Document the gmsh stuff

WIAS-PDELib · Nov 16, 2023 · 91fce0d · 91fce0d
1 parent d921918
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diff --git a/Project.toml b/Project.toml
@@ -18,6 +18,7 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 
 [weakdeps]

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -2,7 +2,12 @@
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 ExtendableGrids = "cfc395e8-590f-11e8-1f13-43a2532b2fa8"
+Gmsh = "705231aa-382f-11e9-3f0c-b7cb4346fdeb"
 GridVisualize = "5eed8a63-0fb0-45eb-886d-8d5a387d12b8"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 SimplexGridFactory = "57bfcd06-606e-45d6-baf4-4ba06da0efd5"
 Triangulate = "f7e6ffb2-c36d-4f8f-a77e-16e897189344"
+
+[compat]
+Documenter = "1"
+julia = "1.9"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,40 +1,38 @@
-ENV["MPLBACKEND"]="agg"
-using Documenter, ExtendableGrids, Literate, GridVisualize, SimplexGridFactory
+ENV["MPLBACKEND"] = "agg"
+using Documenter, ExtendableGrids, Literate, GridVisualize, SimplexGridFactory, Gmsh
 import CairoMakie, Triangulate
 
-CairoMakie.activate!(type="svg",visible=false)
+CairoMakie.activate!(; type = "svg", visible = false)
 
-example_md_dir  = joinpath(@__DIR__,"src","examples")
+example_md_dir = joinpath(@__DIR__, "src", "examples")
 
-
-
-examples1d=joinpath(@__DIR__,"..","examples","examples1d.jl")
+examples1d = joinpath(@__DIR__, "..", "examples", "examples1d.jl")
 include(examples1d)
-examples2d=joinpath(@__DIR__,"..","examples","examples2d.jl")
+examples2d = joinpath(@__DIR__, "..", "examples", "examples2d.jl")
 include(examples2d)
-examples3d=joinpath(@__DIR__,"..","examples","examples3d.jl")
+examples3d = joinpath(@__DIR__, "..", "examples", "examples3d.jl")
 include(examples3d)
 
 include("makeplots.jl")
 
 function mkdocs()
+    Literate.markdown(examples1d, example_md_dir; documenter = false, info = false)
+    Literate.markdown(examples2d, example_md_dir; documenter = false, info = false)
+    Literate.markdown(examples3d, example_md_dir; documenter = false, info = false)
+
+    generated_examples = joinpath.("examples", filter(x -> endswith(x, ".md"), readdir(example_md_dir)))
 
-    Literate.markdown(examples1d, example_md_dir, documenter=false,info=false)
-    Literate.markdown(examples2d, example_md_dir, documenter=false,info=false)
-    Literate.markdown(examples3d, example_md_dir, documenter=false,info=false)
-
-    generated_examples=joinpath.("examples",filter(x->endswith(x, ".md"),readdir(example_md_dir)))
-
-    makeplots(example_md_dir, Plotter=CairoMakie)
-
-    makedocs(sitename="ExtendableGrids.jl",
-             modules = [ExtendableGrids],
-             clean = false, 
+    makeplots(example_md_dir; Plotter = CairoMakie)
+
+    makedocs(; sitename = "ExtendableGrids.jl",
+             modules = [ExtendableGrids, Base.get_extension(ExtendableGrids, :ExtendableGridsGmshExt)],
+             clean = false,
+             warnonly = true,
              doctest = true,
              authors = "J. Fuhrmann, Ch. Merdon",
-             repo="https://github.com/j-fu/ExtendableGrids.jl",
-             pages=[
-                 "Home"=>"index.md",
+             repo = "https://github.com/j-fu/ExtendableGrids.jl",
+             pages = [
+                 "Home" => "index.md",
                  "adjacency.md",
                  "vectorofconstants.md",
                  "typehierarchy.md",
@@ -52,12 +50,12 @@ function mkdocs()
                  "refinement.md",
                  "regionedit.md",
                  "tokenstream.md",
+                 "gmsh.md",
                  "allindex.md",
-                 "Examples" => generated_examples
+                 "Examples" => generated_examples,
              ])
 end
 
 mkdocs()
 
-deploydocs(repo = "github.com/j-fu/ExtendableGrids.jl.git")
-
+deploydocs(; repo = "github.com/j-fu/ExtendableGrids.jl.git")
diff --git a/ext/ExtendableGridsGmshExt.jl b/ext/ExtendableGridsGmshExt.jl
@@ -20,6 +20,7 @@ import ExtendableGrids: Edge1D, Triangle2D, Quadrilateral2D, Tetrahedron3D, Hexa
 #using ExtendableGrids
 using StatsBase: countmap
 using Bijections
+using UUIDs: uuid1
 
 """
 ````
@@ -160,13 +161,15 @@ function simplexgrid_to_gmshfile(grid::ExtendableGrid; filename::String = "")
         # This possibility is new in 1.9, see
         # https://github.com/JuliaLang/julia/blob/release-1.9/NEWS.md#new-language-features
         gmsh.model = simplexgrid_to_mod(grid)
+        mod = gmsh.model
     else
-        simplexgrid_to_mod(grid)
+        mod = simplexgrid_to_mod(grid)
     end
 
     if filename != ""
         gmsh.write(filename)
     end
+    return mod
 end
 
 """
@@ -186,13 +189,15 @@ function mixedgrid_to_gmshfile(grid::ExtendableGrid; filename::String = "")
         # This possibility is new in 1.9, see
         # https://github.com/JuliaLang/julia/blob/release-1.9/NEWS.md#new-language-features
         gmsh.model = mixedgrid_to_mod(grid)
+        mod = gmsh.model
     else
-        mixedgrid_to_mod(grid)
+        mod = mixedgrid_to_mod(grid)
     end
 
     if filename != ""
         gmsh.write(filename)
     end
+    return mod
 end
 
 #---------------------------------------------------------------------------------------------
@@ -592,7 +597,7 @@ function simplexgrid_to_mod(grid::ExtendableGrid)
     # gmsh.initialize()
     gmsh.option.setNumber("General.Terminal", 1)
     #(fbase,fext)=splitext(filename)
-    gmsh.model.add("fbase")
+    gmsh.model.add("model" * string(uuid1())[1:8])
 
     Tc = typeof(grid[Coordinates][1, 1])
     Ti = typeof(grid[CellNodes][1, 1])
@@ -682,7 +687,7 @@ function mixedgrid_to_mod(grid::ExtendableGrid)
     # gmsh.initialize()
     gmsh.option.setNumber("General.Terminal", 1)
     #(fbase,fext)=splitext(filename)
-    gmsh.model.add("fbase")
+    gmsh.model.add("model" * string(uuid1())[1:8])
 
     # formatting the coordinates correctly
     coords = grid[Coordinates]

diff --git a/src/ExtendableGrids.jl b/src/ExtendableGrids.jl
@@ -13,16 +13,14 @@ using Random
 using Dates
 using LinearAlgebra
 
-
-if  !isdefined(Base, :get_extension)
+if !isdefined(Base, :get_extension)
     using Requires
 end
 
-
 include("adjacency.jl")
-export Adjacency,VariableTargetAdjacency,FixedTargetAdjacency
-export atranspose,num_targets,num_sources,num_links,append!, max_num_targets_per_source
-export asparse,tryfix,makevar
+export Adjacency, VariableTargetAdjacency, FixedTargetAdjacency
+export atranspose, num_targets, num_sources, num_links, append!, max_num_targets_per_source
+export asparse, tryfix, makevar
 
 include("serialadjacency.jl")
 export SerialVariableTargetAdjacency
@@ -45,50 +43,45 @@ export AbstractElementGeometry1D
 export Edge1D
 
 export AbstractElementGeometry2D
-export Polygon2D,Triangle2D,Quadrilateral2D,Pentagon2D,Hexagon2D,Parallelogram2D,Rectangle2D,Circle2D
+export Polygon2D, Triangle2D, Quadrilateral2D, Pentagon2D, Hexagon2D, Parallelogram2D, Rectangle2D, Circle2D
 
 export AbstractElementGeometry3D
-export Polyhedron3D,Tetrahedron3D, Hexahedron3D,Parallelepiped3D,RectangularCuboid3D,Prism3D,TrianglePrism3D,Sphere3D
+export Polyhedron3D, Tetrahedron3D, Hexahedron3D, Parallelepiped3D, RectangularCuboid3D, Prism3D, TrianglePrism3D, Sphere3D
 
 export AbstractElementGeometry4D
-export Polychoron4D,HyperCube4D
+export Polychoron4D, HyperCube4D
 
 export dim_element
 
-
 include("coordinatesystem.jl")
-export coordinatesystems,CoordinateSystems
+export coordinatesystems, CoordinateSystems
 export AbstractCoordinateSystem
-export Cartesian1D,Cartesian2D,Cartesian3D
-export Cylindrical2D,Cylindrical3D
-export Polar2D,Polar1D ,Spherical3D,Spherical1D  
-
-
+export Cartesian1D, Cartesian2D, Cartesian3D
+export Cylindrical2D, Cylindrical3D
+export Polar2D, Polar1D, Spherical3D, Spherical1D
 
 include("extendablegrid.jl")
 export ExtendableGrid
 export instantiate, veryform
 export AbstractGridComponent
-export AbstractGridAdjacency,AbstractElementGeometries,AbstractElementRegions
+export AbstractGridAdjacency, AbstractElementGeometries, AbstractElementRegions
 export Coordinates, CellNodes, BFaceNodes
 export CellGeometries, BFaceGeometries
 export CellRegions, BFaceRegions, BEdgeRegions
 export NumCellRegions, NumBFaceRegions, NumBEdgeRegions
 export CoordinateSystem
-export AbstractGridFloatArray1D,AbstractGridFloatArray2D
-export AbstractGridIntegerArray1D,AbstractGridIntegerArray2D
+export AbstractGridFloatArray1D, AbstractGridFloatArray2D
+export AbstractGridIntegerArray1D, AbstractGridIntegerArray2D
 export index_type, coord_type
 export dim_space, dim_grid
-export num_nodes, num_cells, num_bfaces, num_bedges 
+export num_nodes, num_cells, num_bfaces, num_bedges
 export num_cellregions, num_bfaceregions, num_bedgeregions
 export gridcomponents
-export seemingly_equal 
+export seemingly_equal
 
 include("subgrid.jl")
 export subgrid
 
-
-
 include("shape_specs.jl")
 export refcoords_for_geometry
 export num_nodes
@@ -103,7 +96,6 @@ export Tangent4ElemType!
 export xrefFACE2xrefCELL
 export xrefFACE2xrefOFACE
 
-
 include("derived.jl")
 export Coordinates
 export CellVolumes, CellFaces, CellEdges, CellFaceSigns, CellFaceOrientations, CellEdgeSigns
@@ -126,7 +118,7 @@ include("more.jl")
 export BFaceCells, BFaceNormals, BFaceEdges, BEdgeNodes
 
 include("voronoi.jl")
-export tricircumcenter!,VoronoiFaceCenters
+export tricircumcenter!, VoronoiFaceCenters
 
 include("meshrefinements.jl")
 export split_grid_into
@@ -138,9 +130,7 @@ include("adaptive_meshrefinements.jl")
 export bulk_mark
 export RGB_refine
 
-
-
-include("assemblytypes.jl");
+include("assemblytypes.jl")
 export AssemblyType
 export AT_NODES, ON_CELLS, ON_FACES, ON_IFACES, ON_BFACES, ON_EDGES, ON_BEDGES
 export ItemType4AssemblyType
@@ -151,13 +141,12 @@ export GridComponentRegions4AssemblyType
 export GridComponentUniqueGeometries4AssemblyType
 export GridComponentAssemblyGroups4AssemblyType
 
-include("l2gtransformations.jl");
+include("l2gtransformations.jl")
 export L2GTransformer, update_trafo!, eval_trafo!, mapderiv!
 
 include("cellfinder.jl")
 export CellFinder
-export gFindLocal!, gFindBruteForce!, interpolate,interpolate!
-
+export gFindLocal!, gFindBruteForce!, interpolate, interpolate!
 
 include("commongrids.jl")
 export reference_domain
@@ -167,36 +156,31 @@ export grid_unitsquare, grid_unitsquare_mixedgeometries
 export grid_triangle
 export ringsector
 
-
 include("regionedit.jl")
 export cellmask!, bfacemask!, bedgemask!, rect!
 
-
 include("arraytools.jl")
-export glue,geomspace,linspace
+export glue, geomspace, linspace
 
 include("simplexgrid.jl")
 export simplexgrid, geomspace, glue
 export XCoordinates, YCoordinates, ZCoordinates
 export writefile
 
 include("tokenstream.jl")
-export TokenStream, gettoken, expecttoken,trytoken
+export TokenStream, gettoken, expecttoken, trytoken
 
 include("io.jl")
 export writeVTK
 
 include("seal.jl")
 
-
-@static if  !isdefined(Base, :get_extension)
+@static if !isdefined(Base, :get_extension)
     function __init__()
-        @require Gmsh = "705231aa-382f-11e9-3f0c-b7cb4346fdeb"  begin
+        @require Gmsh="705231aa-382f-11e9-3f0c-b7cb4346fdeb" begin
             include("../ext/ExtendableGridsGmshExt.jl")
         end
     end
 end
 
-
-
 end # module
diff --git a/src/io.jl b/src/io.jl
@@ -189,7 +189,6 @@ function simplexgrid(file::String; format = "")
     simplexgrid(coord, cells, regions, faces, bregions)
 end
 
-# Implementations in Gmsh extension
 function simplexgrid_from_gmsh end
 
 function simplexgrid_to_gmsh end