Standardize yml; compat LinearMapsAA v0.12; to v0.2 (#53)

* Standardize yml

* Standardize make.jl

* Compat to v0.2

* Fix typos

Author: JeffFessler

.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

.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'

Project.toml

@@ -1,7 +1,7 @@
 name = "SPECTrecon"
 uuid = "ab1be465-a7f0-4423-9048-0ee774b70ed9"
 authors = ["Zongyu Li and Jeff Fessler and group"]
-version = "0.1"
+version = "0.2"
 
 [deps]
 AbstractFFTs = "621f4979-c628-5d54-868e-fcf4e3e8185c"
@@ -13,10 +13,10 @@ LinearMapsAA = "599c1a8e-b958-11e9-0d14-b1e6b2ecea07"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
 
 [compat]
-AbstractFFTs = "1.0"
+AbstractFFTs = "1"
 FFTW = "1"
 ImageFiltering = "0.6, 0.7"
 LinearInterpolators = "0.1"
-LinearMapsAA = "0.11"
+LinearMapsAA = "0.12"
 OffsetArrays = "1"
 julia = "1.10"

_typos.toml

@@ -0,0 +1,11 @@
+[default]
+extend-ignore-identifiers-re = [
+    "thid",
+    "iy",
+    "iy",
+]
+
+[files]
+extend-exclude = [
+    "*.ipynb",
+]

docs/lit/examples/1-overview.jl

@@ -218,7 +218,7 @@ mul!(tmp, A', views)
 
 The pixel dimensions `deltas` can (and should!) be values with units.
 
-Here is an example ... (todo)
+Here is an example with units ... (todo)
 
 using UnitfulRecipes
 using Unitful: mm

docs/make.jl

@@ -2,8 +2,8 @@ execute = isempty(ARGS) || ARGS[1] == "run"
 
 org, reps = :JuliaImageRecon, :SPECTrecon
 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"
@@ -23,9 +23,7 @@ binder_root_url =
 
 
 repo = eval(:($reps))
-DocMeta.setdocmeta!(repo, :DocTestSetup, :(using $reps); recursive=true)
-
-#ENV["JULIA_DEBUG"] = "Literate"
+Documenter.DocMeta.setdocmeta!(repo, :DocTestSetup, :(using $reps); recursive=true)
 
 # preprocessing
 inc1 = "include(\"../../../inc/reproduce.jl\")"
@@ -79,7 +77,7 @@ format = Documenter.HTML(;
     assets = ["assets/custom.css"],
 )
 
-makedocs(;
+Documenter.makedocs(;
     modules = [repo],
     authors = "Jeff Fessler & Zongyu Li & contributors",
     sitename = "$repo.jl",
@@ -93,7 +91,7 @@ makedocs(;
 )
 
 if isci
-    deploydocs(;
+    Documenter.deploydocs(;
         repo = "github.com/$base",
         devbranch = "main",
         devurl = "dev",

src/spectplan.jl

@@ -16,10 +16,10 @@ Struct for storing key factors for a SPECT system model
 - `psfs [px,pz,ny,nview]` point spread function, must be 4D, with `px and `pz` odd, and symmetric for each slice
 - `nview` number of views, must be integer
 - `viewangle` set of view angles, must be from 0 to 2π
-- `interpmeth` interpolation method, :one means 1d, :two means 2d
-- `mode` pre-allcoation method, :fast means faster, :mem means use less memory
-- `dy` voxel size in y direction (dx is the same value)
-- `nthread` number of CPU threads used to process data, must be integer
+- `interpmeth` interpolation method: `:one` means 1d; `:two` means 2d
+- `mode` pre-allocation method: `:fast` means faster; `:mem` means use less memory
+- `dy` voxel size in y direction (`dx` is the same value)
+- `nthread` number of CPU threads used to process data; must be integer
 - `planrot` Vector of struct `PlanRotate`
 - `planpsf` Vector of struct `PlanPSF`
 Currently code assumes the following:

time/SPECTplan.jl

@@ -50,5 +50,6 @@ function SPECTplan_time()
 end
 
 
-# run all functions, time may vary on different machines, will alllocate ~100 MB memory.
+# Run all functions; time may vary on different machines.
+# Will allocate ~100 MB memory.
 SPECTplan_time()