diff options
Diffstat (limited to 'src/python/CMakeLists.txt')
| -rw-r--r-- | src/python/CMakeLists.txt | 432 |
1 files changed, 432 insertions, 0 deletions
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt new file mode 100644 index 00000000..9e128d30 --- /dev/null +++ b/src/python/CMakeLists.txt @@ -0,0 +1,432 @@ +project(Cython) + +function( add_GUDHI_PYTHON_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 = ${THE_LIB_FILE_NAME}") + set(GUDHI_PYTHON_LIBRARIES "${GUDHI_PYTHON_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 = ${UNIX_LIB_FILE_NAME}") + set(GUDHI_PYTHON_LIBRARIES "${GUDHI_PYTHON_LIBRARIES}'${UNIX_LIB_FILE_NAME}', " PARENT_SCOPE) + endif(WIN32) + endif(EXISTS ${THE_LIB}) +endfunction( add_GUDHI_PYTHON_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 setup.py.in configure_file +function( add_gudhi_debug_info DEBUG_INFO ) + set(GUDHI_PYTHON_DEBUG_INFO "${GUDHI_PYTHON_DEBUG_INFO} \"${DEBUG_INFO}\\n\" \\\n" PARENT_SCOPE) +endfunction( add_gudhi_debug_info ) + +if(PYTHONINTERP_FOUND) + if(CYTHON_FOUND) + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_reader', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'simplex_tree', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'rips_complex', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'cubical_complex', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'periodic_cubical_complex', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'persistence_graphical_tools', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'reader_utils', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'witness_complex', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'strong_witness_complex', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'bottleneck', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'nerve_gic', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'subsampling', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'tangential_complex', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'alpha_complex', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'euclidean_witness_complex', ") + set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'euclidean_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(SCIPY_FOUND) + add_gudhi_debug_info("Scipy version ${SCIPY_VERSION}") + endif() + + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ") + + # Gudhi and CGAL compilation option + if(MSVC) + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ") + else(MSVC) + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ") + endif(MSVC) + if(CMAKE_COMPILER_IS_GNUCXX) + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ") + endif(CMAKE_COMPILER_IS_GNUCXX) + if (CMAKE_CXX_COMPILER_ID MATCHES Intel) + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ") + endif(CMAKE_CXX_COMPILER_ID MATCHES Intel) + if (DEBUG_TRACES) + # For programs to be more verbose + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ") + endif() + + if (EIGEN3_FOUND) + add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}") + # No problem, even if no CGAL found + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") + endif (EIGEN3_FOUND) + + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'off_reader', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'simplex_tree', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'rips_complex', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'cubical_complex', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'periodic_cubical_complex', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'reader_utils', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'witness_complex', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'strong_witness_complex', ") + if (NOT CGAL_VERSION VERSION_LESS 4.11.0) + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'bottleneck', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'nerve_gic', ") + endif () + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'subsampling', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'tangential_complex', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'alpha_complex', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'euclidean_witness_complex', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'euclidean_strong_witness_complex', ") + endif () + + if(CGAL_FOUND) + can_cgal_use_cxx11_thread_local() + if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) + if(CMAKE_BUILD_TYPE MATCHES Debug) + add_GUDHI_PYTHON_lib("${Boost_THREAD_LIBRARY_DEBUG}") + else() + add_GUDHI_PYTHON_lib("${Boost_THREAD_LIBRARY_RELEASE}") + endif() + message("** Add Boost ${Boost_LIBRARY_DIRS}") + set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") + endif() + # Add CGAL compilation args + if(CGAL_HEADER_ONLY) + add_gudhi_debug_info("CGAL header only version ${CGAL_VERSION}") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") + else(CGAL_HEADER_ONLY) + add_gudhi_debug_info("CGAL version ${CGAL_VERSION}") + add_GUDHI_PYTHON_lib("${CGAL_LIBRARY}") + set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") + message("** Add CGAL ${CGAL_LIBRARIES_DIR}") + # If CGAL is not header only, CGAL library may link with boost system, + if(CMAKE_BUILD_TYPE MATCHES Debug) + add_GUDHI_PYTHON_lib("${Boost_SYSTEM_LIBRARY_DEBUG}") + else() + add_GUDHI_PYTHON_lib("${Boost_SYSTEM_LIBRARY_RELEASE}") + endif() + set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") + message("** Add Boost ${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 = ${GMP_LIBRARIES}") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ") + add_GUDHI_PYTHON_lib("${GMP_LIBRARIES}") + set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ") + message("** Add gmp ${GMP_LIBRARIES_DIR}") + if(GMPXX_FOUND) + add_gudhi_debug_info("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ") + add_GUDHI_PYTHON_lib("${GMPXX_LIBRARIES}") + set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ") + message("** Add gmpxx ${GMPXX_LIBRARIES_DIR}") + endif(GMPXX_FOUND) + endif(GMP_FOUND) + endif(CGAL_FOUND) + + # Specific for Mac + if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.12', ") + set(GUDHI_PYTHON_EXTRA_LINK_ARGS "${GUDHI_PYTHON_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 ${GUDHI_INCLUDE_DIRECTORIES}) + set(GUDHI_PYTHON_INCLUDE_DIRS "${GUDHI_PYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ") + endforeach() + set(GUDHI_PYTHON_INCLUDE_DIRS "${GUDHI_PYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_PYTHON_PATH}/include', ") + + if (TBB_FOUND AND WITH_GUDHI_USE_TBB) + add_gudhi_debug_info("TBB version ${TBB_INTERFACE_VERSION} found and used") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ") + if(CMAKE_BUILD_TYPE MATCHES Debug) + add_GUDHI_PYTHON_lib("${TBB_DEBUG_LIBRARY}") + add_GUDHI_PYTHON_lib("${TBB_MALLOC_DEBUG_LIBRARY}") + else() + add_GUDHI_PYTHON_lib("${TBB_RELEASE_LIBRARY}") + add_GUDHI_PYTHON_lib("${TBB_MALLOC_RELEASE_LIBRARY}") + endif() + set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ") + message("** Add tbb ${TBB_LIBRARY_DIRS}") + set(GUDHI_PYTHON_INCLUDE_DIRS "${GUDHI_PYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ") + endif() + + if(UNIX AND WITH_GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS) + set( GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}") + endif(UNIX AND WITH_GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS) + + # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention + configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY) + + # Generate gudhi/__init__.py + file(MAKE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/gudhi") + configure_file("gudhi/__init__.py.in" "${CMAKE_CURRENT_BINARY_DIR}/gudhi/__init__.py" @ONLY) + + # Other .py files + file(COPY "gudhi/persistence_graphical_tools.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi") + + 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(python ALL DEPENDS gudhi.so + COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests") + + install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)") + + # Test examples + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + # 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 4.11.0) + if (NOT CGAL_VERSION VERSION_LESS 4.11.0) + # 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 4.11.0) + + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + # 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 4.11.0) + + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + # Euclidean witness + add_gudhi_py_test(test_euclidean_witness_complex) + + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + + # 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) + if(MATPLOTLIB_FOUND) + if(NUMPY_FOUND) + if(SCIPY_FOUND) + if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/") + # User warning - Sphinx is a static pages generator, and configured to work fine with user_version + # Images and biblio warnings because not found on developper version + if (GUDHI_PYTHON_PATH STREQUAL "src/python") + set (GUDHI_SPHINX_MESSAGE "${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) + + # Set missing or not modules + set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES") + else(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + message("++ Python documentation module will not be compiled because it requires a Eigen3 and CGAL version >= 4.11.0") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES") + endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + else(SCIPY_FOUND) + message("++ Python documentation module will not be compiled because scipy was not found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES") + endif(SCIPY_FOUND) + else(NUMPY_FOUND) + message("++ Python documentation module will not be compiled because numpy was not found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES") + endif(NUMPY_FOUND) + else(MATPLOTLIB_FOUND) + message("++ Python documentation module will not be compiled because matplotlib was not found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES") + endif(MATPLOTLIB_FOUND) + else(SPHINX_PATH) + message("++ Python documentation module will not be compiled because sphinx and sphinxcontrib-bibtex were not found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES") + endif(SPHINX_PATH) + + + # Set missing or not modules + set(GUDHI_MODULES ${GUDHI_MODULES} "python" CACHE INTERNAL "GUDHI_MODULES") + else(CYTHON_FOUND) + message("++ Python module will not be compiled because cython was not found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES") + endif(CYTHON_FOUND) +else(PYTHONINTERP_FOUND) + message("++ Python module will not be compiled because no Python interpreter was found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES") +endif(PYTHONINTERP_FOUND) |