Allow for GeometryBasics v0.5

.github/workflows/ci.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6' # Replace this with the minimum Julia version that your package supports. E.g. if your package requires Julia 1.5 or higher, change this to '1.5'.
+          - '1.9' # Replace this with the minimum Julia version that your package supports. E.g. if your package requires Julia 1.5 or higher, change this to '1.5'.
           - '1'   # Leave this line unchanged. '1' will automatically expand to the latest stable 1.x release of Julia.
           - 'nightly' 
         os:

.gitignore

@@ -3,7 +3,8 @@
 *.jl.mem
 .repl_history.jl
 .DS_Store
-/Manifest.toml
+/Manifest*.toml
 docs/Manifest.toml
 docs/build
 QUARRY
+quarry

CHANGELOG.md

@@ -0,0 +1,63 @@
+# Changelog
+
+All notable changes to this project since V1.0 will be documented in this file.
+
+## [2.0]
+- Allow for GeometryBasics v0.5 along with 0.4
+- Breaking: with GeometryBasics v0.5, a MetaMesh has 
+  to be provided as input for Tetrahedralize. 
+  The RawTetGenIO based API is not affected. Users who
+  rely on the RawTetGenIO based API can use  `TetGen="1,2"` 
+  in their `[compat]` section.
+- Breaking: remove deprecated `tetunsuitable`. Use `tetunsuitable!` instead
+
+## [1.5.1] - 2024-02-27
+
+- Fix version check for `MemoryRef`
+- Add  ci for apple silicon
+
+## [1.5.0] - 2023-11-15
+
+- Fix imports/named using from GeometryBasics
+- add juliaformatter
+- @deprecate tetunsuitable tetunsuitable!
+- Pass pointer to unsafe_convert
+- Test for type of return value of unsuitable function
+- fix for 1.11 memory handling
+
+## [1.4.0] - 2022-06-02
+- allow to input stl files
+
+## [1.3.0] - 2021-10-05
+
+- Switch Julia package to MIT license (after the FFTW model).
+- Remove checking of error catching from tests due to problems on windows.
+- Point3f0->Point3f (GeometryBasics version)
+- Add stl loading functionality
+- Switch Julia package to MIT license (after the FFTW model).
+
+## [1.2.1] - 2021-09-13
+- allow for GeometryBasics 0.4
+
+## [1.2.0] - 2021-05-26
+
+- Added example for RawTetGenIO and holes
+- Created holes for tetrahedralize(::Mesh, ...)
+- Added test example for mesh API with holes
+
+## [1.1.1] - 2021-01-02
+
+- Bump version compat for StaticArrays
+
+## [1.1.0] - 2020-12-22
+
+- Thank you travis and bye bye
+- Update of upstream patch version of TetGen to "August 18, 2018".
+- Formally this still appears to be 1.5.1 , and it is manifest in TetGen_jll 1.5.1+1
+- Catch errors thrown by TetGen in a rc variable, throw julia error if rc!=0
+- Handle unsuitable callback to allow local refinement.
+
+## [1.0.0] - 2020-11-30
+- Dependency on artifacts
+- Refactoring. API of API.jl stays the same.
+- Provide array based API. and RawTetGenIO

Project.toml

@@ -1,7 +1,7 @@
 name = "TetGen"
 uuid = "c5d3f3f7-f850-59f6-8a2e-ffc6dc1317ea"
 authors = ["SimonDanisch <sdanisch@gmail.com>", "Juergen Fuhrmann <juergen.fuhrmann@wias-berlin.de"]
-version = "1.5.1"
+version = "2.0.0"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
@@ -13,13 +13,9 @@ TetGen_jll = "b47fdcd6-d2c1-58e9-bbba-c1cee8d8c179"
 
 [compat]
 DocStringExtensions = "0.8,0.9"
-GeometryBasics = "0.2, 0.3, 0.4"
+GeometryBasics = "0.4, 0.5"
+LinearAlgebra = "1"
+Printf = "1"
 StaticArrays = "1"
 TetGen_jll = "1.5.3"
-julia = "1.6"
-
-[extras]
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[targets]
-test = ["Test"]
+julia = "1.9"

README.md

@@ -4,6 +4,7 @@
 [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/JuliaGeometry/TetGen.jl/blob/master/LICENSE)
 [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://JuliaGeometry.github.io/TetGen.jl/stable)
 [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://JuliaGeometry.github.io/TetGen.jl/dev)
+[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 
 The `TetGen.jl` package is a Julia wrapper for the C++ project [TetGen](https://wias-berlin.de/software/index.jsp?id=TetGen&lang=1). This wrapper enables TetGen based tetrahedral meshing, and (constrained) 3D Delaunay and Voronoi tesselation.
 
@@ -63,7 +64,7 @@ Plotted with Makie:
 ```julia
 using TetGen
 let
-    tetunsuitable() do pa,pb,pc,pd
+    tetunsuitable!() do pa,pb,pc,pd
         vol=det(hcat(pb-pa,pc-pa,pd-pa))/6
         center=0.25*(pa+pb+pc+pd)-[0.5,0.5,0.5]
         vol> 0.05*norm(center)^2.5

docs/make.jl

@@ -4,7 +4,6 @@ function make_all()
     makedocs(;
              sitename = "TetGen.jl",
              modules = [TetGen],
-             warnonly = true,
              clean = false,
              doctest = false,
              authors = "Simon Danisch, Juergen Fuhrmann",

docs/src/index.md

@@ -5,6 +5,12 @@ tetrahedralizations,  constrained  Delaunay  tetrahedralizations,  and
 quality tetrahedral  meshes. TetGen.jl  provides a Julia  interface to
 TetGen.
 
+
+```@docs
+TetGen
+```
+
+
 ## Mesh based API
 This API uses instances of types from [GeometryBasics.jl](https://github.com/JuliaGeometry/GeometryBasics.jl) 
 to describe input and output of TetGen.
@@ -14,6 +20,8 @@ Modules = [TetGen]
 Pages = ["api.jl"]
 ```
 
+
+
 ## Raw API
 This API is closer to TetGen's C++ API in the sense that
 input and output are described using arrays of integers
@@ -40,3 +48,8 @@ tetunsuitable!
   Link to preprint  [here](http://doi.org/10.20347/WIAS.PREPRINT.1762). 
 
 
+## Internal API
+```@autodocs
+Modules = [TetGen]
+Pages = ["meshes.jl", "jltetgenio.jl", "cpptetgenio.jl"]
+```

src/TetGen.jl

@@ -1,16 +1,19 @@
-module TetGen
-using DocStringExtensions
-using TetGen_jll
+"""
+    TetGen
 
+$(read(joinpath(@__DIR__,"..","README.md"),String))
+"""
+module TetGen
+using DocStringExtensions: DocStringExtensions, SIGNATURES, TYPEDEF,
+                           TYPEDFIELDS, TYPEDSIGNATURES
 import GeometryBasics
-using GeometryBasics: Polygon, MultiPolygon, Point, Point3f, LineFace, Polytope, Line,
-                      Simplex, connect, Triangle, NSimplex, Tetrahedron,
-                      TupleView, TriangleFace, SimplexFace, LineString, Mesh, TetrahedronP, TriangleP,
-                      NgonFace, Ngon, faces, coordinates, metafree, meta, faces
-
-using Printf
+using GeometryBasics: Point, Point3f, LineFace, Polytope, Triangle, NSimplex,
+                      TriangleFace, SimplexFace, Mesh, Tetrahedron, Triangle,
+                      NgonFace, faces, coordinates
 
-using StaticArrays
+using Printf: Printf
+using StaticArrays: StaticArrays, SVector
+using TetGen_jll: TetGen_jll, libtet
 
 include("cpptetgenio.jl")
 include("jltetgenio.jl")
@@ -19,7 +22,7 @@ include("meshes.jl")
 include("api.jl")
 
 export tetrahedralize
-export tetunsuitable!, tetunsuitable
+export tetunsuitable!
 export TetGenError
 export RawTetGenIO, facetlist!, RawFacet
 export numberofpoints, numberoftetrahedra, numberoftrifaces, numberofedges

src/api.jl

@@ -1,25 +1,36 @@
 """
-$(SIGNATURES)
+    voronoi(points::Vector{Point{3, T}})  where {T <: AbstractFloat}
 
 Create voronoi diagram of point set.    
 
 Returns a mesh of triangles.
 """
 function voronoi(points::Vector{Point{3, T}}) where {T <: AbstractFloat}
     result = tetrahedralize(JLTetGenIO(points), "Qw")
-    Mesh{Triangle}(result)
+    return Mesh{Triangle}(result)
 end
 
 """
 $(SIGNATURES)
 
 Tetrahedralize a mesh of polygons with optional facet markers.
-Returns a mesh of tetrahdra.
+Returns a mesh of tetrahdra. 
+
+With `GeometryBasics` version 0.4, the input mesh has to be a `GeometryBasics.Mesh` with
+possible metadata. With `GeometryBasics` version 0.5, the input mesh has to be a `GeometryBasics.MetaMesh`.
+
+Default command is "Qp", creating the Delaunay
+triangulation of the point set. See the list of
+possible flags in the documentation of [`tetrahedralize(::RawTetGenIO, flags)`](@ref).
 """
-function TetGen.tetrahedralize(mesh::Mesh{3, Float64, <:TetGen.Ngon}, command = "Qp";
+function TetGen.tetrahedralize(mesh, command = "Qp";
                                marker = :markers, holes = Point{3, Float64}[])
     f = faces(mesh)
-    kw_args = Any[:facets => metafree(f), :holes => holes]
+    if pkgversion(GeometryBasics) < v"0.5"
+        kw_args = Any[:facets => GeometryBasics.metafree(f), :holes => holes]
+    else
+        kw_args = Any[:facets => f, :holes => holes]
+    end
     if hasproperty(f, marker)
         push!(kw_args, :facetmarkers => getproperty(f, marker))
     end
@@ -28,14 +39,15 @@ function TetGen.tetrahedralize(mesh::Mesh{3, Float64, <:TetGen.Ngon}, command =
     return Mesh{Tetrahedron}(result)
 end
 
-"""
-$(SIGNATURES)
-
-Tetrahedralize a domain described by a mesh of triangles.
-Returns a mesh of tetrahdra.
-"""
-function TetGen.tetrahedralize(mesh::Mesh{3, Float64, <:TetGen.Triangle}, command = "Qp")
-    tio = JLTetGenIO(coordinates(mesh); facets = faces(mesh))
-    result = tetrahedralize(tio, command)
-    Mesh{Tetrahedron}(result)
-end
+# JF: probably this case is included in the case above
+# """
+# $(SIGNATURES)
+#
+# Tetrahedralize a domain described by a mesh of triangles.
+# Returns a mesh of tetrahdra.
+# """
+# function TetGen.tetrahedralize(mesh, command = "Qp")
+#     tio = JLTetGenIO(coordinates(mesh); facets = faces(mesh))
+#     result = tetrahedralize(tio, command)
+#     return Mesh{Tetrahedron}(result)
+# end

src/cpptetgenio.jl

@@ -149,5 +149,3 @@ function tetunsuitable!(unsuitable::Function; check_signature = true)
     c_wrap_tetunsuitable = @cfunction(jl_wrap_tetunsuitable, Cint, (Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cdouble}))
     ccall((:tetunsuitable_callback, libtet), Cvoid, (Ptr{Cvoid},), c_wrap_tetunsuitable)
 end
-
-@deprecate tetunsuitable(unsuitable::Function; kwargs...) tetunsuitable!(unsuitable::Function; kwargs...)

src/meshes.jl

@@ -23,10 +23,10 @@ function GeometryBasics.Mesh{P}(x::JLTetGenIO{T}) where {P <: Polytope{N, T} whe
     Mesh{Polytope(P, Point{3, T})}(x)
 end
 
-function GeometryBasics.Mesh{TetrahedronP{ET, P}}(x::JLTetGenIO) where {ET, P}
-    Mesh(convert(Vector{P}, x.points), x.tetrahedra)
+function GeometryBasics.Mesh{Tetrahedron{ET}}(x::JLTetGenIO) where {ET}
+    Mesh(x.points, x.tetrahedra)
 end
 
-function GeometryBasics.Mesh{TriangleP{3, ET, P}}(x::JLTetGenIO) where {ET, P}
-    Mesh(convert(Vector{P}, x.points), x.trifaces)
+function GeometryBasics.Mesh{Triangle{3, ET}}(x::JLTetGenIO) where {ET}
+    Mesh(x.points, x.trifaces)
 end

test/Project.toml

@@ -0,0 +1,14 @@
+[deps]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
+GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[compat]
+Aqua = "0.8"
+ExplicitImports = "1.10"
+GeometryBasics = "0.4, 0.5"
+LinearAlgebra = "1"
+Printf = "1"

test/runtests.jl

@@ -1,9 +1,7 @@
-using TetGen
-using TetGen: JLPolygon, JLFacet, Point
-using GeometryBasics
-using GeometryBasics: Mesh, Triangle, Tetrahedron, TriangleFace, QuadFace,
-                      PointMeta, NgonFaceMeta, meta, faces, metafree
-using GeometryBasics.StructArrays
+using ExplicitImports, Aqua
+using TetGen: TetGen, JLPolygon, JLFacet, Point, tetrahedralize
+using GeometryBasics: GeometryBasics
+using GeometryBasics: Mesh, Triangle, Tetrahedron, TriangleFace, QuadFace, faces
 using Test
 
 @testset "mesh based API" begin
@@ -22,11 +20,20 @@ using Test
 
     markers = Cint[-1, -2, 0, 0, 0, 0]
     # attach some additional information to our faces!
-    mesh = Mesh(points, meta(facets; markers = markers))
+    if pkgversion(GeometryBasics) < v"0.5"
+        mesh = Mesh(points, GeometryBasics.meta(facets; markers))
+    else
+        mesh = GeometryBasics.MetaMesh(points, facets; markers)
+    end
     result = tetrahedralize(mesh)
     @test result isa Mesh
 
     # Make it similar to the README example
+    if pkgversion(GeometryBasics) < v"0.5"
+        mesh = Mesh(points, facets)
+    else
+        mesh = GeometryBasics.MetaMesh(points, facets)
+    end
     result = tetrahedralize(mesh, "vpq1.414a0.1")
     @test result isa Mesh
 
@@ -44,7 +51,11 @@ using Test
                                    [1, 3, 4],
                                    [2, 3, 4]]
 
-    tetmesh = Mesh(tetpoints, tetfacets)
+    if pkgversion(GeometryBasics) < v"0.5"
+        tetmesh = Mesh(tetpoints, tetfacets)
+    else
+        tetmesh = GeometryBasics.MetaMesh(tetpoints, tetfacets)
+    end
     result = tetrahedralize(tetmesh, "pQqAa0.01")
     @test result isa Mesh
 
@@ -81,8 +92,13 @@ using Test
                             [4, 8, 5, 1] .+ 8]
 
     markers = ones(Cint, 12)
-    mesh = Mesh(points, meta(facets; markers = markers))
-    resultx = tetrahedralize(mesh, "pQqAa1.0"; holes = [Point{3, Float64}(0, 0, 0)])
+
+    if pkgversion(GeometryBasics) < v"0.5"
+        mesh = Mesh(points, GeometryBasics.meta(facets; markers = markers))
+    else
+        mesh = GeometryBasics.MetaMesh(points, facets; markers = markers)
+    end
+    result = tetrahedralize(mesh, "pQqAa1.0"; holes = [Point{3, Float64}(0, 0, 0)])
     @test result isa Mesh
 
     # s = Sphere{Float64}(Point(0.0, 0.0, 0.0), 2.0)
@@ -262,3 +278,18 @@ end
     end
     @test test_error_output()
 end
+
+@testset "ExplicitImports" begin
+    @test ExplicitImports.check_no_implicit_imports(TetGen) === nothing
+    @test ExplicitImports.check_no_stale_explicit_imports(TetGen) === nothing
+end
+
+@testset "Aqua" begin
+    Aqua.test_all(TetGen)
+end
+
+if isdefined(Docs, :undocumented_names)
+    @testset "UndocumentedNames" begin
+        @test isempty(Docs.undocumented_names(TetGen))
+    end
+end