Merge branch 'main' into bk-joss-paper

Author: boriskaus

.github/workflows/CI.yml

@@ -6,6 +6,12 @@ on:
     branches:
       - main
     tags: '*'
+
+# Cancel redundant CI tests automatically
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+  
 jobs:
   run_tests:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
@@ -16,16 +22,30 @@ jobs:
         version:
           - '1.9'
           - '1.10'
+          - '1.11'
           - 'nightly'
         os:
           - ubuntu-latest
-          - macOS-latest
+          - macos-13
           - windows-latest
         arch:
           - x64
+        include:
+          - os: macOS-latest
+            arch: aarch64
+            version: '1.9'           
+          - os: macOS-latest
+            arch: aarch64
+            version: '1.10'
+          - os: macOS-latest
+            arch: aarch64
+            version: '1.11'
+          - os: macOS-latest
+            arch: aarch64
+            version: 'nightly'          
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}

.github/workflows/Documenter.yml

@@ -30,11 +30,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: '1.9'
           show-versioninfo: true
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
         env:
           PYTHON: ""

.github/workflows/SpellCheck.yml

@@ -10,6 +10,6 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.18.2
+        uses: crate-ci/typos@v1.25.0
         with:
             args: --exclude **/*.txt --exclude **/*.pvsm

.gitignore

@@ -22,3 +22,4 @@ tutorial/test.tiff
 *.jld2
 *.tiff
 *.nc
+!/test/test_files/ISCTest.xml

.typos.toml

@@ -2,6 +2,9 @@
 MOR = "MOR"
 dum = "dum"
 Shepard = "Shepard"
+arange = "arange"
+iy = "iy"
+nin = "nin"
 
 [files]
 extend-exclude = ["tutorials/*.pvsm"]

Project.toml

@@ -1,14 +1,15 @@
 name = "GeophysicalModelGenerator"
 uuid = "3700c31b-fa53-48a6-808a-ef22d5a84742"
 authors = ["Boris Kaus", "Marcel Thielmann"]
-version = "0.7.0"
+version = "0.7.10"
 
 [deps]
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 FFMPEG = "c87230d0-a227-11e9-1b43-d7ebe4e7570a"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+GDAL_jll = "a7073274-a066-55f0-b90d-d619367d196c"
 GeoParams = "e018b62d-d9de-4a26-8697-af89c310ae38"
 Geodesy = "0ef565a4-170c-5f04-8de2-149903a85f3d"
 GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
@@ -19,51 +20,64 @@ JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LightXML = "9c8b4983-aa76-5018-a973-4c85ecc9e179"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MeshIO = "7269a6da-0436-5bbc-96c2-40638cbb6118"
+NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+WhereTheWaterFlows = "ea906314-1493-4d22-a0af-f886a20c9fba"
 WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 
 [weakdeps]
+Chmy = "33a72cf0-4690-46d7-b987-06506c2248b9"
 GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 GMT = "5752ebe1-31b9-557e-87aa-f909b540aa54"
+GridapGmsh = "3025c34a-b394-11e9-2a55-3fee550c04c8"
 
 [extensions]
+Chmy_utils = "Chmy"
 GLMakie_Visualisation = "GLMakie"
 GMT_utils = "GMT"
+Gmsh_utils = "GridapGmsh"
 
 [compat]
+Chmy = "0.1.20"
 Colors = "0.9 - 0.12"
 Downloads = "1"
 FFMPEG = "0.4"
 FileIO = "1"
-GLMakie = "0.8, 0.9"
-GMT = "1"
-GeoParams = "0.2 - 0.5"
+GDAL_jll = "300.900.0 - 301.901.0"
+GLMakie = "0.8, 0.9, 0.10"
+GMT = "1.0 - 1.14"
+GeoParams = "0.2 - 0.6"
 Geodesy = "1"
 GeometryBasics = "0.1 - 0.4"
 Glob = "1.2 - 1.3"
+GridapGmsh = "0.5 - 0.7"
 ImageIO = "0.1 - 0.6"
 Interpolations = "0.14, 0.15"
+JLD2 = "0.4, 0.5"
 LightXML = "0.8, 0.9"
-JLD2 = "0.4"
 MeshIO = "0.1 - 0.4"
 NearestNeighbors = "0.2 - 0.4"
+NCDatasets = "0.14"
 Parameters = "0.9 - 0.12"
 SpecialFunctions = "1.0, 2"
 StaticArrays = "1"
+WhereTheWaterFlows = "0.10, 0.11"
 WriteVTK = "1"
 julia = "1.9"
 
 [extras]
+Chmy = "33a72cf0-4690-46d7-b987-06506c2248b9"
 GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 GMT = "5752ebe1-31b9-557e-87aa-f909b540aa54"
+KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "GMT", "StableRNGs"]
+test = ["Test", "GMT", "StableRNGs", "GridapGmsh", "Chmy","KernelAbstractions"]

README.md

@@ -10,6 +10,8 @@
 
 Creating consistent 3D images of geophysical and geological datasets and turning that into an input model for geodynamic simulations is often challenging. The aim of this package is to help with this, by providing a number of routines to easily import data and create a consistent 3D visualisation from it in the VTK-toolkit format, which can for example be viewed with [Paraview](https://www.paraview.org). In addition, we provide a range of tools that helps to generate input models to perform geodynamic simulations and import the results of such simulations back into julia.
 
+A short summary of the package and its features are given below. For a detailed description of the package and to learn how to use it, have a look at the [documentation](https://juliageodynamics.github.io/GeophysicalModelGenerator.jl/dev/).
+
 ![README_img](./docs/src/assets/img/Readme_pic.png)
 ### Contents
 - [Geophysical Model Generator](#geophysical-model-generator)
@@ -41,17 +43,17 @@ The best way to learn how to use this is to install the package (see below) and
 ## Installation
 First, you need to install julia on your machine. We recommend to use the binaries from [https://julialang.org](https://julialang.org).
 Next, start julia and switch to the julia package manager using `]`, after which you can add the package.
-```julia
+```julia-repl
 julia> ]
-(@v1.10) pkg> add GeophysicalModelGenerator
+(@1.6) pkg> add GeophysicalModelGenerator
 ```
 You can test whether it works on your system with
-```julia
+```julia-repl
 julia> ]
-(@v1.10) pkg> test GeophysicalModelGenerator
+(@1.6) pkg> test GeophysicalModelGenerator
 ```
 and use it with
-```julia
+```julia-repl
 julia> using GeophysicalModelGenerator
 ```
 

SECURITY.md

@@ -0,0 +1,30 @@
+# Security Policy
+
+We take security issues seriously. We appreciate all efforts
+to responsibly disclose any security issues and will make every
+effort to acknowledge contributions.
+
+
+## Supported Versions
+
+The current stable release following the interpretation of
+[semantic versioning (SemVer)](https://julialang.github.io/Pkg.jl/dev/compatibility/#Version-specifier-format-1)
+used in the Julia ecosystem is supported with security updates.
+
+
+## Reporting a Vulnerability
+
+To report a security issue, please use the GitHub Security Advisory
+["Report a Vulnerability"](https://github.com/JuliaGeodynamics/GeophysicalModelGenerator.jl/security/advisories/new)
+tab.
+
+We will send a response indicating the next steps in handling your report.
+After the initial reply to your report, we will keep you informed of the
+progress towards a fix and full announcement, and may ask for additional
+information or guidance.
+
+Please report security bugs in third-party modules directly to the person
+or team maintaining the module.
+
+Public notifications of vulnerabilities will be shared in community channels
+such as Slack.

docs/make.jl

@@ -105,13 +105,15 @@ makedocs(;
             "19 - Jura tutorial" =>  "man/Tutorial_Jura.md",
             "20 - 2D model setups" => "man/Tutorial_NumericalModel_2D.md",
             "21 - 3D model setups" => "man/Tutorial_NumericalModel_3D.md",
-            "22 - Build geometry from polygons" =>  "man/tutorial_Polygon_structures.md"
+            "22 - 3D model setups" => "man/Tutorial_VolcanoModel_3D.md",
+            "23 - Build geometry from polygons" =>  "man/tutorial_Polygon_structures.md"
         ],
         "User Guide" => Any[
             "Installation" =>  "man/installation.md",
             "Data Structures" =>  "man/datastructures.md",
             "Data Import" =>  "man/dataimport.md",
             "Projection" =>  "man/projection.md",
+            "ASAGI" => "man/asagi_io.md",
             "Paraview output" => "man/paraview_output.md",
             "Paraview collection" => "man/paraview_collection.md",
             "Surfaces" =>  "man/surfaces.md",
@@ -120,7 +122,10 @@ makedocs(;
             "Gravity code" => "man/gravity_code.md",
             "Numerical model setups" => "man/geodynamic_setups.md",
             "LaMEM" => "man/lamem.md",
+            "pTatin" => "man/ptatin.md",
+            "Chmy" => "man/Tutorial_Chmy_MPI.md",
             "Profile Processing" => "man/profile_processing.md",
+            "Gmsh" => "man/gmsh.md",
             "Movies" => "man/movies.md"            
         ],
         "List of functions"  => "man/listfunctions.md",