Merge remote-tracking branch 'origin/main'

Author: boriskaus

.github/workflows/CI.yml

@@ -62,7 +62,7 @@ jobs:
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-runtest@latest
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: false  # or true if you want CI to fail when Codecov fails

.github/workflows/Format.yml

@@ -0,0 +1,105 @@
+name: 'Format'
+
+on:
+  pull_request_target:
+    paths: ['**/*.jl']
+    types: [opened, synchronize, reopened, ready_for_review]
+
+permissions:
+  contents: read
+  actions: write
+  pull-requests: write
+
+jobs:
+  runic:
+    runs-on: ubuntu-latest
+    if: github.event.pull_request.draft == false
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          ref: ${{github.event.pull_request.head.ref}}
+          repository: ${{github.event.pull_request.head.repo.full_name}}
+          fetch-depth: 0
+
+      - name: Add upstream remote
+        run: |
+          git remote add upstream https://github.com/${{ github.repository }}
+          git fetch upstream
+
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+          arch: 'x64'
+      - uses: julia-actions/cache@v2
+
+      - name: Install Runic
+        run: |
+          julia --project=@runic -e 'using Pkg; Pkg.add("Runic")'
+          curl -o git-runic https://raw.githubusercontent.com/fredrikekre/Runic.jl/master/bin/git-runic
+          chmod +x git-runic
+          sudo mv git-runic /usr/local/bin
+
+      - name: Run Runic
+        id: runic
+        run: |
+          set +e
+          MERGE_BASE=$(git merge-base upstream/${{ github.base_ref }} HEAD) || exit 1
+          DIFF=$(git runic --diff $MERGE_BASE)
+          EXIT_CODE=$?
+
+          echo "exit_code=$EXIT_CODE" >> $GITHUB_OUTPUT
+          echo "diff<<EOF" >> $GITHUB_OUTPUT
+          echo "$DIFF" >> $GITHUB_OUTPUT
+          echo "EOF" >> $GITHUB_OUTPUT
+
+          # if Runic failed, bail out
+          [ $EXIT_CODE -eq 2 ] && exit 1 || exit 0
+
+      - name: Find comment
+        uses: peter-evans/find-comment@v3
+        id: find-comment
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-author: 'github-actions[bot]'
+          body-includes: '<!-- runic-format-summary -->'
+
+      - name: Comment formatting suggestions
+        if: steps.runic.outputs.exit_code == 1
+        uses: peter-evans/create-or-update-comment@v4
+        with:
+          comment-id: ${{ steps.find-comment.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            <!-- runic-format-summary -->
+
+            Your PR requires formatting changes to meet the project's style guidelines.
+            Please consider running [Runic](https://github.com/fredrikekre/Runic.jl) (`git runic ${{ github.base_ref }}`) to apply these changes.
+
+            <details>
+            <summary>Click here to view the suggested changes.</summary>
+
+            ```diff
+            ${{ steps.runic.outputs.diff }}
+            ```
+
+            </details>
+          edit-mode: replace
+
+      - name: Update stale comment
+        if: steps.runic.outputs.exit_code == 0 && steps.find-comment.outputs.comment-id
+        uses: peter-evans/create-or-update-comment@v4
+        with:
+          comment-id: ${{ steps.find-comment.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            <!-- runic-format-summary -->
+
+            Your PR no longer requires formatting changes. Thank you for your contribution!
+          edit-mode: replace
+
+      # XXX: if Github ever supports allow-failure (actions/runner#2347)
+      #- name: Propagate exit code
+      #  run: |
+      #    exit ${{ steps.runic.outputs.exit_code }}

.github/workflows/SpellCheck.yml

@@ -10,6 +10,6 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.26.8
+        uses: crate-ci/typos@v1.28.1
         with:
             args: --exclude **/*.txt --exclude **/*.pvsm

.github/workflows/draft-pdf.yml

@@ -20,6 +20,9 @@ tutorial/test.tiff
 *.vtr
 *.vts
 *.jld2
+*.swm
+*.swn
+*.swo
 *.tiff
 *.nc
 !/test/test_files/ISCTest.xml

.gitignore

@@ -5,6 +5,7 @@ Shepard = "Shepard"
 arange = "arange"
 iy = "iy"
 nin = "nin"
+tect = "tect"
 
 [files]
 extend-exclude = ["tutorials/*.pvsm","docs/paper/paper.bib"]

.typos.toml

@@ -1,7 +1,7 @@
 name = "GeophysicalModelGenerator"
 uuid = "3700c31b-fa53-48a6-808a-ef22d5a84742"
 authors = ["Boris Kaus", "Marcel Thielmann"]
-version = "0.7.12"
+version = "0.7.13"
 
 [deps]
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
@@ -51,7 +51,7 @@ FFMPEG = "0.4"
 FileIO = "1"
 GDAL_jll = "300.900.0 - 301.901.0"
 GLMakie = "0.8, 0.9, 0.10, 0.11"
-GeoParams = "0.2 - 0.6"
+GeoParams = "0.2 - 0.7"
 Geodesy = "1"
 GeometryBasics = "0.1 - 0.4"
 Glob = "1.2 - 1.3"

Project.toml

@@ -15,39 +15,39 @@ println("Loading Chmy-GMG tools")
 
 Creates a GMG `CartGrid` data structure from a `Chmy` grid object
 """
-function create_CartGrid(grid::StructuredGrid; ylevel=0.0)
+function create_CartGrid(grid::StructuredGrid; ylevel = 0.0)
 
-    coord1D     = Vector.(coords(grid, Vertex()))
+    coord1D = Vector.(coords(grid, Vertex()))
     coord1D_cen = Vector.(coords(grid, Center()))
-    N           = length.(coord1D)
-    L           = extent(grid, Vertex())
-    X₁          = origin(grid, Vertex())  
-    Δ           = spacing(grid)
-    ConstantΔ   = false;
+    N = length.(coord1D)
+    L = extent(grid, Vertex())
+    X₁ = origin(grid, Vertex())
+    Δ = spacing(grid)
+    ConstantΔ = false
     if isa(grid, UniformGrid)
         ConstantΔ = true
     end
-    if ndims(grid)==2
+    if ndims(grid) == 2
         # we need a special treatment of this, as all GMG routines work with 3D coordinates
-        X₁  = (X₁[1], ylevel, X₁[2]) 
-        L   = (L[1], 0.0, L[2]) 
-        Δ   = (Δ[1], 0.0, Δ[2])
-        N   = (N[1],1,N[2])
+        X₁ = (X₁[1], ylevel, X₁[2])
+        L = (L[1], 0.0, L[2])
+        Δ = (Δ[1], 0.0, Δ[2])
+        N = (N[1], 1, N[2])
         coord1D = (coord1D[1], [0.0], coord1D[2])
         coord1D_cen = (coord1D_cen[1], [0.0], coord1D_cen[2])
     end
-    Xₙ          = X₁ .+ L
-    
+    Xₙ = X₁ .+ L
 
-    return CartGrid(ConstantΔ,N,Δ,L,X₁,Xₙ,coord1D, coord1D_cen)
+
+    return CartGrid(ConstantΔ, N, Δ, L, X₁, Xₙ, coord1D, coord1D_cen)
 end
 
 # all functions to be ported
 function_names = (:add_box!, :add_sphere!, :add_ellipsoid!, :add_cylinder!, :add_layer!, :add_polygon!, :add_slab!, :add_stripes!, :add_volcano!)
 
 for fn in function_names
 
-    @eval begin 
+    @eval begin
         """
             $($fn)( Phase::Field, 
                     Temp::Field,
@@ -56,22 +56,24 @@ for fn in function_names
 
         Sets `$($fn)` function for `Chmy` fields and grids.           
         """
-        function $fn(  Phase::Field, 
-                            Temp::Field,
-                            Grid::StructuredGrid;      # required input
-                            kwargs...)  
+        function $fn(
+                Phase::Field,
+                Temp::Field,
+                Grid::StructuredGrid;      # required input
+                kwargs...
+            )
 
             CartGrid = create_CartGrid(Grid)
 
             cell = false
-            if all(location(Phase).==Center()) 
+            if all(location(Phase) .== Center())
                 cell = true
             end
-            
-            return ($fn)(Phase, Temp, CartGrid; cell=cell, kwargs...)
+
+            return ($fn)(Phase, Temp, CartGrid; cell = cell, kwargs...)
         end
     end
-    
+
 end
 
 
@@ -80,28 +82,30 @@ function_names = (:above_surface, :below_surface)
 
 for fn in function_names
 
-    @eval begin 
+    @eval begin
         """
             $($fn)( Grid::StructuredGrid, field::Field, DataSurface_Cart::CartData; kwargs...) 
 
         Sets `$($fn)` function for `Chmy` grids and the field `field` which can be either on vertices or centers           
         """
-        function $fn( Grid::StructuredGrid,
-                      field::Field, 
-                      DataSurface_Cart::CartData;     
-                      kwargs...)  
+        function $fn(
+                Grid::StructuredGrid,
+                field::Field,
+                DataSurface_Cart::CartData;
+                kwargs...
+            )
 
             CartGrid = create_CartGrid(Grid)
-            
+
             cell = false
-            if all(location(field).==Center()) 
+            if all(location(field) .== Center())
                 cell = true
             end
 
-            return ($fn)(CartGrid, DataSurface_Cart; cell=cell, kwargs...)
+            return ($fn)(CartGrid, DataSurface_Cart; cell = cell, kwargs...)
         end
     end
-    
+
 end