From a07bdd5d2a388b0ea8cedf4470286ae8e67561ee Mon Sep 17 00:00:00 2001
From: Jamie Morton <jamietmorton@gmail.com>
Date: Wed, 6 Jul 2016 11:13:20 -0700
Subject: [PATCH] Updating travis

---
 .coveragerc        | 18 ++++++++++++++++++
 .travis.yml        |  5 ++++-
 Makefile           |  6 +++++-
 README.md          |  4 ++++
 gneiss/balances.py | 40 ++++++++++++++++++++++++++++++++++++++--
 5 files changed, 69 insertions(+), 4 deletions(-)
 create mode 100644 .coveragerc

diff --git a/.coveragerc b/.coveragerc
new file mode 100644
index 0000000..a2831f1
--- /dev/null
+++ b/.coveragerc
@@ -0,0 +1,18 @@
+# this file is based on the examples provided on scikit-learn's .coveragerc
+
+[run]
+omit =
+    */tests*
+    */__init__.py
+source = gneiss
+branch = True
+include = */gneiss/*
+
+[report]
+exclude_lines =
+    pragma: no cover
+    raise NotImplementedError
+    if __name__ == .__main__.:
+omit =
+    */tests*
+    */__init__.py
diff --git a/.travis.yml b/.travis.yml
index c9ed192..ea76eec 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -14,6 +14,7 @@ before_install:
   # Update conda itself
   - conda update --yes conda
   # Useful for debugging any issues with conda
+  - conda info -a
 install:
   - conda create --yes -n test_env python=$PYVERSION --file ci/conda_requirements.txt -c biocore
   - conda install --yes -n test_env cython
@@ -21,7 +22,9 @@ install:
   - pip install -r ci/pip_requirements.txt
   - pip install -e .
 script:
-  - make all
+  - WITH_COVERAGE=TRUE make all
+after_success:
+  - coveralls
 notifications:
   webhooks:
     on_success: change
diff --git a/Makefile b/Makefile
index 23e878e..e0a02d1 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,10 @@
 .DEFAULT_GOAL := help
 
-TEST_COMMAND = nosetests --with-doctest
+ifeq ($(WITH_COVERAGE), TRUE)
+	TEST_COMMAND = COVERAGE_FILE=.coverage coverage run --rcfile .coveragerc setup.py nosetests --with-doctest
+else
+	TEST_COMMAND = nosetests --with-doctest
+endif
 
 help:
 	@echo 'Use "make test" to run all the unit tests and docstring tests.'
diff --git a/README.md b/README.md
index a1b960d..455ffce 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,9 @@
 # gneiss
 
+
+[[https://coveralls.io/github/biocore/micronota?branch=master][https://coveralls.io/repos/biocore/micronota/badge.svg?branch=master&service=github]]
+[[https://travis-ci.org/biocore/micronota][https://travis-ci.org/biocore/micronota.svg?branch=master]]
+
 Canonically pronouced *nice*
 
 A compositional statistics and visualization toolbox
diff --git a/gneiss/balances.py b/gneiss/balances.py
index 4893b08..8ac511a 100644
--- a/gneiss/balances.py
+++ b/gneiss/balances.py
@@ -134,6 +134,14 @@ def _count_matrix(treenode):
 
 
 def default_layout(node):
+    """
+    Specifies the layout for the ete.TreeStyle object.
+
+    Parameters
+    ----------
+    node: ete.Tree
+        Input node for specifying which attributes.
+    """
     if node.is_leaf():
         # Add node name to leaf nodes
         N = AttrFace("name", fsize=14, fgcolor="black")
@@ -157,6 +165,34 @@ def barchart_layout(node, name='name',
                     fsize=14, fgcolor="black",
                     alpha=0.5,
                     rotation=270):
+    """
+    Specifies the layout for the ete.TreeStyle object.
+
+    Parameters
+    ----------
+    node: ete.Tree
+        Input node for specifying which attributes.
+    name: str, optional
+        Attribute to look up the name of the node.
+    width: int, optional
+        Width of the barchart.
+    height: int, optional
+        Height of the barchart.
+    colors: list of str, optional
+        List of HTML colors to color the barchart values.
+    min_value: int, optional
+        Minimum value to set the scale of the chart.
+    max_value: int, optional
+        Maximum value to set the scale of the chart.
+    fsize: int, optional
+        Font size on the leafs.
+    fgcolor: str, optional
+        Font color of the leafs.
+    alpha: float, optional
+        Transparency of the barchart.
+    rotation: int, optional
+        Orientation of the barchart.
+    """
     if colors is None:
         colors = ['#0000FF']
     if node.is_leaf():
@@ -172,7 +208,7 @@ def barchart_layout(node, name='name',
         else:
             weight = node.weight
         C = BarChartFace(values=weight, width=width, height=height,
-                         colors=['#0000FF'], min_value=min_value,
+                         colors=colors, min_value=min_value,
                          max_value=max_value)
         # Let's make the sphere transparent
         C.opacity = alpha
@@ -269,7 +305,7 @@ def balanceplot(balances, tree,
 
     See Also
     --------
-    TreeNode.levelorder
+    skbio.TreeNode.levelorder
     """
     ete_tree = _attach_balances(balances, tree)