Switch to AlgebraOfGraphics (#113)

Project.toml

@@ -5,7 +5,6 @@ version = "0.4.4"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
-Compose = "a81c6b42-2e10-5240-aca2-a61377ecd94b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
@@ -21,7 +20,6 @@ pandoc_jll = "c5432543-76ad-5c9d-82bf-db097047a5e2"
 
 [compat]
 CodeTracking = "1.0"
-Compose = "0.9"
 DataFrames = "0.22, 1.0, 1.1"
 Latexify = "0.15"
 LiveServer = "0.6"

docs/Project.toml

@@ -4,18 +4,17 @@ authors = ["Rik Huijzer <[email protected]>"]
 version = "0.1.0"
 
 [deps]
+AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67"
 Books = "939d5c6b-51ae-42e7-97ca-7564d0d4ad91"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
-Gadfly = "c91e804a-d5a3-530f-b6f0-dfbca275c004"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 
-# Only setting compat entries when there is not already one in the main Project.toml.
 [compat]
-Gadfly = "1.3"
 Latexify = "0.15"
 MCMCChains = "4.9"

docs/contents/demo.md

@@ -274,7 +274,7 @@ _gen/my_data_mean-sco.md
 
 ## Plots {#sec:plots}
 
-Conversions for Gadfly are also included, see @fig:example_plot.
+Conversions for AlgebraOfGraphics are also included, see @fig:example_plot.
 This is actually a bit tricky, because we want to show vector graphics (SVG) on the web, but these are not supported (well) by LaTeX.
 Therefore, portable network graphics (PNG) images are passed to LaTeX via cairosvg;
 I found that this tool does the best conversions without relying on Cairo and/or Fontconfig, which are not so stable in combination with Compose in my experience.
@@ -284,7 +284,7 @@ _gen/example_plot-sco.md
 ```
 
 If the output is a string instead of the output you expected, then check whether you load the related packages in time.
-For example, for this Gadfly plot, you need to load Gadfly.jl together with Books.jl for Requires.jl to work.
+For example, for this plot, you need to load AlgebraOfGraphics.jl together with Books.jl so that Requires.jl will load the code for handling AlgebraOfGraphics objects.
 
 For multiple images, use `Options.(objects, paths)`:
 
@@ -298,13 +298,13 @@ Resulting in @fig:example_plot_2 and @fig:example_plot_3:
 _gen/multiple_example_plots.md
 ```
 
-For changing the size, use `ImageOptions`:
+For changing the size, use `axis` from AlgebraOfGraphics:
 
 ```{.include}
 _gen/image_options_plot-sco.md
 ```
 
-Or, use the combination for setting captions and size
+And, for adjusting the caption, use `Options`:
 
 ```{.include}
 _gen/combined_options_plot-sco.md

docs/src/BooksDocs.jl

@@ -5,11 +5,12 @@ import MCMCChains
 import Statistics
 import TOML
 
+using AlgebraOfGraphics
 using Books
+using CairoMakie
 using CodeTracking
 using DataFrames
 using Dates
-using Gadfly
 
 include("includes.jl")
 

docs/src/includes.jl

@@ -135,28 +135,33 @@ module_example_definition() = code_block("""
 
 function example_plot()
     I = 1:30
-    Gadfly.plot(x=I, y=I.^2)
+    df = (x=I, y=I.^2)
+    xy = data(df) * mapping(:x, :y)
+    fg = draw(xy)
 end
 
 function multiple_example_plots()
     paths = ["example_plot_$i" for i in 2:3]
     I = 1:30
+    df = (x=I, y=I.*2, z=I.^3)
     objects = [
-        plot(x=I, y=I),
-        plot(x=I, y=I.^3)
+        draw(data(df) * mapping(:x, :y))
+        draw(data(df) * mapping(:x, :z))
     ]
     Options.(objects, paths)
 end
 
 function image_options_plot()
     I = 1:0.1:30
-    p = plot(x=I, y=sin.(I), Geom.line)
-    ImageOptions(p; width=6inch, height=2inch)
+    df = (x=I, y=sin.(I))
+    xy = data(df) * visual(Lines) * mapping(:x, :y)
+    axis = (width = 600, height = 140)
+    draw(xy; axis)
 end
 
 function combined_options_plot()
-    imageoptions = image_options_plot()
-    Options(imageoptions; caption="Sine function")
+    p = image_options_plot()
+    Options(p; caption="Sine function")
 end
 
 chain() = MCMCChains.Chains([1])

src/Books.jl

@@ -24,7 +24,6 @@ include("ci.jl")
 include("build.jl")
 include("serve.jl")
 include("output.jl")
-include("outputs/compose.jl")
 include("outputs/dataframes.jl")
 include("showcode.jl")
 include("generate.jl")
@@ -37,7 +36,7 @@ export gen
 export serve
 
 function __init__()
-    @require Gadfly="c91e804a-d5a3-530f-b6f0-dfbca275c004" include("outputs/gadfly.jl")
+    @require AlgebraOfGraphics="cbdf2221-f076-402e-a563-3d30da359d67" include("outputs/aog.jl")
 end
 
 end # module

src/output.jl

@@ -167,7 +167,7 @@ This passes the objects through show to use the overrides that package creators
 ```jldoctest
 julia> using MCMCChains
 
-julia> chn = Chains([1]);
+julia> chn = Chains([1]; info=(start_time=[1.0], stop_time=[1.0]));
 
 julia> string(chn)
 "MCMC chain (1×1×1 Array{Int64, 3})"

src/outputs/aog.jl

@@ -0,0 +1,36 @@
+@debug "Loading AlgebraOfGraphics support into Books via Requires"
+
+using AlgebraOfGraphics
+using CairoMakie
+
+function convert_output(path, fg::AlgebraOfGraphics.FigureGrid; caption=nothing, label=nothing)
+    im_dir = joinpath(BUILD_DIR, "im")
+    mkpath(im_dir)
+
+    if isnothing(path)
+        # Not determining some random name here, because it would require cleanups too.
+        msg = """
+            It is not possible to write an image without specifying a path.
+            Use `Options(p; filename=filename)` where `p` is a AlgebraOfGraphics plot.
+            """
+        throw(ErrorException(msg))
+    end
+    file, _ = method_name(path)
+
+    println("Writing plot images for $file")
+    svg_filename = "$file.svg"
+    svg_path = joinpath(im_dir, svg_filename)
+    # Explicit rm due to https://github.com/JuliaIO/FileIO.jl/issues/338.
+    rm(svg_path; force=true)
+    AlgebraOfGraphics.save(svg_path, fg)
+
+    png_filename = "$file.png"
+    png_path = joinpath(im_dir, png_filename)
+    rm(png_path; force=true)
+    px_per_unit = 3 # Ensure high resolution.
+    AlgebraOfGraphics.save(png_path, fg; px_per_unit)
+
+    im_link = joinpath("im", svg_filename)
+    caption, label = caption_label(path, caption, label)
+    pandoc_image(file, png_path; caption, label)
+end

test/Project.toml

@@ -1,12 +1,11 @@
 [deps]
+AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-Gadfly = "c91e804a-d5a3-530f-b6f0-dfbca275c004"
 MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
-# Only setting compat entries when there is not already one in the main Project.toml.
 [compat]
 Documenter = "0.26"
-Gadfly = "1.3"
 MCMCChains = "4.9"

test/generate.jl

@@ -1,4 +1,5 @@
-import Gadfly
+using AlgebraOfGraphics
+using CairoMakie
 using DataFrames
 
 @testset "generate" begin
@@ -28,8 +29,13 @@ using DataFrames
 
     @test contains(B.convert_output(nothing, DataFrame(A = [1])), "---")
 
+    X = 1:30
+    df = (x=X, y=X.*2)
+    xy = data(df) * mapping(:x, :y)
+    fg = draw(xy)
+
     mktemp() do path, io
-        @test contains(B.convert_output(path, Gadfly.plot()), ".png")
+        @test contains(B.convert_output(path, fg), ".png")
     end
     im_dir = joinpath(B.BUILD_DIR, "im")
     rm(im_dir; force=true, recursive=true)