Merge pull request #9 from timbitz/master

Update for Julia 1.0

.travis.yml

@@ -3,7 +3,7 @@ os:
   - linux
   - osx
 julia:
-  - 0.5
+  - 1.0
   - nightly
 notifications:
   email: false

README.md

@@ -6,7 +6,9 @@ A Julia interface to working with [Suffix Arrays](http://en.wikipedia.org/wiki/S
 
 You can use the package by running:
 ```julia
-Pkg.add("SuffixArrays")
+using Pkg
+add("SuffixArrays")
+#Pkg.add("SuffixArrays") for julia prior to v0.7
 using SuffixArrays
 sa = suffixsort("banana")
 sa.index # access the underlying sorted suffix array; returned indices are currently 0-based

REQUIRE

@@ -1 +1 @@
-julia 0.5
+julia 1.0

src/SuffixArrays.jl

@@ -2,13 +2,13 @@ module SuffixArrays
 
 export suffixsort
 
-immutable SuffixArray{S<:AbstractString,N<:Signed}
+struct SuffixArray{S<:AbstractString,N<:Signed}
     string::S
     n::Int
     index::Array{N,1}
 end
 
-function SuffixArray{S}(s::S)
+function SuffixArray(s::S) where S <: AbstractString
     n = length(s)
     index = zeros(n <= typemax(Int8)  ? Int8  : 
                   n <= typemax(Int16) ? Int16 : 

src/sais.jl

@@ -25,7 +25,7 @@
  =#
 
 #= Suffixsorting =#
-type IntArray
+mutable struct IntArray
     a::Array{Int,1}
     pos::Int
 end

test/runtests.jl

@@ -1,12 +1,12 @@
 using SuffixArrays
-using Base.Test
+using Test
+
+readstring(s) = read(s, String) 
 
 function test_suffix(args)
     for file in args
         T = open(readstring,file)
-        tic()
-        SA = suffixsort(T)
-        t = toq()
+        t = @elapsed SA = suffixsort(T)
         println("Sorting '$file' took: $t")
         @test sufcheck(T,SA.index) == 0
     end
@@ -69,6 +69,12 @@ function sufcheck(T,SA)
     return 0
 end
 
+function initwalk(dir, files)
+   files = walkdir("$dir/src", files)
+   files = walkdir("$dir/test", files)
+   files
+end
+
 function walkdir(dir,files)
     t = readdir(dir)
     for f in t
@@ -83,5 +89,5 @@ function walkdir(dir,files)
     return unique(files)
 end
 
-files = walkdir(dirname(dirname(@__FILE__)),[])
+files = initwalk(dirname(dirname(@__FILE__)),[])
 test_suffix(files)