diff options
Diffstat (limited to 'cython/CMakeLists.txt')
| -rw-r--r-- | cython/CMakeLists.txt | 376 |
1 files changed, 203 insertions, 173 deletions
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt index 96c2acb3..afca9d60 100644 --- a/cython/CMakeLists.txt +++ b/cython/CMakeLists.txt @@ -1,20 +1,65 @@ cmake_minimum_required(VERSION 2.8) project(Cython) +function( add_gudhi_cython_lib THE_LIB ) + if(EXISTS ${THE_LIB}) + get_filename_component(THE_LIB_FILE_NAME ${THE_LIB} NAME_WE) + if(WIN32) + message("++ ${THE_LIB} => THE_LIB_FILE_NAME = ${THE_LIB_FILE_NAME}") + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${THE_LIB_FILE_NAME}', " PARENT_SCOPE) + else(WIN32) + STRING(REGEX REPLACE "lib" "" UNIX_LIB_FILE_NAME ${THE_LIB_FILE_NAME}) + message("++ ${THE_LIB} => UNIX_LIB_FILE_NAME = ${UNIX_LIB_FILE_NAME}") + set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${UNIX_LIB_FILE_NAME}', " PARENT_SCOPE) + endif(WIN32) + endif(EXISTS ${THE_LIB}) +endfunction( add_gudhi_cython_lib ) + +# THE_TEST is the python test file name (without .py extension) containing tests functions +function( add_gudhi_py_test THE_TEST ) + # use ${PYTHON_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python + # use py.test no cache provider, otherwise a .cache file is created in sources by py.test + add_test(NAME ${THE_TEST}_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py) +endfunction( add_gudhi_py_test ) + + if(CYTHON_FOUND) - message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}") + message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - 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}'${BOOST_SYSTEM_LIB_NAME}', ") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ") + + # This is because of https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/tss.h + # CGAL is using boost thread if thread_local is not ready (requires XCode 8 for Mac). + # The test in https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/config.h + # #if __has_feature(cxx_thread_local) || \ + # ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \ + # ( _MSC_VER >= 1900 ) + # #define CGAL_CAN_USE_CXX11_THREAD_LOCAL + # #endif + set(CGAL_CAN_USE_CXX11_THREAD_LOCAL " + int main() { + #ifndef __has_feature + #define __has_feature(x) 0 // Compatibility with non-clang compilers. + #endif + #if __has_feature(cxx_thread_local) || \ + ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \ + ( _MSC_VER >= 1900 ) + bool has_feature_thread_local = true; + #else + // Explicit error of compilation for CMake test purpose - has_feature_thread_local is not defined + #endif + bool result = has_feature_thread_local; + } ") + check_cxx_source_compiles("${CGAL_CAN_USE_CXX11_THREAD_LOCAL}" CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) + + if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) + add_gudhi_cython_lib(${Boost_THREAD_LIBRARY}) + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") + endif() # Gudhi and CGAL compilation option if(MSVC) @@ -25,9 +70,9 @@ if(CYTHON_FOUND) 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") + if (CMAKE_CXX_COMPILER_ID MATCHES Intel) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ") - endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") + endif(CMAKE_CXX_COMPILER_ID MATCHES Intel) if (DEBUG_TRACES) # For programs to be more verbose set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ") @@ -38,101 +83,40 @@ if(CYTHON_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${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 "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_user.rst") + set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'") 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 + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'") + set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'") + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'") + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) 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 "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst") - endif (NOT CGAL_VERSION VERSION_LESS 4.6.0) + "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n") + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) if(CGAL_FOUND) # Add CGAL compilation args if(CGAL_HEADER_ONLY) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${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) + add_gudhi_cython_lib(${CGAL_LIBRARIES}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") + # If CGAL is not header only, CGAL library may link with boost system, + add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY}) + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") 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}'${GMP_LIBRARIES_DIR}', ") + add_gudhi_cython_lib(${GMP_LIBRARIES}) + 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', ") + add_gudhi_cython_lib(${GMPXX_LIBRARIES}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ") endif(GMPXX_FOUND) endif(GMP_FOUND) @@ -153,132 +137,178 @@ if(CYTHON_FOUND) if (TBB_FOUND) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ") - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'tbb', 'tbbmalloc', ") + add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY}) + add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY}) set(GUDHI_CYTHON_LIBRARY_DIRS "${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 "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY) + if(UNIX) + set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}") + endif(UNIX) - # Generate cythonize_gudhi.py file to cythonize Gudhi - configure_file(cythonize_gudhi.py.in "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" @ONLY) + # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention + configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.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" + OUTPUT gudhi.so WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace") + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace") - add_custom_target(cython ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" + add_custom_target(cython ALL DEPENDS 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) + # For installation purpose + # TODO(VR) : files matching pattern mechanism is copying all cython directory + install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING + PATTERN "*.so" + PATTERN "*.dylib" + PATTERN "*.pyd") # Test examples - add_test(NAME alpha_complex_from_points_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_from_points_example.py") - set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + # Bottleneck and Alpha + add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" + -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) - add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) - set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + # Tangential + add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) - add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" - -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) - set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_gudhi_py_test(test_tangential_complex) - add_test(NAME bottleneck_basic_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/bottleneck_basic_example.py") - set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + # Witness complex AND Subsampling + add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + # Subsampling + add_gudhi_py_test(test_subsampling) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + # Bottleneck + add_test(NAME bottleneck_basic_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py") + + add_gudhi_py_test(test_bottleneck_distance) + endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) + + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + # Alpha + add_test(NAME alpha_complex_from_points_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py") + + add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) + + add_gudhi_py_test(test_alpha_complex) + + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) + # Euclidean witness + add_gudhi_py_test(test_euclidean_witness_complex) + + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) + + # Cubical add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) - set_tests_properties(periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME random_cubical_complex_persistence_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/random_cubical_complex_persistence_example.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" 10 10 10) - set_tests_properties(random_cubical_complex_persistence_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_gudhi_py_test(test_cubical_complex) + + # Rips add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) - set_tests_properties(rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) - set_tests_properties(rips_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") add_test(NAME rips_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_from_points_example.py) - set_tests_properties(rips_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py) + + add_gudhi_py_test(test_rips_complex) + # Simplex tree add_test(NAME simplex_tree_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/simplex_tree_example.py) - set_tests_properties(simplex_tree_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py) - add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) - set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") + add_gudhi_py_test(test_simplex_tree) + # Witness add_test(NAME witness_complex_from_nearest_landmark_table_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/witness_complex_from_nearest_landmark_table.py) - set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}") - - # 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) + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py) + + add_gudhi_py_test(test_witness_complex) + + # Reader utils + add_gudhi_py_test(test_reader_utils) + + # Documentation generation is available through sphinx - requires all modules + if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/") + # User warning - Sphinx is a static pages generator, and configured to work fine with user_version + # Images and biblio warnings because not found on developper version + if (GUDHI_CYTHON_PATH STREQUAL "src/cython") + set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss") + endif() + # sphinx target requires gudhi.so, because conf.py reads gudhi version from it + add_custom_target(sphinx + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx + DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" + COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM) + + add_test(NAME sphinx_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest) + + endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) endif(CYTHON_FOUND) |