new docs and bugfixes from juliacon

.github/workflows/CI.yml

@@ -58,6 +58,7 @@ jobs:
       - uses: julia-actions/julia-docdeploy@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          RASTERDATASOURCES_PATH: "."
       - name: Run doctests
         shell: julia --project=docs --color=yes {0}
         run: |

.gitignore

@@ -4,3 +4,7 @@
 /Manifest.toml
 /docs/Manifest.toml
 /docs/build/
+node_modules/
+package-lock.json
+Manifest.toml
+.vscode

Project.toml

@@ -12,6 +12,7 @@ DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 EvoTrees = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5"
 GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
+GeoInterface = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
 Lasso = "b4fcebef-c861-5a0f-a7e2-ba9dc32b180a"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Loess = "4345ca2d-374a-55d4-8d30-97f9976e7612"
@@ -42,15 +43,15 @@ SpeciesDistributionModelsMakieExt = "Makie"
 CategoricalDistributions = "0.1.14"
 Distances = "0.10"
 MLJGLMInterface = "0.3.7"
-Rasters = "0.10.1, 0.11"
+Rasters = "0.10.1, 0.11, 0.12"
 StatisticalMeasures = "0.1.5"
 StatsModels = "0.7.3"
 julia = "1.9"
 
 [extras]
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
-Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 MLJModels = "d491faf4-2d78-11e9-2867-c94bc002c0b7"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 

docs/Project.toml

@@ -1,3 +1,15 @@
 [deps]
+ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterVitepress = "4710194d-e776-4893-9690-8d956a29c365"
+EvoTrees = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5"
+GBIF2 = "dedd4f52-e074-43bf-924d-d6bce14ad628"
+MLJGLMInterface = "caf8df21-4939-456d-ac9c-5fefbfb04c0c"
+Maxnet = "81f79f80-22f2-4e41-ab86-00c11cf0f26f"
+NaturalEarth = "436b0209-26ab-4e65-94a9-6526d86fea76"
+RasterDataSources = "3cb90ccd-e1b6-4867-9617-4276c8b2ca36"
+Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689"
 SpeciesDistributionModels = "3ef73bbf-0321-4d3b-9a2e-5fbebc8e35da"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"

docs/make.jl

@@ -1,25 +1,22 @@
+using Documenter, DocumenterVitepress
 using SpeciesDistributionModels
-using Documenter
-
-DocMeta.setdocmeta!(SpeciesDistributionModels, :DocTestSetup, :(using SpeciesDistributionModels); recursive=true)
 
 makedocs(;
     modules=[SpeciesDistributionModels],
-    authors="Tiem van der Deure <[email protected]>, Rafael Schouten <[email protected]>",
-    repo="https://github.com/tiemvanderdeure/SpeciesDistributionModels.jl/blob/{commit}{path}#{line}",
+    authors= "Tiem van der Deure <[email protected]>, Rafael Schouten <[email protected]>",
     sitename="SpeciesDistributionModels.jl",
-    format=Documenter.HTML(;
-        prettyurls=get(ENV, "CI", "false") == "true",
-        canonical="https://tiemvanderdeure.github.io/SpeciesDistributionModels.jl",
-        edit_link="master",
-        assets=String[],
+    format=DocumenterVitepress.MarkdownVitepress(
+        repo = "github.com/tiemvanderdeure/SpeciesDistributionModels.jl",
+        devurl = "dev",
+        devbranch = "master",
     ),
-    pages=[
-        "Home" => "index.md",
-    ],
+    warnonly = true
 )
 
-deploydocs(;
+deploydocs(; 
     repo="github.com/tiemvanderdeure/SpeciesDistributionModels.jl",
-    devbranch="master",
-)
+    target = "build", # this is where Vitepress stores its output
+    branch = "gh-pages",
+    devbranch = "master",
+    push_preview = true
+)

docs/package.json

@@ -0,0 +1,16 @@
+{
+    "scripts": {
+        "docs:dev": "vitepress dev build/.documenter",
+        "docs:build": "vitepress build build/.documenter",
+        "docs:preview": "vitepress preview build/.documenter"
+    },
+    "devDependencies": {
+        "markdown-it-mathjax3": "^4.3.2",
+        "vitepress": "^1.2.3",
+        "vitepress-plugin-tabs": "^0.5.0"
+    },
+    "dependencies": {
+        "markdown-it": "^14.0.0",
+        "markdown-it-footnote": "^4.0.0"
+    }
+}

docs/src/.vitepress/config.mts

@@ -0,0 +1,66 @@
+import { defineConfig } from 'vitepress'
+import { tabsMarkdownPlugin } from 'vitepress-plugin-tabs'
+import mathjax3 from "markdown-it-mathjax3";
+import footnote from "markdown-it-footnote";
+
+// https://vitepress.dev/reference/site-config
+export default defineConfig({
+  base: 'REPLACE_ME_DOCUMENTER_VITEPRESS',// TODO: replace this in makedocs!
+  title: 'REPLACE_ME_DOCUMENTER_VITEPRESS',
+  description: 'Species distirbution modelling in Julia',
+  lastUpdated: true,
+  cleanUrls: true,
+  outDir: 'REPLACE_ME_DOCUMENTER_VITEPRESS', // This is required for MarkdownVitepress to work correctly...
+  head: [['link', { rel: 'icon', href: 'REPLACE_ME_DOCUMENTER_VITEPRESS_FAVICON' }]],
+  ignoreDeadLinks: true,
+
+  markdown: {
+    math: true,
+    config(md) {
+      md.use(tabsMarkdownPlugin),
+      md.use(mathjax3),
+      md.use(footnote)
+    },
+    theme: {
+      light: "github-light",
+      dark: "github-dark"}
+  },
+  themeConfig: {
+    outline: 'deep',
+    logo: 'REPLACE_ME_DOCUMENTER_VITEPRESS',
+    search: {
+      provider: 'local',
+      options: {
+        detailedView: true
+      }
+    },
+    nav: [
+      { text: 'Getting started', link: '/getting_started' },
+      { text: 'Examples', items:
+        [
+          { text: 'Distribution of Eucalyptus regnans', link: '/eucalyptus_regnans' }, 
+        ]
+      },
+      { text: 'API', link: '/api' },
+      { text: 'Ecosystem',
+        items: [
+          { text: 'Rasters.jl', link: 'https://rafaqz.github.io/Rasters.jl/dev/' },
+          { text: 'MLJ.jl', link: 'https://juliaai.github.io/MLJ.jl/dev/' },
+          { text: 'GBIF2.jl', link: 'https://rafaqz.github.io/GBIF2.jl/dev/' },
+          { text: 'RasterDataSources.jl', link: 'http://docs.ecojulia.org/RasterDataSources.jl/dev/' },
+         ]
+       },
+    ],
+    editLink: 'REPLACE_ME_DOCUMENTER_VITEPRESS',
+    socialLinks: [
+      { icon: 'github', link: 'REPLACE_ME_DOCUMENTER_VITEPRESS' }
+    ],
+    footer: {
+      message: 'Made with <a href="https://luxdl.github.io/DocumenterVitepress.jl/dev/" target="_blank"><strong>DocumenterVitepress.jl</strong></a><br>',
+      copyright: `© Copyright ${new Date().getUTCFullYear()}.`
+    }
+  }
+})
+
+
+

docs/src/.vitepress/theme/index.ts

@@ -0,0 +1,19 @@
+// .vitepress/theme/index.ts
+import { h } from 'vue'
+import type { Theme } from 'vitepress'
+import DefaultTheme from 'vitepress/theme'
+
+import { enhanceAppWithTabs } from 'vitepress-plugin-tabs/client'
+import './style.css'
+
+export default {
+  extends: DefaultTheme,
+  Layout() {
+    return h(DefaultTheme.Layout, null, {
+      // https://vitepress.dev/guide/extending-default-theme#layout-slots
+    })
+  },
+  enhanceApp({ app, router, siteData }) {
+    enhanceAppWithTabs(app)
+  }
+} satisfies Theme