Merge pull request #964 from paulromano/unit-tests

Expand unit test suite and report coverage

.gitignore

@@ -101,3 +101,5 @@ examples/jupyter/plots
 .cache/
 .tox/
 .python-version
+.coverage
+htmlcov

.travis.yml

@@ -18,29 +18,27 @@ env:
   global:
     - FC=gfortran
     - MPI_DIR=/usr
-    - PHDF5_DIR=/usr
-    - HDF5_DIR=/usr
+    - HDF5_ROOT=/usr
     - OMP_NUM_THREADS=2
     - OPENMC_CROSS_SECTIONS=$HOME/nndc_hdf5/cross_sections.xml
     - OPENMC_ENDF_DATA=$HOME/endf-b-vii.1
     - OPENMC_MULTIPOLE_LIBRARY=$HOME/multipole_lib
     - PATH=$PATH:$HOME/NJOY2016/build
+    - DISPLAY=:99.0
   matrix:
-    - OPENMC_CONFIG="^hdf5-debug$"
-    - OPENMC_CONFIG="^omp-hdf5-debug$"
-    - OPENMC_CONFIG="^mpi-hdf5-debug$"
-    - OPENMC_CONFIG="^phdf5-debug$"
-
+    - OMP=n MPI=n PHDF5=n
+    - OMP=y MPI=n PHDF5=n
+    - OMP=n MPI=y PHDF5=n
+    - OMP=n MPI=y PHDF5=y
 before_install:
   - 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
-
 install:
   - ./tools/ci/travis-install.sh
-
 before_script:
   - ./tools/ci/travis-before-script.sh
-
 script:
   - ./tools/ci/travis-script.sh
+after_success:
+  - coveralls

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8.12 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.0 FATAL_ERROR)
 project(openmc Fortran C CXX)
 
 # Setup output directories
@@ -21,11 +21,6 @@ if (${UNIX})
   add_definitions(-DUNIX)
 endif()
 
-# Set MACOSX_RPATH
-if(POLICY CMP0042)
-  cmake_policy(SET CMP0042 NEW)
-endif()
-
 #===============================================================================
 # Command line options
 #===============================================================================
@@ -506,68 +501,3 @@ install(TARGETS ${program} libopenmc
 install(DIRECTORY src/relaxng DESTINATION share/openmc)
 install(FILES man/man1/openmc.1 DESTINATION share/man/man1)
 install(FILES LICENSE DESTINATION "share/doc/${program}" RENAME copyright)
-
-find_package(PythonInterp)
-if(PYTHONINTERP_FOUND)
-  if(debian)
-    install(CODE "execute_process(
-                    COMMAND ${PYTHON_EXECUTABLE} setup.py install
-                    --root=debian/openmc --install-layout=deb
-                    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})")
-  else()
-    install(CODE "set(ENV{PYTHONPATH} \"${CMAKE_INSTALL_PREFIX}/lib/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages\")")
-    install(CODE "execute_process(
-                    COMMAND ${PYTHON_EXECUTABLE} setup.py install
-                    --prefix=${CMAKE_INSTALL_PREFIX}
-                    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})")
-  endif()
-endif()
-
-#===============================================================================
-# Regression tests
-#===============================================================================
-
-# This allows for dashboard configuration
-include(CTest)
-
-# Get a list of all the tests to run
-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 ${test} PATH)
-
-  if (DEFINED ENV{MEM_CHECK})
-    # Generate input files if needed
-    if (NOT EXISTS "${TEST_PATH}/geometry.xml")
-      execute_process(COMMAND ${PYTHON_EXECUTABLE} ${TEST_NAME} --build-inputs
-        WORKING_DIRECTORY ${TEST_PATH})
-    endif()
-
-    # Add serial test
-    add_test(NAME ${TEST_NAME}
-      WORKING_DIRECTORY ${TEST_PATH}
-      COMMAND $<TARGET_FILE:openmc>)
-  else()
-    # Check serial/parallel
-    if (${MPI_ENABLED})
-      # Preform a parallel test
-      add_test(NAME ${TEST_NAME}
-        WORKING_DIRECTORY ${TEST_PATH}
-        COMMAND ${PYTHON_EXECUTABLE} ${TEST_NAME} --exe $<TARGET_FILE:openmc>
-        --mpi_exec ${MPI_DIR}/mpiexec)
-    else()
-      # Perform a serial test
-      add_test(NAME ${TEST_NAME}
-        WORKING_DIRECTORY ${TEST_PATH}
-        COMMAND ${PYTHON_EXECUTABLE} ${TEST_NAME} --exe $<TARGET_FILE:openmc>)
-    endif()
-  endif()
-endforeach(test)

docs/source/conf.py

@@ -27,8 +27,9 @@ except ImportError:
 MOCK_MODULES = ['numpy', 'numpy.polynomial', 'numpy.polynomial.polynomial',
                 'numpy.ctypeslib', 'scipy', 'scipy.sparse', 'scipy.interpolate',
                 'scipy.integrate', 'scipy.optimize', 'scipy.special',
-                'scipy.stats', 'h5py', 'pandas', 'uncertainties', 'matplotlib',
-                'matplotlib.pyplot','openmoc', 'openmc.data.reconstruct']
+                'scipy.stats', 'scipy.spatial', 'h5py', 'pandas', 'uncertainties',
+                'matplotlib', 'matplotlib.pyplot','openmoc',
+                'openmc.data.reconstruct']
 sys.modules.update((mod_name, MagicMock()) for mod_name in MOCK_MODULES)
 
 import numpy as np

docs/source/devguide/index.rst

@@ -10,9 +10,10 @@ as debugging.
 
 .. toctree::
     :numbered:
-    :maxdepth: 3
+    :maxdepth: 2
 
     styleguide
     workflow
+    tests
     user-input
     docbuild

docs/source/devguide/tests.rst

@@ -0,0 +1,73 @@
+.. _devguide_tests:
+
+==========
+Test Suite
+==========
+
+Running Tests
+-------------
+
+The OpenMC test suite consists of two parts, a regression test suite and a unit
+test suite. The regression test suite is based on regression or integrated
+testing where different types of input files are configured and the full OpenMC
+code is executed. Results from simulations are compared with expected
+results. The unit tests are primarily intended to test individual
+functions/classes in the OpenMC Python API.
+
+The test suite relies on the third-party `pytest <https://pytest.org>`_
+package. To run either or both the regression and unit test suites, it is
+assumed that you have OpenMC fully installed, i.e., the :ref:`scripts_openmc`
+executable is available on your :envvar:`PATH` and the :mod:`openmc` Python
+module is importable. In development where it would be onerous to continually
+install OpenMC every time a small change is made, it is recommended to install
+OpenMC in development/editable mode. With setuptools, this is accomplished by
+running::
+
+    python setup.py develop
+
+or using pip (recommended)::
+
+    pip install -e .[test]
+
+It is also assumed that you have cross section data available that is pointed to
+by the :envvar:`OPENMC_CROSS_SECTIONS` and :envvar:`OPENMC_MULTIPOLE_LIBRARY`
+environment variables. Furthermore, to run unit tests for the :mod:`openmc.data`
+module, it is necessary to have ENDF/B-VII.1 data available and pointed to by
+the :envvar:`OPENMC_ENDF_DATA` environment variable. All data sources can be
+obtained using the ``tools/ci/travis-before-script.sh`` script.
+
+To execute the test suite, go to the ``tests/`` directory and run::
+
+    pytest
+
+If you want to collect information about source line coverage in the Python API,
+you must have the `pytest-cov <https://pypi.python.org/pypi/pytest-cov>`_ plugin
+installed and run::
+
+    pytest --cov=../openmc --cov-report=html
+
+Adding Tests to the Regression Suite
+------------------------------------
+
+To add a new test to the regression test suite, create a sub-directory in the
+``tests/regression_tests/`` directory. To configure a test you need to add the
+following files to your new test directory:
+
+    * OpenMC input XML files, if they are not generated through the Python API
+    * **test.py** - Python test driver script; please refer to other tests to
+      see how to construct. Any output files that are generated during testing
+      must be removed at the end of this script.
+    * **inputs_true.dat** - ASCII file that contains Python API-generated XML
+      files concatenated together. When the test is run, inputs that are
+      generated are compared to this file.
+    * **results_true.dat** - ASCII file that contains the expected results from
+      the test. The file *results_test.dat* is compared to this file during the
+      execution of the python test driver script. When the above files have been
+      created, generate a *results_test.dat* file and copy it to this name and
+      commit. It should be noted that this file should be generated with basic
+      compiler options during openmc configuration and build (e.g., no MPI, no
+      debug/optimization).
+
+In addition to this description, please see the various types of tests that are
+already included in the test suite to see how to create them. If all is
+implemented correctly, the new test will automatically be discovered by pytest.

docs/source/devguide/workflow.rst

@@ -89,139 +89,6 @@ features and bug fixes. The general steps for contributing are as follows:
 6. After the pull request has been thoroughly vetted, it is merged back into the
    *develop* branch of mit-crpg/openmc.
 
-.. _test suite:
-
-OpenMC Test Suite
------------------
-
-The purpose of this test suite is to ensure that OpenMC compiles using various
-combinations of compiler flags and options, and that all user input options can
-be used successfully without breaking the code. The test suite is comprised of
-regression tests where different types of input files are configured and the
-full OpenMC code is executed. Results from simulations are compared with
-expected results. The test suite is comprised of many build configurations
-(e.g. debug, mpi, hdf5) and the actual tests which reside in sub-directories
-in the tests directory. We recommend to developers to test their branches
-before submitting a formal pull request using gfortran and Intel compilers
-if available.
-
-The test suite is designed to integrate with cmake using ctest_.  It is
-configured to run with cross sections from NNDC_ augmented with 0 K elastic
-scattering data for select nuclides as well as multipole data. To download the
-proper data, run the following commands:
-
-.. code-block:: sh
-
-    wget -O nndc_hdf5.tar.xz $(cat <openmc_root>/.travis.yml | grep anl.box | awk '{print $2}')
-    tar xJvf nndc_hdf5.tar.xz
-    export OPENMC_CROSS_SECTIONS=$(pwd)/nndc_hdf5/cross_sections.xml
-
-    git clone --branch=master git://github.com/smharper/windowed_multipole_library.git wmp_lib
-    tar xzvf wmp_lib/multipole_lib.tar.gz
-    export OPENMC_MULTIPOLE_LIBRARY=$(pwd)/multipole_lib
-
-The test suite can be run on an already existing build using:
-
-.. code-block:: sh
-
-    cd build
-    make test
-
-or
-
-.. code-block:: sh
-
-    cd build
-    ctest
-
-There are numerous ctest_ command line options that can be set to have
-more control over which tests are executed.
-
-Before running the test suite python script, the following environmental
-variables should be set if the default paths are incorrect:
-
-    * **FC** - The command for a Fortran compiler (e.g. gfotran, ifort).
-
-        * Default - *gfortran*
-
-    * **CC** - The command for a C compiler (e.g. gcc, icc).
-
-        * Default - *gcc*
-
-    * **CXX** - The command for a C++ compiler (e.g. g++, icpc).
-
-        * Default - *g++*
-
-    * **MPI_DIR** - The path to the MPI directory.
-
-        * Default - */opt/mpich/3.2-gnu*
-
-    * **HDF5_DIR** - The path to the HDF5 directory.
-
-        * Default - */opt/hdf5/1.8.16-gnu*
-
-    * **PHDF5_DIR** - The path to the parallel HDF5 directory.
-
-        * Default - */opt/phdf5/1.8.16-gnu*
-
-To run the full test suite, the following command can be executed in the
-tests directory:
-
-.. code-block:: sh
-
-    python run_tests.py
-
-A subset of build configurations and/or tests can be run. To see how to use
-the script run:
-
-.. code-block:: sh
-
-    python run_tests.py --help
-
-As an example, say we want to run all tests with debug flags only on tests
-that have cone and plot in their name. Also, we would like to run this on
-4 processors. We can run:
-
-.. code-block:: sh
-
-    python run_tests.py -j 4 -C debug -R "cone|plot"
-
-Note that standard regular expression syntax is used for selecting build
-configurations and tests. To print out a list of build configurations, we
-can run:
-
-.. code-block:: sh
-
-    python run_tests.py -p
-
-Adding tests to test suite
-++++++++++++++++++++++++++
-
-To add a new test to the test suite, create a sub-directory in the tests
-directory that conforms to the regular expression *test_*. To configure
-a test you need to add the following files to your new test directory,
-*test_name* for example:
-
-    * OpenMC input XML files
-    * **test_name.py** - Python test driver script, please refer to other
-      tests to see how to construct. Any output files that are generated
-      during testing must be removed at the end of this script.
-    * **inputs_true.dat** - ASCII file that contains Python API-generated XML
-      files concatenated together. When the test is run, inputs that are
-      generated are compared to this file.
-    * **results_true.dat** - ASCII file that contains the expected results
-      from the test. The file *results_test.dat* is compared to this file
-      during the execution of the python test driver script. When the
-      above files have been created, generate a *results_test.dat* file and
-      copy it to this name and commit. It should be noted that this file
-      should be generated with basic compiler options during openmc
-      configuration and build (e.g., no MPI/HDF5, no debug/optimization).
-
-In addition to this description, please see the various types of tests that
-are already included in the test suite to see how to create them. If all is
-implemented correctly, the new test directory will automatically be added
-to the CTest framework.
-
 Private Development
 -------------------
 
@@ -236,6 +103,27 @@ changes you've made in your private repository back to mit-crpg/openmc
 repository, simply follow the steps above with an extra step of pulling a branch
 from your private repository into a public fork.
 
+.. _devguide_editable:
+
+Working in "Development" Mode
+-----------------------------
+
+If you are making changes to the Python API during development, it is highly
+suggested to install the Python API in development/editable mode using
+pip_. From the root directory of the OpenMC repository, run:
+
+.. code-block:: sh
+
+    pip install -e .[test]
+
+This installs the OpenMC Python package in `"editable" mode
+<https://pip.pypa.io/en/stable/reference/pip_install/#editable-installs>`_ so
+that 1) it can be imported from a Python interpreter and 2) any changes made are
+immediately reflected in the installed version (that is, you don't need to keep
+reinstalling it). While the same effect can be achieved using the
+:envvar:`PYTHONPATH` environment variable, this is generally discouraged as it
+can interfere with virtual environments.
+
 .. _git: http://git-scm.com/
 .. _GitHub: https://github.com/
 .. _git flow: http://nvie.com/git-model
@@ -247,3 +135,4 @@ from your private repository into a public fork.
 .. _Bitbucket: https://bitbucket.org
 .. _ctest: http://www.cmake.org/cmake/help/v2.8.12/ctest.html
 .. _NNDC:  http://www.nndc.bnl.gov/endf/b7.1/acefiles.html
+.. _pip: https://pip.pypa.io/en/stable/

docs/source/quickinstall.rst

@@ -57,7 +57,6 @@ are no longer supported.
 
 .. _Personal Package Archive: https://launchpad.net/~paulromano/+archive/staging
 .. _APT package manager: https://help.ubuntu.com/community/AptGet/Howto
-.. _HDF5: http://www.hdfgroup.org/HDF5/
 
 ---------------------------------------
 Installing from Source on Ubuntu 15.04+
@@ -83,9 +82,12 @@ building and installing OpenMC from source.
 Installing from Source on Linux or Mac OS X
 -------------------------------------------
 
-All OpenMC source code is hosted on GitHub_. If you have git_, the gfortran_
-compiler, CMake_, and HDF5_ installed, you can download and install OpenMC be
-entering the following commands in a terminal:
+All OpenMC source code is hosted on `GitHub
+<https://github.com/mit-crpg/openmc>`_. If you have `git
+<https://git-scm.com>`_, the `gcc <https://gcc.gnu.org/>`_ compiler suite,
+`CMake <http://www.cmake.org>`_, and `HDF5 <https://www.hdfgroup.org/HDF5/>`_
+installed, you can download and install OpenMC be entering the following
+commands in a terminal:
 
 .. code-block:: sh
 
@@ -104,11 +106,15 @@ should specify an installation directory where you have write access, e.g.
 
     cmake -DCMAKE_INSTALL_PREFIX=$HOME/.local ..
 
+The :mod:`openmc` Python package must be installed separately. The easiest way
+to install it is using `pip <https://pip.pypa.io/en/stable/>`_, which is
+included by default in Python 2.7 and Python 3.4+. From the root directory of
+the OpenMC distribution/repository, run:
+
+.. code-block:: sh
+
+    pip install .
+
 If you want to build a parallel version of OpenMC (using OpenMP or MPI),
 directions can be found in the :ref:`detailed installation instructions
 <usersguide_build>`.
-
-.. _GitHub: https://github.com/mit-crpg/openmc
-.. _git: http://git-scm.com
-.. _gfortran: http://gcc.gnu.org/wiki/GFortran
-.. _CMake: http://www.cmake.org

docs/source/usersguide/install.rst

@@ -6,17 +6,18 @@ Installation and Configuration
 
 .. currentmodule:: openmc
 
+.. _install_conda:
+
 ----------------------------------------
 Installing on Linux/Mac with conda-forge
 ----------------------------------------
 
-`Conda <http://conda.pydata.org/docs/>`_ is an open source package management
-system and environment management system for installing multiple versions of
-software packages and their dependencies and switching easily between
-them. `conda-forge <https://conda-forge.github.io/>`_ is a community-led conda
-channel of installable packages. For instructions on installing conda, please
-consult their `documentation
-<http://conda.pydata.org/docs/install/quick.html>`_.
+Conda_ is an open source package management system and environment management
+system for installing multiple versions of software packages and their
+dependencies and switching easily between them. `conda-forge
+<https://conda-forge.github.io/>`_ is a community-led conda channel of
+installable packages. For instructions on installing conda, please consult their
+`documentation <http://conda.pydata.org/docs/install/quick.html>`_.
 
 Once you have `conda` installed on your system, add the `conda-forge` channel to
 your configuration with:
@@ -38,6 +39,8 @@ It is possible to list all of the versions of OpenMC available on your platform
 
     conda search openmc --channel conda-forge
 
+.. _install_ppa:
+
 -----------------------------
 Installing on Ubuntu with PPA
 -----------------------------
@@ -68,9 +71,11 @@ are no longer supported.
 .. _Personal Package Archive: https://launchpad.net/~paulromano/+archive/staging
 .. _APT package manager: https://help.ubuntu.com/community/AptGet/Howto
 
---------------------
-Building from Source
---------------------
+.. _install_source:
+
+----------------------
+Installing from Source
+----------------------
 
 .. _prerequisites:
 
@@ -191,8 +196,8 @@ switch to the source of the latest stable release, run the following commands::
     git checkout master
 
 .. _GitHub: https://github.com/mit-crpg/openmc
-.. _git: http://git-scm.com
-.. _ssh: http://en.wikipedia.org/wiki/Secure_Shell
+.. _git: https://git-scm.com
+.. _ssh: https://en.wikipedia.org/wiki/Secure_Shell
 
 .. _usersguide_build:
 
@@ -258,14 +263,15 @@ should be used:
 Compiling with MPI
 ++++++++++++++++++
 
-To compile with MPI, set the :envvar:`FC` and :envvar:`CC` environment variables
-to the path to the MPI Fortran and C wrappers, respectively. For example, in a
-bash shell:
+To compile with MPI, set the :envvar:`FC`, :envvar:`CC`, and :envvar:`CXX`
+environment variables to the path to the MPI Fortran, C, and C++ wrappers,
+respectively. For example, in a bash shell:
 
 .. code-block:: sh
 
-    export FC=mpif90
+    export FC=mpifort
     export CC=mpicc
+    export CXX=mpicxx
     cmake /path/to/openmc
 
 Note that in many shells, environment variables can be set for a single command,
@@ -273,7 +279,7 @@ i.e.
 
 .. code-block:: sh
 
-    FC=mpif90 CC=mpicc cmake /path/to/openmc
+    FC=mpifort CC=mpicc CXX=mpicxx cmake /path/to/openmc
 
 Selecting HDF5 Installation
 +++++++++++++++++++++++++++
@@ -349,7 +355,7 @@ follows:
 .. code-block:: sh
 
     mkdir build && cd build
-    FC=ifort CC=icc FFLAGS=-mmic cmake -Dopenmp=on ..
+    FC=ifort CC=icc CXX=icpc FFLAGS=-mmic cmake -Dopenmp=on ..
     make
 
 Note that unless an HDF5 build for the Intel Xeon Phi (Knights Corner) is
@@ -364,18 +370,54 @@ Testing Build
 
 To run the test suite, you will first need to download a pre-generated cross
 section library along with windowed multipole data. Please refer to our
-:ref:`test suite` documentation for further details.
+:ref:`devguide_tests` documentation for further details.
 
---------------------
-Python Prerequisites
---------------------
+---------------------
+Installing Python API
+---------------------
 
-OpenMC's :ref:`Python API <pythonapi>` works with either Python 2.7 or Python
-3.2+. In addition to Python itself, the API relies on a number of third-party
-packages. All prerequisites can be installed using `conda
-<http://conda.pydata.org/docs/>`_ (recommended), `pip
-<https://pip.pypa.io/en/stable/>`_, or through the package manager in most Linux
-distributions.
+If you installed OpenMC using :ref:`Conda <install_conda>` or :ref:`PPA
+<install_ppa>`, no further steps are necessary in order to use OpenMC's
+:ref:`Python API <pythonapi>`. However, if you are :ref:`installing from source
+<install_source>`, the Python API is not installed by default when ``make
+install`` is run because in many situations it doesn't make sense to install a
+Python package in the same location as the ``openmc`` executable (for example,
+if you are installing the package into a `virtual environment
+<https://docs.python.org/3/tutorial/venv.html>`_). The easiest way to install
+the :mod:`openmc` Python package is to use pip_, which is included by default in
+Python 2.7 and Python 3.4+. From the root directory of the OpenMC
+distribution/repository, run:
+
+.. code-block:: sh
+
+    pip install .
+
+pip will first check that all :ref:`required third-party packages
+<usersguide_python_prereqs>` have been installed, and if they are not present,
+they will be installed by downloading the appropriate packages from the Python
+Package Index (`PyPI <https://pypi.org/>`_). However, do note that since pip
+runs the ``setup.py`` script which requires NumPy, you will have to first
+install NumPy:
+
+.. code-block:: sh
+
+    pip install numpy
+
+Installing in "Development" Mode
+--------------------------------
+
+If you are primarily doing development with OpenMC, it is strongly recommended
+to install the Python package in :ref:`"editable" mode <devguide_editable>`.
+
+.. _usersguide_python_prereqs:
+
+Prerequisites
+-------------
+
+The Python API works with either Python 2.7 or Python 3.2+. In addition to
+Python itself, the API relies on a number of third-party packages. All
+prerequisites can be installed using Conda_ (recommended), pip_, or through the
+package manager in most Linux distributions.
 
 .. admonition:: Required
    :class: error
@@ -457,3 +499,5 @@ schemas.xml file in your own OpenMC source directory.
 .. _RELAX NG: http://relaxng.org/
 .. _NNDC: http://www.nndc.bnl.gov/endf/b7.1/acefiles.html
 .. _ctest: http://www.cmake.org/cmake/help/v2.8.12/ctest.html
+.. _Conda: https://conda.io/docs/
+.. _pip: https://pip.pypa.io/en/stable/

docs/source/usersguide/scripts.rst

@@ -168,8 +168,8 @@ ENDF/B-VII.1. It has the following optional arguments:
 
 This script downloads `ENDF/B-VII.1 ACE data
 <http://www.nndc.bnl.gov/endf/b7.1/acefiles.html>`_ from NNDC and converts it to
-an HDF5 library for use with OpenMC. This data is used for OpenMC's regression
-test suite. This script has the following optional arguments:
+an HDF5 library for use with OpenMC. This script has the following optional
+arguments:
 
 -b, --batch     Suppress standard in
 

openmc/cell.py

@@ -211,14 +211,7 @@ class Cell(IDManagerMixin):
     @fill.setter
     def fill(self, fill):
         if fill is not None:
-            if isinstance(fill, string_types):
-                if fill.strip().lower() != 'void':
-                    msg = 'Unable to set Cell ID="{0}" to use a non-Material ' \
-                          'or Universe fill "{1}"'.format(self._id, fill)
-                    raise ValueError(msg)
-                fill = None
-
-            elif isinstance(fill, Iterable):
+            if isinstance(fill, Iterable):
                 for i, f in enumerate(fill):
                     if f is not None:
                         cv.check_type('cell.fill[i]', f, openmc.Material)

openmc/examples.py

@@ -587,7 +587,7 @@ def slab_mg(reps=None, as_macro=True):
 
     # Define the materials file
     model.xs_data = xs
-    model.materials.cross_sections = "../1d_mgxs.h5"
+    model.materials.cross_sections = "../../1d_mgxs.h5"
 
     # Define surfaces.
     # Assembly/Problem Boundary

openmc/geometry.py

@@ -14,8 +14,9 @@ class Geometry(object):
 
     Parameters
     ----------
-    root_universe : openmc.Universe, optional
-        Root universe which contains all others
+    root : openmc.Universe or Iterable of openmc.Cell, optional
+        Root universe which contains all others, or an iterable of cells that
+        should be used to create a root universe.
 
     Attributes
     ----------
@@ -27,11 +28,17 @@ class Geometry(object):
 
     """
 
-    def __init__(self, root_universe=None):
+    def __init__(self, root=None):
         self._root_universe = None
         self._offsets = {}
-        if root_universe is not None:
-            self.root_universe = root_universe
+        if root is not None:
+            if isinstance(root, openmc.Universe):
+                self.root_universe = root
+            else:
+                univ = openmc.Universe()
+                for cell in root:
+                    univ.add_cell(cell)
+                self._root_universe = univ
 
     @property
     def root_universe(self):
@@ -249,7 +256,7 @@ class Geometry(object):
 
         for cell in self.get_all_cells().values():
             if cell.fill_type == 'lattice':
-                if cell.fill not in lattices:
+                if cell.fill.id not in lattices:
                     lattices[cell.fill.id] = cell.fill
 
         return lattices
@@ -306,9 +313,7 @@ class Geometry(object):
             elif not matching and name in material_name:
                 materials.add(material)
 
-        materials = list(materials)
-        materials.sort(key=lambda x: x.id)
-        return materials
+        return sorted(materials, key=lambda x: x.id)
 
     def get_cells_by_name(self, name, case_sensitive=False, matching=False):
         """Return a list of cells with matching names.
@@ -346,9 +351,7 @@ class Geometry(object):
             elif not matching and name in cell_name:
                 cells.add(cell)
 
-        cells = list(cells)
-        cells.sort(key=lambda x: x.id)
-        return cells
+        return sorted(cells, key=lambda x: x.id)
 
     def get_cells_by_fill_name(self, name, case_sensitive=False, matching=False):
         """Return a list of cells with fills with matching names.
@@ -393,9 +396,7 @@ class Geometry(object):
                 elif not matching and name in fill_name:
                     cells.add(cell)
 
-        cells = list(cells)
-        cells.sort(key=lambda x: x.id)
-        return cells
+        return sorted(cells, key=lambda x: x.id)
 
     def get_universes_by_name(self, name, case_sensitive=False, matching=False):
         """Return a list of universes with matching names.
@@ -433,9 +434,7 @@ class Geometry(object):
             elif not matching and name in universe_name:
                 universes.add(universe)
 
-        universes = list(universes)
-        universes.sort(key=lambda x: x.id)
-        return universes
+        return sorted(universes, key=lambda x: x.id)
 
     def get_lattices_by_name(self, name, case_sensitive=False, matching=False):
         """Return a list of lattices with matching names.
@@ -473,9 +472,7 @@ class Geometry(object):
             elif not matching and name in lattice_name:
                 lattices.add(lattice)
 
-        lattices = list(lattices)
-        lattices.sort(key=lambda x: x.id)
-        return lattices
+        return sorted(lattices, key=lambda x: x.id)
 
     def determine_paths(self, instances_only=False):
         """Determine paths through CSG tree for cells and materials.

openmc/lattice.py

@@ -54,25 +54,6 @@ class Lattice(IDManagerMixin):
         self._outer = None
         self._universes = None
 
-    def __eq__(self, other):
-        if not isinstance(other, Lattice):
-            return False
-        elif self.id != other.id:
-            return False
-        elif self.name != other.name:
-            return False
-        elif np.any(self.pitch != other.pitch):
-            return False
-        elif self.outer != other.outer:
-            return False
-        elif np.any(self.universes != other.universes):
-            return False
-        else:
-            return True
-
-    def __ne__(self, other):
-        return not self == other
-
     @property
     def name(self):
         return self._name
@@ -579,7 +560,11 @@ class RectLattice(Lattice):
 
     @property
     def ndim(self):
-        return len(self.pitch)
+        if self.pitch is not None:
+            return len(self.pitch)
+        else:
+            raise ValueError('Number of dimensions cannot be determined until '
+                             'the lattice pitch has been set.')
 
     @property
     def shape(self):
@@ -622,12 +607,12 @@ class RectLattice(Lattice):
             element coordinate system
 
         """
-        ix = floor((point[0] - self.lower_left[0])/self.pitch[0])
-        iy = floor((point[1] - self.lower_left[1])/self.pitch[1])
+        ix = int(floor((point[0] - self.lower_left[0])/self.pitch[0]))
+        iy = int(floor((point[1] - self.lower_left[1])/self.pitch[1]))
         if self.ndim == 2:
             idx = (ix, iy)
         else:
-            iz = floor((point[2] - self.lower_left[2])/self.pitch[2])
+            iz = int(floor((point[2] - self.lower_left[2])/self.pitch[2]))
             idx = (ix, iy, iz)
         return idx, self.get_local_coordinates(point, idx)
 
@@ -1034,10 +1019,10 @@ class HexLattice(Lattice):
             iz = 1
         else:
             z = point[2] - self.center[2]
-            iz = floor(z/self.pitch[1] + 0.5*self.num_axial)
+            iz = int(floor(z/self.pitch[1] + 0.5*self.num_axial))
         alpha = y - x/sqrt(3.)
-        ix = floor(x/(sqrt(0.75) * self.pitch[0]))
-        ia = floor(alpha/self.pitch[0])
+        ix = int(floor(x/(sqrt(0.75) * self.pitch[0])))
+        ia = int(floor(alpha/self.pitch[0]))
 
         # Check four lattice elements to see which one is closest based on local
         # coordinates

openmc/material.py

@@ -15,7 +15,7 @@ from .mixin import IDManagerMixin
 
 
 # Units for density supported by OpenMC
-DENSITY_UNITS = ['g/cm3', 'g/cc', 'kg/cm3', 'atom/b-cm', 'atom/cm3', 'sum',
+DENSITY_UNITS = ['g/cm3', 'g/cc', 'kg/m3', 'atom/b-cm', 'atom/cm3', 'sum',
                  'macro']
 
 
@@ -49,7 +49,7 @@ class Material(IDManagerMixin):
     density : float
         Density of the material (units defined separately)
     density_units : str
-        Units used for `density`. Can be one of 'g/cm3', 'g/cc', 'kg/cm3',
+        Units used for `density`. Can be one of 'g/cm3', 'g/cc', 'kg/m3',
         'atom/b-cm', 'atom/cm3', 'sum', or 'macro'.  The 'macro' unit only
         applies in the case of a multi-group calculation.
     depletable : bool
@@ -312,7 +312,7 @@ class Material(IDManagerMixin):
 
         Parameters
         ----------
-        units : {'g/cm3', 'g/cc', 'kg/cm3', 'atom/b-cm', 'atom/cm3', 'sum', 'macro'}
+        units : {'g/cm3', 'g/cc', 'kg/m3', 'atom/b-cm', 'atom/cm3', 'sum', 'macro'}
             Physical units of density.
         density : float, optional
             Value of the density. Must be specified unless units is given as

openmc/mgxs/mgxs.py

@@ -10,6 +10,7 @@ import itertools
 
 from six import add_metaclass, string_types
 import numpy as np
+import h5py
 
 import openmc
 import openmc.checkvalue as cv
@@ -1682,13 +1683,8 @@ class MGXS(object):
         ValueError
             When this method is called before the multi-group cross section is
             computed from tally data.
-        ImportError
-            When h5py is not installed.
 
         """
-
-        import h5py
-
         # Make directory if it does not exist
         if not os.path.exists(directory):
             os.makedirs(directory)

openmc/mixin.py

@@ -45,14 +45,24 @@ class IDManagerMixin(object):
 
     @id.setter
     def id(self, uid):
-        cls = type(self)
-        name = cls.__name__
+        # The first time this is called for a class, we search through the MRO
+        # to determine which class actually holds next_id and used_ids. Since
+        # next_id is an integer (immutable), we can't modify it directly through
+        # the instance without just creating a new attribute
+        try:
+            cls = self._id_class
+        except AttributeError:
+            for cls in self.__class__.__mro__:
+                if 'next_id' in cls.__dict__:
+                    break
+
         if uid is None:
             while cls.next_id in cls.used_ids:
                 cls.next_id += 1
             self._id = cls.next_id
             cls.used_ids.add(cls.next_id)
         else:
+            name = cls.__name__
             cv.check_type('{} ID'.format(name), uid, Integral)
             cv.check_greater_than('{} ID'.format(name), uid, 0, equality=True)
             if uid in cls.used_ids:

openmc/model/triso.py

@@ -12,11 +12,7 @@ from abc import ABCMeta, abstractproperty, abstractmethod
 
 from six import add_metaclass
 import numpy as np
-try:
-    import scipy.spatial
-    _SCIPY_AVAILABLE = True
-except ImportError:
-    _SCIPY_AVAILABLE = False
+import scipy.spatial
 
 import openmc
 import openmc.checkvalue as cv
@@ -742,7 +738,7 @@ def _close_random_pack(domain, particles, contraction_rate):
         outer_pf = (4/3 * pi * (outer_diameter[0]/2)**3 * n_particles /
                     domain.volume)
 
-        j = floor(-log10(outer_pf - inner_pf))
+        j = int(floor(-log10(outer_pf - inner_pf)))
         outer_diameter[0] = (outer_diameter[0] - 0.5**j * contraction_rate *
                              initial_outer_diameter / n_particles)
 
@@ -837,10 +833,6 @@ def _close_random_pack(domain, particles, contraction_rate):
         if rods:
             inner_diameter[0] = rods[0][0]
 
-    if not _SCIPY_AVAILABLE:
-        raise ImportError('SciPy must be installed to perform '
-                          'close random packing.')
-
     n_particles = len(particles)
     diameter = 2*domain.particle_radius
 

openmc/region.py

@@ -39,10 +39,8 @@ class Region(object):
     def __eq__(self, other):
         if not isinstance(other, type(self)):
             return False
-        elif str(self) != str(other):
-            return False
         else:
-            return True
+            return str(self) == str(other)
 
     def __ne__(self, other):
         return not self == other
@@ -463,7 +461,7 @@ class Union(Region, MutableSequence):
         if memo is None:
             memo = {}
 
-        clone = copy.deepcopy(self)
+        clone = deepcopy(self)
         clone[:] = [n.clone(memo) for n in self]
         return clone
 
@@ -584,6 +582,6 @@ class Complement(Region):
         if memo is None:
             memo = {}
 
-        clone = copy.deepcopy(self)
+        clone = deepcopy(self)
         clone.node = self.node.clone(memo)
         return clone

openmc/settings.py

@@ -60,6 +60,8 @@ class Settings(object):
         type are 'variance', 'std_dev', and 'rel_err'. The threshold value
         should be a float indicating the variance, standard deviation, or
         relative error used.
+    log_grid_bins : int
+        Number of bins for logarithmic energy grid search
     max_order : None or int
         Maximum scattering order to apply globally when in multi-group mode.
     multipole_library : str
@@ -220,19 +222,12 @@ class Settings(object):
         # Uniform fission source subelement
         self._ufs_mesh = None
 
-        # Domain decomposition subelement
-        self._dd_mesh_dimension = None
-        self._dd_mesh_lower_left = None
-        self._dd_mesh_upper_right = None
-        self._dd_nodemap = None
-        self._dd_allow_leakage = False
-        self._dd_count_interactions = False
-
         self._resonance_scattering = {}
         self._volume_calculations = cv.CheckedList(
             VolumeCalculation, 'volume calculations')
 
         self._create_fission_neutrons = None
+        self._log_grid_bins = None
 
     @property
     def run_mode(self):
@@ -362,30 +357,6 @@ class Settings(object):
     def ufs_mesh(self):
         return self._ufs_mesh
 
-    @property
-    def dd_mesh_dimension(self):
-        return self._dd_mesh_dimension
-
-    @property
-    def dd_mesh_lower_left(self):
-        return self._dd_mesh_lower_left
-
-    @property
-    def dd_mesh_upper_right(self):
-        return self._dd_mesh_upper_right
-
-    @property
-    def dd_nodemap(self):
-        return self._dd_nodemap
-
-    @property
-    def dd_allow_leakage(self):
-        return self._dd_allow_leakage
-
-    @property
-    def dd_count_interactions(self):
-        return self._dd_count_interactions
-
     @property
     def resonance_scattering(self):
         return self._resonance_scattering
@@ -398,6 +369,10 @@ class Settings(object):
     def create_fission_neutrons(self):
         return self._create_fission_neutrons
 
+    @property
+    def log_grid_bins(self):
+        return self._log_grid_bins
+
     @run_mode.setter
     def run_mode(self, run_mode):
         cv.check_value('run mode', run_mode, _RUN_MODES)
@@ -696,85 +671,6 @@ class Settings(object):
         cv.check_length('UFS mesh upper-right corner', ufs_mesh.upper_right, 3)
         self._ufs_mesh = ufs_mesh
 
-    @dd_mesh_dimension.setter
-    def dd_mesh_dimension(self, dimension):
-        # TODO: remove this when domain decomposition is merged
-        warnings.warn('This feature is not yet implemented in a release '
-                      'version of openmc')
-
-        cv.check_type('DD mesh dimension', dimension, Iterable, Integral)
-        cv.check_length('DD mesh dimension', dimension, 3)
-
-        self._dd_mesh_dimension = dimension
-
-    @dd_mesh_lower_left.setter
-    def dd_mesh_lower_left(self, lower_left):
-        # TODO: remove this when domain decomposition is merged
-        warnings.warn('This feature is not yet implemented in a release '
-                      'version of openmc')
-
-        cv.check_type('DD mesh lower left corner', lower_left, Iterable, Real)
-        cv.check_length('DD mesh lower left corner', lower_left, 3)
-
-        self._dd_mesh_lower_left = lower_left
-
-    @dd_mesh_upper_right.setter
-    def dd_mesh_upper_right(self, upper_right):
-        # TODO: remove this when domain decomposition is merged
-        warnings.warn('This feature is not yet implemented in a release '
-                      'version of openmc')
-
-        cv.check_type('DD mesh upper right corner', upper_right, Iterable, Real)
-        cv.check_length('DD mesh upper right corner', upper_right, 3)
-
-        self._dd_mesh_upper_right = upper_right
-
-    @dd_nodemap.setter
-    def dd_nodemap(self, nodemap):
-        # TODO: remove this when domain decomposition is merged
-        warnings.warn('This feature is not yet implemented in a release '
-                      'version of openmc')
-
-        cv.check_type('DD nodemap', nodemap, Iterable)
-
-        nodemap = np.array(nodemap).flatten()
-
-        if self._dd_mesh_dimension is None:
-            msg = 'Must set DD mesh dimension before setting the nodemap'
-            raise ValueError(msg)
-        else:
-            len_nodemap = np.prod(self._dd_mesh_dimension)
-
-        if len(nodemap) < len_nodemap or len(nodemap) > len_nodemap:
-            msg = 'Unable to set DD nodemap with length "{0}" which ' \
-                  'does not have the same dimensionality as the domain ' \
-                  'mesh'.format(len(nodemap))
-            raise ValueError(msg)
-
-        self._dd_nodemap = nodemap
-
-    @dd_allow_leakage.setter
-    def dd_allow_leakage(self, allow):
-
-        # TODO: remove this when domain decomposition is merged
-        warnings.warn('This feature is not yet implemented in a release '
-                      'version of openmc')
-
-        cv.check_type('DD allow leakage', allow, bool)
-
-        self._dd_allow_leakage = allow
-
-    @dd_count_interactions.setter
-    def dd_count_interactions(self, interactions):
-
-        # TODO: remove this when domain decomposition is merged
-        warnings.warn('This feature is not yet implemented in a release '
-                      'version of openmc')
-
-        cv.check_type('DD count interactions', interactions, bool)
-
-        self._dd_count_interactions = interactions
-
     @resonance_scattering.setter
     def resonance_scattering(self, res):
         cv.check_type('resonance scattering settings', res, Mapping)
@@ -812,6 +708,12 @@ class Settings(object):
                       create_fission_neutrons, bool)
         self._create_fission_neutrons = create_fission_neutrons
 
+    @log_grid_bins.setter
+    def log_grid_bins(self, log_grid_bins):
+        cv.check_type('log grid bins', log_grid_bins, Real)
+        cv.check_greater_than('log grid bins', log_grid_bins, 0)
+        self._log_grid_bins = log_grid_bins
+
     def _create_run_mode_subelement(self, root):
         elem = ET.SubElement(root, "run_mode")
         elem.text = self._run_mode
@@ -1033,33 +935,6 @@ class Settings(object):
             subelement = ET.SubElement(root, "ufs_mesh")
             subelement.text = str(self.ufs_mesh.id)
 
-    def _create_dd_subelement(self, root):
-        if self._dd_mesh_lower_left is not None and \
-           self._dd_mesh_upper_right is not None and \
-           self._dd_mesh_dimension is not None:
-
-            element = ET.SubElement(root, "domain_decomposition")
-
-            subelement = ET.SubElement(element, "mesh")
-            subsubelement = ET.SubElement(subelement, "dimension")
-            subsubelement.text = ' '.join(map(str, self._dd_mesh_dimension))
-
-            subsubelement = ET.SubElement(subelement, "lower_left")
-            subsubelement.text = ' '.join(map(str, self._dd_mesh_lower_left))
-
-            subsubelement = ET.SubElement(subelement, "upper_right")
-            subsubelement.text = ' '.join(map(str, self._dd_mesh_upper_right))
-
-            if self._dd_nodemap is not None:
-                subelement = ET.SubElement(element, "nodemap")
-                subelement.text = ' '.join(map(str, self._dd_nodemap))
-
-            subelement = ET.SubElement(element, "allow_leakage")
-            subelement.text = str(self._dd_allow_leakage).lower()
-
-            subelement = ET.SubElement(element, "count_interactions")
-            subelement.text = str(self._dd_count_interactions).lower()
-
     def _create_resonance_scattering_subelement(self, root):
         res = self.resonance_scattering
         if res:
@@ -1085,6 +960,11 @@ class Settings(object):
             elem = ET.SubElement(root, "create_fission_neutrons")
             elem.text = str(self._create_fission_neutrons).lower()
 
+    def _create_log_grid_bins_subelement(self, root):
+        if self._log_grid_bins is not None:
+            elem = ET.SubElement(root, "log_grid_bins")
+            elem.text = str(self._log_grid_bins)
+
     def export_to_xml(self, path='settings.xml'):
         """Export simulation settings to an XML file.
 
@@ -1128,10 +1008,10 @@ class Settings(object):
         self._create_trace_subelement(root_element)
         self._create_track_subelement(root_element)
         self._create_ufs_mesh_subelement(root_element)
-        self._create_dd_subelement(root_element)
         self._create_resonance_scattering_subelement(root_element)
         self._create_volume_calcs_subelement(root_element)
         self._create_create_fission_neutrons_subelement(root_element)
+        self._create_log_grid_bins_subelement(root_element)
 
         # Clean the indentation in the file to be user-readable
         clean_xml_indentation(root_element)

openmc/stats/univariate.py

@@ -194,12 +194,12 @@ class Maxwell(Univariate):
     Parameters
     ----------
     theta : float
-        Effective temperature for distribution
+        Effective temperature for distribution in eV
 
     Attributes
     ----------
     theta : float
-        Effective temperature for distribution
+        Effective temperature for distribution in eV
 
     """
 
@@ -250,16 +250,16 @@ class Watt(Univariate):
     Parameters
     ----------
     a : float
-        First parameter of distribution
+        First parameter of distribution in units of eV
     b : float
-        Second parameter of distribution
+        Second parameter of distribution in units of 1/eV
 
     Attributes
     ----------
     a : float
-        First parameter of distribution
+        First parameter of distribution in units of eV
     b : float
-        Second parameter of distribution
+        Second parameter of distribution in units of 1/eV
 
     """
 
@@ -444,10 +444,9 @@ class Legendre(Univariate):
     def coefficients(self, coefficients):
         cv.check_type('Legendre expansion coefficients', coefficients,
                       Iterable, Real)
-        for l in range(len(coefficients)):
-            coefficients[l] *= (2.*l + 1.)/2.
-        self._legendre_polynomial = np.polynomial.legendre.Legendre(
-            coefficients)
+        l = np.arange(len(coefficients))
+        coeffs = (2.*l + 1.)/2. * np.array(coefficients)
+        self._legendre_polynomial = np.polynomial.Legendre(coeffs)
 
     def to_xml_element(self, element_name):
         raise NotImplementedError

openmc/surface.py

@@ -1376,7 +1376,7 @@ class Cone(Surface):
 
     @property
     def r2(self):
-        return self.coefficients['r2']
+        return self.coefficients['R2']
 
     @x0.setter
     def x0(self, x0):

openmc/tallies.py

@@ -1508,8 +1508,6 @@ class Tally(IDManagerMixin):
         ------
         KeyError
             When this method is called before the Tally is populated with data
-        ImportError
-            When Pandas can not be found on the caller's system
 
         """
 

openmc/universe.py

@@ -92,7 +92,7 @@ class Universe(IDManagerMixin):
             return openmc.Union(regions).bounding_box
         else:
             # Infinite bounding box
-            return openmc.Intersection().bounding_box
+            return openmc.Intersection([]).bounding_box
 
     @name.setter
     def name(self, name):
@@ -322,7 +322,7 @@ class Universe(IDManagerMixin):
         if not isinstance(cell, openmc.Cell):
             msg = 'Unable to add a Cell to Universe ID="{0}" since "{1}" is not ' \
                   'a Cell'.format(self._id, cell)
-            raise ValueError(msg)
+            raise TypeError(msg)
 
         cell_id = cell.id
 
@@ -342,7 +342,7 @@ class Universe(IDManagerMixin):
         if not isinstance(cells, Iterable):
             msg = 'Unable to add Cells to Universe ID="{0}" since "{1}" is not ' \
                   'iterable'.format(self._id, cells)
-            raise ValueError(msg)
+            raise TypeError(msg)
 
         for cell in cells:
             self.add_cell(cell)
@@ -360,7 +360,7 @@ class Universe(IDManagerMixin):
         if not isinstance(cell, openmc.Cell):
             msg = 'Unable to remove a Cell from Universe ID="{0}" since "{1}" is ' \
                   'not a Cell'.format(self._id, cell)
-            raise ValueError(msg)
+            raise TypeError(msg)
 
         # If the Cell is in the Universe's list of Cells, delete it
         if cell.id in self._cells:

pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+python_files = test*.py
+python_classes = NoThanks
+filterwarnings = ignore::UserWarning

readme.rst

@@ -2,7 +2,7 @@
 OpenMC Monte Carlo Particle Transport Code
 ==========================================
 
-|licensebadge| |travisbadge|
+|licensebadge| |travisbadge| |coverallsbadge|
 
 The OpenMC project aims to provide a fully-featured Monte Carlo particle
 transport code based on modern methods. It is a constructive solid geometry,
@@ -74,3 +74,7 @@ OpenMC is distributed under the MIT/X 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)
+
+.. |coverallsbadge| image:: https://coveralls.io/repos/github/mit-crpg/openmc/badge.svg?branch=develop
+   :target: https://coveralls.io/github/mit-crpg/openmc?branch=develop
+   :alt: Code Coverage

setup.py

@@ -26,7 +26,7 @@ with open('openmc/__init__.py', 'r') as f:
 kwargs = {
     'name': 'openmc',
     'version': version,
-    'packages': find_packages(),
+    'packages': find_packages(exclude=['tests*']),
     'scripts': glob.glob('scripts/openmc-*'),
 
     # Data files and librarries

src/volume_calc.F90

@@ -193,11 +193,13 @@ contains
 
       if (this % domain_type == FILTER_MATERIAL) then
         i_material = p % material
-        do i_domain = 1, size(this % domain_id)
-          if (i_material == materials(i_domain) % id) then
-            call check_hit(i_domain, i_material, indices, hits, n_mat)
-          end if
-        end do
+        if (i_material /= MATERIAL_VOID) then
+          do i_domain = 1, size(this % domain_id)
+            if (materials(i_material) % id == this % domain_id(i_domain)) then
+              call check_hit(i_domain, i_material, indices, hits, n_mat)
+            end if
+          end do
+        end if
 
       elseif (this % domain_type == FILTER_CELL) THEN
         do level = 1, p % n_coord

tests/conftest.py

@@ -0,0 +1,17 @@
+from tests.regression_tests import config as regression_config
+
+
+def pytest_addoption(parser):
+    parser.addoption('--exe')
+    parser.addoption('--mpi', action='store_true')
+    parser.addoption('--mpiexec')
+    parser.addoption('--mpi-np')
+    parser.addoption('--update', action='store_true')
+    parser.addoption('--build-inputs', action='store_true')
+
+
+def pytest_configure(config):
+    opts = ['exe', 'mpi', 'mpiexec', 'mpi_np', 'update', 'build_inputs']
+    for opt in opts:
+        if config.getoption(opt) is not None:
+            regression_config[opt] = config.getoption(opt)

tests/convert_precision.py

@@ -1,23 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import glob
-
-dirs = glob.glob('test_*')
-
-for adir in dirs:
-
-    os.chdir(adir)
-
-    files = glob.glob('results.py')
-
-    if len(files) > 0:
-
-        files = files[0]
-        with open(files, 'r') as fh:
-            intxt = fh.read()
-        intxt = intxt.replace('14.8E', '12.6E')
-        with open(files, 'w') as fh:
-            fh.write(intxt)
-
-    os.chdir('..')

tests/readme.rst

@@ -1,58 +1 @@
-=================
-OpenMC Test Suite
-=================
-
-The purpose of this test suite is to ensure that OpenMC compiles using various
-combinations of compiler flags and options and that all user input options can
-be used successfully without breaking the code. The test suite is based on
-regression or integrated testing where different types of input files are
-configured and the full OpenMC code is executed. Results from simulations
-are compared with expected results. The test suite is comprised of many
-build configurations (e.g. debug, mpi, hdf5) and the actual tests which
-reside in sub-directories in the tests directory.
-
-The test suite is designed to integrate with cmake using ctest_. To run the
-full test suite run:
-
-.. code-block:: sh
-
-    python run_tests.py
-
-The test suite is configured to run with cross sections from NNDC_. To
-download these cross sections please do the following:
-
-.. code-block:: sh
-
-    cd ../data
-    python get_nndc.py
-    export CROSS_SECTIONS=<path_to_data_folder>/nndc/cross_sections.xml
-
-The environmental variable **CROSS_SECTIONS** can be used to quickly switch
-between the cross sections  set for the test suite and cross section set for 
-your simulations.
-
-A subset of build configurations and/or tests can be run. To see how to use
-the script run:
-
-.. code-block:: sh
-
-    python run_tests.py --help
-
-As an example, say we want to run all tests with debug flags only on tests
-that have cone and plot in their name. Also, we would like to run this on
-4 processors. We can run:
-
-.. code-block:: sh
-
-    python run_tests.py -j 4 -C debug -R "cone|plot"
-
-Note that standard regular expression syntax is used for selecting build
-configurations and tests. To print out a list of build configurations, we
-can run:
-
-.. code-block:: sh
-
-    python run_tests.py -p
-
-.. _ctest: http://www.cmake.org/cmake/help/v2.8.12/ctest.html
-.. _NNDC:  http://http://www.nndc.bnl.gov/endf/b7.1/acefiles.html
+See docs/source/devguide/tests.rst for information on the OpenMC test suite.

tests/regression_tests/__init__.py

@@ -0,0 +1,9 @@
+# Test configuration options for regression tests
+config = {
+    'exe': 'openmc',
+    'mpi': False,
+    'mpiexec': 'mpiexec',
+    'mpi_np': '2',
+    'update': False,
+    'build_inputs': False
+}

tests/regression_tests/asymmetric_lattice/test.py

@@ -1,13 +1,11 @@
-#!/usr/bin/env python
-
 import os
-import sys
 import glob
 import hashlib
-sys.path.insert(0, os.pardir)
-from testing_harness import PyAPITestHarness
+
 import openmc
 
+from tests.testing_harness import PyAPITestHarness
+
 
 class AsymmetricLatticeTestHarness(PyAPITestHarness):
     def __init__(self, *args, **kwargs):
@@ -90,6 +88,6 @@ class AsymmetricLatticeTestHarness(PyAPITestHarness):
         return outstr
 
 
-if __name__ == '__main__':
+def test_asymmetric_lattice():
     harness = AsymmetricLatticeTestHarness('statepoint.10.h5')
     harness.main()

tests/regression_tests/cmfd_feed/test.py

@@ -0,0 +1,6 @@
+from tests.testing_harness import CMFDTestHarness
+
+
+def test_cmfd_feed():
+    harness = CMFDTestHarness('statepoint.20.h5')
+    harness.main()

tests/regression_tests/cmfd_nofeed/test.py

@@ -0,0 +1,6 @@
+from tests.testing_harness import CMFDTestHarness
+
+
+def test_cmfd_nofeed():
+    harness = CMFDTestHarness('statepoint.20.h5')
+    harness.main()

tests/regression_tests/complex_cell/test.py

@@ -0,0 +1,6 @@
+from tests.testing_harness import TestHarness
+
+
+def test_complex_cell():
+    harness = TestHarness('statepoint.10.h5')
+    harness.main()

tests/regression_tests/confidence_intervals/test.py

@@ -0,0 +1,6 @@
+from tests.testing_harness import TestHarness
+
+
+def test_confidence_intervals():
+    harness = TestHarness('statepoint.10.h5')
+    harness.main()

tests/regression_tests/conftest.py

@@ -0,0 +1,15 @@
+import openmc
+import pytest
+
+
+@pytest.fixture(scope='module', autouse=True)
+def setup_regression_test(request):
+    # Reset autogenerated IDs assigned to OpenMC objects
+    openmc.reset_auto_ids()
+
+    # Change to test directory
+    olddir = request.fspath.dirpath().chdir()
+    try:
+        yield
+    finally:
+        olddir.chdir()

tests/regression_tests/create_fission_neutrons/test.py

@@ -1,11 +1,7 @@
-#!/usr/bin/env python
-
-import os
-import sys
-sys.path.insert(0, os.pardir)
-from testing_harness import PyAPITestHarness
 import openmc
 
+from tests.testing_harness import PyAPITestHarness
+
 
 class CreateFissionNeutronsTestHarness(PyAPITestHarness):
     def _build_inputs(self):
@@ -69,6 +65,6 @@ class CreateFissionNeutronsTestHarness(PyAPITestHarness):
         return outstr
 
 
-if __name__ == '__main__':
+def test_create_fission_neutrons():
     harness = CreateFissionNeutronsTestHarness('statepoint.10.h5')
     harness.main()

tests/regression_tests/density/test.py

@@ -0,0 +1,6 @@
+from tests.testing_harness import TestHarness
+
+
+def test_density():
+    harness = TestHarness('statepoint.10.h5')
+    harness.main()

tests/regression_tests/diff_tally/test.py

@@ -1,15 +1,12 @@
-#!/usr/bin/env python
-
 import glob
 import os
-import sys
 
 import pandas as pd
-
-sys.path.insert(0, os.pardir)
-from testing_harness import PyAPITestHarness
 import openmc
 
+from tests.testing_harness import PyAPITestHarness
+
+
 class DiffTallyTestHarness(PyAPITestHarness):
     def __init__(self, *args, **kwargs):
         super(DiffTallyTestHarness, self).__init__(*args, **kwargs)
@@ -125,6 +122,6 @@ class DiffTallyTestHarness(PyAPITestHarness):
         return df.to_csv(None, columns=cols, index=False, float_format='%.7e')
 
 
-if __name__ == '__main__':
+def test_diff_tally():
     harness = DiffTallyTestHarness('statepoint.3.h5')
     harness.main()

tests/regression_tests/distribmat/test.py

@@ -1,11 +1,7 @@
-#!/usr/bin/env python
-
-import os
-import sys
-sys.path.insert(0, os.pardir)
-from testing_harness import TestHarness, PyAPITestHarness
 import openmc
 
+from tests.testing_harness import TestHarness, PyAPITestHarness
+
 
 class DistribmatTestHarness(PyAPITestHarness):
     def _build_inputs(self):
@@ -103,6 +99,6 @@ class DistribmatTestHarness(PyAPITestHarness):
         return outstr
 
 
-if __name__ == '__main__':
+def test_distribmat():
     harness = DistribmatTestHarness('statepoint.5.h5')
     harness.main()

tests/regression_tests/eigenvalue_genperbatch/test.py

@@ -0,0 +1,6 @@
+from tests.testing_harness import TestHarness
+
+
+def test_eigenvalue_genperbatch():
+    harness = TestHarness('statepoint.7.h5')
+    harness.main()

tests/regression_tests/eigenvalue_no_inactive/test.py

@@ -0,0 +1,6 @@
+from tests.testing_harness import TestHarness
+
+
+def test_eigenvalue_no_inactive():
+    harness = TestHarness('statepoint.10.h5')
+    harness.main()