fix all the things

Author: SimonDanisch

.travis.yml

@@ -2,23 +2,14 @@
 language: julia
 os:
   - linux
-  - osx
-
 julia:
-  - 1.0
-  - 1.5
+  - 1.3
+  - 1
   - nightly
-
 matrix:
   allow_failures:
     - julia: nightly
-
+if: branch = master OR tag IS present OR type = pull_request
 notifications:
   email: false
-
-# uncomment the following lines to override the default test script
-script:
-  - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
-  - julia -e 'using Pkg; Pkg.clone(pwd()); Pkg.build("NetworkLayout"); Pkg.clone("LightGraphs"); Pkg.test("NetworkLayout"; coverage=true)'
-after_success:
-  - julia -e 'using Pkg; cd(Pkg.dir("NetworkLayout")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(process_folder()); Codecov.submit(process_folder())'
+codecov: true

Manifest.toml

@@ -0,0 +1,140 @@
+# This file is machine-generated - editing it directly is not advised
+
+[[Adapt]]
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "42c42f2221906892ceb765dbcb1a51deeffd86d7"
+uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
+version = "2.3.0"
+
+[[Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[DataAPI]]
+git-tree-sha1 = "176e23402d80e7743fc26c19c681bfb11246af32"
+uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
+version = "1.3.0"
+
+[[DataValueInterfaces]]
+git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
+uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464"
+version = "1.0.0"
+
+[[Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[Distributed]]
+deps = ["Random", "Serialization", "Sockets"]
+uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+
+[[EarCut_jll]]
+deps = ["Libdl", "Pkg"]
+git-tree-sha1 = "eabac56550a7d7e0be499125673fbff560eb8b20"
+uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5"
+version = "2.1.5+0"
+
+[[GeometryBasics]]
+deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"]
+git-tree-sha1 = "876a906eab3be990fdcbfe1e43bb3a76f4776f72"
+uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
+version = "0.3.3"
+
+[[InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[IterTools]]
+git-tree-sha1 = "05110a2ab1fc5f932622ffea2a003221f4782c18"
+uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
+version = "1.3.0"
+
+[[IteratorInterfaceExtensions]]
+git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
+uuid = "82899510-4779-5014-852e-03e436cf321d"
+version = "1.0.0"
+
+[[LibGit2]]
+deps = ["Printf"]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+
+[[LinearAlgebra]]
+deps = ["Libdl"]
+uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[[Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[Pkg]]
+deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+
+[[Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[Random]]
+deps = ["Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+
+[[Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+
+[[SparseArrays]]
+deps = ["LinearAlgebra", "Random"]
+uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[[StaticArrays]]
+deps = ["LinearAlgebra", "Random", "Statistics"]
+git-tree-sha1 = "016d1e1a00fabc556473b07161da3d39726ded35"
+uuid = "90137ffa-7385-5640-81b9-e52037218182"
+version = "0.12.4"
+
+[[Statistics]]
+deps = ["LinearAlgebra", "SparseArrays"]
+uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
+[[StructArrays]]
+deps = ["Adapt", "DataAPI", "Tables"]
+git-tree-sha1 = "8099ed9fb90b6e754d6ba8c6ed8670f010eadca0"
+uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
+version = "0.4.4"
+
+[[TableTraits]]
+deps = ["IteratorInterfaceExtensions"]
+git-tree-sha1 = "b1ad568ba658d8cbb3b892ed5380a6f3e781a81e"
+uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
+version = "1.0.0"
+
+[[Tables]]
+deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"]
+git-tree-sha1 = "24a584cf65e2cfabdadc21694fb69d2e74c82b44"
+uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
+version = "1.1.0"
+
+[[Test]]
+deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[UUIDs]]
+deps = ["Random", "SHA"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+
+[[Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

Project.toml

@@ -3,12 +3,11 @@ uuid = "46757867-2c16-5918-afeb-47bfcb05e46a"
 version = "0.3.0"
 
 [deps]
-GeometryTypes = "4d00f742-c7ba-57c2-abde-4428a4b178cb"
+GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [compat]
-GeometryTypes = "0.8.3"
 julia = "1"
 
 [extras]

appveyor.yml

@@ -12,7 +12,7 @@ positions     co-ordinates of the layout
 """
 module Buchheim
 
-using GeometryTypes
+using GeometryBasics
 
 struct Tree{A<:AbstractVector,P<:AbstractVector,F}
     nodes::A

src/buchheim.jl

@@ -16,18 +16,18 @@ julia> locs_x, locs_y = circular_layout(g)
 """
 module Circular
 
-using GeometryTypes
+using GeometryBasics
 
 function layout(adj_matrix::AbstractMatrix)
     layout!(adj_matrix)
 end
 
 function layout!(adj_matrix::AbstractMatrix)
-    if size(adj_matrix,1) == 1
+    if size(adj_matrix, 1) == 1
         return Point{2,Float64}[Point(0.0, 0.0)]
     else
         # Discard the extra angle since it matches 0 radians.
-        θ = range(0, stop=2pi, length=size(adj_matrix,1) + 1)[1:end-1]
+        θ = range(0, stop=2pi, length=size(adj_matrix, 1) + 1)[1:end - 1]
         return Point{2,Float64}[(cos(o), sin(o)) for o in θ]
     end
 end

src/circular.jl

@@ -13,10 +13,10 @@ Output :
 """
 module SFDP
 
-using GeometryTypes
+using GeometryBasics
 using LinearAlgebra: norm
 
-struct Layout{M<:AbstractMatrix, P<:AbstractVector, T<:AbstractFloat}
+struct Layout{M <: AbstractMatrix,P <: AbstractVector,T <: AbstractFloat}
     adj_matrix::M
     positions::P
     tol::T
@@ -26,27 +26,27 @@ struct Layout{M<:AbstractMatrix, P<:AbstractVector, T<:AbstractFloat}
 end
 
 function Layout(
-        adj_matrix, PT::Type{Point{N, T}}=Point{2, Float64};
-        startpositions=(2*rand(typ, size(adj_matrix,1)) .- 1),
+        adj_matrix, PT::Type{Point{N,T}}=Point{2,Float64};
+        startpositions=map(x -> 2 .* rand(PT) .- 1, 1:size(adj_matrix, 1)),
         tol=1.0, C=0.2, K=1.0, iterations=100
-    ) where {N, T}
+    ) where {N,T}
     Layout(adj_matrix, startpositions, T(tol), T(C), T(K), Int(iterations))
 end
 
 layout(adj_matrix, dim::Int; kw_args...) = layout(adj_matrix, Point{dim,Float64}; kw_args...)
 
 function layout(
-        adj_matrix, typ::Type{Point{N, T}}=Point{2, Float64};
-        startpositions = (2*rand(typ, size(adj_matrix,1)) .- 1),
+        adj_matrix, PT::Type{Point{N,T}}=Point{2,Float64};
+        startpositions=map(x -> 2 .* rand(PT) .- 1, 1:size(adj_matrix, 1)),
         kw_args...
-    ) where {N, T}
-    layout!(adj_matrix,startpositions;kw_args...)
+    ) where {N,T}
+    layout!(adj_matrix, startpositions; kw_args...)
 end
 
 function layout!(adj_matrix,
-         startpositions::AbstractVector{Point{N, T}};
+         startpositions::AbstractVector{Point{N,T}};
          kw_args...
-    ) where {N, T}
+    ) where {N,T}
     network = Layout(adj_matrix, Point{N,T}; startpositions=startpositions, kw_args...)
     next = iterate(network)
     while next != nothing
@@ -60,7 +60,7 @@ end
 # then it could take a long time. Furthermore I'm not sure if the iterators are
 # the best solution in this situation
 
-function iterate(network::Layout{M, P, T}) where {M, P, T}
+function iterate(network::Layout{M,P,T}) where {M,P,T}
     return network, (one(T), typemax(T), 0, true, 1, copy(network.positions))
 end
 
@@ -69,20 +69,20 @@ function iterate(network::Layout, state)
     K, C, tol, adj_matrix = network.K, network.C, network.tol, network.adj_matrix
     locs = network.positions; locs0 = copy(locs)
     energy0 = energy; energy = zero(energy)
-    F = eltype(locs); N = size(adj_matrix,1)
+    F = eltype(locs); N = size(adj_matrix, 1)
     for i in 1:N
         force = F(0)
         for j in 1:N
             i == j && continue
             if adj_matrix[i,j] == 1
             # Attractive forces for adjacent nodes
-                force += F(f_attr(locs[i],locs[j],K) * ((locs[j] - locs[i]) / norm(locs[j] - locs[i])))
+                force += F(f_attr(locs[i], locs[j], K) .* ((locs[j] .- locs[i]) / norm(locs[j] .- locs[i])))
             else
             # Repulsive forces
-                force += F(f_repln(locs[i],locs[j],C,K) * ((locs[j] - locs[i]) / norm(locs[j] - locs[i])))
+                force += F(f_repln(locs[i], locs[j], C, K) .* ((locs[j] .- locs[i]) / norm(locs[j] .- locs[i])))
             end
         end
-        locs[i] = locs[i] + step * (force / norm(force))
+        locs[i] = locs[i] .+ step .* (force ./ norm(force))
         energy = energy + norm(force)^2
     end
     step, progress = update_step(step, energy, energy0, progress)
@@ -92,13 +92,13 @@ function iterate(network::Layout, state)
         return nothing
     end
 
-    return network, (step, energy, progress, false, iter+1, locs0)
+    return network, (step, energy, progress, false, iter + 1, locs0)
 end
 
 # Calculate Attractive force
-f_attr(a, b, K) = (norm(a-b)^2) / K
+f_attr(a, b, K) = (norm(a .- b).^2) ./ K
 # Calculate Repulsive force
-f_repln(a, b, C, K) = -C*(K^2) / norm(a-b)
+f_repln(a, b, C, K) = -C .* (K^2) / norm(a .- b)
 
 function update_step(step, energy::T, energy0, progress) where {T}
     # cooldown step
@@ -107,7 +107,7 @@ function update_step(step, energy::T, energy0, progress) where {T}
         progress = progress + 1
         if progress >= 5
             progress = 0
-            step = step/t
+            step = step / t
         end
     else
         progress = 0
@@ -116,14 +116,14 @@ function update_step(step, energy::T, energy0, progress) where {T}
     return step, progress
 end
 
-function dist_tolerance(locs,locs0, K, tol)
+function dist_tolerance(locs, locs0, K, tol)
     # check whether the layout is optimal
     for i in 1:size(locs, 1)
-        if norm(locs[i]-locs0[i]) >= K*tol
+        if norm(locs[i] .- locs0[i]) >= K * tol
             return false
         end
     end
     return true
 end
 
-end #end of module
+end # end of module