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|
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)
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