add tests, requirements

Author: olgabot

.travis.yml

@@ -0,0 +1,38 @@
+language: python
+
+env:
+  - PYTHON=2.7
+  - PYTHON=2.7
+  - PYTHON=3.3
+  - PYTHON=3.4
+
+install:
+  - conda update conda --yes
+  - conda create -n testenv --yes pip python=$PYTHON
+  - conda update conda --yes
+  - source activate testenv
+  - conda install --yes --file requirements.txt
+  - python combat.py
+  - python test.py
+
+before_install:
+  - sudo apt-get update -yq
+  - sudo sh -c "echo ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula select true | debconf-set-selections"
+  - sudo apt-get install msttcorefonts -qq
+  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b
+  - export PATH=/home/travis/miniconda/bin:$PATH
+
+before_script:
+  - conda install --yes -c r r
+
+script:
+  - nosetests --with-doctest
+  # Notebook tests are failing on old matplotlib
+  # because the figures have every so slightly a
+  # different size. Skip until I understand why.
+  - if [ ${DEPS} == modern ] && [ ${PYTHON} != 3.4 ]; then
+    python ipnbdoctest.py examples/*.ipynb;
+    fi
+

R-combat.R

@@ -1,3 +1,5 @@
+source("http://bioconductor.org/biocLite.R")
+biocLite("sva")
 library("sva")
 options(stringsAsFactors=FALSE)
 

requirements.txt

@@ -0,0 +1,2 @@
+pandas
+patsy

test.py

@@ -0,0 +1,8 @@
+#!/usr/bin/env python
+
+import pandas as pd
+
+p = pd.read_table('py-batch.txt', index_col=0)
+r = pd.read_table('r-batch.txt', index_col=0)
+
+assert (p - r).max().max() < 1e-4