fix documentation, all docstrings in output

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: linux-macos-windows
+name: ci
 on:
   pull_request:
     branches:
@@ -20,17 +20,30 @@ jobs:
           - 'nightly'
         os:
           - ubuntu-latest
-          - macos-latest
           - windows-latest
+          - macOS-13 # intel
+          - macOS-14 # arm
         arch:
           - x64
+          - aarch64
+        exclude:
+          - os: ubuntu-latest
+            arch: aarch64
+          - os: windows-latest
+            arch: aarch64
+          - os: macOS-13 
+            arch: aarch64
+          - os: macOS-14
+            version: 1.6
+          - os: macOS-14
+            arch: x64
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:
@@ -41,20 +54,14 @@ jobs:
             ${{ runner.os }}-test-
             ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@v1
-        env:
-          PYTHON: ""
       - uses: julia-actions/julia-runtest@v1
-        env:
-          PYTHON: ""
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
-        with:
-          file: lcov.info
+      - uses: codecov/codecov-action@v4
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1'
@@ -63,16 +70,13 @@ jobs:
             using Pkg
             Pkg.develop(PackageSpec(path=pwd()))
             Pkg.instantiate()'
-        env:
-          PYTHON: ""
       # - run: |
       #     julia --project=docs -e '
       #       using Documenter: doctest
       #       using MYPACKAGE
       #       doctest(MYPACKAGE)'
       - run: julia --project=docs docs/make.jl
         env:
-          PYTHON: ""
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
-
+

.gitignore

@@ -1,8 +1,8 @@
 QUARRY
-.project.jl
+test/*testfile*
 docs/build
-docs/src/examples
+docs/src/*examples
 *~
 Manifest.toml
 .repl_history.jl
-
+quarry

Project.toml

@@ -1,7 +1,7 @@
 name = "ExtendableGrids"
 uuid = "cfc395e8-590f-11e8-1f13-43a2532b2fa8"
 authors = ["Juergen Fuhrmann <[email protected]>", "Christian Merdon  <[email protected]>", "Johannes Taraz  <[email protected]>"]
-version = "1.3.1"
+version = "1.3.2"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
@@ -17,27 +17,33 @@ Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 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]
-Gmsh = "705231aa-382f-11e9-3f0c-b7cb4346fdeb"
-
-[extensions]
-ExtendableGridsGmshExt = "Gmsh"
-
 [compat]
 AbstractTrees = "0.3,0.4"
 Bijections = "0.1.4"
+Dates = "1.6"
 DocStringExtensions = "0.8,0.9"
 ElasticArrays = "1"
 Gmsh = "0.2.2"
+InteractiveUtils = "1.6"
+LinearAlgebra = "1.6"
+Printf = "1.6"
+Random = "1.6"
 Requires = "1.3"
+SparseArrays = "1.6"
 StaticArrays = "1"
 StatsBase = "0.34"
+UUIDs = "1.6"
 WriteVTK = "1.14"
 julia = "1.6"
 
+[extensions]
+ExtendableGridsGmshExt = "Gmsh"
+
 [extras]
 Gmsh = "705231aa-382f-11e9-3f0c-b7cb4346fdeb"
+
+[weakdeps]
+Gmsh = "705231aa-382f-11e9-3f0c-b7cb4346fdeb"

README.md

@@ -18,6 +18,6 @@ Additional functionality:
 
 Companion packages:
 - Visualization of these grids and of functions on them is avaialable in [GridVisualize.jl](https://github.com/j-fu/GridVisualize.jl).
-- The differently licensed [SimplexGridFactory](https://github.com/j-fu/SimplexGridFactory.jl) contains an API which allows to
+- [SimplexGridFactory](https://github.com/j-fu/SimplexGridFactory.jl) contains an API which allows to
   create `ExtendableGrid` objects with  [Triangulate.jl](https://github.com/JuliaGeometry/Triangulate.jl) which wraps the Triangle mesh generator
   by J. Shewchuk and [TetGen.jl](https://github.com/JuliaGeometry/TetGen.jl) which wraps the  TetGen mesh generator by H. Si.

docs/make.jl

@@ -2,16 +2,15 @@ using Documenter, ExtendableGrids, ExampleJuggler, Gmsh
 import CairoMakie
 CairoMakie.activate!(; type = "svg", visible = false)
 ExampleJuggler.verbose!(true)
-
+ExtendableGridsGmshExt=Base.get_extension(ExtendableGrids, :ExtendableGridsGmshExt)
 function mkdocs()
     cleanexamples()
     generated_examples = @docscripts(joinpath(@__DIR__, "..", "examples"),
                                      ["examples1d.jl", "examples2d.jl", "examples3d.jl", "gmsh.jl"],
                                      Plotter=CairoMakie)
     makedocs(; sitename = "ExtendableGrids.jl",
-             modules = [ExtendableGrids, Base.get_extension(ExtendableGrids, :ExtendableGridsGmshExt)],
+             modules = [ExtendableGrids,ExtendableGridsGmshExt],
              clean = false,
-             warnonly = true,
              doctest = true,
              authors = "J. Fuhrmann, Ch. Merdon, J. Taraz",
              repo = "https://github.com/j-fu/ExtendableGrids.jl",
@@ -31,6 +30,7 @@ function mkdocs()
                  "cellfinder.md",
                  "arraytools.md",
                  "gridconstructors.md",
+                 "output.md",
                  "refinement.md",
                  "regionedit.md",
                  "tokenstream.md",

docs/src/gmsh.md

@@ -17,6 +17,35 @@ ExtendableGrids.simplexgrid_from_gmsh
 ExtendableGrids.simplexgrid_to_gmsh
 ExtendableGrids.mixedgrid_from_gmsh
 ExtendableGrids.mixedgrid_to_gmsh
+ExtendableGrids.seal!
 ```
 
 
+
+## Internals
+### Gmsh extension
+```@docs
+ExtendableGridsGmshExt.gmshfile_to_mixedgrid
+ExtendableGridsGmshExt.take_second
+ExtendableGridsGmshExt.gmshfile_to_simplexgrid
+ExtendableGridsGmshExt.test_gmsh_init
+ExtendableGridsGmshExt.mixedgrid_to_gmshfile
+ExtendableGridsGmshExt.multiply_indices
+ExtendableGridsGmshExt.mod_to_mixedgrid
+ExtendableGridsGmshExt.simplexgrid_to_gmshfile
+ExtendableGridsGmshExt.simplexgrid_to_mod
+ExtendableGridsGmshExt.mod_to_simplexgrid
+ExtendableGridsGmshExt.incomplete_mod_to_simplexgrid
+ExtendableGridsGmshExt.use_geoms
+ExtendableGridsGmshExt.use_vta
+```
+
+### seal! method
+```@docs
+ExtendableGrids.faces_of_ndim_simplex
+ExtendableGrids.assemble_bfaces_direct
+ExtendableGrids.decode
+ExtendableGrids.encode
+ExtendableGrids.faces_of_ndim_simplex_direct
+ExtendableGrids.assemble_bfaces
+```

docs/src/gridconstructors.md

@@ -1,9 +1,16 @@
 # Grid constructors
 
+## Tensor product simplex grids
 
-## API
+```@docs
+simplexgrid
+glue
+```
+
+## Various special grids
 ```@autodocs
+Private = false
 Modules = [ExtendableGrids]
-Pages = ["simplexgrid.jl","commongrids.jl"]
+Pages = ["commongrids.jl"]
 ```
 

docs/src/output.md

@@ -0,0 +1,6 @@
+# Grid output
+
+```@docs
+Base.write
+writeVTK
+```

src/ExtendableGrids.jl

@@ -82,7 +82,7 @@ export seemingly_equal, numbers_match
 include("subgrid.jl")
 export subgrid
 export ParentGrid
-export NodeParents, CellParents, FaceParents, BFaceParents, EdgeParents, BEdgeParents
+export NodeParents, CellParents, FaceParents, BFaceParents
 export ParentGridRelation, SubGrid, BoundarySubGrid, RefinedGrid
 
 include("shape_specs.jl")
@@ -93,7 +93,6 @@ export num_edges
 export local_cellfacenodes
 export local_celledgenodes
 export facetype_of_cellface
-export Volume4ElemType
 export Normal4ElemType!
 export Tangent4ElemType!
 export xrefFACE2xrefCELL
@@ -167,7 +166,6 @@ 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

src/commongrids.jl

@@ -38,9 +38,7 @@ function reference_domain(EG::Type{<:AbstractElementGeometry}, T::Type{<:Real} =
 end
 
 """
-````
-    Triangle(coords) -> ExtendableGrid{T,Int32}
-````
+    grid_triangle(coords::AbstractArray{T,2}) where {T}
 
 Generates a single triangle with the given coordinates, that should be a 2 x 3 array
 with the coordinates of the three vertices, e.g. coords = [0.0 0.0; 1.0 0.0; 0.0 1.0]'.
@@ -51,12 +49,20 @@ function grid_triangle(coords::AbstractArray{T,2}) where {T}
     return xgrid
 end
 
-# unit cube as one cell with six boundary regions (bottom, front, right, back, left, top)
+"""
+    grid_unitcube(EG::Type{<:Hexahedron3D}; scale = [1,1,1], shift = [0,0,0])
+
+Unit cube as one cell with six boundary regions (bottom, front, right, back, left, top)
+"""
 function grid_unitcube(EG::Type{<:Hexahedron3D}; scale = [1,1,1], shift = [0,0,0])
     return reference_domain(EG; scale = scale, shift = shift)
 end
 
-# unit cube as six tets with six boundary regions (bottom, front, right, back, left, top)
+"""
+    grid_unitcube(::Type{Tetrahedron3D}; scale = [1,1,1], shift = [0,0,0])
+
+Unit cube as six tets with six boundary regions (bottom, front, right, back, left, top)
+"""
 function grid_unitcube(::Type{Tetrahedron3D}; scale = [1,1,1], shift = [0,0,0])
     xgrid=ExtendableGrid{Float64,Int32}()
     xCoordinates=Array{Float64,2}([0 0 0; 1 0 0; 1 1 0; 0 1 0; 0 0 1; 1 0 1; 1 1 1; 0 1 1]')
@@ -80,14 +86,18 @@ function grid_unitcube(::Type{Tetrahedron3D}; scale = [1,1,1], shift = [0,0,0])
     return xgrid
 end
 
-
-
-# unit square as one cell with four boundary regions (bottom, right, top, left)
+"""
+    grid_unitsquare(EG::Type{<:Quadrilateral2D}; scale = [1,1], shift = [0,0])
+Unit square as one cell with four boundary regions (bottom, right, top, left)
+"""
 function grid_unitsquare(EG::Type{<:Quadrilateral2D}; scale = [1,1], shift = [0,0])
     return reference_domain(EG; scale = scale, shift = shift)
 end
 
-# unit square as two triangles with four boundary regions (bottom, right, top, left)
+"""
+    grid_unitsquare(::Type{<:Triangle2D}; scale = [1,1], shift = [0,0])
+Unit square as two triangles with four boundary regions (bottom, right, top, left)
+"""
 function grid_unitsquare(::Type{<:Triangle2D}; scale = [1,1], shift = [0,0])
     xgrid=ExtendableGrid{Float64,Int32}()
     xCoordinates=Array{Float64,2}([0 0; 1 0; 1 1; 0 1; 0.5 0.5]')
@@ -107,7 +117,10 @@ function grid_unitsquare(::Type{<:Triangle2D}; scale = [1,1], shift = [0,0])
 end
 
 
-# unit square as two triangles with four boundary regions (bottom, right, top, left)
+"""
+    grid_lshape(::Type{<:Triangle2D}; scale = [1,1], shift = [0,0])
+Lshape domain
+"""
 function grid_lshape(::Type{<:Triangle2D}; scale = [1,1], shift = [0,0])
     xgrid=ExtendableGrid{Float64,Int32}()
     xCoordinates=Array{Float64,2}([0 0; 1 0; 1 1; 0 1; -1 1; -1 0; -1 -1; 0 -1]')
@@ -126,7 +139,11 @@ function grid_lshape(::Type{<:Triangle2D}; scale = [1,1], shift = [0,0])
     return xgrid
 end
 
-# unit suqare as mixed triangles and squares with four boundary regions (bottom, right, top, left)
+"""
+    grid_unitsquare_mixedgeometries()
+
+Unit suqare as mixed triangles and squares with four boundary regions (bottom, right, top, left)
+"""
 function grid_unitsquare_mixedgeometries()
 
     xgrid=ExtendableGrid{Float64,Int32}()
@@ -155,10 +172,12 @@ function grid_unitsquare_mixedgeometries()
     return xgrid
 end
 
-#################################
-# Specific tensor product grids #
-#################################
 
+"""
+    ringsector(rad,ang; eltype=Triangle2D)
+
+Sector of ring or full ring (if  `ang[begin]-ang[end]≈2π`)
+"""
 function ringsector(rad,ang; eltype=Triangle2D)
     Tv=Float32
     Ti=Int32

src/io.jl

@@ -17,7 +17,6 @@ exports grid and optional provided data as a vtk file
 
 Each '(key, value)' pair adds another data entry to the vtk file via WriteVTK functionality.
 """
-
 function writeVTK(filename::String, grid::ExtendableGrid{Tc, Ti}; kwargs...) where {Tc, Ti}
     ncells = num_cells(grid)   # get number of cells in grid
     coords = grid[Coordinates] # get coordinates 

src/simplexgrid.jl

@@ -647,11 +647,11 @@ end
 
 
 """
-   function glue(g1,g2;
-            g1regions=1:num_bfaceregions(g1),
-            g2regions=1:num_bfaceregions(g2),
-            interface=0,
-            tol=1.0e-10)
+    glue(g1,g2;
+         g1regions=1:num_bfaceregions(g1),
+         g2regions=1:num_bfaceregions(g2),
+         interface=0,
+         tol=1.0e-10)
 
 Merge two grids along their common boundary facets. 
 
@@ -666,7 +666,7 @@ Merge two grids along their common boundary facets.
 Deprecated:
 - breg: old notation for interface
 """
-function glue(g1,g2;
+function glue(g1::ExtendableGrid,g2::ExtendableGrid;
               g1regions=1:num_bfaceregions(g1),
               g2regions=1:num_bfaceregions(g2),
               breg=nothing,