Refactor code to put rng as first (optional) argument in related functions and make win an arg instead of kwarg

Author: guilgautier

docs/plots/ball_example.jl

@@ -1,12 +1,11 @@
 using PartialRejectionSampling
 const PRS = PartialRejectionSampling
 
-c, w = [0.0, 0.0], 10.0
-win = PRS.SquareWindow(c, w)
-
-r = 4
-hc = PRS.HardCorePointProcess(b, r, win)
+c, r = rand(2), 10
 
+using Random
+rng = Random.MersenneTwister(123)
+@time pts = rand(rng, PRS.BallWindow(c, r), 10)
 @time pts = rand(PRS.BallWindow(c, r), 10)
 
 using Plots

docs/plots/hard_core_graph.jl

@@ -7,7 +7,10 @@ g = LG.grid(dims)
 
 hcg = PRS.HardCoreGraph(g, β)
 
-seed = 123
-@time sample = PRS.generate_sample_prs(hcg; rng=seed)
+using Random
+rng = Random.MersenneTwister(123)
+@time sample = PRS.generate_sample_prs(rng, hcg)
 
-p = plot(hcg, sample, dims; file="docs/plots/output/hard_core_graph.pdf")
+p = plot(hcg, sample, dims, "docs/plots/output/hard_core_graph.pdf")
+
+@time sample = PRS.generate_sample_prs(hcg)

docs/plots/hard_core_graph_pedagogy.jl

@@ -8,8 +8,7 @@ g = LG.grid(dims)
 
 pp = PRS.HardCoreGraph(g, β)
 
-seed = 1
-rng = PRS.getRNG(seed)
+rng = Random.MersenneTwister(123)
 
 path(i) = joinpath("docs/plots/output/hard_core_graph", join([lpad(i, 3, "0"), ".pdf"]))
 
@@ -27,7 +26,6 @@ plot(pp.graph, dims, path(i); nodefillc=c_nodes)
 
 proba = pp.β / (one(pp.β) + pp.β)
 
-rng = PRS.getRNG(rng)
 adj = LG.adjacency_matrix(pp.graph)
 occupied = Random.randsubseq(rng, LG.vertices(pp.graph), proba)
 

docs/plots/hard_core_spatial.jl

@@ -10,8 +10,9 @@ win = PRS.SquareWindow(c, w)
 
 hc = PRS.HardCorePointProcess(b, r, win)
 
-seed = 123
-@time sample = PRS.generate_sample_prs(hc; rng=seed)
-# @time sample = PRS.generate_sample_grid_prs(hc; rng=seed)
+using Random
+rng = Random.MersenneTwister(123)
+@time sample = PRS.generate_sample_prs(rng, hc)
+# @time sample = PRS.generate_sample_grid_prs(rng, hc)
 
 p = plot(hc, sample; title="")

docs/plots/hard_core_spatial_pedagogy.jl

@@ -10,5 +10,6 @@ win = PRS.SquareWindow(c, w)
 
 hc = PRS.HardCorePointProcess(b, r, win)
 
-seed = 123
-pedagogy_generate_sample_prs(hc; rng=seed)
+using Random
+rng = Random.MersenneTwister(123)
+pedagogy_generate_sample_prs(hc; rng=rng)

docs/plots/ising_gibbs_perfect.jl

@@ -7,7 +7,9 @@ H, J = 0.0, 0.01
 
 ising = PRS.Ising(dims, J, H; periodic=periodic)
 
-seed = 123
-@time sample = PRS.generate_sample_gibbs_perfect(ising; rng=seed)
+using Random
+rng = Random.MersenneTwister(123)
+@time sample = PRS.generate_sample_gibbs_perfect(rng, ising)
 
-p = plot(ising, sample, dims...; file="docs/plots/output/ising_gibbs_perfect.pdf")
+p = plot(ising, sample, dims, "docs/plots/output/ising_gibbs_perfect.pdf";
+         nodelabel=nothing)

docs/plots/ising_grid_prs.jl

@@ -7,7 +7,9 @@ H, J = 0.0, 0.01
 
 ising = PRS.Ising(dims, J, H; periodic=periodic)
 
-seed = 123
-@time sample = PRS.generate_sample_grid_prs(ising; rng=seed)
+using Random
+rng = Random.MersenneTwister(123)
+@time sample = PRS.generate_sample_gibbs_perfect(rng, ising)
 
-p = plot(ising, sample, dims...; file="docs/plots/output/ising/ising_grid_prs.pdf")
+p = plot(ising, sample, dims, "docs/plots/output/ising/ising_grid_prs.pdf";
+         nodelabel=nothing)

docs/plots/pattern_free_string_prs.jl

@@ -2,5 +2,7 @@ n = 100
 alph = ["A", "C", "G", "T"]
 pattern = "ACAC"
 pfs = PRS.PatternFreeString(alph, pattern)
-seed = 123
-@time PRS.generate_sample_prs(pfs, n; rng=seed)
+
+using Random
+rng = Random.MersenneTwister(123)
+@time PRS.generate_sample_prs(rng, pfs, n)

docs/plots/pedagogy_graph.jl

@@ -64,50 +64,54 @@ end
 function plot(
     pp::PRS.Ising,
     state,
-    dims=zeros(2);
+    dims=zeros(2),
+    file="";
     kwargs...
 )
     c_nodes = ifelse.(
             state .== 1,
             Colors.colorant"gray",
             Colors.colorant"white")
 
-    plot(pp.graph, dims; nodefillc=c_nodes, kwargs...)
+    plot(pp.graph, dims, file; nodefillc=c_nodes, kwargs...)
 end
 
 function plot(
     pp::PRS.HardCoreGraph,
     state,
-    dims=zeros(2);
+    dims=zeros(2),
+    file="";
     kwargs...
 )
     c_nodes = [Colors.colorant"white" for _ in 1:LG.nv(pp.graph)]
-    c_nodes[state] .= Colors.colorant"black"
+    c_nodes[state] .= Colors.colorant"grey"
 
-    plot(pp.graph, dims; nodefillc=c_nodes, kwargs...)
+    plot(pp.graph, dims, file; nodefillc=c_nodes, kwargs...)
 end
 
 function plot(
     pp::PRS.SinkFreeGraph,
     sample,
-    dims=zeros(2);
+    dims=zeros(2),
+    file="";
     kwargs...
 )
     c_nodes, c_edges = color_sinks(sample)
 
-    plot(sample, dims; nodefillc=c_nodes, edgestrokec=c_edges, kwargs...)
+    plot(sample, dims, file; nodefillc=c_nodes, edgestrokec=c_edges, kwargs...)
 end
 
 function plot(
     pp::PRS.RootedSpanningForest,
     sample,
-    dims=zeros(2);
+    dims=zeros(2),
+    file="";
     kwargs...
 )
     c_nodes, c_edges = color_cycles(sample)
     c_nodes[collect(pp.roots)] .= Colors.colorant"orange"
 
-    plot(sample, dims; nodefillc=c_nodes, edgestrokec=c_edges)
+    plot(sample, dims, file; nodefillc=c_nodes, edgestrokec=c_edges)
 end
 
 function color_cycles(

docs/plots/pedagogy_spatial.jl

@@ -5,20 +5,19 @@ using Plots
 
 # Pedagogy
 function pedagogy_generate_sample_prs(
-        pp::PRS.HardCorePointProcess{T};
-        win::Union{Nothing,PRS.AbstractWindow}=nothing,
-        rng=-1
+    pp::PRS.HardCorePointProcess{T};
+    win::Union{Nothing,PRS.AbstractWindow}=nothing,
+    rng=-1
 )::Vector{T} where {T}
 
     path(i) = joinpath("docs/plots/output/hard_core_spatial", join([lpad(i, 3, "0"), ".pdf"]))
 
-    rng = PRS.getRNG(rng)
     window_ = win === nothing ? PRS.window(pp) : win
 
     n = rand(rng, Distributions.Poisson(pp.β * PRS.volume(window_)))
     points = Matrix{Float64}(undef, PRS.dimension(pp), n)
     for x in eachcol(points)
-        x .= rand(window_; rng=rng)
+        x .= rand(rng, window_)
     end
 
     i = 0
@@ -44,7 +43,7 @@ function pedagogy_generate_sample_prs(
         i+=1
         Plots.savefig(p, path(i))
 
-        resampled = PRS.generate_sample_poisson_union_balls(pp.β, points[:, bad], pp.r; win=window_, rng=rng)
+        resampled = PRS.generate_sample_poisson_union_balls(rng, pp.β, points[:, bad], pp.r, window_)
         pedagogy_plot!(p, resampled, true, 0, "blue", pp.window)
         i+=1
         Plots.savefig(p, path(i))
@@ -61,12 +60,12 @@ function pedagogy_generate_sample_prs(
 end
 
 function pedagogy_plot!(
-        p,
-        points,
-        show_center=true,
-        radius=0,
-        color="white",
-        window=SquareWindow(zeros(2), 1)
+    p,
+    points,
+    show_center=true,
+    radius=0,
+    color="white",
+    window=SquareWindow(zeros(2), 1)
 )
     for x in (points isa Matrix ? eachcol(points) : points)
         if radius > 0
@@ -114,9 +113,9 @@ function plot_disk!(p, center, radius, color=:white)
 end
 
 function plot(
-        pp::PRS.AbstractSpatialPointProcess,
-        points;
-        title=""
+    pp::PRS.AbstractSpatialPointProcess,
+    points;
+    title=""
 )
     p = Plots.plot([0], [0],
             label="", legend=false,