Standardize yml and LazyGrids compat v1 (#84)

* Standardize docs

* Standardize yml

* Compat LazyGrids v1

* Fix size

* Compat for ImageGeoms !?

* Compat ImageGeoms for docs/ too !?

.github/workflows/CompatHelper.yml

@@ -4,11 +4,23 @@ on:
   schedule:
     - cron: 0 0 * * 0 # weekly
   workflow_dispatch:
-
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
+      - 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
@@ -31,3 +43,6 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           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

Project.toml

@@ -9,6 +9,6 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 
 [compat]
-LazyGrids = "0.5"
+LazyGrids = "0.5, 1"
 SpecialFunctions = "1.8, 2"
 julia = "1.10"

docs/Project.toml

@@ -11,3 +11,4 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [compat]
+ImageGeoms = "0.10"

docs/lit/examples/01-overview.jl

@@ -149,13 +149,13 @@ pic1 = phantom(x, y, [ellipse1])
 
 marker = :star
 p0 = jim(x, y, pic0, "Original ellipse";
-    xlabel="x", ylabel="y", prompt=:false)
+    xlabel="x", ylabel="y", size=(700,300), prompt=:false)
 x0,y0 = 7,0
 scatter!([x0], [y0], color=:blue; marker)
 point1 = [cos(ϕ1) -sin(ϕ1); sin(ϕ1) cos(ϕ1)] * [x0; y0] # rotate point
 x1,y1 = point1[1], point1[2]
 p1 = jim(x, y, pic1, "Rotated by ϕ = $ϕ1s";
-    xlabel="x", ylabel="y", prompt=:false)
+    xlabel="x", ylabel="y", size=(700,300), prompt=:false)
 scatter!([x1], [y1], color=:blue; marker)
 jim(p0, p1)
 
@@ -221,15 +221,15 @@ pic1 = phantom(x, y, z, [ellipsoid1])
 
 p0z = jim(x, y, pic0,
     "Original ellipsoid:\n(x,y) slice";
-    xlabel="x", ylabel="y", prompt=:false)
+    xlabel="x", ylabel="y", size=(700,300), prompt=:false)
 x0,y0 = 7,0
 scatter!([x0], [y0], color=:blue; marker)
 Rz(ϕ) = [cos(ϕ) -sin(ϕ) 0; sin(ϕ) cos(ϕ) 0; 0 0 1]
 point1 = Rz(ϕ1) * [x0; y0; 0] # rotate point
 x1,y1 = point1[1], point1[2]
 p1z = jim(x, y, pic1,
     "Rotated about z\nby ϕ = $ϕ1s\n(z out of 'board')";
-    xlabel="x", ylabel="y", prompt=:false)
+    xlabel="x", ylabel="y", size=(700,350), prompt=:false)
 scatter!([x1], [y1], color=:blue; marker)
 jim(p0z, p1z)
 
@@ -285,15 +285,15 @@ pic1 = phantom(x, y, z, [ellipsoid1]); pic1 = selectdim(pic1, 2, 1)
 
 p0y = jim(x, z, pic0,
     "Original ellipsoid:\n (x,z) slice";
-    xlabel="x", ylabel="z", prompt=false)
+    xlabel="x", ylabel="z", size=(700,350), prompt=false)
 x0,z0 = 7,0
 scatter!([x0], [z0], color=:green; marker)
 Ry(θ) = [cos(θ) 0 sin(θ); 0 1 0; -sin(θ) 0 cos(θ)]
 point1 = Ry(θ1) * [x0; 0; z0] # rotate point
 x1,z1 = point1[1], point1[3]
 p1y = jim(x, z, pic1,
     "Rotated about y\nby θ = $θ1s\n(y into 'board')";
-    xlabel="x", ylabel="z", prompt=false)
+    xlabel="x", ylabel="z", size=(700,350), prompt=false)
 scatter!([x1], [z1], color=:green; marker)
 jim(p0y, p1y)
 
@@ -347,15 +347,15 @@ pic1 = phantom(x, y, z, [ellipsoid1]); pic1 = selectdim(pic1, 1, 1)
 
 p0x = jim(y, z, pic0,
     "Original ellipsoid:\n (y,z) slice)";
-    xlabel="y", ylabel="z", prompt=false)
+    xlabel="y", ylabel="z", size=(700,350), prompt=false)
 y0,z0 = 3,0
 scatter!([y0], [z0], color=:red; marker)
 Rx(ψ) = [1 0 0 ; 0 cos(ψ) -sin(ψ); 0 sin(ψ) cos(ψ)]
 point1 = Rx(ψ1) * [0; y0; z0] # rotate point
 y1,z1 = point1[2], point1[3]
 p1x = jim(y, z, pic1,
     "Rotated about x\nby ψ = $ψ1s\n(x out of 'board')";
-    xlabel="y", ylabel="z", prompt=false)
+    xlabel="y", ylabel="z", size=(700,350), prompt=false)
 scatter!([y1], [z1], color=:red; marker)
 jim(p0x, p1x)
 
@@ -441,10 +441,10 @@ pic1 = phantom(x, y, z, [ellipsoid1])
 
 p0a = jim(mid3(pic0),
     "Original ellipsoid\n(central slices)";
-    xlabel="x", ylabel="y", prompt=:false)
+    xlabel="x", ylabel="y", size=(700,320), prompt=:false)
 p1a = jim(mid3(pic1),
     "Rotated\nϕ = $ϕ1s, θ = $θ1s, ψ = $ψ1s";
-    xlabel="x", ylabel="y", prompt=:false)
+    xlabel="x", ylabel="y", size=(700,320), prompt=:false)
 jim(p0a, p1a)
 
 

docs/make.jl

@@ -2,8 +2,8 @@ execute = isempty(ARGS) || ARGS[1] == "run"
 
 org, reps = :JuliaImageRecon, :ImagePhantoms
 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",

test/Project.toml

@@ -8,3 +8,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [compat]
+ImageGeoms = "0.10"

test/helper.jl

@@ -10,8 +10,10 @@ end
 =#
 
 
-# fft cannot handle units so this is a work-around
-function myfft(x::AbstractArray{<:Number})
-    u = oneunit(eltype(x))
-    return fftshift(fft(ifftshift(x) / u)) * u
+if !@isdefined myfft
+    # fft cannot handle units so this is a work-around
+    function myfft(x::AbstractArray{<:Number})
+        u = oneunit(eltype(x))
+        return fftshift(fft(ifftshift(x) / u)) * u
+    end
 end

test/shape2.jl

@@ -13,6 +13,7 @@ using ImageGeoms: ImageGeom, axesf
 using FFTW: fft, fftshift, ifftshift
 using Test: @test, @testset, @inferred
 
+include("helper.jl") # myfft
 
 @testset "circle-square" begin # special constructors
     args = [(1, 5.0f0), (1, 2, 3., 5.0f0), ((1, 2), 3., 5.0f0)]
@@ -178,7 +179,7 @@ end
 
   @testset "spectrum" begin
     (M,N) = (2^10,2^10+5) # odd
-    ig = ImageGeom( dims=(M,N), deltas=(0.02m, 0.025m), offsets=:dsp)
+    ig = ImageGeom(; dims=(M,N), deltas=(0.02m, 0.025m), offsets=:dsp)
     ob = shape((2m, -3m), swidth, π/6, 1.0f0)
     zscale = 1 / (ob.value * IP.area(ob)) # normalize spectra by area