Merge pull request #203 from UT-CHG/v2_master

V2 master

.travis.yml

@@ -5,22 +5,27 @@ python:
     #- "3.2"
     #- "3.3"
     #- "3.4"
-# command to install dependencies
+
 before_install:
-    - sudo apt-get install gfortran libblas-dev liblapack-dev mpich2 libmpich2-dev python-dev python-numpy python-scipy python-matplotlib python-nose python-pip
-    - pip install pyDOE mpi4py
+  - "export DISPLAY=:99.0"
+  - "sh -e /etc/init.d/xvfb start"
+  - sudo apt-get install gfortran libblas-dev liblapack-dev mpich2 libmpich2-dev
+  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - conda update --yes conda
+
+install:
+  - conda install --yes python=$TRAVIS_PYTHON_VERSION pip numpy scipy nose
+  - pip install pyDOE mpi4py
+  - python setup.py install
 
-# install package:
-    - python setup.py install
-# script to run before running tests
-before_script:
-    - mkdir -p shippable/testresults
-# command to run tests
 script:
-    - nosetests --with-xunit --xunit-file=shippable/testresults/nosetests_mpi4py_serial.xml
-    - mpirun -n 2 nosetests --with-xunit --xunit-file=shippable/testresults/nosetests_mpi4py_parallel.xml
-    - pip uninstall -y mpi4py
-    - nosetests --with-xunit --xunit-file=shippable/testresults/nosetests_nompi4py.xml
+  - nosetests
+  - mpirun -n 2 nosetests
+  - pip uninstall -y mpi4py
+  - nosetests
+
 # notification settings
 notifications:
     email:
@@ -34,4 +39,4 @@ notifications:
 branches:
     only:
         - master
-
+        - v2_master

README.md

@@ -20,6 +20,17 @@ You will need to run sphinx-apidoc AND reinstall BET anytime a new module or met
 
 Useful scripts are contained in ``examples/``
 
+Tests
+-----
+
+To run tests in serial call::
+
+    nosetests tests
+
+To run tests in parallel call::
+
+    mpirun -np NPROC nosetets tests
+
 Dependencies
 ------------
 

bet/Comm.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2014-2015 The BET Development Team
+# Copyright (C) 2014-2016 The BET Development Team
 
 """
 This module provides a workaround for people without mpi4py installed
@@ -18,7 +18,9 @@ def __init__(self):
         """
         Initialization
         """
+        #: size, 1
         self.size = 1
+        #: rank, 0
         self.rank = 0
         pass
 
@@ -146,6 +148,11 @@ def Barrier(self):
         """
         pass
 
+    def barrier(self):
+        """
+        Does nothing in serial.
+        """
+        pass
 
 class MPI_for_no_mpi4py(object):
 
@@ -158,9 +165,13 @@ def __init__(self):
         """
         Initialization
         """
+        #: fake sum 
         self.SUM = None
+        #: float type
         self.DOUBLE = float
+        #: int type
         self.INT = int
+        #: bool type
         self.BOOL = bool
 
 try:

bet/__init__.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2014-2015 The BET Development Team
+# Copyright (C) 2014-2016 The BET Development Team
 
 """
 Butler, Estep, Tavener Method
@@ -23,7 +23,10 @@
 postProcess :mod:`~bet.postProcess` provides plotting tools and tools to sort
     samples by probabilities.
 
+sample :mod:`~bet.sample` provides data structures to store sets of samples and
+    their associated arrays.
+
 """
 
 __all__ = ['sampling', 'calculateP', 'postProcess', 'sensitivity', 'util', 
-    'Comm']
+    'Comm', 'sample']