diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-03-28 19:36:31 +0000 |
---|---|---|
committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-03-28 19:36:31 +0000 |
commit | 57d21359ba689f739344d67309be7efa43bf078a (patch) | |
tree | 05a5c7885006b9fead50dc10b66eb91aee633073 | |
parent | 1210ddafd2e26e842e66714d92f6dbfc0c3ba003 (diff) |
Missing a test for cython
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2272 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 223961ca5575e07d0db2c93ee0326864166980d8
-rw-r--r-- | src/cython/CMakeLists.txt | 401 |
1 files changed, 200 insertions, 201 deletions
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index c51d9a1e..7c650102 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -34,9 +34,6 @@ if(PYTHONINTERP_FOUND) find_program( SPHINX_PATH sphinx-build ) elseif(PYTHON_VERSION_MAJOR EQUAL 3) FIND_PROGRAM(CYTHON_PATH cython3) - if(NOT CYTHON_PATH) - message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python is set to 3.X while no cython3 installed.") - endif(NOT CYTHON_PATH) # Unitary tests are available through py.test find_program( PYTEST_PATH py.test ) # Documentation generation is available through sphinx @@ -46,202 +43,204 @@ if(PYTHONINTERP_FOUND) endif(PYTHON_VERSION_MAJOR EQUAL 2) endif(PYTHONINTERP_FOUND) -message("${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_PATH} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}") - -set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ") -set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") -set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") -if(WIN32) - set( returnValue "" ) - find_the_lib (${returnValue} ${Boost_SYSTEM_LIBRARY}) - set(BOOST_SYSTEM_LIB_NAME ${returnValue}) -else() - set(BOOST_SYSTEM_LIB_NAME "boost_system") - endif() -set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${BOOST_SYSTEM_LIB_NAME}', ") - -# Gudhi and CGAL compilation option -if(MSVC) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ") -else(MSVC) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ") -endif(MSVC) -if(CMAKE_COMPILER_IS_GNUCXX) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ") -endif(CMAKE_COMPILER_IS_GNUCXX) -if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ") -endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") -if (DEBUG_TRACES) - # For programs to be more verbose - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ") -endif() - -if (EIGEN3_FOUND) - # No problem, even if no CGAL found - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") -endif (EIGEN3_FOUND) - -# Copy recursively include, cython, example, doc and test repositories before packages finding -# Some tests and doc files are removed in case some packages are not found -file(COPY include DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) -file(COPY cython DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) -file(COPY example DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) -file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) -file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) -# Developper version for doc images -file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png") -file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") -file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.svg") -file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") -# User version for doc images -file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png") -file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") -file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.svg") -file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") -# Biblio -file(GLOB GUDHI_BIB_FILES "${CMAKE_SOURCE_DIR}/biblio/*.bib") -file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") -# Cubical complex perseus doc example -file(GLOB GUDHI_CUBICAL_PERSEUS_FILES "${CMAKE_SOURCE_DIR}/data/bitmap/*cubicalcomplexdoc.txt") -file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") -file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") -file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") -# Persistence graphical tools examples -file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") -file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") - -if (NOT CGAL_VERSION VERSION_LESS 4.8.1) - # If CGAL_VERSION >= 4.8.1, include subsampling - set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'") - set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'") - set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include 'cython/bottleneck_distance.pyx'") -else (NOT CGAL_VERSION VERSION_LESS 4.8.1) - # Remove subsampling unitary tests - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py) - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_sum.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_user.rst") - # Remove tangential complex and bottleneck unitary tests - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_tangential_complex.py) - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_bottleneck_distance.py) - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_sum.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_user.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_sum.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_user.rst") -endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) -if (NOT CGAL_VERSION VERSION_LESS 4.7.0) - # If CGAL_VERSION >= 4.7.0, include alpha - set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'") -else (NOT CGAL_VERSION VERSION_LESS 4.7.0) - # Remove alpha complex unitary tests - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py) - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_sum.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_user.rst") -endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) -if (NOT CGAL_VERSION VERSION_LESS 4.6.0) - # If CGAL_VERSION >= 4.6.0, include euclidean versions of witness complex - set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX - "include 'cython/euclidean_witness_complex.pyx'\ninclude 'cython/euclidean_strong_witness_complex.pyx'\n") -else (NOT CGAL_VERSION VERSION_LESS 4.6.0) - # Remove alpha complex unitary tests - file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_euclidean_witness_complex.py) - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_witness_complex_ref.rst") - file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst") -endif (NOT CGAL_VERSION VERSION_LESS 4.6.0) - -if(CGAL_FOUND) - # Add CGAL compilation args - if(CGAL_HEADER_ONLY) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") - else(CGAL_HEADER_ONLY) - if(WIN32) - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL-vc140-mt-4.7', ") - else(WIN32) - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL', ") - endif(WIN32) - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") - endif(CGAL_HEADER_ONLY) - # GMP and GMPXX are not required, but if present, CGAL will link with them. - if(GMP_FOUND) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ") - if(WIN32) - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'libgmp-10', ") - else(WIN32) - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ") - endif(WIN32) - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ") - if(GMPXX_FOUND) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ") - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmpxx', ") - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ") - endif(GMPXX_FOUND) - endif(GMP_FOUND) -endif(CGAL_FOUND) - -# Specific for Mac -if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.9', ") - set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.9', ") -endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") - -# Loop on INCLUDE_DIRECTORIES PROPERTY -get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES) -foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES}) - set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ") -endforeach() -set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ") - -if (TBB_FOUND) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ") - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'tbb', 'tbbmalloc', ") - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ") - set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ") -endif() - -# set sphinx-build in make files -configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY) -configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY) - -# Generate cythonize_gudhi.py file to cythonize Gudhi -configure_file(cythonize_gudhi.py.in "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" @ONLY) -# Generate gudhi.pyx - Gudhi cython file -configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY) - -add_custom_command( - OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace") - -add_custom_target(cython ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" - COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests") - -if(UNIX) - set( ENV{PYTHONPATH} $ENV{PYTHONPATH}:${CMAKE_CURRENT_BINARY_DIR}/ ) -endif(UNIX) - -# Unitary tests are available through py.test -if(PYTEST_PATH) - add_test( - NAME gudhi_cython_py_test +if(CYTHON_PATH) + message("${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_PATH} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}") + + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") + if(WIN32) + set( returnValue "" ) + find_the_lib (${returnValue} ${Boost_SYSTEM_LIBRARY}) + set(BOOST_SYSTEM_LIB_NAME ${returnValue}) + else() + set(BOOST_SYSTEM_LIB_NAME "boost_system") + endif() + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${BOOST_SYSTEM_LIB_NAME}', ") + + # Gudhi and CGAL compilation option + if(MSVC) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ") + else(MSVC) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ") + endif(MSVC) + if(CMAKE_COMPILER_IS_GNUCXX) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ") + endif(CMAKE_COMPILER_IS_GNUCXX) + if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ") + endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") + if (DEBUG_TRACES) + # For programs to be more verbose + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ") + endif() + + if (EIGEN3_FOUND) + # No problem, even if no CGAL found + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") + endif (EIGEN3_FOUND) + + # Copy recursively include, cython, example, doc and test repositories before packages finding + # Some tests and doc files are removed in case some packages are not found + file(COPY include DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + file(COPY cython DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + file(COPY example DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + # Developper version for doc images + file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png") + file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") + file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.svg") + file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") + # User version for doc images + file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png") + file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") + file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.svg") + file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") + # Biblio + file(GLOB GUDHI_BIB_FILES "${CMAKE_SOURCE_DIR}/biblio/*.bib") + file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") + # Cubical complex perseus doc example + file(GLOB GUDHI_CUBICAL_PERSEUS_FILES "${CMAKE_SOURCE_DIR}/data/bitmap/*cubicalcomplexdoc.txt") + file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") + file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") + file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") + # Persistence graphical tools examples + file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") + file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") + + if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + # If CGAL_VERSION >= 4.8.1, include subsampling + set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'") + set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'") + set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include 'cython/bottleneck_distance.pyx'") + else (NOT CGAL_VERSION VERSION_LESS 4.8.1) + # Remove subsampling unitary tests + file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py) + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_ref.rst") + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_sum.rst") + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_user.rst") + # Remove tangential complex and bottleneck unitary tests + file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_tangential_complex.py) + file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_bottleneck_distance.py) + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_ref.rst") + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_sum.rst") + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_user.rst") + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_ref.rst") + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_sum.rst") + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_user.rst") + endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) + if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + # If CGAL_VERSION >= 4.7.0, include alpha + set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'") + else (NOT CGAL_VERSION VERSION_LESS 4.7.0) + # Remove alpha complex unitary tests + file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py) + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_ref.rst") + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_sum.rst") + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_user.rst") + endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) + if (NOT CGAL_VERSION VERSION_LESS 4.6.0) + # If CGAL_VERSION >= 4.6.0, include euclidean versions of witness complex + set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX + "include 'cython/euclidean_witness_complex.pyx'\ninclude 'cython/euclidean_strong_witness_complex.pyx'\n") + else (NOT CGAL_VERSION VERSION_LESS 4.6.0) + # Remove alpha complex unitary tests + file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_euclidean_witness_complex.py) + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_witness_complex_ref.rst") + file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst") + endif (NOT CGAL_VERSION VERSION_LESS 4.6.0) + + if(CGAL_FOUND) + # Add CGAL compilation args + if(CGAL_HEADER_ONLY) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") + else(CGAL_HEADER_ONLY) + if(WIN32) + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL-vc140-mt-4.7', ") + else(WIN32) + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL', ") + endif(WIN32) + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") + endif(CGAL_HEADER_ONLY) + # GMP and GMPXX are not required, but if present, CGAL will link with them. + if(GMP_FOUND) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ") + if(WIN32) + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'libgmp-10', ") + else(WIN32) + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ") + endif(WIN32) + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ") + if(GMPXX_FOUND) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ") + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmpxx', ") + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ") + endif(GMPXX_FOUND) + endif(GMP_FOUND) + endif(CGAL_FOUND) + + # Specific for Mac + if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.9', ") + set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.9', ") + endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + + # Loop on INCLUDE_DIRECTORIES PROPERTY + get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES) + foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES}) + set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ") + endforeach() + set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ") + + if (TBB_FOUND) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ") + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'tbb', 'tbbmalloc', ") + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ") + set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ") + endif() + + # set sphinx-build in make files + configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY) + configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY) + + # Generate cythonize_gudhi.py file to cythonize Gudhi + configure_file(cythonize_gudhi.py.in "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" @ONLY) + # Generate gudhi.pyx - Gudhi cython file + configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY) + + add_custom_command( + OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${PYTEST_PATH}") - set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") -endif(PYTEST_PATH) - -# Documentation generation is available through sphinx -if(SPHINX_PATH) - if (UNIX) - add_custom_target(sphinx - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc - DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" - COMMAND make html doctest) - else (UNIX) - add_custom_target(sphinx - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc - COMMAND make.bat html doctest) - endif (UNIX) -endif(SPHINX_PATH) + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace") + + add_custom_target(cython ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" + COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests") + + if(UNIX) + set( ENV{PYTHONPATH} $ENV{PYTHONPATH}:${CMAKE_CURRENT_BINARY_DIR}/ ) + endif(UNIX) + + # Unitary tests are available through py.test + if(PYTEST_PATH) + add_test( + NAME gudhi_cython_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} "${PYTEST_PATH}") + set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + endif(PYTEST_PATH) + + # Documentation generation is available through sphinx + if(SPHINX_PATH) + if (UNIX) + add_custom_target(sphinx + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc + DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" + COMMAND make html doctest) + else (UNIX) + add_custom_target(sphinx + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc + COMMAND make.bat html doctest) + endif (UNIX) + endif(SPHINX_PATH) +endif(CYTHON_PATH) |