Update Turkie to new versions of Turing and Makie (#26)

* General updates, update AbstractPlotting to Makie

* Working version

* Patch bump

Author: theogf

.gitignore

@@ -4,4 +4,5 @@ test/Manifest.toml
 test/video.gif
 test/video.webm
 docs/build/
-docs/Manifest.toml
+docs/Manifest.toml
+.vscode/settings.json

Project.toml

@@ -1,21 +1,21 @@
 name = "Turkie"
 uuid = "8156cc02-0533-41cd-9345-13411ebe105f"
 authors = ["Theo Galy-Fajou <[email protected]> and contributors"]
-version = "0.1.3"
+version = "0.1.4"
 
 [deps]
-AbstractPlotting = "537997a7-5e4e-5d89-9595-2241ea00577e"
 ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 OnlineStats = "a15396b6-48d5-5d58-9928-6d29437db91e"
 Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
 
 [compat]
-AbstractPlotting = "0.15, 0.16"
 ColorSchemes = "3.10"
 Colors = "0.12"
 KernelDensity = "0.5, 0.6"
+Makie = "0.13"
 OnlineStats = "1.5"
 Turing = "0.15"
 julia = "1.4"

README.md

@@ -39,7 +39,7 @@ Small example:
 ```julia
 using Turing
 using Turkie
-using Makie # You could also use CairoMakie or another backend
+using GLMakie # You could also use CairoMakie or another backend
 @model function demo(x) # Some random Turing model
     m0 ~ Normal(0, 2)
     s ~ InverseGamma(2, 3)
@@ -76,7 +76,7 @@ If you want to record the video do
 
 ```julia
 using Makie
-record(cb.scene, joinpath(@__DIR__, "video.webm")) do io
+record(cb, joinpath(@__DIR__, "video.webm")) do io
     addIO!(cb, io)
     sample(m,  NUTS(0.65), 300; callback = cb)
 end

src/Turkie.jl

@@ -1,10 +1,10 @@
 module Turkie
 
-using AbstractPlotting: Scene, Point2f0
-using AbstractPlotting: barplot!, lines!, scatter! # Plotting tools
-using AbstractPlotting: Observable, Node, lift, on # Observable tools
-using AbstractPlotting: recordframe! # Recording tools
-using AbstractPlotting.MakieLayout # Layouting tool
+using Makie: Figure, Scene, Point2f0
+using Makie: barplot!, lines!, scatter! # Plotting tools
+using Makie: Observable, Node, lift, on # Observable tools
+using Makie: recordframe! # Recording tools
+using Makie.MakieLayout # Layouting tool
 using Colors, ColorSchemes # Colors tools
 using KernelDensity # To be able to give a KDE
 using OnlineStats # Estimators
@@ -16,6 +16,7 @@ export addIO!, record
 
 include("online_stats_plots.jl")
 
+ # Uses the colorblind scheme of seaborn by default
 const std_colors = ColorSchemes.seaborn_colorblind
 
 name(s::Symbol) = name(Val(s))
@@ -43,7 +44,7 @@ See the docs for some examples.
 TurkieCallback
 
 struct TurkieCallback{TN<:NamedTuple,TD<:AbstractDict}
-    scene::Scene
+    figure::Figure
     data::Dict{Symbol, MovingWindow}
     axis_dict::Dict
     vars::TN
@@ -70,7 +71,7 @@ end
 function TurkieCallback(vars::NamedTuple, params::Dict)
 # Create a scene and a layout
     outer_padding = 5
-    scene, layout = layoutscene(outer_padding, resolution = (1200, 700))
+    fig = Figure(;resolution = (1200, 700), figure_padding=outer_padding)
     window = get!(params, :window, 1000)
     refresh = get!(params, :refresh, false)
     params[:t0] = 0
@@ -81,9 +82,9 @@ function TurkieCallback(vars::NamedTuple, params::Dict)
     for (i, variable) in enumerate(keys(vars))
         plots = vars[variable]
         data[variable] = MovingWindow(window, Float32)
-        axis_dict[(variable, :varname)] = layout[i, 1, Left()] = Label(scene, string(variable), textsize = 30)
+        axis_dict[(variable, :varname)] = fig[i, 1, Left()] = Label(fig, string(variable), textsize = 30)
         axis_dict[(variable, :varname)].padding = (0, 60, 0, 0)   
-        onlineplot!(scene, layout, axis_dict, plots, iter, data, variable, i)
+        onlineplot!(fig, axis_dict, plots, iter, data, variable, i)
     end
     on(iter) do i
         if i > 1 # To deal with autolimits a certain number of samples are needed
@@ -94,16 +95,16 @@ function TurkieCallback(vars::NamedTuple, params::Dict)
             end
         end
     end
-    MakieLayout.trim!(layout)
-    display(scene)
-    TurkieCallback(scene, data, axis_dict, vars, params, iter)
+    MakieLayout.trim!(fig.layout)
+    display(fig)
+    return TurkieCallback(fig, data, axis_dict, vars, params, iter)
 end
 
 function addIO!(cb::TurkieCallback, io)
     cb.params[:io] = io
 end
 
-function (cb::TurkieCallback)(rng, model, sampler, transition, iteration)
+function (cb::TurkieCallback)(rng, model, sampler, transition, state, iteration; kwargs...)
     if iteration == 1
         if cb.params[:refresh]
             refresh_plots!(cb)
@@ -116,7 +117,7 @@ function (cb::TurkieCallback)(rng, model, sampler, transition, iteration)
             fit!(cb.data[variable], Float32(val)) # Update its value
         end
     end
-    cb.iter[] += 1
+    cb.iter[] = cb.iter[] + 1
     if haskey(cb.params, :io)
         recordframe!(cb.params[:io])
     end

src/online_stats_plots.jl

@@ -1,6 +1,6 @@
-function onlineplot!(scene, layout, axis_dict, stats::AbstractVector, iter, data, variable, i)
+function onlineplot!(fig, axis_dict, stats::AbstractVector, iter, data, variable, i)
     for (j, stat) in enumerate(stats)
-        axis_dict[(variable, stat)] = layout[i, j] = Axis(scene, title = "$(name(stat))")
+        axis_dict[(variable, stat)] = fig[i, j] = Axis(fig, title="$(name(stat))")
         limits!(axis_dict[(variable, stat)], 0.0, 10.0, -1.0, 1.0)
         onlineplot!(axis_dict[(variable, stat)], stat, iter, data[variable], data[:iter], i, j)
         tight_ticklabel_spacing!(axis_dict[(variable, stat)])
@@ -19,27 +19,26 @@ onlineplot!(axis, ::Val{:autocov}, args...) = onlineplot!(axis, AutoCov(20), arg
 
 onlineplot!(axis, ::Val{:hist}, args...) = onlineplot!(axis, KHist(50, Float32), args...)
 
-
 # Generic fallback for OnlineStat objects
 function onlineplot!(axis, stat::T, iter, data, iterations, i, j) where {T<:OnlineStat}
     window = data.b
     @eval TStat = $(nameof(T))
     stat = Observable(TStat(Float32))
-    on(iter) do i
+    on(iter) do _
         stat[] = fit!(stat[], last(value(data)))
     end
     statvals = Observable(MovingWindow(window, Float32))
     on(stat) do s
         statvals[] = fit!(statvals[], Float32(value(s)))
     end
-    statpoints = lift(statvals; init = Point2f0.([0], [0])) do v
+    statpoints = map!(Observable(Point2f0.([0], [0])), statvals)  do v
         Point2f0.(value(iterations), value(v))
     end
     lines!(axis, statpoints, color = std_colors[i], linewidth = 3.0)
 end
 
 function onlineplot!(axis, ::Val{:trace}, iter, data, iterations, i, j)
-    trace = lift(iter; init = [Point2f0(0f0, 0f0)]) do i
+    trace = map!(Observable([Point2f0(0, 0)]), iter) do _
         Point2f0.(value(iterations), value(data))
     end
     lines!(axis, trace, color = std_colors[i]; linewidth = 3.0)
@@ -48,15 +47,17 @@ end
 function onlineplot!(axis, stat::KHist, iter, data, iterations, i, j)
     nbins = stat.k
     stat = Observable(KHist(nbins, Float32))
-    on(iter) do i
+    on(iter) do _
         stat[] = fit!(stat[], last(value(data)))
     end
-    hist_vals = lift(stat; init = Point2f0.(range(0, 1, length = nbins), zeros(Float32, nbins))) do h
+    hist_vals = Node(Point2f0.(collect(range(0f0, 1f0, length=nbins)), zeros(Float32, nbins)))
+    on(stat) do h
         edges, weights = OnlineStats.xy(h)
         weights = nobs(h) > 1 ? weights / OnlineStats.area(h) : weights
-        return Point2f0.(edges, weights)
+        hist_vals[] = Point2f0.(edges, weights)
     end
-    barplot!(axis, hist_vals, color = std_colors[i])
+    barplot!(axis, hist_vals; color=std_colors[i])
+    # barplot!(axis, rand(4), rand(4))
 end
 
 function expand_extrema(xs)
@@ -69,19 +70,20 @@ end
 
 function onlineplot!(axis, ::Val{:kde}, iter, data, iterations, i, j)
     interpkde = Observable(InterpKDE(kde([1f0])))
-    on(iter) do i
+    on(iter) do _
         interpkde[] = InterpKDE(kde(value(data)))
     end
-    xs = lift(iter; init = range(0.0, 2.0, length = 200)) do i
-        range(expand_extrema(extrema(value(data)))..., length = 200)
+    xs = Observable(range(0, 2, length=10))
+    on(iter) do _
+        xs[] = range(expand_extrema(extrema(value(data)))..., length = 200)
     end
     kde_pdf = lift(xs) do xs
         pdf.(Ref(interpkde[]), xs)
     end
     lines!(axis, xs, kde_pdf, color = std_colors[i], linewidth = 3.0)
 end
 
-name(s::Val{:histkde}) = "Hist + KDE"
+name(s::Val{:histkde}) = "Hist. + KDE"
 
 function onlineplot!(axis, ::Val{:histkde}, iter, data, iterations, i, j)
     onlineplot!(axis, KHist(50), iter, data, iterations, i, j)
@@ -91,10 +93,10 @@ end
 function onlineplot!(axis, stat::AutoCov, iter, data, iterations, i, j)
     b = length(stat.cross)
     stat = Observable(AutoCov(b, Float32))
-    on(iter) do i
+    on(iter) do _
         stat[] = fit!(stat[], last(value(data)))
     end
-    statvals = lift(stat; init = zeros(Float32, b + 1)) do s
+    statvals = map!(Observable(zeros(Float32, b + 1)), stat) do s
         value(s)
     end
     scatter!(axis, Point2f0.([0.0, b], [-0.1, 1.0]), markersize = 0.0, color = RGBA(0.0, 0.0, 0.0, 0.0)) # Invisible points to keep limits fixed

test/dev_test.jl

@@ -1,3 +1,4 @@
+using Pkg; Pkg.activate("..")
 using Turing
 using Turkie
 using GLMakie # You could also use CairoMakie or another backend
@@ -19,7 +20,7 @@ cb = TurkieCallback(m) # Create a callback function to be given to the sample fu
 chain = sample(m, NUTS(0.65), 30; callback = cb)
 
 
-record(cb.scene, joinpath(@__DIR__, "video.gif")) do io
+record(cb.figure, joinpath(@__DIR__, "video.gif")) do io
     addIO!(cb, io)
     sample(m,  NUTS(0.65), 50; callback = cb)
 end

test/runtests.jl

@@ -1,6 +1,7 @@
 using Turkie
 using Test
 using CairoMakie
+CairoMakie.activate!()
 using OnlineStats
 using Turing
 
@@ -23,7 +24,7 @@ using Turing
         @test Turkie.name(OnlineStats.Mean(Float32)) == "Mean"
 
         cb = TurkieCallback(model; blah=2.0)
-        @test cb.scene isa Scene
+        @test cb.figure isa Figure
         @test sort(collect(keys(cb.data))) == sort(vcat(vars, :iter))
         @test cb.data[:m] isa MovingWindow{Float32}
         @test sort(collect(keys(cb.vars))) == sort(vars)
@@ -41,13 +42,13 @@ using Turing
         @testset "Vector of symbols" begin
             for stat in [:histkde, :kde, :hist, :mean, :var, :trace, :autocov]
                 cb = TurkieCallback(Dict(:m => [stat]))
-                sample(model, MH(), 50; callback = cb) 
+                sample(model, MH(), 50; callback=cb) 
             end
         end 
         @testset "Series" begin
             for stat in [Mean(Float32), Variance(Float32)]
                 cb = TurkieCallback(model, OnlineStats.Series(stat))
-                sample(model, MH(), 50; callback = cb)
+                sample(model, MH(), 50; callback=cb)
             end
         end
     end