Add tests and CI (#2)

.travis.yml

@@ -11,11 +11,11 @@ notifications:
 git:
   depth: 99999999
 
-## uncomment the following lines to allow failures on nightly julia
-## (tests will run but not make your overall status red)
-#matrix:
-#  allow_failures:
-#  - julia: nightly
+# uncomment the following lines to allow failures on nightly julia
+# (tests will run but not make your overall status red)
+matrix:
+ allow_failures:
+ - julia: nightly
 
 ## uncomment and modify the following lines to manually install system packages
 #addons:
@@ -25,8 +25,8 @@ git:
 #before_script: # homebrew for mac
 #  - if [ $TRAVIS_OS_NAME = osx ]; then brew install gcc; fi
 
-## uncomment the following lines to override the default test script
-#script:
+# # uncomment the following lines to override the default test script
+# script:
 #  - julia -e 'Pkg.clone(pwd()); Pkg.build("Microbiome"); Pkg.test("Microbiome"; coverage=true)'
 after_success:
   # push coverage results to Coveralls

README.md

@@ -1,3 +1,5 @@
+[![Build Status](https://travis-ci.org/kescobo/Microbiome.jl.svg?branch=master)](https://travis-ci.org/kescobo/Microbiome.jl)
+
 # Microbiome-related methods for julia
 
 This package provides (or will provide) methods for microbial community

REQUIRE

@@ -2,6 +2,5 @@ julia 0.6-
 RecipesBase
 Distances
 DataFrames
-IterTools
-MultivariateStats
 Clustering
+Colors

src/Microbiome.jl

@@ -11,12 +11,11 @@ export
     getrowdm,
     pcoa,
     eigenvalue,
-    principalcoord
+    principalcoord,
+    relativeabundance
 
-using BioSequences
 using RecipesBase
 using Distances
-using IterTools
 using Colors
 
 using DataFrames: DataFrame

src/abundances.jl

@@ -51,7 +51,7 @@ function relativeabundance(a::AbundanceTable; kind::Symbol=:fraction)
     kind == :percent ? relab = relab .* 100 : true
 
     return AbundanceTable(
-        reshape([a[x,i] / sum(a[:,i]) for i in 1:size(a, 2) for x in 1:size(a, 1) ], size(a, 1), size(a, 2)),
+        reshape(relab, size(a, 1), size(a, 2)),
         a.samples,
         a.features)
 end

test/runtests.jl

@@ -1,4 +1,5 @@
 using Microbiome
+using Distances
 using Base.Test
 
 @testset "Abundances" begin
@@ -12,10 +13,11 @@ using Base.Test
 
     @test typeof(relab_fract) <: AbundanceTable
     @test typeof(relab_perc) <: AbundanceTable
-    @test typeof(relab_filt) <: AbundanceTable
+    @test typeof(filt) <: AbundanceTable
 
     @test size(abund) == (100, 10)
     @test size(relab_fract) == (100, 10)
+    @test size(relab_perc) == (100, 10)
     @test size(filt) == (6, 10)
 
     for i in 1:10
@@ -28,7 +30,11 @@ using Base.Test
 end
 
 @testset "Distances" begin
-    dm = getdm(abund, BrayCurtis())
+    abund = AbundanceTable(
+        rand(100, 10), ["sample_$x" for x in 1:10],
+        ["feature_$x" for x in 1:100])
+
+    dm = getdm(abund, Jaccard()) # TODO: change to BrayCurtis after PR merges in Distances.jl
     p = pcoa(dm, correct_neg=true)
 
     @test size(dm) == (10, 10)