Merge branch 'main' into feature/concrete-region-numbers

Author: j-fu

.codespellrc

@@ -0,0 +1,2 @@
+[codespell]
+ignore-words-list = missings,rcall,linke,fo

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: daily

.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.
+          - 'lts' # Replace this with the minimum Julia version that your package supports.
           - '1'   # Leave this line unchanged. '1' will automatically expand to the latest stable 1.x release of Julia.
           - 'nightly' 
         os:
@@ -25,8 +25,8 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
@@ -43,15 +43,15 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v5
         with:
           file: lcov.info
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
       - run: |

.github/workflows/format_check.yml

@@ -22,7 +22,7 @@ jobs:
         with:
           version: ${{ matrix.julia-version }}
 
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
       - name: Install JuliaFormatter and format
         # This will use the latest version by default but you can set the version like so:
         #

docs/Project.toml

@@ -3,3 +3,6 @@ ColorTypes = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 GridVisualizeTools = "5573ae12-3b76-41d9-b48c-81d0b6e61cc5"
+
+[compat]
+Colors = "0.13"

docs/make.jl

@@ -1,4 +1,4 @@
-using Documenter, GridVisualizeTools, ColorTypes
+using Documenter, GridVisualizeTools, ColorTypes, Colors
 
 function mkdocs()
     DocMeta.setdocmeta!(GridVisualizeTools, :DocTestSetup, :(using GridVisualizeTools, ColorTypes, Colors); recursive = true)

docs/src/index.md

@@ -33,22 +33,26 @@ rgbtuple
 rgbtuple(:red)
 # output
 
-(1.0,1.0,1.0)
+(1.0,0.0,0.0)
 ```
-
 ```@docs
-ColorTypes.RGB
+rgbcolor
 ```
 
-```@example
-using ColorTypes,GridVisualizeTools # hide
-RGB(:red)
+```@jldoctest
+rgbcolor(:red)
+# output
+
+RGB{Float64}(1.0,0.0,0.0)
 ```
-```@example
-using ColorTypes,GridVisualizeTools # hide
-RGB("green")
+```@jldoctest
+rgbcolor(1.0, 0.0, 0.0)
+# output
+
+RGB{Float64}(1.0,0.0,0.0)
 ```
 
+
 ## Visibility handling of grid cells
 
 ```@docs

src/GridVisualizeTools.jl

@@ -7,7 +7,7 @@ using DocStringExtensions: SIGNATURES, TYPEDEF, TYPEDSIGNATURES
 using StaticArraysCore: SVector
 
 include("colors.jl")
-export region_cmap, bregion_cmap, rgbtuple
+export region_cmap, bregion_cmap, rgbtuple, rgbcolor
 
 include("extraction.jl")
 export extract_visible_cells3D, extract_visible_bfaces3D

src/colors.jl

@@ -1,4 +1,4 @@
-"""
+"""depend
 $(SIGNATURES)
 
 Create customized distinguishable colormap for interior regions.
@@ -10,7 +10,7 @@ region_cmap(10)[1]
 
 # output
 
-RGB{Float64}(0.85,0.6,0.6)
+RGB{Float64}(0.85, 0.6, 0.6)
 ```
 
 """
@@ -33,7 +33,7 @@ bregion_cmap(10)[1]
 
 # output
 
-RGB{Float64}(1.0,0.0,0.0)
+RGB{Float64}(1.0, 0.0, 0.0)
 ```
 
 """
@@ -46,66 +46,76 @@ function bregion_cmap(n)
 end
 
 """
-$(SIGNATURES)
+Create color tuple from  color description (e.g. string)
 
-Create RGB color from color name string.
+```jldoctest
+julia> rgbtuple(:red)
+(1.0, 0.0, 0.0)
 
-julia> Colors.RGB("red")
-RGB{Float64}(1.0,0.0,0.0)
+julia> rgbtuple("red")
+(1.0, 0.0, 0.0)
 ```
 """
-function Colors.RGB(c::String)
-    c64 = Colors.color_names[c]
-    Colors.RGB(c64[1] / 255, c64[2] / 255, c64[3] / 255)
-end
+rgbtuple(c) = rgbtuple(parse(Colors.RGB{Float64},c))
 
 """
 $(SIGNATURES)
 
-Create RGB color from color name symbol.
+Create color tuple from  RGB color.
 
 ```jldoctest
-julia> Colors.RGB(:red)
-RGB{Float64}(1.0,0.0,0.0)
+julia> rgbtuple(RGB(0.0,1,0))
+(0.0, 1.0, 0.0)
 ```
 """
-Colors.RGB(c::Symbol) = Colors.RGB(String(c))
+rgbtuple(c::Colors.RGB) = (Colors.red(c), Colors.green(c), Colors.blue(c))
+
 
 """
-$(SIGNATURES)
+    rgbcolor(col::Any)
 
-Create RGB color from tuple
+Return Colors.RGB object from string or symbol. 
 
 ```jldoctest
-julia> Colors.RGB((1.0,0,0))
-RGB{Float64}(1.0,0.0,0.0)
+julia> rgbcolor(:red)
+RGB{Float64}(1.0, 0.0, 0.0)
+
+julia> rgbcolor("red")
+RGB{Float64}(1.0, 0.0, 0.0)
 ```
-"""
-Colors.RGB(c::Tuple) = Colors.RGB(c...)
 
 """
-$(SIGNATURES)
+rgbcolor(col::Any) = parse(Colors.RGB{Float64},col) 
 
-Create color tuple from  color description (e.g. string)
 
-```jldoctest
-julia> rgbtuple(:red)
-(1.0, 0.0, 0.0)
+"""
+    rgbcolor(col::RGB)
 
-julia> rgbtuple("red")
-(1.0, 0.0, 0.0)
+Pass through of RGB color object.
+```jldoctest
+julia> rgbcolor(RGB(1.0,0.0, 0.0))
+RGB{Float64}(1.0, 0.0, 0.0)
 ```
-"""
-rgbtuple(c) = rgbtuple(Colors.RGB(c))
 
 """
-$(SIGNATURES)
+rgbcolor(col::Colors.RGB) = col
 
-Create color tuple from  RGB color.
+"""
+    rgbcolor(col::Tuple)
 
+Create RGB color object from tuple
 ```jldoctest
-julia> rgbtuple(RGB(0.0,1,0))
-(0.0, 1.0, 0.0)
+julia> rgbcolor((1.0,0.0, 0.0))
+RGB{Float64}(1.0, 0.0, 0.0)
 ```
+
 """
-rgbtuple(c::Colors.RGB) = (Colors.red(c), Colors.green(c), Colors.blue(c))
+function rgbcolor(col::Tuple)
+    # Base.depwarn(
+    #     "Setting custom colors as `Tuple`, e.g. `color=(0.,0.,1.)` will be removed in the next major release. "*
+    #     "Please use color=RGB(0.,0.,1.) instead.",
+    #     :update_lines,
+    # )
+    return Colors.RGB(col...)
+end
+

src/marching.jl

@@ -17,7 +17,7 @@
 
   Mutates:
   - ixcoord: 3x4 array of plane - tetedge intersection coordinates
-  - ixvalues: 4 element array of fuction values at plane - tetdedge intersections
+  - ixvalues: 4 element array of function values at plane - tetdedge intersections
 
   Returns:
   - nxs,ixcoord,ixvalues
@@ -67,7 +67,7 @@ end
  flevel could be flevels
  xyzcut could be a vector of plane data
  perhaps we can also collect isolines.
- Just an optional collector parameter, defaulting to somethig makie independent.
+ Just an optional collector parameter, defaulting to something makie independent.
 
     Better yet:
 
@@ -114,7 +114,7 @@ Return values: (points, tris, values)
 
 These can be readily turned into a mesh with function values on it.
 
-Caveat: points with similar coordinates are not identified, e.g. an intersection of a plane and an edge will generate as many edge intersection points as there are tetrahedra adjacent to that edge. As a consequence, normal calculations for visualization alway will end up with facet normals, not point normals, and the visual impression of a rendered isosurface will show its piecewise linear genealogy.
+Caveat: points with similar coordinates are not identified, e.g. an intersection of a plane and an edge will generate as many edge intersection points as there are tetrahedra adjacent to that edge. As a consequence, normal calculations for visualization always will end up with facet normals, not point normals, and the visual impression of a rendered isosurface will show its piecewise linear genealogy.
 
 """
 function marching_tetrahedra(coord::Matrix{Tc},

src/markerpoints.jl

@@ -5,7 +5,7 @@ $(SIGNATURES)
 Assume that `points` are nodes of a polyline.
 Place `nmarkers` equidistant markers  at the polyline, under
 the assumption that the points are transformed via the transformation
-matrix M vor visualization.
+matrix M for visualization.
 """
 function markerpoints(points, nmarkers, transform)
     dist(p1, p2) = norm(transform * (p1 - p2))