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-rw-r--r--cython/CMakeLists.txt228
1 files changed, 172 insertions, 56 deletions
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index 17d440ee..09ea28f1 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -16,17 +16,51 @@ 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)
+ 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)
- message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - Sphinx is ${SPHINX_PATH}")
+ set(GUDHI_CYTHON_MODULES "${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', ")
@@ -49,49 +83,86 @@ if(CYTHON_FOUND)
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 '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
- endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+ set(GUDHI_CYTHON_MODULES "${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 '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
- endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+ set(GUDHI_CYTHON_MODULES "${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 '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
- endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+ set(GUDHI_CYTHON_MODULES "${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 '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
- endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+ set(GUDHI_CYTHON_MODULES "${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: ${GUDHI_CYTHON_MISSING_MODULES}")
+ endif()
if(CGAL_FOUND)
can_cgal_use_cxx11_thread_local()
if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
- add_gudhi_cython_lib(${Boost_THREAD_LIBRARY})
+ 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_cython_lib(${CGAL_LIBRARY})
+ 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,
- add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY})
+ if(CMAKE_BUILD_TYPE MATCHES Debug)
+ add_gudhi_cython_lib("${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(${GMP_LIBRARIES})
+ add_gudhi_cython_lib("${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(${GMPXX_LIBRARIES})
+ add_gudhi_cython_lib("${GMPXX_LIBRARIES}")
set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
endif(GMPXX_FOUND)
endif(GMP_FOUND)
@@ -111,9 +182,15 @@ if(CYTHON_FOUND)
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', ")
- add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY})
- add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY})
+ 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()
@@ -151,40 +228,73 @@ if(CYTHON_FOUND)
${PYTHON_EXECUTABLE} "${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)
- # Tangential
- add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
+ 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/tangential_complex_plain_homology_from_off_file_example.py"
- --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
- add_gudhi_py_test(test_tangential_complex)
+ add_gudhi_py_test(test_bottleneck_distance)
- # Witness complex AND Subsampling
- add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+ # 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/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)
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
+ -f human.off -c 2 -r 10 -g 0.3)
- add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+ 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/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)
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
+ -f human.off -c 0 -v)
- # Subsampling
- add_gudhi_py_test(test_subsampling)
+ 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)
- 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
+ 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/bottleneck_basic_example.py")
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
+ -f human.off -n 700 -v)
- add_gudhi_py_test(test_bottleneck_distance)
+ 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)
@@ -194,11 +304,13 @@ if(CYTHON_FOUND)
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
+ 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)
@@ -217,26 +329,30 @@ if(CYTHON_FOUND)
${PYTHON_EXECUTABLE} "${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)
- 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)
+ 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
- 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)
+ 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}
@@ -265,7 +381,7 @@ if(CYTHON_FOUND)
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)
+ 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
@@ -285,5 +401,5 @@ if(CYTHON_FOUND)
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()
endif(CYTHON_FOUND)