Julia 0.4 only

.gitignore

@@ -0,0 +1 @@
+.DS_Store

.travis.yml

@@ -2,7 +2,7 @@ language: julia
 os:
   - linux
 julia:
-  - release
+  - 0.4
   - nightly
 notifications:
   email: false
@@ -12,4 +12,4 @@ script:
   - julia -e 'Pkg.clone(pwd()); Pkg.build("GraphLayout")'
   - julia -e 'Pkg.test("GraphLayout"; coverage=true)'
 after_success:
-  - julia -e 'cd(Pkg.dir("GraphLayout")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
+  - julia -e 'cd(Pkg.dir("GraphLayout")); Pkg.add("Coverage"); using Coverage; Codecov.submit(process_folder())'

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2014 Iain Dunning
+Copyright (c) 2015 Iain Dunning
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

README.md

@@ -4,10 +4,11 @@ Graph layout and visualization algorithms, implemented in Julia.
 
 [![GraphLayout](http://pkg.julialang.org/badges/GraphLayout_0.3.svg)](http://pkg.julialang.org/?pkg=GraphLayout&ver=0.3)
 [![GraphLayout](http://pkg.julialang.org/badges/GraphLayout_0.4.svg)](http://pkg.julialang.org/?pkg=GraphLayout&ver=0.4)
+[![GraphLayout](http://pkg.julialang.org/badges/GraphLayout_0.4.svg)](http://pkg.julialang.org/?pkg=GraphLayout&ver=0.5)
 
-**Development version**: 
-[![Build Status](https://travis-ci.org/IainNZ/GraphLayout.jl.svg)](https://travis-ci.org/IainNZ/GraphLayout.jl)
-[![Coverage Status](https://img.shields.io/coveralls/IainNZ/GraphLayout.jl.svg)](https://coveralls.io/r/IainNZ/GraphLayout.jl)
+**Development version**:
+[![Build Status](https://travis-ci.org/IainNZ/GraphLayout.jl.svg?branch=master)](https://travis-ci.org/IainNZ/GraphLayout.jl)
+[![codecov.io](https://codecov.io/github/IainNZ/GraphLayout.jl/coverage.svg?branch=master)](https://codecov.io/github/IainNZ/GraphLayout.jl?branch=master)
 
 
 The package currently implements the following layout methods:

REQUIRE

@@ -1,5 +1,3 @@
-julia 0.3
-Docile
+julia 0.4
 Requires
-Compose
-Compat
+Compose 0.4

src/GraphLayout.jl

@@ -1,13 +1,8 @@
-
-VERSION >= v"0.4.0" && __precompile__(true)
+__precompile__(true)
 
 module GraphLayout
-    if VERSION < v"0.4.0"
-        using Docile
-    end
     using Requires  # to optionally load JuMP
-    using Compose  # for plotting features
-    using Compat # for v0.3 compatibility
+    using Compose   # for plotting features
 
     typealias AdjList{T} Vector{Vector{T}}
 
@@ -26,7 +21,7 @@ module GraphLayout
     include("tree_heur.jl")
     # Optimal algorithms for tree layout, that require JuMP
     # These methods will be loaded when JuMP is loaded
-    _ordering_ip(args...) = 
+    _ordering_ip(args...) =
         error("JuMP package must be loaded for optimization tree layout")
     @require JuMP include("tree_opt.jl")
 

src/draw.jl

@@ -1,10 +1,10 @@
 using Compose
 import Colors
-@compat typealias ComposeColor Union{Colors.Color, 
-                                     Colors.AlphaColor, 
-                                     Colors.AbstractString}
+typealias ComposeColor Union{Colors.Color,
+                             Colors.AlphaColor,
+                             Colors.AbstractString}
 
-@doc """
+"""
 Given an adjacency matrix and two vectors of X and Y coordinates, returns
 a Compose tree of the graph layout
 
@@ -22,7 +22,7 @@ Arguments:
                      Set to 0 for no arrows. Default: 0.1
     angleoffset      angular width in radians for the arrows. Default: π/9 (20 degrees).
 
-""" ->
+"""
 function compose_layout_adj{S, T<:Real}(
     adj_matrix::Array{S,2},
     locs_x::Vector{T}, locs_y::Vector{T};
@@ -113,12 +113,10 @@ function lineij(locs_x, locs_y, i, j, NODESIZE, ARROWLENGTH, angleoffset)
     return composenode
 end
 
-@doc """
+"""
 Given an adjacency matrix and two vectors of X and Y coordinates, returns
 an SVG of the graph layout.
 
-Requires Compose.jl
-
 Arguments:
     adj_matrix       Adjacency matrix of some type. Non-zero of the eltype
                      of the matrix is used to determine if a link exists,
@@ -134,7 +132,7 @@ Arguments:
     arrowlengthfrac  Fraction of line length to use for arrows.
                      Set to 0 for no arrows. Default: 0.1
     angleoffset      angular width in radians for the arrows. Default: π/9 (20 degrees).
-""" ->
+"""
 function draw_layout_adj{S, T<:Real}(
     adj_matrix::Array{S,2},
     locs_x::Vector{T}, locs_y::Vector{T};

src/spring.jl

@@ -1,4 +1,4 @@
-@doc """
+"""
     Use the spring/repulsion model of Fruchterman and Reingold (1991):
         Attractive force:  f_a(d) =  d^2 / k
         Repulsive force:  f_r(d) = -k^2 / d
@@ -13,7 +13,7 @@
     C          Constant to fiddle with density of resulting layout
     MAXITER    Number of iterations we apply the forces
     INITTEMP   Initial "temperature", controls movement per iteration
-""" ->
+"""
 function layout_spring_adj{T}(adj_matrix::Array{T,2}; C=2.0, MAXITER=100, INITTEMP=2.0)
 
     size(adj_matrix, 1) != size(adj_matrix, 2) && error("Adj. matrix must be square.")

src/stress.jl

@@ -1,4 +1,4 @@
-@doc """
+"""
 Compute graph layout using stress majorization
 
 Inputs:
@@ -51,7 +51,7 @@ Reference:
         publisher={Springer Berlin Heidelberg},
         pages={239--250},
     }
-""" ->
+"""
 function layout_stressmajorize_adj(δ, p::Int=2, w=nothing, X0=randn(size(δ, 1), p);
         maxiter = 400size(X0, 1)^2, abstols=√(eps(eltype(X0))),
         reltols=√(eps(eltype(X0))), abstolx=√(eps(eltype(X0))),
@@ -162,5 +162,3 @@ function LZ(Z, d, w)
     @assert all(isfinite(L))
     L
 end
-
-

src/tree.jl

@@ -1,13 +1,4 @@
-# Uses a macro to switch between .abs and .value depending on Compose version
-macro raw_measure(m)
-    if Pkg.installed("Compose") > v"0.3.18"
-        return :($m.value)
-    else
-        return :($m.abs)
-    end
-end
-
-@doc """
+"""
     Hierachical drawing of directed graphs inspired by the Sugiyama framework.
     In particular see Chapter 13 of 'Hierachical Drawing Algorithms' from
     the 'Handbook of Graph Drawing and Visualization' and the article
@@ -44,7 +35,7 @@ end
     labelpad        Padding around text in vertices
     background      Defaults to nothing. If not-nothing, that value
                     will be used for the background color
-""" ->
+"""
 function layout_tree{T}(adj_list::AdjList{T},
                         labels::Vector;
                         filename    = "",
@@ -87,7 +78,7 @@ function layout_tree{T}(adj_list::AdjList{T},
     elseif ordering == :optimal
         layer_verts = _ordering_ip(adj_list, layers, layer_verts)
     end
-    
+
 
     # 4     Vertex coordinates [to straighten edges]
     # 4.1   Place y coordinates in layers
@@ -108,8 +99,8 @@ function layout_tree{T}(adj_list::AdjList{T},
     if length(labels) == orig_n
         extents = text_extents("sans",10pt,labels...)
         for (i,(width,height)) in enumerate(extents)
-            widths[i] = @raw_measure width
-            heights[i] = @raw_measure height
+            widths[i]  = width.value
+            heights[i] = height.value
         end
     end
     locs_x = _coord_ip(adj_list, layers, layer_verts, orig_n, widths, xsep)

src/tree_heur.jl

@@ -1,9 +1,9 @@
-@doc """
+"""
     Assigns layers using the longest path method.
 
     Arguments:
     adj_list        Directed graph in adjacency list format
-""" ->
+"""
 function _layer_assmt_longestpath{T}(adj_list::AdjList{T})
     n = length(adj_list)
     layers = fill(-1, n)
@@ -142,4 +142,4 @@ function _ordering_barycentric{T}(adj_list::AdjList{T}, layers, layer_verts)
     end
 
     return layer_verts
-end
+end

src/tree_opt.jl

@@ -9,7 +9,7 @@ using JuMP
 ########################################################################
 
 
-@doc """
+"""
     Given a layer assignment, decide a permutation for each layer
     that minimizes edge crossings using integer programming.
 
@@ -28,7 +28,7 @@ using JuMP
 
     Returns:
     new_layer_verts An improved dictionary of layer => vertices (opt. perm.)
-""" ->
+"""
 function _ordering_ip{T}(adj_list::AdjList{T}, layers, layer_verts)
     num_layers = maximum(layers)
 
@@ -145,7 +145,7 @@ function _coord_ip{T}(adj_list::AdjList{T}, layers, layer_verts, orig_n, widths,
         for i in 1:length(layer_verts[L])-1
             a = layer_verts[L][i]
             b = layer_verts[L][i+1]
-            @addConstraint(m, x[L,b] - x[L,a] >= 
+            @addConstraint(m, x[L,b] - x[L,a] >=
                 (widths[a] + widths[b])/2 + xsep)
         end
     end

test/REQUIRE

@@ -1,4 +1,3 @@
 FactCheck
 JuMP
-Cbc
-Clp
+GLPKMathProgInterface