workflow update

.github/dependabot.yml

@@ -2,7 +2,12 @@
 
 version: 2
 updates:
-  - package-ecosystem: github-actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+
+  - package-ecosystem: "julia"
     directory: "/"
     schedule:
       interval: "weekly"

.github/workflows/Documentation.yml

@@ -3,21 +3,29 @@ name: Documentation
 on:
   pull_request:
     paths-ignore:
-      - 'README.md'
+      - 'readme.md'
   push:
-    paths-ignore:
-      - 'README.md'
     branches:
       - 'main'
       - 'release-'
+    paths-ignore:
+      - 'readme.md'
     tags: '*'
 
 jobs:
   build:
+    # These permissions are needed to:
+    # - Deploy the documentation: https://documenter.juliadocs.org/stable/man/hosting/#Permissions
+    # - Delete old caches: https://github.com/julia-actions/cache#usage
+    permissions:
+      actions: write
+      contents: write
+      pull-requests: read
+      statuses: write
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v7
+      - uses: julia-actions/setup-julia@v3
         with:
           version: '1'
       - name: CacheArtifacts
@@ -33,15 +41,15 @@ jobs:
             ${{ runner.os }}-
       - name: InstallDependencies
         run: |
-          julia --project=docs/ -e '
+          julia --color=yes --project=docs/ -e '
             ENV["JULIA_PKG_SERVER"] = ""
             using Pkg
             Pkg.develop(PackageSpec(path=pwd()))
             Pkg.instantiate()'
       - name: BuildAndDeploy
+        run: julia --color=yes --project=docs/ docs/make.jl
         env:
 # https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#Authentication:-GITHUB_TOKEN
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # for previews
           ssh: ${{ secrets.DOCUMENTER_KEY }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia --project=docs/ docs/make.jl

.github/workflows/SpellCheck.yml

@@ -8,6 +8,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Actions Repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
       - name: Check spelling
         uses: crate-ci/typos@master

.github/workflows/clean.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gh-pages branch
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           ref: gh-pages
       - name: Delete preview and history + push changes

Project.toml

@@ -1,7 +1,10 @@
 name = "Examples"
 uuid = "940e8692-a183-489f-acd6-ad125fa6e02d"
-authors = ["Jeff Fessler <fessler@umich.edu> and others"]
+authors = ["Jeff Fessler and others"]
 version = "0.0.1"
 
+[workspace]
+projects = ["docs"]
+
 [compat]
-julia = "1.7"
+julia = "1.12.6"

docs/lit/mri/2-cs-wl-l1-2d.jl

@@ -206,6 +206,3 @@ p3 = jim(Xpogm, "POGM recon")
 p5 = jim(X0 - Xtrue, "X0 error", clim=(0,2))
 p6 = jim(Xpogm - Xtrue, "Xpogm error", clim=(0,2))
 pe = jim(p2, p3, p5, p6)
-
-
-include("../../inc/reproduce.jl")

docs/lit/mri/3-2d-t.jl

@@ -207,5 +207,3 @@ anim3 = @animate for it in 1:nt
     )
 end
 gif(anim3; fps = 6)
-
-include("../../inc/reproduce.jl")

docs/lit/mri/4-cs-sense-2d.jl

@@ -376,6 +376,3 @@ but aliasing artifacts (ripples)
 were greatly reduced
 by the CS-SENSE reconstruction method.
 =#
-
-
-include("../../inc/reproduce.jl")

docs/lit/mri/5-l-plus-s.jl

@@ -411,5 +411,3 @@ any(any4, (out_pgm, out_fpgm, out_pogm)) && throw("unexpected restart")
 
 As expected, POGM converged the fastest here.
 =#
-
-include("../../inc/reproduce.jl")

docs/lit/mri/6-precon.jl

@@ -300,6 +300,3 @@ p5 = plot(
 
 #
 isinteractive() && prompt();
-
-
-include("../../inc/reproduce.jl")

docs/lit/mri/95-varpro1.jl

@@ -442,5 +442,3 @@ plot(p2r,
 
 - affine fit via LS and WLS and ML
 =#
-
-include("../../inc/reproduce.jl")

docs/lit/mri/99-varpro2.jl

@@ -338,5 +338,3 @@ plot!(annotation = (24, 200, "CRB = $(roundr(crb_std.rb))", :red))
 - Newton's method?
 - Units?
 =#
-
-include("../../inc/reproduce.jl")

docs/make.jl

@@ -22,6 +22,7 @@ binder_root_url =
     "https://mybinder.org/v2/gh/$base/gh-pages?filepath=generated"
 
 repo = eval(:($reps))
+
 # preprocessing
 inc1 = "include(\"../../inc/reproduce.jl\")"