Illustrate mid3 with xticks in documentation

.github/workflows/CompatHelper.yml

@@ -1,20 +1,48 @@
 name: CompatHelper
+
 on:
   schedule:
     - cron: 0 0 * * 0 # weekly
   workflow_dispatch:
-
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@latest
+        with:
+          version: '1'
+          # arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }} # need ssh
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
 
 # based on:
 # https://github.com/JuliaRegistries/CompatHelper.jl

.github/workflows/SpellCheck.yml

@@ -0,0 +1,13 @@
+name: Spell Check
+
+on: [pull_request]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v4
+      - name: Check spelling
+        uses: crate-ci/typos@master

.github/workflows/TagBot.yml

@@ -1,9 +1,11 @@
 name: TagBot
+
 on:
   issue_comment:
     types:
       - created
   workflow_dispatch:
+
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'

docs/lit/examples/1-examples.jl

@@ -12,7 +12,7 @@ This page illustrates the Julia package
 
 # Packages needed here.
 
-using MIRTjim: jim, prompt
+using MIRTjim: jim, prompt, mid3
 using AxisArrays: AxisArray
 using ColorTypes: RGB
 using OffsetArrays: OffsetArray
@@ -71,7 +71,7 @@ jim(zo, "OffsetArray example")
 =#
 
 f3 = reshape(1:(9*7*6), (9, 7, 6))
-jim(f3, "3D")
+jim(f3, "3D"; size=(600, 300))
 
 
 # One can specify how many images per row or column for such a mosaic.
@@ -80,7 +80,28 @@ x11 = reshape(1:(5*6*11), (5, 6, 11))
 jim(x11, "nrow=3"; nrow=3)
 
 #
-jim(x11, "ncol=6"; ncol=6)
+jim(x11, "ncol=6"; ncol=6, size=(600, 200))
+
+
+#=
+## Central slices with `mid3`
+The `mid3` function shows the central x-y, y-z, and x-z slices
+[(axial, coronal, sagittal) planes](https://en.wikipedia.org/wiki/Anatomical_plane).
+Making useful `xticks` and `yticks` in this case takes some fiddling.
+=#
+x,y,z = -20:20, -10:10, 1:30
+xc = reshape(x, :, 1, 1)
+yc = reshape(y, 1, :, 1)
+zc = reshape(z, 1, 1, :)
+rx = reshape(range(2, 19, length(z)), size(zc))
+ry = reshape(range(2, 9, length(z)), size(zc))
+cone = @. abs2(xc / rx) + abs2(yc / ry) < 1
+jim(mid3(cone); color=:cividis, title="mid3")
+xticks = ([1, length(x), length(x)+length(z)],
+ ["$(x[begin])", "$(x[end]), $(z[begin])", "$(z[end])"])
+yticks = ([1, length(y), length(y)+length(z)],
+ ["$(y[begin])", "$(y[end]), $(z[begin])", "$(z[end])"])
+Plots.plot!(;xticks , yticks)
 
 
 #=
@@ -115,7 +136,7 @@ jim(x, y, zu, "units" ;
 x = range(-2,2,201) * 1u"m"
 y = range(-1.2,1.2,150) * 1u"m" # Δy ≢ Δx
 z = @. sqrt(x^2 + (y')^2) ≤ 1u"m"
-jim(x, y, z, "Axis units with unequal spacing"; color=:cividis)
+jim(x, y, z, "Axis units with unequal spacing"; color=:cividis, size=(600,350))
 
 
 #=

docs/lit/examples/2-yflip.jl

@@ -37,7 +37,8 @@ This is a typical convention in "image processing" of digital images
 that lack any physical coordinates for their axes.
 =#
 
-ji = (args...; kwargs...) -> jim(args...; kwargs..., prompt=false)
+ji = (args...; kwargs...) ->
+ jim(args...; size=(700,400), kwargs..., prompt=false)
 jim(
     ji(i1, "2D default"),
     ji(i1, yflip=false, "2D yflip=false"),

docs/make.jl

@@ -2,8 +2,8 @@ execute = isempty(ARGS) || ARGS[1] == "run"
 
 org, reps = :JeffFessler, :MIRTjim
 eval(:(using $reps))
-using Documenter
-using Literate
+import Documenter
+import Literate
 
 # https://juliadocs.github.io/Documenter.jl/stable/man/syntax/#@example-block
 ENV["GKSwstype"] = "100"
@@ -23,7 +23,7 @@ binder_root_url =
 
 
 repo = eval(:($reps))
-DocMeta.setdocmeta!(repo, :DocTestSetup, :(using $reps); recursive=true)
+Documenter.DocMeta.setdocmeta!(repo, :DocTestSetup, :(using $reps); recursive=true)
 
 # preprocessing
 inc1 = "include(\"../../../inc/reproduce.jl\")"
@@ -77,7 +77,7 @@ format = Documenter.HTML(;
     assets = ["assets/custom.css"],
 )
 
-makedocs(;
+Documenter.makedocs(;
     modules = [repo],
     authors = "Jeff Fessler and contributors",
     sitename = "$repo.jl",
@@ -90,7 +90,7 @@ makedocs(;
 )
 
 if isci
-    deploydocs(;
+    Documenter.deploydocs(;
         repo = "github.com/$base",
         devbranch = "main",
         devurl = "dev",

src/MIRTjim.jl

@@ -1,6 +1,9 @@
 """
 Module `MIRTjim` exports the "jiffy image display" method `jim`,
-and the two helper methods `caller_name` and `prompt`.
+and the helper methods:
+- `caller_name`
+- `mid3`
+- `prompt`
 """
 module MIRTjim
 

test/isplot.jl

@@ -1,6 +1,8 @@
 using Plots
 using Test: @test
 
-macro isplot(ex) # @isplot macro to streamline tests
-    :(@test $(esc(ex)) isa Plots.Plot)
+if !isdefined(Main, Symbol("@isplot"))
+    macro isplot(ex) # @isplot macro to streamline tests
+        :(@test $(esc(ex)) isa Plots.Plot)
+    end
 end

test/runtests.jl

@@ -5,10 +5,6 @@ using MIRTjim
 
 ENV["GKSwstype"] = "100"
 
-macro isplot(ex) # @isplot macro to streamline tests
-    :(@test $(esc(ex)) isa Plots.Plot)
-end
-
 @testset "MIRTjim" begin
     include("jim.jl")