Merge branch 'main' into cf

.github/workflows/Documenter.yml

@@ -1,53 +1,45 @@
-# Sample workflow for building and deploying a VitePress site to GitHub Pages
-#
-name: Documenter
+name: Documentation
 
 on:
-  # Runs on pushes targeting the `main` branch. Change this to `master` if you're
-  # using the `master` branch as the default branch.
   push:
     branches:
       - main
-    tags: ['*']
+    tags: '*'
   pull_request:
 
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-
-# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+# Sets permissions of the GITHUB_TOKEN
 permissions:
   contents: write
   pages: write
   id-token: write
   statuses: write
 
-# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
-# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
 concurrency:
   group: pages
-  cancel-in-progress: false
+  cancel-in-progress: true
 
 jobs:
-  # Build job
   build:
     runs-on: ubuntu-latest
+    env:
+      DISPLAY: ':0'
     steps:
       - name: Checkout
         uses: actions/checkout@v4
       - name: Setup Julia
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
       - name: Pull Julia cache
-        uses: julia-actions/cache@v1
-      - name: Install documentation dependencies
-        run: sudo apt-get update && sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev libcairo2-dev libfreetype6-dev libffi-dev libjpeg-dev libpng-dev libz-dev
-      - name: Install custom documentation dependencies
-        run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs -e 'using Pkg; pkg"dev ."; Pkg.instantiate(); Pkg.precompile(); Pkg.status()'
+        uses: julia-actions/cache@v2
+      - name: Install GLMakie dependencies
+        run: sudo apt-get update && sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev
+      - name: Install Julia dependencies
+        run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs -e 'using Pkg; Pkg.Registry.update(); pkg"dev ."; Pkg.instantiate(); Pkg.precompile(); Pkg.status()'
       - name: Build and deploy
         env:
           RASTERDATASOURCES_PATH: "."
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-          GKSwstype: "100" # https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+          GKSwstype: "100"
           JULIA_DEBUG: "Documenter"
           DATADEPS_ALWAYS_ACCEPT: true
         run: |

Project.toml

@@ -1,7 +1,7 @@
 name = "Rasters"
 uuid = "a3a2b9e3-a471-40c9-b274-f788e487c689"
 authors = ["Rafael Schouten <[email protected]>"]
-version = "0.12.1"
+version = "0.13.0"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
@@ -54,7 +54,7 @@ Adapt = "2, 3.0, 4"
 Aqua = "0.8"
 ArchGDAL = "0.9, 0.10"
 CFTime = "0.1"
-ColorTypes = "0.10, 0.11"
+ColorTypes = "0.10, 0.11, 0.12"
 CommonDataModel = "0.2.3, 0.3"
 ConstructionBase = "1"
 CoordinateTransformations = "0.6.2"
@@ -106,6 +106,7 @@ RasterDataSources = "3cb90ccd-e1b6-4867-9617-4276c8b2ca36"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 Shapefile = "8e980c4a-a4fe-5da2-b3a7-4b4b0353a2f4"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 

docs/Project.toml

@@ -9,19 +9,25 @@ DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterVitepress = "4710194d-e776-4893-9690-8d956a29c365"
 GBIF2 = "dedd4f52-e074-43bf-924d-d6bce14ad628"
+GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 GeoInterface = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
+GeoMakie = "db073c08-6b98-4ee5-b6a4-5efafb3259c6"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
 MLJGLMInterface = "caf8df21-4939-456d-ac9c-5fefbfb04c0c"
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 Maxnet = "81f79f80-22f2-4e41-ab86-00c11cf0f26f"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
+NaNStatistics = "b946abbf-3ea7-4610-9019-9858bfdeaf2d"
+NaturalEarth = "436b0209-26ab-4e65-94a9-6526d86fea76"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Proj = "c94c279d-25a6-4763-9509-64d165bea63e"
 RasterDataSources = "3cb90ccd-e1b6-4867-9617-4276c8b2ca36"
 Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689"
 Shapefile = "8e980c4a-a4fe-5da2-b3a7-4b4b0353a2f4"
 SpeciesDistributionModels = "3ef73bbf-0321-4d3b-9a2e-5fbebc8e35da"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 
 [sources]
-SpeciesDistributionModels = {url = "https://github.com/tiemvanderdeure/SpeciesDistributionModels.jl/"}
+SpeciesDistributionModels = {url = "https://github.com/tiemvanderdeure/SpeciesDistributionModels.jl/"}

docs/logo.jl

@@ -0,0 +1,53 @@
+ENV["RASTERDATASOURCES_PATH"] = "~/Data"
+using Rasters, RasterDataSources
+import ArchGDAL
+using CairoMakie
+
+layers = (:evenness, :range, :contrast, :correlation)
+st = RasterStack(EarthEnv{HabitatHeterogeneity}, layers)
+ausbounds = X(110 .. 190), Y(-55 .. 5) # Roughly cut out Australia and New Zealand!
+aus = st[ausbounds...] |> Rasters.trim
+
+# colorbar attributes
+colormap = :batlow
+flipaxis = false
+tickalign=1
+width = 13
+ticksize = 13
+# figure
+fig = with_theme(theme_dark()) do
+    fig = Figure(; size=(600, 600),
+        backgroundcolor=:transparent
+        )
+    ax = Axis(fig[1,1],
+        backgroundcolor=:transparent
+        )
+    plt = Makie.heatmap!(ax, aus[:correlation]; colormap)
+    ylims!(ax, -50, 15)
+    xlims!(ax, 110, 180)
+    hidedecorations!(ax)
+    fig
+end
+
+mkpath(joinpath(@__DIR__, "src", "assets"))
+save(joinpath(@__DIR__, "src", "assets", "logo.png"), fig; px_per_unit=2)
+save(joinpath(@__DIR__, "src", "assets", "favicon.png"), fig; px_per_unit=0.25)
+
+# do tiling for background image
+function tile_background()
+    grid_color = RGBAf(0.55, 0.55, 0.55, 0.16)
+    fig = Figure(; figure_padding= 0, size=(600, 600),
+        backgroundcolor=:transparent
+        )
+    ax = Axis(fig[1,1], backgroundcolor=:transparent,
+        xgridcolor = grid_color, ygridcolor = grid_color,)
+    hidespines!(ax, :r, :b)
+    hidedecorations!(ax, grid=false)
+    ax.topspinecolor = grid_color
+    ax.leftspinecolor = grid_color
+    ax.xticks = 1:9
+    ax.yticks = 1:10
+    fig
+end
+fig = tile_background()
+save(joinpath(@__DIR__, "src", "assets", "rect_pattern.png"), fig; px_per_unit=2)

docs/make.jl

@@ -10,9 +10,9 @@ CairoMakie.activate!(type = "png")
 # Plots warnings are brWarn doctests. They don't warn the second time.
 # Downloads also show op in doctests. So download everything first.
 function flush_info_and_warnings()
-    # RasterStack(AWAP, (:tmin, :tmax); date=DateTime(2001, 1, 1))
-    # RasterStack(EarthEnv{HabitatHeterogeneity}, (:evenness, :range, :contrast, :correlation))
-    # RasterStack(WorldClim{BioClim}, (1, 3, 5, 7, 12))
+    RasterStack(AWAP, (:tmin, :tmax); date=DateTime(2001, 1, 1))
+    RasterStack(EarthEnv{HabitatHeterogeneity}, (:evenness, :range, :contrast, :correlation))
+    RasterStack(WorldClim{BioClim}, (1, 3, 5, 7, 12))
     st = RasterStack(WorldClim{Climate}; month=1);
     plot(st)
 end

docs/package.json

@@ -5,12 +5,16 @@
     "docs:preview": "vitepress preview build/.documenter"
   },
   "devDependencies": {
+    "@types/d3-format": "^3.0.4",
+    "@types/node": "^22.10.1",
     "markdown-it-mathjax3": "^4.3.2",
-    "vitepress": "^1.2.3",
+    "rollup-plugin-delete": "^2.0.0",
+    "vitepress": "^1.5.0",
     "vitepress-plugin-tabs": "^0.5.0"
   },
   "dependencies": {
-    "markdown-it": "^14.0.0",
+    "d3-format": "^3.1.0",
+    "markdown-it": "^14.1.0",
     "markdown-it-footnote": "^4.0.0"
   }
 }