Merge branch 'main' into mt_tutorial

.github/workflows/Documenter.yml

@@ -0,0 +1,48 @@
+# Note: this workflow is copied from the Trixi.jl package
+name: Documentation
+on:
+  push:
+    branches:
+      - 'main'
+    tags: '*'
+    paths-ignore:
+      - '.zenodo.json'
+      - '.github/workflows/benchmark.yml'
+      - '.github/workflows/CI.yml'
+      - '.github/workflows/CompatHelper.yml'
+  pull_request:
+    paths-ignore:
+      - '.zenodo.json'
+      - '.github/workflows/CI.yml'
+      - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/TagBot.yml'
+      - 'benchmark/**'
+      - 'utils/**'
+  workflow_dispatch:
+
+# Cancel redundant CI tests automatically
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1.9'
+          show-versioninfo: true
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+        env:
+          PYTHON: ""
+      - name: Install dependencies
+        run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+          GKSwstype: 100 # To make GitHub Action work, disable showing a plot window with the GR backend of the Plots package
+        run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs --color=yes docs/make.jl

.github/workflows/cleanup_caches.yml

@@ -0,0 +1,29 @@
+name: cleanup caches by a branch
+on:
+  pull_request:
+    types:
+      - closed
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Cleanup
+        run: |
+          gh extension install actions/gh-actions-cache
+
+          echo "Fetching list of cache key"
+          cacheKeysForPR=$(gh actions-cache list -R $REPO -B $BRANCH -L 100 | cut -f 1 )
+
+          ## Setting this to not fail the workflow while deleting cache keys.
+          set +e
+          echo "Deleting caches..."
+          for cacheKey in $cacheKeysForPR
+          do
+              gh actions-cache delete $cacheKey -R $REPO -B $BRANCH --confirm
+          done
+          echo "Done"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          REPO: ${{ github.repository }}
+          BRANCH: refs/pull/${{ github.event.pull_request.number }}/merge

docs/.gitignore

@@ -0,0 +1 @@
+gmt.history

docs/Project.toml

@@ -1,7 +1,8 @@
 [deps]
-GeoParams = "e018b62d-d9de-4a26-8697-af89c310ae38"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-
+GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
+GMT = "5752ebe1-31b9-557e-87aa-f909b540aa54"
+GeophysicalModelGenerator = "3700c31b-fa53-48a6-808a-ef22d5a84742"
 
 [compat]
-Documenter = "0.26"
+Documenter = "1"

docs/gmt.history

@@ -3,6 +3,6 @@ BEGIN GMT 6.5.0
 B	afWSen
 J	X
 JX	X15c/0
-R	0/1/0.1/1
+R	0/1/0/0.9
 @L	1
 END

docs/make.jl

@@ -1,7 +1,12 @@
-using GeophysicalModelGenerator
-using .GeophysicalModelGenerator
 using Documenter
 
+push!(LOAD_PATH, dirname(@__DIR__))
+
+using GeophysicalModelGenerator
+
+# Importing these activates package extensions
+import GLMakie, GMT
+
 #DocMeta.setdocmeta!(GeophysicalModelGenerator, :DocTestSetup, :(using GeophysicalModelGenerator); recursive=true)
 
 # Get GeophysicalModelGenerator.jl root directory
@@ -48,6 +53,7 @@ open(joinpath(@__DIR__, "src", "man", "code_of_conduct.md"), "w") do io
     println(io, "> ", line)
   end
 end
+
 open(joinpath(@__DIR__, "src", "man", "contributing.md"), "w") do io
     # Point to source license file
     println(io, """
@@ -67,7 +73,7 @@ open(joinpath(@__DIR__, "src", "man", "contributing.md"), "w") do io
 
 makedocs(;
     modules=[GeophysicalModelGenerator],
-    authors="Marcel Thielmann, Boris Kaus",
+    authors="Boris Kaus, Marcel Thielmann",
     sitename="GeophysicalModelGenerator.jl",
     format=Documenter.HTML(;
         prettyurls=get(ENV, "CI", "false") == "true",
@@ -76,21 +82,21 @@ makedocs(;
         "Home" => "index.md",
         "Tutorials" => Any[
             "Overview" =>  "man/tutorials.md",
-            "3D seismic tomography from ASCII" =>  "man/tutorial_load3DSeismicData.md",
-            "3D seismic tomography from netCDF" =>  "man/tutorial_loadregular3DSeismicData_netCDF.md",
-            "Visualize Moho topography" =>  "man/tutorial_MohoTopo.md",
-            "Create GMT-based topography" =>  "man/tutorial_GMT_Topography.md",
-            "Coastlines" =>  "man/tutorial_Coastlines.md",
-            "Import screenshots" =>  "man/tutorial_Screenshot_To_Paraview.md",
-            "Interpolate irregular 3D seismic tomography" =>  "man/tutorial_loadirregular3DSeismicData.md",
-            "ETOPO1 Topography and geological maps" =>  "man/tutorial_GMT_Topography_GeologicalMap.md",
-            "ISC earthquake data" =>  "man/tutorial_ISC_data.md",
-            "Plot GPS vectors" =>  "man/tutorial_GPS.md",
-            "Read UTM data" =>  "man/tutorial_UTM.md",
-            "VoteMaps" =>  "man/Tutorial_Votemaps.md",
-            "Kilometer-scale volcano" =>  "man/tutorial_local_Flegrei.md",
-            "Generating LaMEM model" =>  "man/LaPalma_example.md",
-            "Create movies" =>  "man/tutorial_time_Seismicity.md"
+            "1 - 3D seismic tomography from ASCII" =>  "man/tutorial_load3DSeismicData.md",
+            "2 - 3D seismic tomography from netCDF" =>  "man/tutorial_loadregular3DSeismicData_netCDF.md",
+            "3 - Visualize Moho topography" =>  "man/tutorial_MohoTopo.md",
+            "4 - Create GMT-based topography" =>  "man/tutorial_GMT_Topography.md",
+            "5 - Coastlines" =>  "man/tutorial_Coastlines.md",
+            "6 - Import screenshots" =>  "man/tutorial_Screenshot_To_Paraview.md",
+            "7 - Interpolate irregular 3D seismic tomography" =>  "man/tutorial_loadirregular3DSeismicData.md",
+            "8 - ETOPO1 Topography and geological maps" =>  "man/tutorial_GMT_Topography_GeologicalMap.md",
+            "9 - ISC earthquake data" =>  "man/tutorial_ISC_data.md",
+            "10 - Plot GPS vectors" =>  "man/tutorial_GPS.md",
+            "11 - Read UTM data" =>  "man/tutorial_UTM.md",
+            "12 - VoteMaps" =>  "man/Tutorial_Votemaps.md",
+            "13 - Campi Flegrei" =>  "man/tutorial_local_Flegrei.md",
+            "14 - Cartesian Volcano Model" =>  "man/LaPalma_example.md",
+            "15 - Create movies" =>  "man/tutorial_time_Seismicity.md"
         ],
         "User Guide" => Any[
             "Installation" =>  "man/installation.md",
@@ -110,6 +116,8 @@ makedocs(;
         "Code of Conduct" => "man/code_of_conduct.md",
         "License" => "man/license.md"
     ],
+    pagesonly=true,
+    warnonly=true
 )
 
 deploydocs(;