test correlations of lsp/rsp and rw/rsp

.github/workflows/CI.yml

@@ -1,15 +1,7 @@
 name: CI
 on:
-  pull_request:
-    branches:
-      - main
-      - dev
-  push:
-    branches:
-      - main
-      - dev
-    tags: '*'
-  workflow_dispatch:
+  - pull_request
+  - push
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
@@ -18,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - 'lts'
+          # - 'lts' cant do lts testing with [sources] in Project.toml
           - '1'
           - 'pre'
         os:
@@ -47,28 +39,3 @@ jobs:
       - uses: codecov/codecov-action@v5
         with:
           file: lcov.info
-  docs:
-    name: Documentation
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v2
-        with:
-          version: '1'
-      - run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
-            Pkg.instantiate()'
-      - run: |
-          julia --project=docs -e '
-            using Documenter: doctest, DocMeta
-            using ConScape
-            DocMeta.setdocmeta!(ConScape, :DocTestSetup, :(using ConScape); recursive=true)
-            doctest(ConScape)'
-        env:
-          COLUMNS: 120
-      - run: julia --project=docs docs/make.jl
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

Project.toml

@@ -6,15 +6,15 @@ version = "0.3.0"
 ArnoldiMethod = "ec485272-7323-5ecc-a04f-4719b315124d"
 CommonSolve = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2"
 ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
-DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+GeometryOps = "3251bfac-6a57-4b6d-aa61-ac1fef2975ab"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
-LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-ProgressLogging = "33c8b6b6-d38a-422a-b730-caa89a2f386c"
 Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689"
+ReadOnlyArrays = "988b38a3-91fc-5605-94a2-ee2116b3bd83"
 SimpleWeightedGraphs = "47aef6b3-ad0c-573a-a1e2-d07658019622"
+SortTileRecursiveTree = "746ee33f-1797-42c2-866d-db2fce69d14d"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+WoodburyMatrices = "efce3f68-66dc-5838-9240-27a6d6f5f9b6"
 
 [weakdeps]
 LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
@@ -23,22 +23,39 @@ LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
 ConScapeLinearSolveExt = "LinearSolve"
 
 [compat]
+Aqua = "0.8"
+ArchGDAL = "0.10"
 ArnoldiMethod = "0.0.4, 0.4"
 CommonSolve = "0.2"
 ConstructionBase = "1.5.8"
-DelimitedFiles = "1"
+GeometryOps = "0.1"
 Graphs = "1"
-LaTeXStrings = "1.1"
+LinearAlgebra = "1"
 LinearSolve = "2.38.0"
+OldConScape = "0.3"
 Plots = "1.4"
-ProgressLogging = "0.1"
-Rasters = "0.14"
+Rasters = "0.14.5"
+ReadOnlyArrays = "0.2.0"
+SafeTestsets = "0.1"
 SimpleWeightedGraphs = "1.1"
+SortTileRecursiveTree = "0.1"
+SparseArrays = "1"
+Statistics = "1"
+Test = "1"
+WoodburyMatrices = "1.0.0"
 julia = "1.10"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
+OldConScape = "3ba2d6f2-f651-5162-bda8-601e45ce5244"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[sources]
+OldConScape = {url = "https://github.com/ConScape/ConScape.jl", rev = "old"}
 
 [targets]
-test = ["ArchGDAL","Plots"]
+test = ["Aqua", "ArchGDAL", "OldConScape", "Plots", "SafeTestsets", "Statistics", "Test"]

docs/.gitignore

@@ -1,2 +1,5 @@
 build/
-site/
+node_modules/
+package-lock.json
+Manifest.toml
+.vscode

docs/.vscode/settings.json

@@ -0,0 +1 @@
+{}

docs/Project.toml

@@ -1,5 +1,8 @@
 [deps]
+ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+ConScape = "2ba2d6f2-f651-5162-bda8-601e45ce5244"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-
-[compat]
-Documenter = "1"
+DocumenterQuarto = "4710194d-e776-4893-9690-8d956a29c365"
+JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
+Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689"

docs/make.jl

@@ -1,21 +1,10 @@
 using Documenter
-using ConScape
+using DocumenterQuarto
+using DocumenterQuarto.Quarto
 
-ENV["COLUMNS"] = 120
-ENV["LINES"] = 30
+Quarto.render(joinpath(@__DIR__, "src"))
 
-DocMeta.setdocmeta!(ConScape, :DocTestSetup, :(using ConScape); recursive=true)
-
-makedocs(
-    sitename = "ConScape",
-    format = Documenter.HTML(),
-    modules = [ConScape],
-)
-
-# Documenter can also automatically deploy documentation to gh-pages.
-# See "Hosting Documentation" and deploydocs() in the Documenter manual
-# for more information.
-deploydocs(
-    repo = "github.com/ConScape/ConScape.jl.git",
-    devbranch = "main",
-)
+deploydocs(;
+    repo="github.com/ConScape/ConScape.jl",
+    push_preview=true,
+)

docs/src/.gitignore

@@ -0,0 +1,4 @@
+/.quarto/
+*.html
+*.tif
+/site_libs/

docs/src/Project.toml

@@ -0,0 +1,9 @@
+[deps]
+ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+ConScape = "2ba2d6f2-f651-5162-bda8-601e45ce5244"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterQuarto = "73f83fcb-c367-40db-89b6-8fd94701aaf2"
+JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
+Optim = "429524aa-4258-5aef-a3af-852621145aeb"
+Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689"

docs/src/_quarto.yml

@@ -0,0 +1,82 @@
+project:
+    type: book
+    output-dir: "../build"
+
+book:
+    page-navigation: true
+    title: "ConScape.jl"
+    # site-url: "https://conscape.github.io/site" 
+    repo-url: https://github.com/ConScape/ConScape.jl
+    author: 
+        name: "Bram van Moorter and Rafael Schouten"
+        email: "rafaelschouten@gmail.com"
+    date: "2025-05-08"
+    chapters:
+        # logo: "images/stickerConScape.png"
+        # pinned: true
+        - part: index.qmd
+          chapters:
+            - quick_start.qmd
+            - faq.qmd 
+            - glossary.qmd
+            - background.qmd
+        - part: applications/index.qmd
+          chapters:
+            - applications/GI.qmd
+            - applications/EIA.qmd
+        - part: "Tutorials"
+          chapters:
+            # - notebooks/index.qmd
+            - notebooks/nbk_getting_started.qmd
+            - notebooks/nbk_landmarks.qmd
+            - notebooks/nbk_windowing.qmd
+            - notebooks/nbk_distance_metrics.qmd
+            - notebooks/nbk_cost.qmd
+            - notebooks/nbk_functionality_variants.qmd
+        - api.qmd 
+    navbar: 
+        background: primary
+        right: 
+        - text: Version
+          menu: 
+            - text: dev
+
+    search: 
+        location: sidebar
+        type: textbox
+
+    twitter-card: true
+    open-graph: true
+    repo-actions: [issue]
+
+toc-title: "Table of Contents"
+
+execute:
+    echo: false
+    output: true
+    cache: false
+    freeze: false
+
+bibliography: references.bib
+
+format:
+    html:
+        include-in-header: 
+            file: _static/versions.html
+        code-link: true
+        number-sections: false
+        resources: 
+            # - _static/style.css
+            - _static/versions.html
+            # - _static/theme.scss
+        theme: 
+            light: 
+                # - _static/theme.scss
+                - flatly
+            dark: 
+                # - _static/theme.scss
+                - darkly
+        code-overflow: wrap
+        toc: true
+        # css: _static/style.css
+        css: styles.css

docs/src/_static/style.css

@@ -0,0 +1,4 @@
+.dropdown-item {
+    text-align: right;
+    display: block;  
+}

docs/src/_static/theme.scss

@@ -0,0 +1,3 @@
+/*-- scss:defaults --*/
+
+$primary: darken(#bb64f5, 10%);