ci: standardize linting, import hygiene, and CI workflows (#20)

- Move the Aqua.jl and JET.jl checks into a self-contained `test/linting.jl` (JET runs on Julia v1.12+ only).
- Add ExplicitImports.jl import-hygiene checks and drop the unused `Configurations` dependency.
- Add a package-scoped `Aqua.test_ambiguities` check alongside `Aqua.test_all(…; ambiguities = false)`.
- Standardize the GitHub Actions workflow: pin actions to their latest majors, restrict the Julia matrix to `1` and `lts`, and drop the `os`/`arch` matrix (single `ubuntu-latest` runner).
- Add a pre-commit config (Runic, typos, whitespace/EOF hygiene) and apply the resulting fixes.

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

Author: adrhill

.github/workflows/CI.yml

@@ -24,33 +24,31 @@ jobs:
         version:
           - 'lts'
           - '1'
-          - 'pre'
     steps:
-      - uses: actions/checkout@v5
-      - uses: julia-actions/setup-julia@v2
+      - uses: actions/checkout@v7
+      - uses: julia-actions/setup-julia@v3
         with:
           version: ${{ matrix.version }}
-          arch: x64
-      - uses: julia-actions/cache@v2
+      - uses: julia-actions/cache@v3
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v5
+      - uses: codecov/codecov-action@v7
         with:
           files: lcov.info
-  
+
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     permissions:
       contents: write
       statuses: write
     steps:
-      - uses: actions/checkout@v5
-      - uses: julia-actions/setup-julia@v2
+      - uses: actions/checkout@v7
+      - uses: julia-actions/setup-julia@v3
         with:
           version: '1'
-      - uses: julia-actions/cache@v2
+      - uses: julia-actions/cache@v3
       - name: Configure doc environment
         run: |
           julia --project=docs/ --color=yes -e '
@@ -72,11 +70,11 @@ jobs:
     name: Runic formatting
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      # - uses: julia-actions/setup-julia@v2
+      - uses: actions/checkout@v7
+      # - uses: julia-actions/setup-julia@v3
       #   with:
       #     version: '1'
-      # - uses: julia-actions/cache@v2
+      # - uses: julia-actions/cache@v3
       - uses: fredrikekre/runic-action@v1
         with:
-          version: '1'
+          version: '1'

.gitignore

@@ -5,4 +5,4 @@ Manifest.toml
 /test/Manifest.toml
 /docs/Manifest.toml
 /docs/build/
-settings.json
+settings.json

.pre-commit-config.yaml

@@ -2,4 +2,26 @@ repos:
   - repo: https://github.com/fredrikekre/runic-pre-commit
     rev: v1.0.0
     hooks:
-      - id: runic
+      - id: runic
+
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.48.0
+    hooks:
+      - id: typos
+        # report and fail (no --write-changes, so no in-place edits);
+        # --force-exclude makes staged files honor _typos.toml excludes
+        args: [--force-exclude]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+        # ReferenceTests golden files: trailing space and the missing
+        # final newline are significant output, never "fix" them
+        exclude: ^test/references/
+      - id: end-of-file-fixer
+        exclude: ^test/references/
+      - id: check-merge-conflict
+      - id: check-added-large-files
+      - id: check-toml
+      - id: check-yaml

CHANGELOG.md

@@ -2,7 +2,7 @@
 
 ## Version `v2.1.0`
 * ![Feature][badge-feature] Support overlays over batches of images ([#17])
-* ![Maintenance][badge-maintenance] Test type inferrence with JET.jl ([#19])
+* ![Maintenance][badge-maintenance] Test type inference with JET.jl ([#19])
 * ![Maintenance][badge-maintenance] Format with Runic
 
 ## Version `v2.0.1`
@@ -24,7 +24,7 @@
 
 ## Version `v1.2.0`
 * ![Feature][badge-feature] Add heatmap overlays ([#5][pr-5])
-* ![Feature][badge-feature] Add color channel reduction presets `:sumabs` and `:abssum` ([#6][pr-6]) 
+* ![Feature][badge-feature] Add color channel reduction presets `:sumabs` and `:abssum` ([#6][pr-6])
 
 ## Version `v1.1.0`
 * ![Feature][badge-feature] Access color schemes through their symbols ([#3][pr-3])
@@ -66,4 +66,4 @@
 [badge-security]: https://img.shields.io/badge/security-black.svg
 [badge-experimental]: https://img.shields.io/badge/experimental-lightgrey.svg
 [badge-maintenance]: https://img.shields.io/badge/maintenance-gray.svg
-[badge-docs]: https://img.shields.io/badge/docs-orange.svg
+[badge-docs]: https://img.shields.io/badge/docs-orange.svg

Project.toml

@@ -5,7 +5,6 @@ version = "2.1.0-DEV"
 
 [deps]
 ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
-Configurations = "5218b696-f38b-4ac9-8b61-a12ec717816d"
 ImageCore = "a09fc81d-aa75-5fe9-8630-4744c3626534"
 ImageTransformations = "02fcd773-0e25-5acc-982a-7f6622650795"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
@@ -14,7 +13,6 @@ XAIBase = "9b48221d-a747-4c1b-9860-46a1d8ba24a7"
 
 [compat]
 ColorSchemes = "3"
-Configurations = "0.17"
 ImageCore = "0.9, 0.10"
 ImageTransformations = "0.10"
 Interpolations = "0.15, 0.16"

README.md

@@ -25,6 +25,10 @@ To install this package and its dependencies, open the Julia REPL and run
 ## Related packages
 * [TextHeatmaps.jl](https://github.com/Julia-XAI/TextHeatmaps.jl):
   Sibling package for visualization of sentiment analysis and input space attributions of NLP models.
-* [Julia-XAI](https://github.com/Julia-XAI): 
+* [Julia-XAI](https://github.com/Julia-XAI):
   VisionHeatmaps.jl was designed to visualize explanations from the Julia-XAI ecosystem
-  and provides methods for the interface defined by [XAIBase.jl](https://github.com/Julia-XAI/XAIBase.jl).
+  and provides methods for the interface defined by [XAIBase.jl](https://github.com/Julia-XAI/XAIBase.jl).
+
+## Acknowledgements
+
+Adrian Hill gratefully acknowledges funding from the German Federal Ministry of Education and Research under the grant BIFOLD26B.

docs/src/example.md

@@ -10,7 +10,7 @@ asset_dir = HTTP.URI("https://raw.githubusercontent.com/Julia-XAI/VisionHeatmaps
 img = load(joinpath(asset_dir, "img1.png")) # load image file
 ```
 
-You might use an input space attribution method 
+You might use an input space attribution method
 (for example from [ExplainableAI.jl](https://github.com/Julia-XAI/ExplainableAI.jl))
 to determine which parts of the input contributed most to the "saxophone" class.
 
@@ -43,9 +43,9 @@ heatmap(x) |> only
 ```
 
 ## Custom heatmapping pipelines
- 
+
 VisionHeatmaps internally applies a sequence of image transformations in what we call a [`Pipeline`](@ref).
-The default pipeline corresponds to: 
+The default pipeline corresponds to:
 ```@example 1
 pipe = NormReduction() |> ExtremaColormap() |> FlipImage()
 ```
@@ -124,8 +124,8 @@ heatmap(x, pipe) |> only
 pipe = NormReduction() |> ExtremaColormap(:viridis) |> FlipImage()
 heatmap(x, pipe) |> only
 ```
- 
-We strongly suggest to only use sequential color schemes with `ExtremaColormap` 
+
+We strongly suggest to only use sequential color schemes with `ExtremaColormap`
 and divergent color schemes with `CenteredColormap`.
 
 !!! tip "ColorSchemes.jl catalogue"
@@ -147,7 +147,7 @@ heatmap(x, img, pipe) |> only
 Let's assume we computed an input space attribution `batch` for the following images.
 
 ```@example 1
-imgs = [load(joinpath(asset_dir, f)) for f in ("img1.png", "img2.png", "img3.png", "img4.png", "img5.png")] # load image files 
+imgs = [load(joinpath(asset_dir, f)) for f in ("img1.png", "img2.png", "img3.png", "img4.png", "img5.png")] # load image files
 ```
 
 Once again, we assume that `batch` is in WHCN format:

docs/src/index.md

@@ -31,7 +31,7 @@ AbsSumReduction
 ### Manipulating array dimensions
 ```@docs
 FlipImage
-PermuteDims 
+PermuteDims
 DropDims
 ```
 

src/VisionHeatmaps.jl

@@ -6,7 +6,6 @@ using ImageTransformations: imresize
 using Interpolations: Lanczos
 using ImageCore
 using XAIBase: Explanation, AbstractXAIMethod, analyze
-using Configurations: @option
 
 const AbstractImage{T <: Union{Number, Colorant}} = AbstractArray{T, 2}
 const AbstractImageBatch{T <: Union{Number, Colorant}} = AbstractArray{T, 3}

src/heatmap.jl

@@ -37,7 +37,7 @@ heatmap(x) = heatmap(x, DEFAULT_PIPELINE)
 """
     heatmap(expl::Explanation)
     heatmap(expl::Explanation, pipeline)
-    heatmap(expl::Explanation, image)   
+    heatmap(expl::Explanation, image)
     heatmap(expl::Explanation, image, pipeline)
 
 Visualize `Explanation` from XAIBase as a vision heatmap.