diff options
Diffstat (limited to 'cython/CMakeLists.txt')
| -rw-r--r-- | cython/CMakeLists.txt | 405 |
1 files changed, 0 insertions, 405 deletions
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt deleted file mode 100644 index 09ea28f1..00000000 --- a/cython/CMakeLists.txt +++ /dev/null @@ -1,405 +0,0 @@ -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 ) - if(PYTEST_FOUND) - # 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) - endif() -endfunction( add_gudhi_py_test ) - -# Set gudhi.__debug_info__ -# WARNING : to be done before gudhi.pyx.in configure_file -function( add_gudhi_debug_info DEBUG_INFO ) - set(GUDHI_CYTHON_DEBUG_INFO "${GUDHI_CYTHON_DEBUG_INFO} \"${DEBUG_INFO}\\n\" \\\n" PARENT_SCOPE) -endfunction( add_gudhi_debug_info ) - - -if(CYTHON_FOUND) - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}off_reader;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}simplex_tree;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}rips_complex;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}cubical_complex;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}periodic_cubical_complex;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}reader_utils;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}witness_complex;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}strong_witness_complex;") - - add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}") - add_gudhi_debug_info("Cython version ${CYTHON_VERSION}") - if(PYTEST_FOUND) - add_gudhi_debug_info("Pytest version ${PYTEST_VERSION}") - endif() - if(MATPLOTLIB_FOUND) - add_gudhi_debug_info("Matplotlib version ${MATPLOTLIB_VERSION}") - endif() - if(NUMPY_FOUND) - add_gudhi_debug_info("Numpy version ${NUMPY_VERSION}") - endif() - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;") - else() - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;") - endif() - - message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_VERSION} - 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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ") - - # 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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ") - endif(CMAKE_COMPILER_IS_GNUCXX) - if (CMAKE_CXX_COMPILER_ID MATCHES Intel) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ") - 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', ") - endif() - - if (EIGEN3_FOUND) - add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}") - # No problem, even if no CGAL found - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") - endif (EIGEN3_FOUND) - - if (NOT CGAL_VERSION VERSION_LESS 4.8.1) - set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}bottleneck_distance;") - set(GUDHI_CYTHON_NERVE_GIC "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/nerve_gic.pyx'") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}nerve_gic;") - else() - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}bottleneck_distance;") - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}nerve_gic;") - endif () - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) - set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}subsampling;") - set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}tangential_complex;") - else() - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}subsampling;") - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}tangential_complex;") - endif () - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}alpha_complex;") - else() - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}alpha_complex;") - endif () - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) - set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX - "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_witness_complex;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_strong_witness_complex;") - else() - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_witness_complex;") - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_strong_witness_complex;") - endif () - - add_gudhi_debug_info("Installed modules are: ${GUDHI_CYTHON_MODULES}") - if(GUDHI_CYTHON_MISSING_MODULES) - add_gudhi_debug_info("Missing modules are: ${GUDHI_CYTHON_MISSING_MODULES}") - endif() - - if(CGAL_FOUND) - can_cgal_use_cxx11_thread_local() - if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) - if(CMAKE_BUILD_TYPE MATCHES Debug) - add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_DEBUG}") - else() - add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_RELEASE}") - endif() - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") - endif() - # Add CGAL compilation args - if(CGAL_HEADER_ONLY) - add_gudhi_debug_info("CGAL header only version ${CGAL_VERSION}") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") - else(CGAL_HEADER_ONLY) - add_gudhi_debug_info("CGAL version ${CGAL_VERSION}") - add_gudhi_cython_lib("${CGAL_LIBRARY}") - 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, - if(CMAKE_BUILD_TYPE MATCHES Debug) - add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_DEBUG}") - else() - add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_RELEASE}") - endif() - 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) - add_gudhi_debug_info("GMP_LIBRARIES = ${GMP_LIBRARIES}") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ") - add_gudhi_cython_lib("${GMP_LIBRARIES}") - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ") - if(GMPXX_FOUND) - add_gudhi_debug_info("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ") - add_gudhi_cython_lib("${GMPXX_LIBRARIES}") - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ") - endif(GMPXX_FOUND) - endif(GMP_FOUND) - endif(CGAL_FOUND) - - # Specific for Mac - if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.12', ") - set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.12', ") - 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 AND WITH_GUDHI_USE_TBB) - add_gudhi_debug_info("TBB version ${TBB_INTERFACE_VERSION} found and used") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ") - if(CMAKE_BUILD_TYPE MATCHES Debug) - add_gudhi_cython_lib("${TBB_DEBUG_LIBRARY}") - add_gudhi_cython_lib("${TBB_MALLOC_DEBUG_LIBRARY}") - else() - add_gudhi_cython_lib("${TBB_RELEASE_LIBRARY}") - add_gudhi_cython_lib("${TBB_MALLOC_RELEASE_LIBRARY}") - endif() - 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() - - if(UNIX) - set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}") - endif(UNIX) - - # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention - configure_file(setup.py.in "${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 gudhi.so - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace") - - add_custom_target(cython ALL DEPENDS gudhi.so - COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests") - - # For installation purpose - # TODO(VR) : files matching pattern mechanism is copying all cython directory - install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING - PATTERN "*.so" - PATTERN "*.dylib" - PATTERN "*.pyd") - - # Test examples - 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) - - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - # 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 -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) - - add_gudhi_py_test(test_tangential_complex) - - # 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_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) - endif() - - # 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) - - # Cover complex - file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - add_test(NAME cover_complex_nerve_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/nerve_of_a_covering.py" - -f human.off -c 2 -r 10 -g 0.3) - - add_test(NAME cover_complex_coordinate_gic_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/coordinate_graph_induced_complex.py" - -f human.off -c 0 -v) - - add_test(NAME cover_complex_functional_gic_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/functional_graph_induced_complex.py" - -o lucky_cat.off - -f lucky_cat_PCA1 -v) - - add_test(NAME cover_complex_voronoi_gic_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/voronoi_graph_induced_complex.py" - -f human.off -n 700 -v) - - add_gudhi_py_test(test_cover_complex) - 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") - - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - 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) - endif() - - 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${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) - - if(NUMPY_FOUND) - add_test(NAME random_cubical_complex_persistence_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/random_cubical_complex_persistence_example.py" - 10 10 10) - endif() - - add_gudhi_py_test(test_cubical_complex) - - # Rips - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_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/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) - - add_test(NAME rips_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/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) - endif() - - add_test(NAME rips_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/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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py) - - 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${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 MATPLOTLIB_FOUND AND NUMPY_FOUND 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() -endif(CYTHON_FOUND) |