Runic (#166)

docs/Project.toml

@@ -2,6 +2,7 @@
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+DelaunayTriangulation = "927a84f5-c5f4-47a5-9785-b46e178433df"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
 ElasticArrays = "fdbdab4c-e67f-52f5-8c3f-e7b388dad3d4"

docs/liveserver.jl

@@ -5,12 +5,13 @@ Pkg.instantiate()
 import LiveServer
 withenv("LIVESERVER_ACTIVE" => "true") do
  LiveServer.servedocs(;
- launch_browser=true,
- foldername=joinpath(repo_root, "docs"),
- include_dirs=[joinpath(repo_root, "src")],
- skip_dirs=[joinpath(repo_root, "docs/src/tutorials"),
+ launch_browser = true,
+ foldername = joinpath(repo_root, "docs"),
+ include_dirs = [joinpath(repo_root, "src")],
+ skip_dirs = [
+ joinpath(repo_root, "docs/src/tutorials"),
  joinpath(repo_root, "docs/src/applications"),
  joinpath(repo_root, "docs/src/figures"),
  ],
  )
-end
+end

docs/make.jl

@@ -4,8 +4,10 @@ using Literate
 using Test
 using Dates
 
-DocMeta.setdocmeta!(DelaunayTriangulation, :DocTestSetup, :(using DelaunayTriangulation, Test);
- recursive=true)
+DocMeta.setdocmeta!(
+ DelaunayTriangulation, :DocTestSetup, :(using DelaunayTriangulation, Test);
+ recursive = true,
+)
 
 const IS_LIVESERVER = false && get(ENV, "LIVESERVER_ACTIVE", "false") == "true"
 if IS_LIVESERVER
@@ -41,7 +43,7 @@ function add_just_the_code_section(dir, file)
  file_name, file_ext = splitext(file)
  file_path = joinpath(dir, file)
  new_file_path = joinpath(session_tmp, file_name * "_just_the_code" * file_ext)
- cp(file_path, new_file_path, force=true)
+ cp(file_path, new_file_path, force = true)
  folder = splitpath(dir)[end] # literate_tutorials or literate_applications
  open(new_file_path, "a") do io
  write(io, "\n")
@@ -74,7 +76,7 @@ for folder in ("tutorials", "applications")
  # end
  #end
  new_file_path = add_just_the_code_section(dir, file)
- script = Literate.script(file_path, session_tmp, name=splitext(file)[1] * "_just_the_code_cleaned")
+ script = Literate.script(file_path, session_tmp, name = splitext(file)[1] * "_just_the_code_cleaned")
  code = strip(read(script, String))
  @info "[$(ct())] Processing $file: Converting markdown script"
  line_ending_symbol = occursin(code, "\r\n") ? "\r\n" : "\n"
@@ -86,12 +88,12 @@ for folder in ("tutorials", "applications")
  Literate.markdown(
  new_file_path,
  outputdir;
- documenter=true,
- postprocess=editurl_update ∘ post_strip,
- credit=true,
- name=splitext(file)[1],
- execute=false,
- flavor=Literate.DocumenterFlavor(),
+ documenter = true,
+ postprocess = editurl_update ∘ post_strip,
+ credit = true,
+ name = splitext(file)[1],
+ execute = false,
+ flavor = Literate.DocumenterFlavor(),
  )
  end
 end
@@ -127,15 +129,15 @@ const _PAGES = [
  "Voronoi Tessellations" => "tutorials/voronoi.md",
  "Clipped Voronoi Tessellations" => [
  "Clipping to the Convex Hull" => "tutorials/clipped.md",
- "Clipping to a Rectangle" => "tutorials/clipped_rectangle.md"
+ "Clipping to a Rectangle" => "tutorials/clipped_rectangle.md",
  ],
  "Centroidal Voronoi Tessellations" => "tutorials/centroidal.md",
  "Point Location" => "tutorials/point_location.md",
  "Nearest Neighbour Queries" => "tutorials/nearest.md",
  "Convex Hulls" => "tutorials/convex_hull.md",
  "Pole of Inaccessibility" => "tutorials/pole_of_inaccessibility.md",
  "Point-in-Polygon Testing" => "tutorials/point_in_polygon.md",
- "Using Custom Structs for Primitives and Boundaries" => "tutorials/custom_primitive.md"
+ "Using Custom Structs for Primitives and Boundaries" => "tutorials/custom_primitive.md",
  ],
  "Manual" => [
  "Overview" => "manual/overview.md",
@@ -168,7 +170,7 @@ const _PAGES = [
  "Data Structures" => "extended/data_structures.md",
  "Algorithm Internals" => "extended/algorithms.md",
  "Utility Functions" => "extended/utils.md",
- ], 
+ ],
  "Mathematical Details" => [
  "Overview" => "math/overview.md",
  "Delaunay Triangulations" => "math/delaunay.md",
@@ -221,34 +223,38 @@ end
 
 # Make and deploy
 makedocs(;
- modules=[DelaunayTriangulation],
- authors="Daniel VandenHeuvel <danj.vandenheuvel@gmail.com>",
- sitename="DelaunayTriangulation.jl",
- format=Documenter.HTML(;
- prettyurls=IS_CI,
- canonical="https://JuliaGeometry.github.io/DelaunayTriangulation.jl",
- edit_link="main",
- size_threshold=8000 * 2^10,
- size_threshold_warn=1000 * 2^10,
- size_threshold_ignore=["api/triangulation.md", "extended/data_structures.md"],
- collapselevel=1,
- assets=String[],
- mathengine=MathJax3(Dict(
- :loader => Dict("load" => ["[tex]/physics"]),
- :tex => Dict(
- "inlineMath" => [["\$", "\$"], ["\\(", "\\)"]],
- "tags" => "ams",
- "packages" => ["base", "ams", "autoload", "physics"],
+ modules = [DelaunayTriangulation],
+ authors = "Daniel VandenHeuvel <danj.vandenheuvel@gmail.com>",
+ sitename = "DelaunayTriangulation.jl",
+ format = Documenter.HTML(;
+ prettyurls = IS_CI,
+ canonical = "https://JuliaGeometry.github.io/DelaunayTriangulation.jl",
+ edit_link = "main",
+ size_threshold = 8000 * 2^10,
+ size_threshold_warn = 1000 * 2^10,
+ size_threshold_ignore = ["api/triangulation.md", "extended/data_structures.md"],
+ collapselevel = 1,
+ assets = String[],
+ mathengine = MathJax3(
+ Dict(
+ :loader => Dict("load" => ["[tex]/physics"]),
+ :tex => Dict(
+ "inlineMath" => [["\$", "\$"], ["\\(", "\\)"]],
+ "tags" => "ams",
+ "packages" => ["base", "ams", "autoload", "physics"],
+ ),
  ),
- ))),
- linkcheck=false,
- warnonly=true,
- draft=IS_LIVESERVER,
- pages=_PAGES,
- pagesonly=true,
+ ),
+ ),
+ linkcheck = false,
+ warnonly = true,
+ draft = IS_LIVESERVER,
+ pages = _PAGES,
+ pagesonly = true,
 )
 
 deploydocs(;
- repo="github.com/JuliaGeometry/DelaunayTriangulation.jl",
- devbranch="main",
- push_preview=true)
+ repo = "github.com/JuliaGeometry/DelaunayTriangulation.jl",
+ devbranch = "main",
+ push_preview = true,
+)

docs/src/api/triangulation.md

@@ -45,7 +45,6 @@ get_section_index
 map_ghost_vertex
 get_ghost_vertex_range
 all_ghost_vertices
-get_point
 num_points
 get_representative_point_coordinates
 compute_representative_points!

docs/src/applications/cell_simulations.md

@@ -54,7 +54,7 @@ using StatsBase
 using CairoMakie
 Base.@kwdef mutable struct CellModel{P}
  tri::Triangulation{P}
- new_r_cache::Vector{NTuple{2,Float64}} # for r(t + Δt)
+ new_r_cache::Vector{NTuple{2, Float64}} # for r(t + Δt)
  α::Float64
  s::Float64
  Δt::Float64
@@ -103,7 +103,7 @@ function polygon_area(points) # this is the same function from the Interpolation
  rx, ry = getxy(r)
  sx, sy = getxy(s)
  area = px * (qy - ry) + rx * (py - sy)
- for i in 2:(n-1)
+ for i in 2:(n - 1)
  p, q, r = get_point(points, i, i + 1, i - 1)
  px, py = getxy(p)
  qx, qy = getxy(q)
@@ -113,7 +113,7 @@ function polygon_area(points) # this is the same function from the Interpolation
  return area / 2
 end
 function get_voronoi_area(tri::Triangulation, i)
- points = NTuple{2,Float64}[]
+ points = NTuple{2, Float64}[]
  !DelaunayTriangulation.has_vertex(tri, i) && return (0.0, points) # might not be included anymore due to retriangulation
  DelaunayTriangulation.is_boundary_node(tri, i)[1] && return (0.0, points) # to prevent boundary cells from proliferating
  N = get_neighbours(tri, i)
@@ -157,7 +157,7 @@ function proliferate_cells!(cells::CellModel)
  δ = DelaunayTriangulation.distance_to_polygon(p, get_points(tri), poly)
  s, c = sincos(θ)
  q = p .+ (δ * cells.ϵ) .* (c, s)
- add_point!(tri, q; rng=cells.rng)
+ add_point!(tri, q; rng = cells.rng)
  push!(cells.new_r_cache, q)
  end
  return nothing
@@ -174,7 +174,7 @@ function perform_step!(cells::CellModel)
 end
 function simulate_cells(cells::CellModel)
  t = 0.0
- all_points = Vector{Vector{NTuple{2,Float64}}}()
+ all_points = Vector{Vector{NTuple{2, Float64}}}()
  push!(all_points, deepcopy(get_points(cells.tri)))
  while t < cells.final_time
  perform_step!(cells)
@@ -194,23 +194,27 @@ $\beta = 0.25$, $K = 100^2$, and $\epsilon = 0.5$.
 rng = StableRNG(123444)
 a, b, c, d = -2.0, 2.0, -5.0, 5.0
 points = [(a + (b - a) * rand(rng), c + (d - c) * rand(rng)) for _ in 1:10]
-tri = triangulate(points; rng=rng)
-cells = CellModel(; tri=tri, new_r_cache=similar(points), α=5.0, s=2.0, Δt=1e-3,
- β=0.25, K=100.0^2, rng, final_time=25.0, ϵ=0.5)
+tri = triangulate(points; rng = rng)
+cells = CellModel(;
+ tri = tri, new_r_cache = similar(points), α = 5.0, s = 2.0, Δt = 1.0e-3,
+ β = 0.25, K = 100.0^2, rng, final_time = 25.0, ϵ = 0.5,
+)
 results = simulate_cells(cells);
 
-fig = Figure(fontsize=26)
+fig = Figure(fontsize = 26)
 title_obs = Observable(L"t = %$(0.0)")
-ax1 = Axis(fig[1, 1], width=1200, height=400, title=title_obs, titlealign=:left)
+ax1 = Axis(fig[1, 1], width = 1200, height = 400, title = title_obs, titlealign = :left)
 Δt = cells.Δt
 i = Observable(1)
-voronoiplot!(ax1, @lift(voronoi(triangulate(results[$i]; rng), clip=true, rng=rng)),
- color=:darkgreen, strokecolor=:black, strokewidth=2, show_generators=false)
+voronoiplot!(
+ ax1, @lift(voronoi(triangulate(results[$i]; rng), clip = true, rng = rng)),
+ color = :darkgreen, strokecolor = :black, strokewidth = 2, show_generators = false,
+)
 xlims!(ax1, -12, 12)
 ylims!(ax1, -12, 12)
 resize_to_layout!(fig)
 t = 0:Δt:cells.final_time
-record(fig, "cell_simulation.mp4", 1:10:length(t); framerate=60) do ii
+record(fig, "cell_simulation.mp4", 1:10:length(t); framerate = 60) do ii
  i[] = ii
  title_obs[] = L"t = %$(((ii-1) * Δt))"
 end;
@@ -231,7 +235,7 @@ using StatsBase
 using CairoMakie
 Base.@kwdef mutable struct CellModel{P}
  tri::Triangulation{P}
- new_r_cache::Vector{NTuple{2,Float64}} # for r(t + Δt)
+ new_r_cache::Vector{NTuple{2, Float64}} # for r(t + Δt)
  α::Float64
  s::Float64
  Δt::Float64
@@ -270,7 +274,7 @@ function polygon_area(points) # this is the same function from the Interpolation
  rx, ry = getxy(r)
  sx, sy = getxy(s)
  area = px * (qy - ry) + rx * (py - sy)
- for i in 2:(n-1)
+ for i in 2:(n - 1)
  p, q, r = get_point(points, i, i + 1, i - 1)
  px, py = getxy(p)
  qx, qy = getxy(q)
@@ -280,7 +284,7 @@ function polygon_area(points) # this is the same function from the Interpolation
  return area / 2
 end
 function get_voronoi_area(tri::Triangulation, i)
- points = NTuple{2,Float64}[]
+ points = NTuple{2, Float64}[]
  !DelaunayTriangulation.has_vertex(tri, i) && return (0.0, points) # might not be included anymore due to retriangulation
  DelaunayTriangulation.is_boundary_node(tri, i)[1] && return (0.0, points) # to prevent boundary cells from proliferating
  N = get_neighbours(tri, i)
@@ -319,7 +323,7 @@ function proliferate_cells!(cells::CellModel)
  δ = DelaunayTriangulation.distance_to_polygon(p, get_points(tri), poly)
  s, c = sincos(θ)
  q = p .+ (δ * cells.ϵ) .* (c, s)
- add_point!(tri, q; rng=cells.rng)
+ add_point!(tri, q; rng = cells.rng)
  push!(cells.new_r_cache, q)
  end
  return nothing
@@ -332,7 +336,7 @@ function perform_step!(cells::CellModel)
 end
 function simulate_cells(cells::CellModel)
  t = 0.0
- all_points = Vector{Vector{NTuple{2,Float64}}}()
+ all_points = Vector{Vector{NTuple{2, Float64}}}()
  push!(all_points, deepcopy(get_points(cells.tri)))
  while t < cells.final_time
  perform_step!(cells)
@@ -345,23 +349,27 @@ end
 rng = StableRNG(123444)
 a, b, c, d = -2.0, 2.0, -5.0, 5.0
 points = [(a + (b - a) * rand(rng), c + (d - c) * rand(rng)) for _ in 1:10]
-tri = triangulate(points; rng=rng)
-cells = CellModel(; tri=tri, new_r_cache=similar(points), α=5.0, s=2.0, Δt=1e-3,
- β=0.25, K=100.0^2, rng, final_time=25.0, ϵ=0.5)
+tri = triangulate(points; rng = rng)
+cells = CellModel(;
+ tri = tri, new_r_cache = similar(points), α = 5.0, s = 2.0, Δt = 1.0e-3,
+ β = 0.25, K = 100.0^2, rng, final_time = 25.0, ϵ = 0.5,
+)
 results = simulate_cells(cells);
 
-fig = Figure(fontsize=26)
+fig = Figure(fontsize = 26)
 title_obs = Observable(L"t = %$(0.0)")
-ax1 = Axis(fig[1, 1], width=1200, height=400, title=title_obs, titlealign=:left)
+ax1 = Axis(fig[1, 1], width = 1200, height = 400, title = title_obs, titlealign = :left)
 Δt = cells.Δt
 i = Observable(1)
-voronoiplot!(ax1, @lift(voronoi(triangulate(results[$i]; rng), clip=true, rng=rng)),
- color=:darkgreen, strokecolor=:black, strokewidth=2, show_generators=false)
+voronoiplot!(
+ ax1, @lift(voronoi(triangulate(results[$i]; rng), clip = true, rng = rng)),
+ color = :darkgreen, strokecolor = :black, strokewidth = 2, show_generators = false,
+)
 xlims!(ax1, -12, 12)
 ylims!(ax1, -12, 12)
 resize_to_layout!(fig)
 t = 0:Δt:cells.final_time
-record(fig, "cell_simulation.mp4", 1:10:length(t); framerate=60) do ii
+record(fig, "cell_simulation.mp4", 1:10:length(t); framerate = 60) do ii
  i[] = ii
  title_obs[] = L"t = %$(((ii-1) * Δt))"
 end;