Update compat; standardize yml; use Type not DataType; to v0.18 (#133)

* Update compat

* Standardize yml

* Standardize make.jl

* Use Type not DataType

* Use Type not DataType

* Use Type not DataType

* Fix typos

.github/workflows/CompatHelper.yml

@@ -2,20 +2,47 @@ name: CompatHelper
 
 on:
   schedule:
-    - cron: '00 00 * * *'
+    - 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.COMPATHELPER_PRIV }}  # optional
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
 
 # based on:
 # https://github.com/JuliaRegistries/CompatHelper.jl

.github/workflows/Documentation.yml

@@ -40,6 +40,7 @@ jobs:
             Pkg.instantiate()'
       - name: BuildAndDeploy
         env:
+# https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#Authentication:-GITHUB_TOKEN
 #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           ssh: ${{ secrets.DOCUMENTER_KEY }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.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'

.github/workflows/clean.yml

@@ -0,0 +1,28 @@
+# https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#gh-pages-Branch
+
+name: DocPreviewCleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "documenter@juliadocs.github.io"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
+        env:
+            PRNUM: ${{ github.event.number }}

Project.toml

@@ -1,7 +1,7 @@
 name = "MIRT"
 uuid = "7035ae7a-3787-11e9-139a-5545ed3dc201"
 authors = ["fessler <fessler@umich.edu>"]
-version = "0.17.0"
+version = "0.18"
 
 [deps]
 AVSfldIO = "b6189060-daf9-4c28-845a-cc0984b81781"
@@ -25,14 +25,14 @@ Wavelets = "29a6e085-ba6d-5f35-a997-948ac2efa89a"
 [compat]
 AVSfldIO = "0.2"
 FFTW = "1"
-FileIO = "1.9, 1.14"
-FillArrays = "0.12, 0.13"
-ImageFiltering = "0.6, 0.7"
-ImageTransformations = "0.8, 0.9"
-Interpolations = "0.12, 0.13, 0.14"
-LazyGrids = "0.5"
-LinearMapsAA = "0.11"
+FileIO = "1"
+FillArrays = "1"
+ImageFiltering = "0.7"
+ImageTransformations = "0.10"
+Interpolations = "0.15"
+LazyGrids = "1"
+LinearMapsAA = "0.12"
 NFFT = "0.13"
-SpecialFunctions = "1, 2"
-Wavelets = "0.9"
-julia = "1.8"
+SpecialFunctions = "2"
+Wavelets = "0.10"
+julia = "1.10"

_typos.toml

@@ -0,0 +1,9 @@
+[default]
+extend-ignore-identifiers-re = [
+    "allk",
+    "als",
+    "Nd",
+    "iy",
+    "pn",
+    "MIRTio",
+]

doc/start-juno.md

@@ -43,7 +43,7 @@ jim(x, title="test")
 * This test should produce a grayscale image of the famous
 [Shepp-Logan phantom](https://en.wikipedia.org/wiki/Shepp%E2%80%93Logan_phantom) in the Plots tab of Atom.
 * To learn about the jiffy image display function `jim`, type `?jim` at the REPL.
-* Juno and Atom have lots of online documention.
+* Juno and Atom have lots of online documentation.
 I use the `vim-mode-plus` key bindings, installed using Atom preferences.
 
 * To start a Jupyter notebook for Julia, type at the REPL:

doc/start.md

@@ -1,17 +1,22 @@
-* Install Julia (1.5 or later recommended) from https://julialang.org/
-* Explore the extensive documentation at https://docs.julialang.org/
+* Install Julia (1.10 or later recommended) from https://julialang.org
+* Explore the extensive documentation at https://docs.julialang.org
 * Launch Julia and use the `]` key to enter its package manager.
 * Add any packages needed for these notebooks using the `add` command.
 * For example `add Plots` to add the `Plots` package.
 * Other crucial standard packages are `FFTW` `FFTViews`
 * You will also need the package `IJulia` to run any Jupyter demo notebooks.
 * Add MIRT by typing `add MIRT`
-(Automatically loads from https://github.com/JeffFessler/MIRT.jl because MIRT.jl is a registered package.)
+  (Automatically loads from https://github.com/JeffFessler/MIRT.jl
+  because MIRT.jl is a registered package.)
 * Type `precompile` to have Julia precompile the added packages.
-* After you are done adding packages, press the backspace key to return to the REPL prompt.
-* Later if you need to add more packages just type the `]` key again at the REPL prompt to enter the package manager.
-* Julia is under active development so code is updated frequently.  It is a wise to type `up` (short for `update`) at the package manager prompt every week or so to get automatic updates of any packages you have intalled.
+* After you are done adding packages, press the backspace key
+  to return to the REPL prompt.
+* Later if you need to add more packages just type the `]` key again
+  at the REPL prompt to enter the package manager.
+* Julia is under active development so code is updated frequently.
+  It is a wise to type `up` (short for `update`) at the package manager prompt
+  every week or so to get automatic updates of any packages you have installed.
 * For some Julia tutorials see
-http://web.eecs.umich.edu/~fessler/course/551/julia/tutor/
+  http://web.eecs.umich.edu/~fessler/course/551/julia/tutor
 * For some signal processing demos in Julia see
-http://web.eecs.umich.edu/~fessler/course/551/julia/demo/
+  http://web.eecs.umich.edu/~fessler/course/551/julia/demo

docs/make.jl

@@ -2,8 +2,8 @@ execute = isempty(ARGS) || ARGS[1] == "run"
 
 org, reps = :JeffFessler, :MIRT
 eval(:(using $reps))
-using Documenter
-using Literate
+import Documenter
+import Literate
 #using DemoCards
 
 # examples_templates, examples_theme = cardtheme("grid")
@@ -27,7 +27,7 @@ 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\")"
@@ -81,7 +81,7 @@ format = Documenter.HTML(;
     assets = ["assets/custom.css"],
 )
 
-makedocs(;
+Documenter.makedocs(;
     modules = [repo],
     authors = "Jeff Fessler and contributors",
     sitename = "$repo.jl",
@@ -96,7 +96,7 @@ makedocs(;
 # examples_cb()
 
 if isci
-    deploydocs(;
+    Documenter.deploydocs(;
         repo = "github.com/$base",
         devbranch = "main",
         devurl = "dev",

src/algorithm/general/dot-curv.jl

@@ -10,7 +10,7 @@ _curv_type(Tf::Type{<:RealU}, Tx::Type{<:Number}) =
 
 
 """
-    make_dot_curvf(curv::Function, [x, Tf::DataType; w = similar(x)])
+    make_dot_curvf(curv::Function, [x, Tf::Type; w = similar(x)])
 
 Make a function with arguments `(v, x)`
 that computes the dot product between
@@ -53,7 +53,7 @@ Those units are relevant to defining the work array `w`.
 - `x` an array whose `size` and `eltype` is used to allocate `w`
 
 # option
-- `Tf::DataType = typeof(one(eltype(x)))`
+- `Tf::Type = typeof(one(eltype(x)))`
   Specify `eltype` of function `f(x)`, defaulting to unitless.
 - `w = similar(x,  typeof(oneunit(Tf) / oneunit(eltype(x))^2))`
   work space for gradient calculation, with appropriate units (if needed).

src/algorithm/general/dot-grad.jl

@@ -10,7 +10,7 @@ _grad_type(Tf::Type{<:RealU}, Tx::Type{<:Number}) =
 
 
 """
-    make_dot_gradf(grad::Function, [x, Tf::DataType; w = similar(x)])
+    make_dot_gradf(grad::Function, [x, Tf::Type; w = similar(x)])
 
 Make a function with arguments `(v, x)`
 that computes the dot product between
@@ -44,7 +44,7 @@ Those units are relevant to defining the work array `w`.
 # in
 - `grad::Function` see above
 - `x` an array whose `size` and `eltype` is used to allocate `w`
-- `Tf::DataType = typeof(one(eltype(x)))`
+- `Tf::Type = typeof(one(eltype(x)))`
   Specify `eltype` of function `f(x)`, defaulting to unitless.
 
 # option

src/algorithm/general/pogm_restart.jl

@@ -71,7 +71,7 @@ iterate as below for given coefficients ``(\\alpha, \\beta_k, \\gamma_k)``
   - ``x_{k+1} = y_{k+1} + \\beta_k  (y_{k+1} - y_k) + \\gamma_k  (y_{k+1} - x_k)`` : momentum update
 
 Proximal versions of the above for ``g(x) \\neq 0`` are in the below references,
-and use the proximal operater
+and use the proximal operator
 ``prox_g(z) = argmin_x {1/2\\|z-x\\|^2 + g(x)}``.
 
 - Proximal Gradient method (PGM or ISTA) - ``\\beta_k = \\gamma_k = 0``. [BT09]

src/mri/kspace-spiral.jl

@@ -17,7 +17,7 @@ using Interpolations
 Make k-space spiral trajectory based on GE 3T scanner constraints
 
 Option:
-- `N` dimention of reconstructed image
+- `N` dimension of reconstructed image
 - `Nt` # of time points
 - `fov` field of view in cm
 - `dt` time sampling interval out; default `5e-6` sec
@@ -163,7 +163,7 @@ to gradients at 4us.
 
 Multi-shot spiral design
 uses Duyn's approximate slewrate limited design
-augmented with archimedian `gmax` limit
+augmented with archimedean `gmax` limit
 
 # in [args]
 * `D` = FOV; cm