trixi-framework · vincmarks · Apr 28, 2025 · Apr 29, 2025 · Apr 30, 2025 · May 13, 2025
diff --git a/.JuliaFormatter.toml b/.JuliaFormatter.toml
diff --git a/.gitignore b/.gitignore
@@ -6,6 +6,7 @@ solution_*
 *.png
 *.gif
 *.xyz
+!examples/data/geo.xyz
 docs/build
 docs/src/authors.md
 docs/src/changelog.md

diff --git a/Project.toml b/Project.toml
@@ -4,7 +4,10 @@ authors = ["maxbertrand1996 <[email protected]>", "Andrew R. Winter
 version = "0.1.4-DEV"
 
 [deps]
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
+GMT = "5752ebe1-31b9-557e-87aa-f909b540aa54"
+GeophysicalModelGenerator = "3700c31b-fa53-48a6-808a-ef22d5a84742"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
@@ -13,10 +16,14 @@ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 
 [extensions]
+TrixiBottomTopographyGeophysicalModelGeneratorExt = "GeophysicalModelGenerator"
 TrixiBottomTopographyMakieExt = "Makie"
 
 [compat]
+DataFrames = "1.5"
 Downloads = "1.6"
+GMT = "1.0"
+GeophysicalModelGenerator = "0.7.14"
 LinearAlgebra = "1"
 Makie = "0.21, 0.22"
 SparseArrays = "1"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -2,15 +2,22 @@
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Changelog = "5217a498-cd5d-4ec6-b8c2-9b85a09b6e3e"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+GMT = "5752ebe1-31b9-557e-87aa-f909b540aa54"
+GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
+GeophysicalModelGenerator = "3700c31b-fa53-48a6-808a-ef22d5a84742"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 OrdinaryDiffEqLowStorageRK = "b0944070-b475-4768-8dec-fb6eb410534d"
 Trixi = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
+Trixi2Vtk = "bc1476a1-1ca6-4cc3-950b-c312b255ff95"
 TrixiBottomTopography = "86af9953-43df-404b-8eaa-d20d82623a82"
 TrixiShallowWater = "804cb1fc-5b08-4398-a671-a789bfe091b3"
 
 [compat]
 CairoMakie = "0.13"
 Changelog = "1.1"
 Documenter = "1.3"
+GeometryBasics = "0.5"
+Makie = "0.21, 0.22"
 OrdinaryDiffEqLowStorageRK = "1.3"
 Trixi = "0.12"
 TrixiShallowWater = "0.2"
diff --git a/docs/make.jl b/docs/make.jl
@@ -6,75 +6,80 @@ using Changelog: Changelog
 # Copy list of authors to not need to synchronize it manually.
 # Since the authors header exists twice we create a unique identifier for the docs section.
 authors_text = read(joinpath(dirname(@__DIR__), "AUTHORS.md"), String)
-authors_text = replace(authors_text,
-                       "in the [LICENSE.md](LICENSE.md) file" => "under [License](@ref)")
-authors_text = replace(authors_text,
-                       "# Authors" => "# [Authors](@id trixi_bt_authors)")
+authors_text =
+    replace(authors_text, "in the [LICENSE.md](LICENSE.md) file" => "under [License](@ref)")
+authors_text = replace(authors_text, "# Authors" => "# [Authors](@id trixi_bt_authors)")
 write(joinpath(@__DIR__, "src", "authors.md"), authors_text)
 
 # Define module-wide setups such that the respective modules are available in doctests
-DocMeta.setdocmeta!(TrixiBottomTopography, :DocTestSetup, :(using TrixiBottomTopography);
-                    recursive = true)
+DocMeta.setdocmeta!(
+    TrixiBottomTopography,
+    :DocTestSetup,
+    :(using TrixiBottomTopography);
+    recursive = true,
+)
 
 # Copy some files from the repository root directory to the docs and modify them
 # as necessary
 # Based on: https://github.com/ranocha/SummationByPartsOperators.jl/blob/0206a74140d5c6eb9921ca5021cb7bf2da1a306d/docs/make.jl#L27-L41
 open(joinpath(@__DIR__, "src", "code_of_conduct.md"), "w") do io
     # Point to source license file
-    println(io,
-            """
-            ```@meta
-            EditURL = "https://github.com/trixi-framework/TrixiBottomTopography.jl/blob/main/CODE_OF_CONDUCT.md"
-            ```
-            """)
+    println(
+        io,
+        """
+        ```@meta
+        EditURL = "https://github.com/trixi-framework/TrixiBottomTopography.jl/blob/main/CODE_OF_CONDUCT.md"
+        ```
+        """,
+    )
     # Write the modified contents
     println(io, "# [Code of Conduct](@id code-of-conduct)")
     println(io, "")
     for line in eachline(joinpath(dirname(@__DIR__), "CODE_OF_CONDUCT.md"))
-        line = replace(line,
-                       "[AUTHORS.md](AUTHORS.md)" => "[Authors](@ref trixi_bt_authors)")
+        line =
+            replace(line, "[AUTHORS.md](AUTHORS.md)" => "[Authors](@ref trixi_bt_authors)")
         println(io, "> ", line)
     end
 end
 
 # Copy contributing information to not need to synchronize it manually
 open(joinpath(@__DIR__, "src", "contributing.md"), "w") do io
     # Point to source license file
-    println(io,
-            """
-            ```@meta
-            EditURL = "https://github.com/trixi-framework/TrixiBottomTopography.jl/blob/main/CONTRIBUTING.md"
-            ```
-            """)
+    println(
+        io,
+        """
+        ```@meta
+        EditURL = "https://github.com/trixi-framework/TrixiBottomTopography.jl/blob/main/CONTRIBUTING.md"
+        ```
+        """,
+    )
     # Write the modified contents
     for line in eachline(joinpath(dirname(@__DIR__), "CONTRIBUTING.md"))
         line = replace(line, "[LICENSE.md](LICENSE.md)" => "[License](@ref)")
-        line = replace(line,
-                       "[AUTHORS.md](AUTHORS.md)" => "[Authors](@ref trixi_bt_authors)")
+        line =
+            replace(line, "[AUTHORS.md](AUTHORS.md)" => "[Authors](@ref trixi_bt_authors)")
         println(io, line)
     end
 end
 
 # Copy contents form README to the starting page to not need to synchronize it manually
 readme_text = read(joinpath(dirname(@__DIR__), "README.md"), String)
-readme_text = replace(readme_text,
-                      "[LICENSE.md](LICENSE.md)" => "[License](@ref)")
-readme_text = replace(readme_text,
-                      "[AUTHORS.md](AUTHORS.md)" => "[Authors](@ref trixi_bt_authors)")
-readme_text = replace(readme_text,
-                      "<p" => "```@raw html\n<p")
-readme_text = replace(readme_text,
-                      "p>" => "p>\n```")
-readme_text = replace(readme_text,
-                      r"\[comment\].*\n" => "")    # remove comments
+readme_text = replace(readme_text, "[LICENSE.md](LICENSE.md)" => "[License](@ref)")
+readme_text =
+    replace(readme_text, "[AUTHORS.md](AUTHORS.md)" => "[Authors](@ref trixi_bt_authors)")
+readme_text = replace(readme_text, "<p" => "```@raw html\n<p")
+readme_text = replace(readme_text, "p>" => "p>\n```")
+readme_text = replace(readme_text, r"\[comment\].*\n" => "")    # remove comments
 write(joinpath(@__DIR__, "src", "index.md"), readme_text)
 
 # Create changelog
-Changelog.generate(Changelog.Documenter(),                            # output type
-                   joinpath(@__DIR__, "..", "NEWS.md"),               # input file
-                   joinpath(@__DIR__, "src", "changelog_tmp.md");     # output file
-                   repo = "trixi-framework/TrixiBottomTopography.jl", # default repository for links
-                   branch = "main",)
+Changelog.generate(
+    Changelog.Documenter(),                            # output type
+    joinpath(@__DIR__, "..", "NEWS.md"),               # input file
+    joinpath(@__DIR__, "src", "changelog_tmp.md");     # output file
+    repo = "trixi-framework/TrixiBottomTopography.jl", # default repository for links
+    branch = "main",
+)
 # Fix edit URL of changelog
 open(joinpath(@__DIR__, "src", "changelog.md"), "w") do io
     for line in eachline(joinpath(@__DIR__, "src", "changelog_tmp.md"))
@@ -89,37 +94,45 @@ rm(joinpath(@__DIR__, "src", "changelog_tmp.md"))
 
 # Make documentation
 makedocs(;
-         modules = [TrixiBottomTopography],
-         authors = "Andrew R. Winters <[email protected]>, Michael Schlottke-Lakemper <[email protected]>",
-         sitename = "TrixiBottomTopography.jl",
-         format = Documenter.HTML(;
-                                  # Disable pretty URLs during manual testing
-                                  prettyurls = get(ENV, "CI", "false") == "true",
-                                  # Set canonical URL to GitHub pages URL
-                                  canonical = "https://trixi-framework.github.io/TrixiBottomTopography.jl/stable",
-                                  edit_link = "main",
-                                  size_threshold_ignore = ["index.md"],),
-         # Explicitly specify documentation structure
-         pages = ["Home" => "index.md",
-             "Overview" => [
-                 "Data conversion" => "conversion.md",
-                 "B-spline structure" => "structure.md",
-                 "B-spline function" => "function.md"
-             ],
-             "TrixiShallowWater.jl examples" => "trixishallowwater_jl_examples.md",
-             "Advanced topics & developers" => ["Development" => "development.md",
-                 "Style guide" => "styleguide.md",
-                 "Testing" => "testing.md"],
-             "Changelog" => "changelog.md",
-             "Authors" => "authors.md",
-             "Contributing" => "contributing.md",
-             "Code of Conduct" => "code_of_conduct.md",
-             "License" => "license.md",
-             "Reference" => "reference.md"])
+    modules = [TrixiBottomTopography],
+    authors = "Andrew R. Winters <[email protected]>, Michael Schlottke-Lakemper <[email protected]>",
+    sitename = "TrixiBottomTopography.jl",
+    format = Documenter.HTML(;
+        # Disable pretty URLs during manual testing
+        prettyurls = get(ENV, "CI", "false") == "true",
+        # Set canonical URL to GitHub pages URL
+        canonical = "https://trixi-framework.github.io/TrixiBottomTopography.jl/stable",
+        edit_link = "main",
+        size_threshold_ignore = ["index.md"],
+    ),
+    # Explicitly specify documentation structure
+    pages = [
+        "Home" => "index.md",
+        "Overview" => [
+            "Data conversion" => "conversion.md",
+            "B-spline structure" => "structure.md",
+            "B-spline function" => "function.md",
+        ],
+        "TrixiShallowWater.jl examples" => "trixishallowwater_jl_examples.md",
+        "Advanced topics & developers" => [
+            "Development" => "development.md",
+            "Style guide" => "styleguide.md",
+            "Testing" => "testing.md",
+        ],
+        "Changelog" => "changelog.md",
+        "Authors" => "authors.md",
+        "Contributing" => "contributing.md",
+        "Code of Conduct" => "code_of_conduct.md",
+        "License" => "license.md",
+        "Reference" => "reference.md",
+    ],
+)
 
 # 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/trixi-framework/TrixiBottomTopography.jl.git",
-           devbranch = "main",
-           push_preview = true)
+deploydocs(
+    repo = "github.com/trixi-framework/TrixiBottomTopography.jl.git",
+    devbranch = "main",
+    push_preview = true,
+)