From 2e01b31ef6ac4b940e1418d6aca45478ca4e7815 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <tim@poisotlab.io>
Date: Mon, 7 Sep 2015 22:24:59 -0400
Subject: [PATCH 1/3] Identation and readme

---
 README.md                 | 5 +++--
 test/reorder_by_module.jl | 5 ++++-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index fbd5583..61e4983 100644
--- a/README.md
+++ b/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.
diff --git a/test/reorder_by_module.jl b/test/reorder_by_module.jl
index 1299821..e42f928 100644
--- a/test/reorder_by_module.jl
+++ b/test/reorder_by_module.jl
@@ -1,11 +1,14 @@
 module TestReorderByModule
   using Base.Test
   using Brim
-  #=testdir = dirname(@__FILE__)=#
+
   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
+
 end

From 8d0e0c9b48c8901d39b6042d2e846618d452140e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <tim@poisotlab.io>
Date: Mon, 7 Sep 2015 22:45:51 -0400
Subject: [PATCH 2/3] New tests for reorder_by_module

---
 REQUIRE                   |  2 +-
 src/Brim.jl               |  2 +-
 test/reorder_by_module.jl | 12 ++++++++++++
 3 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/REQUIRE b/REQUIRE
index f209d7d..c65980e 100644
--- a/REQUIRE
+++ b/REQUIRE
@@ -1,6 +1,6 @@
 julia 0.3
 Cairo
-Color 0.2.10-
+Colors
 DataFrames
 Lexicon
 Logging
diff --git a/src/Brim.jl b/src/Brim.jl
index 5f1cfa6..3a20ab5 100644
--- a/src/Brim.jl
+++ b/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)
diff --git a/test/reorder_by_module.jl b/test/reorder_by_module.jl
index e42f928..436a0f6 100644
--- a/test/reorder_by_module.jl
+++ b/test/reorder_by_module.jl
@@ -2,6 +2,8 @@ module TestReorderByModule
   using Base.Test
   using Brim
 
+  # 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]
@@ -11,4 +13,14 @@ module TestReorderByModule
   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

From b325d26a369f5fa67195517aae819205b007f5d9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <tim@poisotlab.io>
Date: Mon, 7 Sep 2015 22:48:42 -0400
Subject: [PATCH 3/3] Ensure that all swapped submatrices are 2x2

---
 src/permutations.jl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/permutations.jl b/src/permutations.jl
index 3aa64a6..e7ae6cc 100644
--- a/src/permutations.jl
+++ b/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