TST: adds coveralls

.coveragerc

@@ -0,0 +1,19 @@
+# this file is based on the examples provided on scikit-learn's .coveragerc
+# and is adapted from scikit-bio's .coveragerc
+
+[run]
+omit =
+    */tests*
+    */__init__.py
+source = sourcetracker
+branch = True
+include = */sourcetracker/*
+
+[report]
+exclude_lines =
+    pragma: no cover
+    raise NotImplementedError
+    if __name__ == .__main__.:
+omit =
+    */tests*
+    */__init__.py

.gitignore

@@ -69,3 +69,4 @@ target/
 # example output
 data/tiny-test/mixing_proportions
 data/tiny-test/source_loo
+data/tiny-test/example*

.travis.yml

@@ -12,11 +12,14 @@ before_install:
 install:
   - conda create --yes -n st2 python=$PYTHON_VERSION nose numpy scipy h5py flake8 scikit-bio=0.4.0
   - source activate st2
+  - pip install coveralls
   - pip install .
 script:
-  - nosetests
+  - nosetests --with-coverage
   - flake8 sourcetracker setup.py
   - sourcetracker2 gibbs --help
   - cd data/tiny-test/
   - sourcetracker2 gibbs -i otu_table.biom -m map.txt -o example1/
   - sourcetracker2 gibbs -i otu_table.biom -m alt-map.txt -o example2/ --source_sink_column source-or-sink --source_column_value src --sink_column_value snk --source_category_column sample-type
+after_success:
+  - coveralls

README.md

@@ -1,6 +1,5 @@
-[![Build Status](https://travis-ci.org/biota/sourcetracker2.svg?branch=master)](https://travis-ci.org/biota/sourcetracker2)
-
 # SourceTracker2
+[![Build Status](https://travis-ci.org/biota/sourcetracker2.svg?branch=master)](https://travis-ci.org/biota/sourcetracker2) [![Coverage Status](https://coveralls.io/repos/github/biota/sourcetracker2/badge.svg)](https://coveralls.io/github/biota/sourcetracker2)
 
 SourceTracker was originally described in [Knights et al., 2011](http://www.ncbi.nlm.nih.gov/pubmed/21765408).
 If you use this package, please cite the original SourceTracker paper linked