Merge branch 'develop' into photon-new

.gitignore

@@ -95,3 +95,7 @@ examples/jupyter/plots
 *.c
 *.html
 *.so
+
+.cache/
+.tox/
+.python-version

.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
@@ -71,6 +61,7 @@ script:
   - if [[ $OPENMC_CONFIG == "check_source" ]]; then
       ./check_source.py;
     else
-      ./run_tests.py -C $OPENMC_CONFIG -j 2;
+      ./run_tests.py -C $OPENMC_CONFIG -j 2 &&
+      pytest --cov=../openmc unit_tests/;
     fi
   - cd ..

CMakeLists.txt

@@ -119,8 +119,8 @@ if(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
   list(APPEND f90flags -cpp -std=f2008ts -fbacktrace -O2)
   if(debug)
     list(REMOVE_ITEM f90flags -O2)
-    list(APPEND f90flags -g -Wall -pedantic -fbounds-check
-      -ffpe-trap=invalid,overflow,underflow)
+    list(APPEND f90flags -g -Wall -Wno-unused-dummy-argument -pedantic
+      -fbounds-check -ffpe-trap=invalid,overflow,underflow)
     list(APPEND ldflags -g)
   endif()
   if(profile)
@@ -320,10 +320,8 @@ set(LIBOPENMC_FORTRAN_SRC
   src/endf_header.F90
   src/energy_distribution.F90
   src/error.F90
-  src/finalize.F90
   src/geometry.F90
   src/geometry_header.F90
-  src/global.F90
   src/hdf5_interface.F90
   src/initialize.F90
   src/input_xml.F90
@@ -362,6 +360,8 @@ set(LIBOPENMC_FORTRAN_SRC
   src/secondary_nbody.F90
   src/secondary_uncorrelated.F90
   src/set_header.F90
+  src/settings.F90
+  src/simulation_header.F90
   src/simulation.F90
   src/source.F90
   src/source_header.F90
@@ -370,21 +370,37 @@ set(LIBOPENMC_FORTRAN_SRC
   src/string.F90
   src/summary.F90
   src/surface_header.F90
-  src/tally.F90
-  src/tally_filter.F90
-  src/tally_filter_header.F90
-  src/tally_header.F90
-  src/tally_initialize.F90
   src/timer_header.F90
   src/tracking.F90
   src/track_output.F90
-  src/trigger.F90
-  src/trigger_header.F90
   src/urr_header.F90
   src/vector_header.F90
   src/volume_calc.F90
   src/volume_header.F90
-  src/xml_interface.F90)
+  src/xml_interface.F90
+  src/tallies/tally.F90
+  src/tallies/tally_derivative_header.F90
+  src/tallies/tally_filter.F90
+  src/tallies/tally_filter_header.F90
+  src/tallies/tally_filter_azimuthal.F90
+  src/tallies/tally_filter_cell.F90
+  src/tallies/tally_filter_cellborn.F90
+  src/tallies/tally_filter_cellfrom.F90
+  src/tallies/tally_filter_delayedgroup.F90
+  src/tallies/tally_filter_distribcell.F90
+  src/tallies/tally_filter_energy.F90
+  src/tallies/tally_filter_energyfunc.F90
+  src/tallies/tally_filter_material.F90
+  src/tallies/tally_filter_mesh.F90
+  src/tallies/tally_filter_mu.F90
+  src/tallies/tally_filter_particle.F90
+  src/tallies/tally_filter_polar.F90
+  src/tallies/tally_filter_surface.F90
+  src/tallies/tally_filter_universe.F90
+  src/tallies/tally_header.F90
+  src/tallies/trigger.F90
+  src/tallies/trigger_header.F90
+)
 add_library(libopenmc SHARED ${LIBOPENMC_FORTRAN_SRC})
 set_target_properties(libopenmc PROPERTIES OUTPUT_NAME openmc)
 add_executable(${program} src/main.F90)
@@ -415,7 +431,7 @@ target_link_libraries(${program} ${ldflags} libopenmc)
 add_custom_command(TARGET libopenmc POST_BUILD
   COMMAND ${CMAKE_COMMAND} -E copy
   $<TARGET_FILE:libopenmc>
-  ${CMAKE_CURRENT_SOURCE_DIR}/openmc/_$<TARGET_FILE_NAME:libopenmc>
+  ${CMAKE_CURRENT_SOURCE_DIR}/openmc/capi/$<TARGET_FILE_NAME:libopenmc>
   COMMENT "Copying libopenmc to Python module directory")
 
 #===============================================================================
@@ -455,6 +471,11 @@ 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)

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