diff --git a/.github/dependabot.yml b/.github/dependabot.yml index d486ff7..8b46c7d 100644 --- a/.github/dependabot.yml +++ b/.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" diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml index 62578fe..ca0406b 100644 --- a/.github/workflows/Documentation.yml +++ b/.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 diff --git a/.github/workflows/SpellCheck.yml b/.github/workflows/SpellCheck.yml index b156e88..100a157 100644 --- a/.github/workflows/SpellCheck.yml +++ b/.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 diff --git a/.github/workflows/clean.yml b/.github/workflows/clean.yml index b8a8b4d..37357aa 100644 --- a/.github/workflows/clean.yml +++ b/.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 diff --git a/Project.toml b/Project.toml index 44d239a..a1fc74e 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,10 @@ name = "Examples" uuid = "940e8692-a183-489f-acd6-ad125fa6e02d" -authors = ["Jeff Fessler and others"] +authors = ["Jeff Fessler and others"] version = "0.0.1" +[workspace] +projects = ["docs"] + [compat] -julia = "1.7" +julia = "1.12.6" diff --git a/docs/lit/mri/2-cs-wl-l1-2d.jl b/docs/lit/mri/2-cs-wl-l1-2d.jl index ab7bc0e..b577bbe 100644 --- a/docs/lit/mri/2-cs-wl-l1-2d.jl +++ b/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") diff --git a/docs/lit/mri/3-2d-t.jl b/docs/lit/mri/3-2d-t.jl index 7213bdc..2b226f3 100644 --- a/docs/lit/mri/3-2d-t.jl +++ b/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") diff --git a/docs/lit/mri/4-cs-sense-2d.jl b/docs/lit/mri/4-cs-sense-2d.jl index 9b211d4..06c3aa2 100644 --- a/docs/lit/mri/4-cs-sense-2d.jl +++ b/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") diff --git a/docs/lit/mri/5-l-plus-s.jl b/docs/lit/mri/5-l-plus-s.jl index dbf0b68..6acc7e7 100644 --- a/docs/lit/mri/5-l-plus-s.jl +++ b/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") diff --git a/docs/lit/mri/6-precon.jl b/docs/lit/mri/6-precon.jl index f0f65b4..09c9303 100644 --- a/docs/lit/mri/6-precon.jl +++ b/docs/lit/mri/6-precon.jl @@ -300,6 +300,3 @@ p5 = plot( # isinteractive() && prompt(); - - -include("../../inc/reproduce.jl") diff --git a/docs/lit/mri/95-varpro1.jl b/docs/lit/mri/95-varpro1.jl index 3ce7b17..fc82816 100644 --- a/docs/lit/mri/95-varpro1.jl +++ b/docs/lit/mri/95-varpro1.jl @@ -442,5 +442,3 @@ plot(p2r, - affine fit via LS and WLS and ML =# - -include("../../inc/reproduce.jl") diff --git a/docs/lit/mri/99-varpro2.jl b/docs/lit/mri/99-varpro2.jl index 5c3eb6f..0085680 100644 --- a/docs/lit/mri/99-varpro2.jl +++ b/docs/lit/mri/99-varpro2.jl @@ -338,5 +338,3 @@ plot!(annotation = (24, 200, "CRB = $(roundr(crb_std.rb))", :red)) - Newton's method? - Units? =# - -include("../../inc/reproduce.jl") diff --git a/docs/make.jl b/docs/make.jl index 655b372..2e849ab 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -22,6 +22,7 @@ binder_root_url = "https://mybinder.org/v2/gh/$base/gh-pages?filepath=generated" repo = eval(:($reps)) + # preprocessing inc1 = "include(\"../../inc/reproduce.jl\")" diff --git a/README.md b/readme.md similarity index 100% rename from README.md rename to readme.md