "608a59af-f2a3-5ad4-90b4-758bdf3122a7" | ||
| ComplexityMeasures = "ab4b797d-85ee-42ba-b621-05d793b346a2" | ||
| CoordinateTransformations = "150eb455-5306-5404-9cee-2592286d6298" | ||
| DelayEmbeddings = "5732040d-69e3-5649-938a-b6b4f237613f" | ||
| Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" | ||
| Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" | ||
| DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8" | ||
| DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4" | ||
| ImageTransformations = "02fcd773-0e25-5acc-982a-7f6622650795" | ||
| Rotations = "6038ab10-8711-5258-84ad-4b1120ba62dc" | ||
| SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" | ||
| StateSpaceSets = "40b095a5-5852-4c12-98c7-d43bf788e795" | ||
| StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" | ||
| Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" | ||
| TestImages = "5e47fb64-e119-507b-a336-dd2b206d9990" | ||
| TimeseriesSurrogates = "c804724b-8c18-5caa-8579-6025a0767c70" |
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| cd(@__DIR__) | ||
|
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| import Downloads | ||
| Downloads.download( | ||
| "https://raw.githubusercontent.com/JuliaDynamics/doctheme/master/apply_style.jl", | ||
| joinpath(@__DIR__, "apply_style.jl") | ||
| ) | ||
| include("apply_style.jl") | ||
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| using DelayEmbeddings | ||
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| DelayEmbeddings_PAGES = [ | ||
| "index.md", | ||
| "embed.md", | ||
| "separated.md", | ||
| "unified.md", | ||
| ] | ||
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| makedocs( | ||
| modules = [DelayEmbeddings, StateSpaceSets], | ||
| format = Documenter.HTML( | ||
| prettyurls = CI, | ||
| assets = [ | ||
| asset("https://fonts.googleapis.com/css?family=Montserrat|Source+Code+Pro&display=swap", class=:css), | ||
| ], | ||
| collapselevel = 3, | ||
| ), | ||
| sitename = "DelayEmbeddings.jl", | ||
| authors = "George Datseris", | ||
| pages = DelayEmbeddings_PAGES, | ||
| doctest = false, | ||
| draft = false, | ||
| ) | ||
|
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| if CI | ||
| deploydocs( | ||
| repo = "github.com/JuliaDynamics/DelayEmbeddings.jl.git", | ||
| target = "build", | ||
| push_preview = true | ||
| ) | ||
| end |
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