Merge pull request #12 from PoisotLab/dev-reorder

✅  new tests

README.md

@@ -6,5 +6,6 @@
 [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.16579.svg)](http://dx.doi.org/10.5281/zenodo.16579)
 [![Documentation Status](https://readthedocs.org/projects/brimjl/badge/?version=latest)](https://readthedocs.org/projects/brimjl/?badge=latest)
 
-Various ways to optimize the modularity of bipartite networks using BRIM in
-`Julia`. General purpose, but mostly used for biological and ecological datasets.
+This package offers ways to optimize the modularity of bipartite networks using
+BRIM in `Julia`. It should be reasonably general purpose, but has only be used
+for biological and ecological datasets so far.

REQUIRE

@@ -1,6 +1,6 @@
 julia 0.3
 Cairo
-Color 0.2.10-
+Colors
 DataFrames
 Lexicon
 Logging

src/Brim.jl

@@ -2,7 +2,7 @@ module Brim
 
 # Dependencies
 using Cairo
-using Color
+using Colors
 using DataFrames
 using Logging
 Logging.configure(output=open("brim.log", "a"), level=INFO)

src/permutations.jl

@@ -33,7 +33,7 @@ end
 Performs a constrained swap: the marginals are conserved.
 """
 function constrained_swap(A::Array{Int64, 2})
-  # TODO checks
+  @assert size(A) == (2, 2)
   const c1 = [1 0; 0 1]
   const c2 = [0 1; 1 0]
   if A == c2
@@ -48,6 +48,7 @@ Perfoms a free swap: the matrix cells are shuffled. The marginals are not
 (necessarily) conserved.
 """
 function free_swap(A::Array{Int64, 2})
+  @assert size(A) == (2, 2)
   return reshape(A[shuffle([1, 2, 3, 4])], (2, 2))
 end
 

test/reorder_by_module.jl

@@ -1,11 +1,26 @@
 module TestReorderByModule
   using Base.Test
   using Brim
-  #=testdir = dirname(@__FILE__)=#
+
+  # Test 1 - simple case
+
   A = [1 0 0; 0 0 1; 0 1 0]
   S = [0 1 0; 1 0 0; 0 0 1; 0 1 0; 0 0 1; 0 0 1]
   C = [1 0 0; 0 1 0; 0 0 1; 0 1 0; 0 0 1; 0 0 1]
+
   M = no_empty_modules!(Modular(A, S))
+
   reorder_by_module!(M)
   @test sum(abs(M.S .- C)) == 0
+
+  # Test 2 - more complex case
+
+  A = [0 0 0 1 1 1; 1 1 1 0 0 0; 0 0 0 1 1 1; 1 1 1 0 0 0; 0 0 0 1 1 1; 1 1 1 0 0 0]
+  M = recursive_brim!(partition_random(A))
+  reorder_by_module!(M)
+
+  target = [1 0; 1 0; 1 0; 0 1; 0 1; 0 1; 1 0; 1 0; 1 0; 0 1; 0 1; 0 1]
+
+  @test hash(M.S) == hash(target)
+
 end