Reduce dependency on Makie recipes (#23)

* recipe conversion

* CI bump

.github/workflows/ci.yml

@@ -21,12 +21,12 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        version: [1.6, 1]
+        version: [1.9, 1]
         arch: [x64]
         os: [ubuntu-latest]
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Julia Setup
         uses: julia-actions/setup-julia@v1
         with:
@@ -45,10 +45,12 @@ jobs:
         uses: julia-actions/julia-processcoverage@v1
         if:  ${{ startsWith(matrix.os, 'ubuntu') && (matrix.version == '1') }}
       - name: Coverage Upload
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v4
         if:  ${{ startsWith(matrix.os, 'ubuntu') && (matrix.version == '1') }}
         with:
           file: lcov.info
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       - name: Setup Node for Percy
         if: ${{ matrix.version == '1' }}
         uses: actions/setup-node@v3

.github/workflows/documenter.yml

@@ -16,7 +16,7 @@ jobs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/cache@v1
         with:
           cache-compiled: "true"

.github/workflows/style.yml

@@ -20,19 +20,19 @@ jobs:
     permissions: write-all
     strategy:
       matrix:
-        julia-version: [1.6]
+        julia-version: [1.9]
     steps:
       - uses: julia-actions/setup-julia@latest
         with:
           version: ${{ matrix.julia-version }}
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Instantiate `format` environment and format
+        shell: julia --color=yes -O0 {0}
         run: |
-          julia -e'
           using Pkg; Pkg.activate()
           Pkg.add("JuliaFormatter")
           using JuliaFormatter
-          format(".", YASStyle())'
+          format(".", YASStyle())
       - uses: reviewdog/action-suggester@v1
         if: github.event_name == 'pull_request'
         with:

.gitignore

@@ -22,7 +22,9 @@ docs/site/
 # committed for packages, but should be committed for applications that require a static
 # environment.
 Manifest.toml
+Manifest-v*.toml
 
 # Editor files
 .vscode/*
 *~
+coverage/lcov.info

Project.toml

@@ -1,10 +1,9 @@
 name = "BoxCox"
 uuid = "1248164d-f7a6-4bdb-8e8d-8c4a187b3ce6"
 authors = ["Phillip Alday <[email protected]>"]
-version = "0.2.4"
+version = "0.3.0"
 
 [deps]
-Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
@@ -32,10 +31,9 @@ BoxCoxStatsModelsExt = ["StatsModels", "Tables"]
 
 [compat]
 Aqua = "0.6"
-Compat = "3.29, 4"
 DocStringExtensions = "0.9"
 LinearAlgebra = "1"
-Makie = "0.19.0, 0.20"
+Makie = "0.19, 0.20"
 MixedModels = "4"
 NLopt = "0.6, 1"
 PrecompileTools = "1"
@@ -47,12 +45,11 @@ StatsBase = "0.33, 0.34"
 StatsFuns = "1"
 StatsModels = "0.6, 0.7"
 Tables = "1"
-julia = "1.6"
+julia = "1.9"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
-Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 MixedModels = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316"
 RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b"
 StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"

docs/Project.toml

@@ -9,4 +9,4 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
 
 [compat]
-Documenter = "0.27"
+Documenter = "1.3"

docs/make.jl

@@ -5,7 +5,6 @@ using BoxCox
 makedocs(; root=joinpath(dirname(pathof(BoxCox)), "..", "docs"),
          sitename="BoxCox",
          doctest=true,
-         strict=true,
          pages=["index.md",
                 "mixed-models.md",
                 "api.md"])

docs/src/mixed-models.md

@@ -5,8 +5,7 @@ CurrentModule = BoxCox
 ```
 
 BoxCox.jl supports finding fitting the Box-Cox transformation to a `LinearMixedModel` from MixedModels.jl.
-On Julia 1.9 and above, this support is done via a package extension and so the user pays no dependency or precompilation penalty when this functionality is not used.
-On Julia 1.6 to 1.8, this functionality is defined unconditionally (thus incurring the dependency and precompilation penalty), but neither the `@formula` macro nor the `MixedModel` type are re-exported, so MixedModels.jl must still be loaded to use this functionality.
+This support is done via a package extension and so the user pays no dependency or precompilation penalty when this functionality is not used.
 
 
 Let us examine the classic sleepstudy dataset from MixedModels.jl. First, we load the necessary packages.
@@ -77,7 +76,7 @@ model_bc = fit(MixedModel,
                 dataset(:sleepstudy))
 ```
 
-For our original model on the untransformed scale, the intercept was approximately 250, which means that the average response time was about 250 milliseconds. 
+For our original model on the untransformed scale, the intercept was approximately 250, which means that the average response time was about 250 milliseconds.
 For the model on the speed scale, we have an intercept about approximately 4, which means that the average response speed is about 4 responses per second, which implies that the the average response time is 250 milliseconds.
 In other words, our new results are compatible with our previous estimates.
 

ext/BoxCoxMakieExt.jl

@@ -5,32 +5,17 @@ using Makie
 
 using BoxCox: _loglikelihood_boxcox!,
               _loglikelihood_boxcox,
-              qr, chisqinvcdf, @compat,
+              qr, chisqinvcdf,
               @setup_workload, @compile_workload
 
 # XXX it would be great to have a 1-1 aspect ratio here,
 # but this seems like something that should be done upstream
-function Makie.convert_arguments(P::Type{<:Makie.QQNorm}, x::BoxCoxTransformation, args...;
-                                 qqline=:fitrobust, kwargs...)
-    return convert_arguments(P, x.(x.y), args...; qqline, kwargs...)
+function Makie.qqnorm!(ax::Axis, bc::BoxCoxTransformation, args...; kwargs...)
+    return qqnorm!(ax, bc.(bc.y), args...; kwargs...)
 end
 
-function Makie.convert_arguments(P::Type{<:Union{Makie.Scatter,Makie.Lines}},
-                                 bc::BoxCoxTransformation, args...;
-                                 λ=nothing, n_steps=21, kwargs...)
-    if isnothing(λ)
-        # TODO: cache this somehow so we're not computing it twice
-        # when also plotting the CI
-        ci = confint(bc; fast=true)
-        lower = first(ci) - 0.05 * abs(first(ci))
-        upper = last(ci) + 0.05 * abs(last(ci))
-        λ = range(lower, upper; length=n_steps)
-    end
-    sort!(collect(λ))
-
-    @compat (; X, y) = bc
-    ll = _loglikelihood_boxcox(X, y, λ)
-    return convert_arguments(P, λ, ll, args...; kwargs...)
+function Makie.qqnorm(bc::BoxCoxTransformation, args...; kwargs...)
+    return qqnorm(bc.(bc.y), args...; kwargs...)
 end
 
 function BoxCox._loglikelihood_boxcox(X::AbstractMatrix{<:Number}, y::Vector{<:Number},
@@ -54,97 +39,50 @@ function BoxCox._loglikelihood_boxcox(::Nothing, y::Vector{<:Number},
     return ll
 end
 
-function Makie.convert_arguments(P::Type{<:Makie.VLines}, bc::BoxCoxTransformation, args...;
-                                 kwargs...)
-    return convert_arguments(P, bc.λ, args...; kwargs...)
-end
-
-@recipe(BCPlot, boxcox) do scene
-    s_theme = default_theme(scene, Scatter)
-    l_theme = default_theme(scene, Lines)
-    automatic = Makie.automatic
-    scatline = Attributes(; color=l_theme.color,
-                          colormap=l_theme.colormap,
-                          # colorscale = l_theme.colorscale,
-                          colorrange=get(l_theme.attributes, :colorrange, automatic),
-                          linestyle=l_theme.linestyle,
-                          linewidth=l_theme.linewidth,
-                          markercolor=automatic,
-                          markercolormap=theme(scene, :colormap),
-                          markercolorrange=get(s_theme.attributes, :colorrange, automatic),
-                          markersize=s_theme.markersize,
-                          strokecolor=s_theme.strokecolor,
-                          strokewidth=s_theme.strokewidth,
-                          marker=s_theme.marker,
-                          inspectable=theme(scene, :inspectable),
-                          cycle=[:color])
-    return merge(scatline, Attributes(; conf_level=0.95, n_steps=10, λ=nothing))
-end
-
-function Makie.plot!(p::BCPlot)
-    # markercolor is the same as linecolor if left automatic
-    # RGBColors -> union of all colortypes that `to_color` accepts + returns
-    real_markercolor = Observable{Makie.RGBColors}()
-    map!(real_markercolor, p.color, p.markercolor) do col, mcol
-        if mcol === Makie.automatic
-            return to_color(col)
-        else
-            return to_color(mcol)
-        end
-    end
-
-    bc = p[1][]
-    n_steps = p.n_steps[]
-    λ = p.λ[]
-    # TODO use splines
-    scatterlines!(p, bc; λ, n_steps,
-                  p.strokecolor, p.strokewidth, p.marker, p.markersize,
-                  color=real_markercolor, p.linestyle, p.linewidth, p.colormap, # p.colorscale,
-                  p.colorrange, p.inspectable)
-    # seem to be hitting some buggy behavior in Makie
-    # vlines!(p, bc; λ,
-    #         p.color, linestyle=:dash, p.linewidth, p.colormap, # p.colorscale,
-    #         p.colorrange, p.inspectable)
-    return plot
+function BoxCox.boxcoxplot(bc::BoxCoxTransformation; kwargs...)
+    fig = Figure()
+    boxcoxplot!(Axis(fig[1, 1]), bc; kwargs...)
+    return fig
 end
 
-BoxCox.boxcoxplot!(ax, bc::BoxCoxTransformation; kwargs...) = bcplot!(ax, bc; kwargs...)
-BoxCox.boxcoxplot(bc::BoxCoxTransformation; kwargs...) = bcplot(bc; kwargs...)
+function BoxCox.boxcoxplot!(ax::Axis, bc::BoxCoxTransformation;
+                            xlabel="λ",
+                            ylabel="log likelihood",
+                            n_steps=21,
+                            λ=nothing,
+                            conf_level=nothing,
+                            attributes...)
+    ax.xlabel = xlabel
+    ax.ylabel = ylabel
 
-function Makie.plot!(ax::Axis, P::Type{<:BCPlot}, allattrs::Makie.Attributes, bc)
-    allattrs = merge(default_theme(P), allattrs)
-    plot = Makie.plot!(ax.scene, P, allattrs, bc)
+    ci = nothing
 
-    if haskey(allattrs, :title)
-        ax.title = allattrs.title[]
-    end
-    if haskey(allattrs, :xlabel)
-        ax.xlabel = allattrs.xlabel[]
-    else
-        ax.xlabel = "λ"
-    end
-    if haskey(allattrs, :ylabel)
-        ax.ylabel = allattrs.ylabel[]
-    else
-        ax.ylabel = "log likelihood"
-    end
-    # scatterlines!(ax, bc)
-    # the ylim error doesn't happen if we do this here
-    vlines!(ax, bc; bc.λ, linestyle=:dash, color=:black)
-    if haskey(allattrs, :conf_level)
-        level = allattrs.conf_level[]
-        lltarget = loglikelihood(bc) - chisqinvcdf(1, level) / 2
+    if !isnothing(conf_level)
+        lltarget = loglikelihood(bc) - chisqinvcdf(1, conf_level) / 2
         hlines!(ax, lltarget; linestyle=:dash, color=:black)
-        ci = confint(bc; level)
+        ci = confint(bc; level=conf_level)
         vlines!(ax, ci; linestyle=:dash, color=:black)
-        text = "$(round(Int, 100 * level))% CI"
+        text = "$(round(Int, 100 * conf_level))% CI"
         text!(ax, first(ci) + 0.05 * abs(first(ci)), lltarget; text)
     end
+
+    if isnothing(λ)
+        ci = @something(ci, confint(bc; fast=true))
+        lower = first(ci) - 0.05 * abs(first(ci))
+        upper = last(ci) + 0.05 * abs(last(ci))
+        λ = range(lower, upper; length=n_steps)
+    end
+    sort!(collect(λ))
+
+    (; X, y) = bc
+    ll = _loglikelihood_boxcox(X, y, λ)
+
+    scatterlines!(ax, λ, ll; attributes...)
+    vlines!(ax, bc.λ; linestyle=:dash, color=:black)
+
     return plot
 end
 
-Makie.plottype(::BoxCoxTransformation) = BCPlot
-
 @setup_workload begin
     # Putting some things in `@setup_workload` instead of `@compile_workload` can reduce the size of the
     # precompile file and potentially make loading faster.

src/BoxCox.jl

@@ -1,6 +1,5 @@
 module BoxCox
 
-using Compat
 using DocStringExtensions
 using LinearAlgebra
 # we use NLopt because that's what MixedModels uses and this was developed
@@ -140,25 +139,29 @@ end
 
 """
     boxcoxplot(bc::BoxCoxTransformation; kwargs...)
-    boxcoxplot!(axis, bc::BoxCoxTransformation; λ=nothing, n_steps=21)
+    boxcoxplot!(axis::Axis, bc::BoxCoxTransformation;
+                λ=nothing, n_steps=21, xlabel="λ", ylabel="log likelihood",
+                conf_level=nothing, attributes...)
 
 Create a diagnostic plot for the Box-Cox transformation.
 
+The mutating method for `Axis` returns the (modified) original `Axis`.
+The non-mutating method returns a `Figure`.
+
 If λ is `nothing`, the range of possible values for the λ parameter is automatically determined,
 with a total of `n_steps`. If `λ` is a vector of numbers, then the λ parameter is evaluated at
 each element of that vector.
 
-!!! note
-    You must load an appropriate Makie backend (e.g., CairoMakie or GLMakie) to actually render a plot.
+If `conf_level` is `nothing`, then no confidence interval is displayed.
+
+`attributes` are forwarded to `scatterlines!`.
 
 !!! note
     A meaningful plot is only possible when `bc` has not been `empty!`'ed.
 
-!!! compat "Julia 1.6"
-    The plotting functionality is defined unconditionally.
-
-!!! compat "Julia 1.9"
+!!! note
     The plotting functionality interface is defined as a package extension and only loaded when Makie is available.
+    You must load an appropriate Makie backend (e.g., CairoMakie or GLMakie) to actually render a plot.
 """
 function boxcoxplot!(::Any, ::PowerTransformation; kwargs...)
     # specialize slightly so that they can't just throw Any and get this message
@@ -227,11 +230,7 @@ If a `LinearMixedModel` is provided, then `X` and `y` are extracted from the mod
     The formula interface is only available if StatsModels.jl is loaded either directly or via another package
     such GLM.jl or MixedModels.jl.
 
-!!! compat "Julia 1.6"
-    - The formula interface is defined unconditionally, but `@formula` is not loaded.
-    - The MixedModels interface is defined unconditionally.
-
-!!! compat "Julia 1.9"
+!!! note
     - The formula interface is defined as a package extension.
     - The MixedModels interface is defined as a package extension.
 
@@ -427,12 +426,6 @@ function Base.show(io::IO, t::BoxCoxTransformation)
     return nothing
 end
 
-if !isdefined(Base, :get_extension)
-    include("../ext/BoxCoxMakieExt.jl")
-    include("../ext/BoxCoxMixedModelsExt.jl")
-    include("../ext/BoxCoxStatsModelsExt.jl")
-end
-
 @setup_workload begin
     # Putting some things in `@setup_workload` instead of `@compile_workload` can reduce the size of the
     # precompile file and potentially make loading faster.