Merge pull request #922 from paulromano/unittest

Set up unit testing infrastructure
2026-07-28 06:05:58 -04:00 · 2017-11-07 11:36:45 -05:00 · 2017-11-07 11:36:45 -05:00 · 1abb1bfa1b
commit 1abb1bfa1b
parent 8047f6c134 1c8fbf5367
11 changed files with 179 additions and 179 deletions
--- a/.gitignore
+++ b/.gitignore
@ -97,3 +97,7 @@ examples/jupyter/plots
 *.c
 *.html
 *.so
+
+.cache/
+.tox/
+.python-version
--- 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 six numpy scipy h5py=2.5 pandas;
-      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;
@ -52,7 +38,11 @@ before_install:
      export HDF5_DIR=/usr;
    fi

-install: true
+install:
+  - if [[ $OPENMC_CONFIG != "check_source" ]]; then
+      pip install numpy cython;
+      pip install -e .[test];
+    fi

 before_script:
  - if [[ $OPENMC_CONFIG != "check_source" ]]; then
@ -72,5 +62,6 @@ script:
      ./check_source.py;
    else
      ./run_tests.py -C $OPENMC_CONFIG -j 2;
+      pytest --cov=../openmc unit_tests/;
    fi
  - cd ..
--- 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)
--- a/CTestConfig.cmake
+++ b/CTestConfig.cmake
@ -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 "")
--- a/MANIFEST.in
+++ b/MANIFEST.in
@ -0,0 +1,35 @@
+include CMakeLists.txt
+include LICENSE
+include schemas.xml
+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
--- a/14
+++ b/14
@ -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
--- 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:

--- 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)
--- 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, find_packages
 try:
    from Cython.Build import cythonize
    have_cython = True
@ -28,47 +23,53 @@ 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': 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',
-          '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'
-          ]}
+    # Metadata
+    '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',
+        'Intended Audience :: Developers',
+        'Intended Audience :: End Users/Desktop',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: MIT License',
+        'Natural Language :: English',
+        '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',
+    ],

-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', 'ipython', 'matplotlib',
+        'pandas>=0.17.0', 'lxml', 'uncertainties'
+    ],

-        # Optional dependencies
-        'extras_require': {
-            'decay': ['uncertainties'],
-            'plot': ['matplotlib', 'ipython'],
-            'vtk': ['vtk', 'silomesh'],
-            'validate': ['lxml']
-        },
-
-    })
+    # Optional dependencies
+    'extras_require': {
+        'test': ['pytest', 'pytest-cov'],
+        'vtk': ['vtk', 'silomesh'],
+    },
+}

 # If Cython is present, add resonance reconstruction capability
 if have_cython:
--- a/tests/run_tests.py
+++ b/tests/run_tests.py
@ -10,43 +10,43 @@ 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',
-                  help="Number of parallel jobs.")
-parser.add_option('-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',
-                  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",
-                  dest="list_build_configs", default=False,
-                  help="List out build configurations.")
-parser.add_option("-p", "--project", dest="project", default="",
-                  help="project name for build")
-parser.add_option("-D", "--dashboard", dest="dash",
-                  help="Dash name -- Experimental, Nightly, Continuous")
-parser.add_option("-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",
-                  help="Activate CTest scripting mode for coverage, valgrind\
-                        and dashboard capability.")
-(options, args) = parser.parse_args()
+parser = ArgumentParser()
+parser.add_argument('-j', '--parallel', dest='n_procs', default='1',
+                    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.")
+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_argument('-l', '--list', action="store_true",
+                    dest="list_build_configs", default=False,
+                    help="List out build configurations.")
+parser.add_argument("-p", "--project", dest="project", default="",
+                    help="project name for build")
+parser.add_argument("-D", "--dashboard", dest="dash",
+                    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.")
+parser.add_argument("-s", "--script", action="store_true", dest="script",
+                    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 =  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
@ -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.'
@ -243,12 +244,12 @@ class Test(object):
            return

        # Default make string
-        make_list = ['make','-s']
+        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 +266,14 @@ 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)
@ -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)})
@ -308,7 +309,7 @@ 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 +321,10 @@ 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 +334,21 @@ 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 +359,17 @@ 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 +391,8 @@ 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()

@ -447,16 +442,16 @@ 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:
-        ctest_vars.update({'tests' : ''})
+    if args.regex_tests is None:
+        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}'.
-                          format(options.regex_tests)})
+        ctest_vars.update({'tests': 'INCLUDE {0}'.
+                          format(args.regex_tests)})

    # Main part of code that does the ctest execution.
    # It is broken up by two modes, script and non-script
--- a/tests/test_element_wo/test_element_wo.py
+++ b/tests/test_element_wo/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.