API modernization: argmin rename, ratio keyword arg, highpass! variants (v1.0.0)

.claude/freshen-package-status

@@ -0,0 +1,11 @@
+DONE: design review
+DONE: API review
+DONE: update .gitignore
+DONE: format with runic
+DONE: add Aqua.jl
+DONE: remove deprecations
+DONE: add ExplicitImports.jl
+DONE: limit struct mutability
+DONE: improve test coverage
+DONE: add and improve docstrings
+TODO: add or improve documentation

.github/workflows/CI.yml

@@ -13,17 +13,15 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
-          - '1.1'
+          - '1.10'
           - '1'
-#          - 'nightly'
         os:
           - ubuntu-latest
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
@@ -42,6 +40,6 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info

.github/workflows/Documenter.yml

@@ -10,11 +10,14 @@ jobs:
       name: Documentation
       runs-on: ubuntu-latest
       steps:
-        - uses: actions/checkout@v2
+        - uses: actions/checkout@v4
         - name: Install HolyLab Registry
           run: julia -e 'using Pkg; Pkg.Registry.add([RegistrySpec(name="General"),RegistrySpec(url="https://github.com/HolyLab/HolyLabRegistry")]);'
-        - uses: julia-actions/julia-buildpkg@latest
-        - uses: julia-actions/julia-docdeploy@latest
+        - uses: julia-actions/setup-julia@v2
+          with:
+            version: '1'
+        - uses: julia-actions/julia-buildpkg@v1
+        - uses: julia-actions/julia-docdeploy@v1
           env:
             GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
             DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.gitignore

@@ -3,3 +3,7 @@
 *.jl.mem
 deps/deps.jl
 Manifest.toml
+Manifest-v*.toml
+docs/Manifest.toml
+docs/Manifest-v*.toml
+docs/build/

Project.toml

@@ -1,7 +1,7 @@
 name = "RegisterCore"
 uuid = "67712758-55e7-5c3c-8e85-dda1d7758434"
+version = "1.0.0"
 authors = ["Tim Holy <tim.holy@gmail.com>"]
-version = "0.2.5"
 
 [deps]
 CenterIndexedArrays = "46a7138f-0d70-54e1-8ada-fb8296f91f24"
@@ -10,16 +10,23 @@ ImageFiltering = "6a3955dd-da59-5b1f-98d4-e7296123deb5"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 
 [compat]
+Aqua = "0.8"
 CenterIndexedArrays = "0.2"
+ExplicitImports = "1"
 ImageCore = "0.8.1, 0.9, 0.10"
 ImageFiltering = "0.5, 0.6, 0.7"
+ImageMetadata = "0.9"
+Interpolations = "0.13, 0.14, 0.15, 0.16"
 Requires = "1"
+Test = "1"
 julia = "^1.1"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 ImageMetadata = "bc367c6b-8a6b-528e-b4bd-a4b897500b49"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["ImageMetadata", "Interpolations", "Test"]
+test = ["Aqua", "ExplicitImports", "ImageMetadata", "Interpolations", "Test"]

README.md

@@ -1,8 +1,10 @@
 # RegisterCore
 
+[![CI](https://github.com/HolyLab/RegisterCore.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/HolyLab/RegisterCore.jl/actions/workflows/CI.yml)
 [![codecov](https://codecov.io/gh/HolyLab/RegisterCore.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/HolyLab/RegisterCore.jl)
+[![Aqua QA](https://juliatesting.github.io/Aqua.jl/dev/assets/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
+[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://HolyLab.github.io/RegisterCore.jl/stable)
+[![](https://img.shields.io/badge/docs-dev-blue.svg)](https://HolyLab.github.io/RegisterCore.jl/dev)
 
 This package defines low-level types and operations used for a larger image registration infrastructure.
-The documentation gives something of a big-picture overview:
-
-[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://HolyLab.github.io/RegisterCore.jl/dev)
+The documentation gives a big-picture overview of the key concepts.

docs/Project.toml

@@ -2,4 +2,4 @@
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 
 [compat]
-Documenter = "~0.23"
+Documenter = "1"

docs/make.jl

@@ -7,7 +7,11 @@ makedocs(
         prettyurls = get(ENV, "CI", nothing) == "true"
     ),
     modules = [RegisterCore],
-    pages = ["index.md", "api.md"]
+    checkdocs = :exports,
+    pages = [
+        "Overview" => "index.md",
+        "API Reference" => "api.md",
+    ]
 )
 
 deploydocs(

docs/src/api.md

@@ -1,15 +1,22 @@
 # API
 
+```@docs
+RegisterCore
+```
+
 ## Types
 
 ```@docs
 NumDenom
+MismatchArray
+ColonFun
+PreprocessSNF
 ```
 
-## Functions related to NumDenom
+## MismatchArray functions
 
 ```@docs
-indmin_mismatch
+argmin_mismatch
 maxshift
 mismatcharrays
 ratio
@@ -20,7 +27,7 @@ separate
 
 ```@docs
 highpass
-PreprocessSNF
+highpass!
 paddedview
 trimmedview
 ```

docs/src/index.md

@@ -74,7 +74,7 @@ corresponds to an identical shift in the opposite direction.
 
 ## NumDenom
 
-Mismatch computations actually return two numbers, conventionaly
+Mismatch computations actually return two numbers, conventionally
 called `num` and `denom` packed into a type called `NumDenom`.
 `num` represents the "numerator" of the mismatch,
 and always holds the sum-of-squared-differences.  In our example above,
@@ -88,6 +88,31 @@ julia> sum((img[1:end-1,:] - img[2:end,:]).^2)
 24
 ```
 
+`NumDenom` supports vector-space arithmetic, which enables interpolation
+of mismatch arrays. A brief example without `RegisterMismatch`:
+
+```jldoctest
+julia> using RegisterCore
+
+julia> a = NumDenom(3.0, 10.0)
+NumDenom(3.0,10.0)
+
+julia> b = NumDenom(1.0, 6.0)
+NumDenom(1.0,6.0)
+
+julia> a + b
+NumDenom(4.0,16.0)
+
+julia> 0.5 * a
+NumDenom(1.5,5.0)
+
+julia> ratio(a, 0.0)
+0.3
+
+julia> ratio(NumDenom(0.0, 1e-6), 0.0)
+0.0
+```
+
 One key thing to note is that this sum-of-squared-differences
 includes  *only overlapping pixels*.
 In the example above, `D[2,0]` is `NumDenom(16, 22)`, and the 16