From 7653be0a5e1ce0fece431711129faad45083c72c Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Fri, 29 Sep 2017 09:45:42 -0500
Subject: [PATCH 01/13] Use argparse in run_tests.py instead of optparse

---
 tests/run_tests.py | 78 +++++++++++++++++++++-------------------------
 1 file changed, 36 insertions(+), 42 deletions(-)

diff --git a/tests/run_tests.py b/tests/run_tests.py
index 50e9313df3..a3320823a8 100755
--- a/tests/run_tests.py
+++ b/tests/run_tests.py
@@ -10,35 +10,35 @@ import glob
 import socket
 from subprocess import call, check_output
 from collections import OrderedDict
-from optparse import OptionParser
+from argparse import ArgumentParser
 
 # Command line parsing
-parser = OptionParser()
-parser.add_option('-j', '--parallel', dest='n_procs', default='1',
+parser = ArgumentParser()
+parser.add_argument('-j', '--parallel', dest='n_procs', default='1',
                   help="Number of parallel jobs.")
-parser.add_option('-R', '--tests-regex', dest='regex_tests',
+parser.add_argument('-R', '--tests-regex', dest='regex_tests',
                   help="Run tests matching regular expression. \
                   Test names are the directories present in tests folder.\
                   This uses standard regex syntax to select tests.")
-parser.add_option('-C', '--build-config', dest='build_config',
+parser.add_argument('-C', '--build-config', dest='build_config',
                   help="Build configurations matching regular expression. \
                         Specific build configurations can be printed out with \
                         optional argument -p, --print. This uses standard \
                         regex syntax to select build configurations.")
-parser.add_option('-l', '--list', action="store_true",
+parser.add_argument('-l', '--list', action="store_true",
                   dest="list_build_configs", default=False,
                   help="List out build configurations.")
-parser.add_option("-p", "--project", dest="project", default="",
+parser.add_argument("-p", "--project", dest="project", default="",
                   help="project name for build")
-parser.add_option("-D", "--dashboard", dest="dash",
+parser.add_argument("-D", "--dashboard", dest="dash",
                   help="Dash name -- Experimental, Nightly, Continuous")
-parser.add_option("-u", "--update", action="store_true", dest="update",
+parser.add_argument("-u", "--update", action="store_true", dest="update",
                   help="Allow CTest to update repo. (WARNING: may overwrite\
                         changes that were not pushed.")
-parser.add_option("-s", "--script", action="store_true", dest="script",
+parser.add_argument("-s", "--script", action="store_true", dest="script",
                   help="Activate CTest scripting mode for coverage, valgrind\
                         and dashboard capability.")
-(options, args) = parser.parse_args()
+args = parser.parse_args()
 
 # Default compiler paths
 FC='gfortran'
@@ -173,7 +173,7 @@ class Test(object):
 
     # Sets the build name that will show up on the CDash
     def get_build_name(self):
-        self.build_name =  options.project + '_' + self.name
+        self.build_name =  args.project + '_' + self.name
         return self.build_name
 
     # Sets up build options for various tests. It is used both
@@ -246,9 +246,9 @@ class Test(object):
         make_list = ['make','-s']
 
         # Check for parallel
-        if options.n_procs is not None:
+        if args.n_procs is not None:
             make_list.append('-j')
-            make_list.append(options.n_procs)
+            make_list.append(args.n_procs)
 
         # Run make
         rc = call(make_list)
@@ -265,14 +265,14 @@ class Test(object):
         ctest_list = ['ctest']
 
         # Check for parallel
-        if options.n_procs is not None:
+        if args.n_procs is not None:
             ctest_list.append('-j')
-            ctest_list.append(options.n_procs)
+            ctest_list.append(args.n_procs)
 
         # Check for subset of tests
-        if options.regex_tests is not None:
+        if args.regex_tests is not None:
             ctest_list.append('-R')
-            ctest_list.append(options.regex_tests)
+            ctest_list.append(args.regex_tests)
 
         # Run ctests
         rc = call(ctest_list)
@@ -308,7 +308,7 @@ add_test('hdf5-debug_valgrind', debug=True, valgrind=True)
 add_test('hdf5-debug_coverage', debug=True, coverage=True)
 
 # Check to see if we should just print build configuration information to user
-if options.list_build_configs:
+if args.list_build_configs:
     for key in tests:
         print('Configuration Name: {0}'.format(key))
         print('  Debug Flags:..........{0}'.format(tests[key].debug))
@@ -320,10 +320,10 @@ if options.list_build_configs:
     exit()
 
 # Delete items of dictionary that don't match regular expression
-if options.build_config is not None:
+if args.build_config is not None:
     to_delete = []
     for key in tests:
-        if not re.search(options.build_config, key):
+        if not re.search(args.build_config, key):
             to_delete.append(key)
     for key in to_delete:
         del tests[key]
@@ -333,27 +333,21 @@ if options.build_config is not None:
 # Experimental, Nightly, Continuous. On the CDash end, these can be
 # reorganized into groups when a hostname, dashboard and build name
 # are matched.
-if options.dash is None:
+if args.dash is None:
     dash = 'Experimental'
     submit = ''
 else:
-    dash = options.dash
+    dash = args.dash
     submit = 'ctest_submit()'
 
 # Check for update command, which will run git fetch/merge and will delete
 # any changes to repo that were not pushed to remote origin
-if options.update:
-    update = 'ctest_update()'
-else:
-    update = ''
+update = 'ctest_update()' if args.update else ''
 
 # Check for CTest scipts mode
 # Sets up whether we should use just the basic ctest command or use
 # CTest scripting to perform tests.
-if not options.dash is None or options.script:
-    script_mode = True
-else:
-    script_mode = False
+script_mode = (args.dash is not None or args.script)
 
 # Setup CTest script vars. Not used in non-script mode
 pwd = os.getcwd()
@@ -364,17 +358,17 @@ ctest_vars = {
     'dashboard': dash,
     'submit': submit,
     'update': update,
-    'n_procs': options.n_procs
+    'n_procs': args.n_procs
 }
 
 # Check project name
-subprop = """set_property(GLOBAL PROPERTY SubProject {0})"""
-if options.project == "" :
-    ctest_vars.update({'subproject':''})
-elif options.project == 'develop':
-    ctest_vars.update({'subproject':''})
+subprop = "set_property(GLOBAL PROPERTY SubProject {0})"
+if args.project == "" :
+    ctest_vars.update({'subproject': ''})
+elif args.project == 'develop':
+    ctest_vars.update({'subproject': ''})
 else:
-    ctest_vars.update({'subproject':subprop.format(options.project)})
+    ctest_vars.update({'subproject': subprop.format(args.project)})
 
 # Set up default valgrind tests (subset of all tests)
 # Currently takes too long to run all the tests with valgrind
@@ -396,8 +390,8 @@ if not script_mode:
 for key in to_delete:
     del tests[key]
 
-# Check if tests empty
-if len(list(tests.keys())) == 0:
+# Check if tests is empty
+if not tests:
     print('No tests to run.')
     exit()
 
@@ -447,7 +441,7 @@ for key in iter(tests):
     # Check for user custom tests
     # INCLUDE is a CTest command that allows for a subset
     # of tests to be executed. Only used in script mode.
-    if options.regex_tests is None:
+    if args.regex_tests is None:
         ctest_vars.update({'tests' : ''})
 
         # No user tests, use default valgrind tests
@@ -456,7 +450,7 @@ for key in iter(tests):
                               format(valgrind_default_tests)})
     else:
         ctest_vars.update({'tests' : 'INCLUDE {0}'.
-                          format(options.regex_tests)})
+                          format(args.regex_tests)})
 
     # Main part of code that does the ctest execution.
     # It is broken up by two modes, script and non-script

From 2673880a9c95f710d531a67598119280be2dbe0e Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Fri, 29 Sep 2017 11:09:50 -0500
Subject: [PATCH 02/13] Move test_element_wo to unit tests

---
 tests/{test_element_wo => unit_tests}/test_element_wo.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)
 rename tests/{test_element_wo => unit_tests}/test_element_wo.py (92%)

diff --git a/tests/test_element_wo/test_element_wo.py b/tests/unit_tests/test_element_wo.py
similarity index 92%
rename from tests/test_element_wo/test_element_wo.py
rename to tests/unit_tests/test_element_wo.py
index e2a5726f19..7b9487f73d 100644
--- a/tests/test_element_wo/test_element_wo.py
+++ b/tests/unit_tests/test_element_wo.py
@@ -5,13 +5,11 @@ import sys
 
 import numpy as np
 
-sys.path.insert(0, os.pardir)
-sys.path.insert(0, os.path.join(os.pardir, os.pardir))
 from openmc import Material
 from openmc.data import NATURAL_ABUNDANCE, atomic_mass
 
 
-if __name__ == '__main__':
+def test_element_wo():
     # This test doesn't require an OpenMC run.  We just need to make sure the
     # element.expand() method expands elements with the proper nuclide
     # compositions.

From 232f40e1193c1e520025e30334f5ad3bc9cf30da Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Fri, 29 Sep 2017 11:11:18 -0500
Subject: [PATCH 03/13] Only install via setuptools

---
 setup.py | 65 +++++++++++++++++++++++++-------------------------------
 1 file changed, 29 insertions(+), 36 deletions(-)

diff --git a/setup.py b/setup.py
index 7ca824ab01..8d482b8626 100755
--- a/setup.py
+++ b/setup.py
@@ -3,13 +3,8 @@
 import glob
 import sys
 import numpy as np
-try:
-    from setuptools import setup
-    have_setuptools = True
-except ImportError:
-    from distutils.core import setup
-    have_setuptools = False
 
+from setuptools import setup
 try:
     from Cython.Build import cythonize
     have_cython = True
@@ -28,11 +23,12 @@ else:
 with open('openmc/__init__.py', 'r') as f:
     version = f.readlines()[-1].split()[-1].strip("'")
 
-kwargs = {'name': 'openmc',
-          'version': version,
-          'packages': ['openmc', 'openmc.capi', 'openmc.data', 'openmc.mgxs',
-                       'openmc.model', 'openmc.stats'],
-          'scripts': glob.glob('scripts/openmc-*'),
+kwargs = {
+    'name': 'openmc',
+    'version': version,
+    'packages': ['openmc', 'openmc.capi', 'openmc.data', 'openmc.mgxs',
+                 'openmc.model', 'openmc.stats'],
+    'scripts': glob.glob('scripts/openmc-*'),
 
           # Data files and librarries
           'package_data': {
@@ -42,33 +38,30 @@ kwargs = {'name': 'openmc',
 
           # Metadata
           'author': 'Will Boyd',
-          'author_email': 'wbinventor@gmail.com',
-          'description': 'OpenMC Python API',
-          'url': 'https://github.com/mit-crpg/openmc',
-          'classifiers': [
-              'Intended Audience :: Developers',
-              'Intended Audience :: End Users/Desktop',
-              'Intended Audience :: Science/Research',
-              'License :: OSI Approved :: MIT License',
-              'Natural Language :: English',
-              'Programming Language :: Python',
-              'Topic :: Scientific/Engineering'
-          ]}
+    'author_email': 'wbinventor@gmail.com',
+    'description': 'OpenMC Python API',
+    'url': 'https://github.com/mit-crpg/openmc',
+    'classifiers': [
+        'Intended Audience :: Developers',
+        'Intended Audience :: End Users/Desktop',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: MIT License',
+        'Natural Language :: English',
+        'Programming Language :: Python',
+        'Topic :: Scientific/Engineering'
+    ],
 
-if have_setuptools:
-    kwargs.update({
-        # Required dependencies
-        'install_requires': ['six', 'numpy>=1.9', 'h5py', 'scipy', 'pandas>=0.17.0'],
+    # Required dependencies
+    'install_requires': ['six', 'numpy>=1.9', 'h5py', 'scipy',
+                         'pandas>=0.17.0', 'lxml'],
 
-        # Optional dependencies
-        'extras_require': {
-            'decay': ['uncertainties'],
-            'plot': ['matplotlib', 'ipython'],
-            'vtk': ['vtk', 'silomesh'],
-            'validate': ['lxml']
-        },
-
-    })
+    # Optional dependencies
+    'extras_require': {
+        'decay': ['uncertainties'],
+        'plot': ['matplotlib', 'ipython'],
+        'vtk': ['vtk', 'silomesh'],
+    },
+}
 
 # If Cython is present, add resonance reconstruction capability
 if have_cython:

From 819744bbcba2f53a15d4cdd257be3580f2ad0f12 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Fri, 29 Sep 2017 14:30:57 -0500
Subject: [PATCH 04/13] Add a MANIFEST.in and tox.ini file

---
 .gitignore  | 4 ++++
 MANIFEST.in | 2 ++
 tox.ini     | 9 +++++++++
 3 files changed, 15 insertions(+)
 create mode 100644 MANIFEST.in
 create mode 100644 tox.ini

diff --git a/.gitignore b/.gitignore
index a0cfd5c7ff..35f45e747b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -97,3 +97,7 @@ examples/jupyter/plots
 *.c
 *.html
 *.so
+
+.cache/
+.tox/
+.python-version
diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000000..bd3bec5689
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,2 @@
+include readme.rst
+include openmc/data/reconstruct.pyx
diff --git a/tox.ini b/tox.ini
new file mode 100644
index 0000000000..951bd8cd0c
--- /dev/null
+++ b/tox.ini
@@ -0,0 +1,9 @@
+[tox]
+envlist = py{34,36}
+[testenv]
+commands = pytest tests/unit_tests
+deps =
+     pytest
+     numpy
+     cython
+passenv = OPENMC_CROSS_SECTIONS

From 12848904cb119e2c7b83eaffefa033b2424a58f8 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Mon, 2 Oct 2017 14:01:51 -0500
Subject: [PATCH 05/13] Remove unused files at root

---
 CTestConfig.cmake | 25 -------------------------
 Makefile          | 14 --------------
 2 files changed, 39 deletions(-)
 delete mode 100644 CTestConfig.cmake
 delete mode 100644 Makefile

diff --git a/CTestConfig.cmake b/CTestConfig.cmake
deleted file mode 100644
index e127a8ddf2..0000000000
--- a/CTestConfig.cmake
+++ /dev/null
@@ -1,25 +0,0 @@
-## This file should be placed in the root directory of your project.
-## Then modify the CMakeLists.txt file in the root directory of your
-## project to incorporate the testing dashboard.
-## # The following are required to uses Dart and the Cdash dashboard
-##   ENABLE_TESTING()
-##   INCLUDE(CTest)
-
-# Generic information about CDASH site
-set(CTEST_PROJECT_NAME "OpenMC")
-set(CTEST_NIGHTLY_START_TIME "01:00:00 UTC")
-set(CTEST_DROP_METHOD "http")
-set(CTEST_DROP_SITE "openmc.mit.edu")
-set(CTEST_DROP_LOCATION "/cdash/submit.php?project=OpenMC")
-set(CTEST_DROP_SITE_CDASH TRUE)
-
-# Set file size larger to see more output
-set(CTEST_CUSTOM_MAXIMUM_FAILED_TEST_OUTPUT_SIZE "20000")
-set(CTEST_CUSTOM_MAXIMUM_PASSED_TEST_OUTPUT_SIZE "20000")
-
-# User/password to CDASH site
-# Please contact Nick Horelik <nhorelik@mit.edu> or
-# Bryan Herman <bherman@mit.edu> if you want to push
-# test suite information to our CDASH site.
-set(CTEST_DROP_SITE_USER "")
-set(CTEST_DROP_SITE_PASSWORD "")
diff --git a/Makefile b/Makefile
deleted file mode 100644
index 990f22d9d3..0000000000
--- a/Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-all:
-	mkdir -p build
-	cmake -H. -Bbuild
-	make -s -C build
-clean:
-	make -s -C build clean
-distclean:
-	rm -fr build
-test:
-	make -s -C build test
-install:
-	make -s -C build install
-
-.PHONY: all clean distclean test install

From d21d158a5bf3bd21ed49e37a5240e707b053d559 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Mon, 2 Oct 2017 14:06:14 -0500
Subject: [PATCH 06/13] Add MANIFEST.in and update setup.py

---
 MANIFEST.in | 36 +++++++++++++++++++++++++++++++++++-
 setup.py    | 27 +++++++++++++++++----------
 2 files changed, 52 insertions(+), 11 deletions(-)

diff --git a/MANIFEST.in b/MANIFEST.in
index bd3bec5689..04436bf1df 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,2 +1,36 @@
-include readme.rst
+include CMakeLists.txt
+include LICENSE
+include schemas.xml
+include tox.ini
 include openmc/data/reconstruct.pyx
+include docs/source/_templates/layout.html
+include docs/sphinxext/LICENSE
+recursive-include . *.rst
+recursive-include cmake *.cmake
+recursive-include docs *.css
+recursive-include docs *.dia
+recursive-include docs *.png
+recursive-include docs *.py
+recursive-include docs *.svg
+recursive-include docs *.tex
+recursive-include docs *.txt
+recursive-include docs Makefile
+recursive-include examples *.h5
+recursive-include examples *.ipynb
+recursive-include examples *.png
+recursive-include examples *.py
+recursive-include examples *.xml
+recursive-include man *.1
+recursive-include src *.F90
+recursive-include src *.c
+recursive-include src *.cc
+recursive-include src *.cpp
+recursive-include src *.h
+recursive-include src *.hpp
+recursive-include src *.rnc
+recursive-include src *.rng
+recursive-include tests *.dat
+recursive-include tests *.h5
+recursive-include tests *.py
+recursive-include tests *.xml
+prune docs/build
diff --git a/setup.py b/setup.py
index 8d482b8626..354098ea35 100755
--- a/setup.py
+++ b/setup.py
@@ -26,29 +26,36 @@ with open('openmc/__init__.py', 'r') as f:
 kwargs = {
     'name': 'openmc',
     'version': version,
-    'packages': ['openmc', 'openmc.capi', 'openmc.data', 'openmc.mgxs',
-                 'openmc.model', 'openmc.stats'],
+    'packages': find_packages(),
     'scripts': glob.glob('scripts/openmc-*'),
 
-          # Data files and librarries
-          'package_data': {
-              'openmc.capi': ['libopenmc.{}'.format(suffix)],
-              'openmc.data': ['mass.mas12', 'fission_Q_data_endfb71.h5']
-          },
+    # Data files and librarries
+    'package_data': {
+        'openmc.capi': ['libopenmc.{}'.format(suffix)],
+        'openmc.data': ['mass.mas12', 'fission_Q_data_endfb71.h5']
+    },
 
-          # Metadata
-          'author': 'Will Boyd',
+    # Metadata
+    'author': 'Will Boyd',
     'author_email': 'wbinventor@gmail.com',
     'description': 'OpenMC Python API',
     'url': 'https://github.com/mit-crpg/openmc',
     'classifiers': [
+        'Development Status :: 4 - Beta',
         'Intended Audience :: Developers',
         'Intended Audience :: End Users/Desktop',
         'Intended Audience :: Science/Research',
         'License :: OSI Approved :: MIT License',
         'Natural Language :: English',
-        'Programming Language :: Python',
         'Topic :: Scientific/Engineering'
+        'Programming Language :: Python :: 2',
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.2',
+        'Programming Language :: Python :: 3.3',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
     ],
 
     # Required dependencies

From 00f6bbe26608e78b7de6447084f15abff76e3559 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Fri, 13 Oct 2017 16:21:34 -0500
Subject: [PATCH 07/13] Run unit tests on Travis

---
 .travis.yml    |  6 ++++--
 CMakeLists.txt |  5 +++++
 setup.py       | 17 +++++++++--------
 3 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 64fbdc9df2..bb2c500c9a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -41,7 +41,7 @@ before_install:
   - conda update -q conda
   - conda info -a
   - if [[ $OPENMC_CONFIG != "check_source" ]]; then
-      conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION six numpy scipy h5py=2.5 pandas;
+      conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION pip numpy cython;
       source activate test-environment;
       sudo add-apt-repository ppa:nschloe/hdf5-backports -y;
       sudo apt-get update -q;
@@ -52,7 +52,8 @@ before_install:
       export HDF5_DIR=/usr;
     fi
 
-install: true
+install:
+  - pip install -e .[test]
 
 before_script:
   - if [[ $OPENMC_CONFIG != "check_source" ]]; then
@@ -73,4 +74,5 @@ script:
     else
       ./run_tests.py -C $OPENMC_CONFIG -j 2;
     fi
+  - pytest unit_tests/
   - cd ..
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 905555a050..0b0bef14ea 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -468,6 +468,11 @@ file(GLOB_RECURSE TESTS ${CMAKE_CURRENT_SOURCE_DIR}/tests/test_*.py)
 
 # Loop through all the tests
 foreach(test ${TESTS})
+  # Remove unit tests
+  if(test MATCHES ".*unit_tests.*")
+    continue()
+  endif()
+
   # Get test information
   get_filename_component(TEST_NAME ${test} NAME)
   get_filename_component(TEST_PATH ${test} PATH)
diff --git a/setup.py b/setup.py
index 354098ea35..e064efa68c 100755
--- a/setup.py
+++ b/setup.py
@@ -4,7 +4,7 @@ import glob
 import sys
 import numpy as np
 
-from setuptools import setup
+from setuptools import setup, find_packages
 try:
     from Cython.Build import cythonize
     have_cython = True
@@ -36,9 +36,9 @@ kwargs = {
     },
 
     # Metadata
-    'author': 'Will Boyd',
-    'author_email': 'wbinventor@gmail.com',
-    'description': 'OpenMC Python API',
+    'author': 'The OpenMC Development Team',
+    'author_email': 'openmc-dev@googlegroups.com',
+    'description': 'OpenMC',
     'url': 'https://github.com/mit-crpg/openmc',
     'classifiers': [
         'Development Status :: 4 - Beta',
@@ -59,13 +59,14 @@ kwargs = {
     ],
 
     # Required dependencies
-    'install_requires': ['six', 'numpy>=1.9', 'h5py', 'scipy',
-                         'pandas>=0.17.0', 'lxml'],
+    'install_requires': [
+        'six', 'numpy>=1.9', 'h5py', 'scipy', 'ipython', 'matplotlib',
+        'pandas>=0.17.0', 'lxml', 'uncertainties'
+    ],
 
     # Optional dependencies
     'extras_require': {
-        'decay': ['uncertainties'],
-        'plot': ['matplotlib', 'ipython'],
+        'test': ['pytest'],
         'vtk': ['vtk', 'silomesh'],
     },
 }

From 215220bb060def96323fc316b5c75749db323e6a Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Sat, 14 Oct 2017 13:15:01 -0500
Subject: [PATCH 08/13] Don't pip install or run unit tests for check_source
 configuration

---
 .travis.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index bb2c500c9a..bb7a7da377 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -53,7 +53,9 @@ before_install:
     fi
 
 install:
-  - pip install -e .[test]
+  - if [[ $OPENMC_CONFIG != "check_source" ]]; then
+      pip install -e .[test];
+    fi
 
 before_script:
   - if [[ $OPENMC_CONFIG != "check_source" ]]; then
@@ -73,6 +75,6 @@ script:
       ./check_source.py;
     else
       ./run_tests.py -C $OPENMC_CONFIG -j 2;
+      pytest unit_tests/;
     fi
-  - pytest unit_tests/
   - cd ..

From ef7261cd713040780ddafc3b74cdf9c31e5945cd Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Sat, 14 Oct 2017 14:06:24 -0500
Subject: [PATCH 09/13] Try using default pip/virtualenv on Travis instead of
 conda

---
 .travis.yml | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index bb7a7da377..0de30b20a4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -28,21 +28,7 @@ matrix:
       env: OPENMC_CONFIG="check_source"
 
 before_install:
-  # ============== Handle Python third-party packages ==============
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    fi
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
-  - conda info -a
   - if [[ $OPENMC_CONFIG != "check_source" ]]; then
-      conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION pip numpy cython;
-      source activate test-environment;
       sudo add-apt-repository ppa:nschloe/hdf5-backports -y;
       sudo apt-get update -q;
       sudo apt-get install libhdf5-serial-dev libhdf5-mpich-dev -y;
@@ -54,6 +40,7 @@ before_install:
 
 install:
   - if [[ $OPENMC_CONFIG != "check_source" ]]; then
+      pip install numpy cython;
       pip install -e .[test];
     fi
 

From 3d32f57c6ff3157143a089de096a5ef7b237a706 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Tue, 17 Oct 2017 15:13:30 -0500
Subject: [PATCH 10/13] Add coverage to unit tests

---
 .travis.yml | 2 +-
 setup.py    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 0de30b20a4..b4462ed0e7 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -62,6 +62,6 @@ script:
       ./check_source.py;
     else
       ./run_tests.py -C $OPENMC_CONFIG -j 2;
-      pytest unit_tests/;
+      pytest --cov=../openmc unit_tests/;
     fi
   - cd ..
diff --git a/setup.py b/setup.py
index e064efa68c..271fac0f00 100755
--- a/setup.py
+++ b/setup.py
@@ -66,7 +66,7 @@ kwargs = {
 
     # Optional dependencies
     'extras_require': {
-        'test': ['pytest'],
+        'test': ['pytest', 'pytest-cov'],
         'vtk': ['vtk', 'silomesh'],
     },
 }

From 3955e901b46781503cffc636eba15c54c1e55b09 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Wed, 18 Oct 2017 10:51:45 -0500
Subject: [PATCH 11/13] Remove tox.ini for now, update install instructions

---
 MANIFEST.in                        |  1 -
 docs/source/usersguide/install.rst | 17 ++++++++++-------
 tox.ini                            |  9 ---------
 3 files changed, 10 insertions(+), 17 deletions(-)
 delete mode 100644 tox.ini

diff --git a/MANIFEST.in b/MANIFEST.in
index 04436bf1df..04348222fa 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,7 +1,6 @@
 include CMakeLists.txt
 include LICENSE
 include schemas.xml
-include tox.ini
 include openmc/data/reconstruct.pyx
 include docs/source/_templates/layout.html
 include docs/sphinxext/LICENSE
diff --git a/docs/source/usersguide/install.rst b/docs/source/usersguide/install.rst
index 497e09b4d5..09fc4520c0 100644
--- a/docs/source/usersguide/install.rst
+++ b/docs/source/usersguide/install.rst
@@ -414,16 +414,19 @@ distributions.
       various HDF5 files, h5py is needed to provide access to data within these
       files from Python.
 
-.. admonition:: Optional
-   :class: note
-
    `Matplotlib <http://matplotlib.org/>`_
       Matplotlib is used to providing plotting functionality in the API like the
       :meth:`Universe.plot` method and the :func:`openmc.plot_xs` function.
 
    `uncertainties <https://pythonhosted.org/uncertainties/>`_
-      Uncertainties are optionally used for decay data in the :mod:`openmc.data`
-      module.
+      Uncertainties are used for decay data in the :mod:`openmc.data` module.
+
+   `lxml <http://lxml.de/>`_
+      lxml is used for the :ref:`scripts_validate` script and various other
+      parts of the Python API.
+
+.. admonition:: Optional
+   :class: note
 
    `Cython <http://cython.org/>`_
       Cython is used for resonance reconstruction for ENDF data converted to
@@ -437,8 +440,8 @@ distributions.
       The silomesh package is needed to convert voxel and track files to SILO
       format.
 
-   `lxml <http://lxml.de/>`_
-      lxml is used for the :ref:`scripts_validate` script.
+   `pytest <https://docs.pytest.org>`_
+      The pytest framework is used for unit testing the Python API.
 
 .. _usersguide_nxml:
 
diff --git a/tox.ini b/tox.ini
deleted file mode 100644
index 951bd8cd0c..0000000000
--- a/tox.ini
+++ /dev/null
@@ -1,9 +0,0 @@
-[tox]
-envlist = py{34,36}
-[testenv]
-commands = pytest tests/unit_tests
-deps =
-     pytest
-     numpy
-     cython
-passenv = OPENMC_CROSS_SECTIONS

From e510fc799213a226756f21a0760b8d1d486671e6 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Wed, 18 Oct 2017 11:23:10 -0500
Subject: [PATCH 12/13] Add license badge on readme.rst

---
 readme.rst | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/readme.rst b/readme.rst
index 34d2a5d099..75e4a1438f 100644
--- a/readme.rst
+++ b/readme.rst
@@ -2,8 +2,7 @@
 OpenMC Monte Carlo Particle Transport Code
 ==========================================
 
-.. image:: https://travis-ci.org/mit-crpg/openmc.svg?branch=develop
-    :target: https://travis-ci.org/mit-crpg/openmc
+|licensebadge| |travisbadge|
 
 The OpenMC project aims to provide a fully-featured Monte Carlo particle
 transport code based on modern methods. It is a constructive solid geometry,
@@ -55,3 +54,11 @@ OpenMC is distributed under the MIT/X license_.
 .. _Troubleshooting section: http://openmc.readthedocs.io/en/stable/usersguide/troubleshoot.html
 .. _Issues: https://github.com/mit-crpg/openmc/issues
 .. _license: http://openmc.readthedocs.io/en/stable/license.html
+
+.. |licensebadge| image:: https://img.shields.io/github/license/mit-crpg/openmc.svg
+   :target: http://openmc.readthedocs.io/en/latest/license.html
+   :alt: License
+
+.. |travisbadge| image:: https://travis-ci.org/mit-crpg/openmc.svg?branch=develop
+   :target: https://travis-ci.org/mit-crpg/openmc
+   :alt: Travis CI build status (Linux)

From 1c8fbf536747971af6f6b4a9a50755378fb2e24c Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Tue, 7 Nov 2017 08:28:29 -0600
Subject: [PATCH 13/13] PEP8 fixes in run_tests.py

---
 tests/run_tests.py | 61 +++++++++++++++++++++++-----------------------
 1 file changed, 31 insertions(+), 30 deletions(-)

diff --git a/tests/run_tests.py b/tests/run_tests.py
index a3320823a8..6e6b886a50 100755
--- a/tests/run_tests.py
+++ b/tests/run_tests.py
@@ -15,38 +15,38 @@ from argparse import ArgumentParser
 # Command line parsing
 parser = ArgumentParser()
 parser.add_argument('-j', '--parallel', dest='n_procs', default='1',
-                  help="Number of parallel jobs.")
+                    help="Number of parallel jobs.")
 parser.add_argument('-R', '--tests-regex', dest='regex_tests',
-                  help="Run tests matching regular expression. \
-                  Test names are the directories present in tests folder.\
-                  This uses standard regex syntax to select tests.")
+                    help="Run tests matching regular expression. \
+                    Test names are the directories present in tests folder.\
+                    This uses standard regex syntax to select tests.")
 parser.add_argument('-C', '--build-config', dest='build_config',
-                  help="Build configurations matching regular expression. \
-                        Specific build configurations can be printed out with \
-                        optional argument -p, --print. This uses standard \
-                        regex syntax to select build configurations.")
+                    help="Build configurations matching regular expression. \
+                    Specific build configurations can be printed out with \
+                    optional argument -p, --print. This uses standard \
+                    regex syntax to select build configurations.")
 parser.add_argument('-l', '--list', action="store_true",
-                  dest="list_build_configs", default=False,
-                  help="List out build configurations.")
+                    dest="list_build_configs", default=False,
+                    help="List out build configurations.")
 parser.add_argument("-p", "--project", dest="project", default="",
-                  help="project name for build")
+                    help="project name for build")
 parser.add_argument("-D", "--dashboard", dest="dash",
-                  help="Dash name -- Experimental, Nightly, Continuous")
+                    help="Dash name -- Experimental, Nightly, Continuous")
 parser.add_argument("-u", "--update", action="store_true", dest="update",
-                  help="Allow CTest to update repo. (WARNING: may overwrite\
-                        changes that were not pushed.")
+                    help="Allow CTest to update repo. (WARNING: may overwrite\
+                    changes that were not pushed.")
 parser.add_argument("-s", "--script", action="store_true", dest="script",
-                  help="Activate CTest scripting mode for coverage, valgrind\
-                        and dashboard capability.")
+                    help="Activate CTest scripting mode for coverage, valgrind\
+                    and dashboard capability.")
 args = parser.parse_args()
 
 # Default compiler paths
-FC='gfortran'
-CC='gcc'
-CXX='g++'
-MPI_DIR='/opt/mpich/3.2-gnu'
-HDF5_DIR='/opt/hdf5/1.8.16-gnu'
-PHDF5_DIR='/opt/phdf5/1.8.16-gnu'
+FC = 'gfortran'
+CC = 'gcc'
+CXX = 'g++'
+MPI_DIR = '/opt/mpich/3.2-gnu'
+HDF5_DIR = '/opt/hdf5/1.8.16-gnu'
+PHDF5_DIR = '/opt/phdf5/1.8.16-gnu'
 
 # Script mode for extra capability
 script_mode = False
@@ -115,6 +115,7 @@ endif()
 # Define test data structure
 tests = OrderedDict()
 
+
 def cleanup(path):
     """Remove generated output files."""
     for dirpath, dirnames, filenames in os.walk(path):
@@ -173,7 +174,7 @@ class Test(object):
 
     # Sets the build name that will show up on the CDash
     def get_build_name(self):
-        self.build_name =  args.project + '_' + self.name
+        self.build_name = args.project + '_' + self.name
         return self.build_name
 
     # Sets up build options for various tests. It is used both
@@ -211,7 +212,7 @@ class Test(object):
             os.environ['HDF5_ROOT'] = PHDF5_DIR
         else:
             os.environ['HDF5_ROOT'] = HDF5_DIR
-        rc = call(['ctest', '-S', 'ctestscript.run','-V'])
+        rc = call(['ctest', '-S', 'ctestscript.run', '-V'])
         if rc != 0:
             self.success = False
             self.msg = 'Failed on ctest script.'
@@ -243,7 +244,7 @@ class Test(object):
             return
 
         # Default make string
-        make_list = ['make','-s']
+        make_list = ['make', '-s']
 
         # Check for parallel
         if args.n_procs is not None:
@@ -282,7 +283,7 @@ class Test(object):
 
 
 # Simple function to add a test to the global tests dictionary
-def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
+def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,
              phdf5=False, valgrind=False, coverage=False):
     tests.update({name: Test(name, debug, optimize, mpi, openmp, phdf5,
                              valgrind, coverage)})
@@ -363,7 +364,7 @@ ctest_vars = {
 
 # Check project name
 subprop = "set_property(GLOBAL PROPERTY SubProject {0})"
-if args.project == "" :
+if args.project == "":
     ctest_vars.update({'subproject': ''})
 elif args.project == 'develop':
     ctest_vars.update({'subproject': ''})
@@ -442,14 +443,14 @@ for key in iter(tests):
     # INCLUDE is a CTest command that allows for a subset
     # of tests to be executed. Only used in script mode.
     if args.regex_tests is None:
-        ctest_vars.update({'tests' : ''})
+        ctest_vars.update({'tests': ''})
 
         # No user tests, use default valgrind tests
         if test.valgrind:
-            ctest_vars.update({'tests' : 'INCLUDE {0}'.
+            ctest_vars.update({'tests': 'INCLUDE {0}'.
                               format(valgrind_default_tests)})
     else:
-        ctest_vars.update({'tests' : 'INCLUDE {0}'.
+        ctest_vars.update({'tests': 'INCLUDE {0}'.
                           format(args.regex_tests)})
 
     # Main part of code that does the ctest execution.