Move to Julia extensions (v1.9) + fix an export (#152)

* remove requires dep

* add makie weak deap

* fix standardize export

* move plotting function to extension file

* port uncertain data to extensions file

* correct codecov

* more powerful plotting

* remove uncertain data

* remove requires

* make proper module structure for surrogates plot

* finish everything

* correct display of surroplot in docs

* remove global `using StatsBase`

Author: Datseris

.codecov.yml

@@ -2,7 +2,7 @@ name = "TimeseriesSurrogates"
 uuid = "c804724b-8c18-5caa-8579-6025a0767c70"
 authors = ["Kristian Agasøster Haaga <kahaaga@gmail.com>", "George Datseris"]
 repo = "https://github.com/JuliaDynamics/TimeseriesSurrogates.jl.git"
-version = "2.4.0"
+version = "2.5.0"
 
 [deps]
 AbstractFFTs = "621f4979-c628-5d54-868e-fcf4e3e8185c"
@@ -14,13 +14,20 @@ Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LombScargle = "fc60dff9-86e7-5f2f-a8a0-edeadbb75bd9"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsAPI = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StateSpaceSets = "40b095a5-5852-4c12-98c7-d43bf788e795"
 Wavelets = "29a6e085-ba6d-5f35-a997-948ac2efa89a"
 
+[weakdeps]
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+# UncertainData = "dcd9ba68-c27b-5cea-ae21-829cd07325bf"
+
+[extensions]
+TimeseriesSurrogatesVisualizations = "Makie"
+# TimeseriesSurrogatesUncertainData = "UncertainData"
+
 [compat]
 AbstractFFTs = "1"
 DSP = "^0.5.2, 0.6, ^1, 0.7"
@@ -29,12 +36,12 @@ Distances = "0.10, 1"
 Distributions = "0.21, 1, 0.23, 0.24, 0.25"
 Interpolations = "^0.12, ^1, 0.13, 0.14"
 LombScargle = "1"
-Requires = "^0.5.2, ^1"
+Makie = "≥ 0.19"
 StatsAPI = "1.6"
 StatsBase = "^0.32.0, ^1, 0.33"
 StateSpaceSets = "1"
 Wavelets = "^0.8.0, 0.9, 1"
-julia = "^1.1"
+julia = "^1.9"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

Project.toml

@@ -0,0 +1,5 @@
+# sample regex patterns
+ignore:
+  - "src/deprecated.jl"
+  - "plotting/*"
+  - "ext/*"

codecov.yml

@@ -108,16 +108,15 @@ noiseradius
 
 TimeseriesSurrogates.jl has defined a simple function `surroplot(x, s)`.
 This comes into scope when `using Makie` (you also need a plotting backend).
+This functionality requires you to be using Julia 1.9 or later versions.
 
-To load the function, do:
+Example:
 
 ```@example MAIN
 using TimeseriesSurrogates
-using CairoMakie, Makie
-using TimeseriesSurrogates, CairoMakie, Makie
-ts = AR1() # create a realization of a random AR(1) process
-s = surrogate(ts, AAFT())
-fig = surroplot(ts, s)
+using CairoMakie
+x = AR1() # create a realization of a random AR(1) process
+fig = surroplot(x, AAFT())
 save("surroplot.png", fig); # hide
 ```
 

docs/src/index.md

@@ -0,0 +1,10 @@
+module TimeseriesSurrogatesUncertainData
+
+using TimeseriesSurrogates
+import UncertainData: UncertainDataset, UncertainIndexDataset, UncertainValueDataset, resample
+
+TimeseriesSurrogates.surrogate(x::UncertainDataset, method::Surrogate) = surrogate(resample(x), method)
+TimeseriesSurrogates.surrogate(x::UncertainValueDataset, method::Surrogate) = surrogate(resample(x), method)
+TimeseriesSurrogates.surrogate(x::UncertainIndexDataset, method::Surrogate) = surrogate(resample(x), method)
+
+end

ext/TimeseriesSurrogatesUncertainData.jl

@@ -0,0 +1,43 @@
+module TimeseriesSurrogatesVisualizations
+
+using TimeseriesSurrogates, Makie
+
+function TimeseriesSurrogates.surroplot(x, s;
+        cx = "#191E44", cs = ("#7143E0", 0.9), resolution = (500, 500),
+        nbins = 50,
+    )
+
+    t = 1:length(x)
+    fig = Makie.Figure(resolution = resolution)
+
+    # Time series
+    ax1, _ = Makie.lines(fig[1,1], t, x; color = cx, linewidth = 2)
+    Makie.lines!(ax1, t, s; color = cs, linewidth = 2)
+
+    # Binned multitaper periodograms
+    p, psurr = TimeseriesSurrogates.DSP.mt_pgram(x), TimeseriesSurrogates.DSP.mt_pgram(s)
+    ax3 = Makie.Axis(fig[2,1]; yscale = log10)
+    Makie.lines!(ax3, p.freq, p.power; color = cx, linewidth = 3)
+    Makie.lines!(ax3, psurr.freq, psurr.power; color = cs, linewidth = 3)
+
+    # Histograms
+    ax4 = Makie.Axis(fig[3,1])
+    Makie.hist!(ax4, x; label = "original", bins = nbins, color = cx)
+    Makie.hist!(ax4, s; label = "surrogate", bins = nbins, color = cs)
+    Makie.axislegend(ax4)
+
+    ax1.xlabel = "time step"
+    ax1.ylabel = "value"
+    ax3.xlabel = "frequency"
+    ax3.ylabel = "power"
+    ax4.xlabel = "binned value"
+    ax4.ylabel = "histogram"
+    return fig
+end
+
+function TimeseriesSurrogates.surroplot(x, method::Surrogate; kwargs...)
+    s = surrogate(x, method)
+    return surroplot(x, s; kwargs...)
+end
+
+end

ext/TimeseriesSurrogatesVisualizations.jl

@@ -10,20 +10,18 @@ end TimeseriesSurrogates
 using Random
 using Distributions
 using Distances # Will be used by the LombScargle method
-using StatsBase
 using AbstractFFTs
 using DSP
 using Interpolations
 using Wavelets
-using Requires
 using StateSpaceSets
-standardize = StateSpaceSets.standardize
 export standardize
 
 include("core/api.jl")
 include("core/surrogate_test.jl")
 
 include("utils/testsystems.jl")
+include("plotting/surrogate_plot.jl")
 
 # The different surrogate routines
 include("methods/randomshuffle.jl")
@@ -43,20 +41,5 @@ include("methods/trend_based.jl")
 # Methods for irregular time series
 include("methods/lombscargle.jl")
 
-# Visualization routine for time series + surrogate + periodogram/acf/histogram
-using Requires
-function __init__()
-    @require UncertainData="dcd9ba68-c27b-5cea-ae21-829cd07325bf" begin
-        include("utils/uncertaindatasets.jl")
-    end
-    @require Makie="ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" begin
-        include("plotting/surrogate_plot.jl")
-    end
-end
-
-export surroplot_path
-function surroplot_path()
-    joinpath(@__DIR__, "plotting", "surrogate_plot.jl")
-end
 
 end # module

src/TimeseriesSurrogates.jl

@@ -1,47 +1,15 @@
-using TimeseriesSurrogates.StatsBase
-using TimeseriesSurrogates.DSP
-
 """
     surroplot(x, s; kwargs...) → fig
+    surroplot(x, method::Surrogate; kwargs...) → fig
 
 Plot a timeseries `x` along with its surrogate realization `s`, and compare the
-power spectrum and histogram of the two time series.
+power spectrum and histogram of the two time series. If given a method to generate
+surrogates, create a surrogate from `x` and plot it.
 
 ## Keyword arguments
 - `cx` and `cs`: Colors of the original and the surrogate time series, respectively.
 - `nbins`: The number of bins for the histograms.
 - `resolution`: A tuple giving the resolution of the figure.
 """
-function surroplot(x, s;
-        cx = "#1B1B1B", cs = ("#2DB9C5", 0.9), resolution = (500, 500),
-        nbins = 50,
-    )
-
-    t = 1:length(x)
-    fig = Makie.Figure(resolution = resolution)
-
-    # Time series
-    ax1, _ = Makie.lines(fig[1,1], t, x; color = cx)
-    Makie.lines!(ax1, t, s; color = cs)
-
-    # Binned multitaper periodograms
-    p, psurr = DSP.mt_pgram(x), DSP.mt_pgram(s)
-    ax3 = Makie.Axis(fig[2,1]; yscale = log10)
-    Makie.lines!(ax3, p.freq, p.power; color = cx)
-    Makie.lines!(ax3, psurr.freq, psurr.power; color = cs)
-
-    # Histograms
-    ax4 = Makie.Axis(fig[3,1])
-    Makie.hist!(ax4, x; label = "original", bins = nbins, color = cx)
-    Makie.hist!(ax4, s; label = "surrogate", bins = nbins, color = cs)
-    Makie.axislegend(ax4)
-
-    ax1.xlabel = "time step"
-    ax1.ylabel = "value"
-    ax3.xlabel = "frequency"
-    ax3.ylabel = "power"
-    ax4.xlabel = "binned value"
-    ax4.ylabel = "histogram"
-    return fig
-end
+function surroplot end
 export surroplot