Finish and tag v1 (#2)

* remove old files

* export Syxtems

* make compilable

* add docs

* better read me and module

* buildable docs

* tests pass as far as I can tell

* ad cairomakie to the docbuild

Author: Datseris

.gitignore

@@ -5,4 +5,5 @@ docs/build
 deps/build.log
 Manifest.toml
 *.scss
-*.css
+*.css
+*style.jl

CHANGELOG.md

@@ -7,6 +7,8 @@ version = "1"
 DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [compat]
 DynamicalSystemsBase = "3"

CITATION.bib

@@ -1,15 +1,26 @@
-# DynamicalSystemsBase.jl
+# PredefinedDynamicalSystems.jl
 
-[![](https://img.shields.io/badge/docs-dev-blue.svg)](https://JuliaDynamics.github.io/DynamicalSystemsBase.jl/dev)
-[![](https://img.shields.io/badge/DOI-10.1007/978-3-030-91032-7-purple)](https://link.springer.com/book/10.1007/978-3-030-91032-7)
-[![CI](https://github.com/JuliaDynamics/DynamicalSystemsBase.jl/workflows/CI/badge.svg)](https://github.com/JuliaDynamics/DynamicalSystemsBase.jl/actions?query=workflow%3ACI)
-[![codecov](https://codecov.io/gh/JuliaDynamics/DynamicalSystemsBase.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/JuliaDynamics/DynamicalSystemsBase.jl)
-[![Package Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/DynamicalSystemsBase)](https://pkgs.genieframework.com?packages=DynamicalSystemsBase)
+[![](https://img.shields.io/badge/docs-dev-blue.svg)](https://JuliaDynamics.github.io/PredefinedDynamicalSystems.jl/dev)
+[![CI](https://github.com/JuliaDynamics/PredefinedDynamicalSystems.jl/workflows/CI/badge.svg)](https://github.com/JuliaDynamics/PredefinedDynamicalSystems.jl/actions?query=workflow%3ACI)
+[![Package Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/PredefinedDynamicalSystems)](https://pkgs.genieframework.com?packages=PredefinedDynamicalSystems)
 
-A Julia package that defines the `DynamicalSystem` interface and many concrete implementations used in the [DynamicalSystems.jl](https://juliadynamics.github.io/DynamicalSystems.jl/dev/) ecosystem.
+Module which contains pre-defined dynamical systems that can be used by the [DynamicalSystems.jl](https://juliadynamics.github.io/DynamicalSystems.jl/dev/) library.
+To install it, run `import Pkg; Pkg.add("PredefinedDynamicalSystems")`.
 
-To install it, run `import Pkg; Pkg.add("DynamicalSystemsBase")`.
-Typically, you do not want to use `DynamicalSystemsBase` directly,
-as downstream analysis packages re-export it.
+Predefined systems exist as functions that
+return a `DynamicalSystem` instance. They are accessed like:
+```julia
+ds = PredefinedDynamicalSystems.lorenz(u0; ρ = 32.0)
+```
+The alias `Systems` is also exported as a deprecation.
 
-All further information is provided in the documentation, which you can either find [online](https://juliadynamics.github.io/DynamicalSystemsBase.jl/dev/) or build locally by running the `docs/make.jl` file.
+**This module is provided purely as a convenience.
+Nothing here is tested, nor guaranteed to be stable in future versions.
+It is not recommended to use this module for anything else besides
+on-the-spot demonstrative examples.**
+
+For some systems, a Jacobian function is also defined.
+The naming convention for the Jacobian function is `\$(name)_jacob`.
+So, for the above example we have `J = Systems.lorenz_jacob`.
+
+All available systems are provided in the documentation, which you can either find [online](https://juliadynamics.github.io/PredefinedDynamicalSystems.jl/dev/) or build locally by running the `docs/make.jl` file.

Project.toml

@@ -1,4 +1,5 @@
 [deps]
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
 PredefinedDynamicalSystems = "31e2f376-db9e-427a-b76e-a14f56347a14"

README.md

@@ -1,35 +1,13 @@
 cd(@__DIR__)
-CI = get(ENV, "CI", nothing) == "true" || get(ENV, "GITHUB_TOKEN", nothing) !== nothing
-using PredefinedDynamicalSystems # comes from global environment in CI
-using Documenter
-using DocumenterTools: Themes
-ENV["JULIA_DEBUG"] = "Documenter"
 
-# %% JuliaDynamics theme
-# It includes themeing for the HTML build
-# and themeing for the Makie plotting
-
-using DocumenterTools: Themes
-for file in ("juliadynamics-lightdefs.scss", "juliadynamics-darkdefs.scss", "juliadynamics-style.scss")
-    filepath = joinpath(@__DIR__, file)
-    if !isfile(filepath)
-        download("https://raw.githubusercontent.com/JuliaDynamics/doctheme/master/$file", joinpath(@__DIR__, file))
-    end
-end
-# create the themes
-for w in ("light", "dark")
-    header = read(joinpath(@__DIR__, "juliadynamics-style.scss"), String)
-    theme = read(joinpath(@__DIR__, "juliadynamics-$(w)defs.scss"), String)
-    write(joinpath(@__DIR__, "juliadynamics-$(w).scss"), header*"\n"*theme)
-end
-# compile the themes
-Themes.compile(joinpath(@__DIR__, "juliadynamics-light.scss"), joinpath(@__DIR__, "src/assets/themes/documenter-light.css"))
-Themes.compile(joinpath(@__DIR__, "juliadynamics-dark.scss"), joinpath(@__DIR__, "src/assets/themes/documenter-dark.css"))
-
-# %% Build docs
-ENV["JULIA_DEBUG"] = "Documenter"
+import Downloads
+Downloads.download(
+    "https://raw.githubusercontent.com/JuliaDynamics/doctheme/master/apply_style.jl",
+    joinpath(@__DIR__, "apply_style.jl")
+)
+include("apply_style.jl")
 
-include("style.jl")
+using PredefinedDynamicalSystems
 
 makedocs(
     modules = [PredefinedDynamicalSystems],