1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
|
cmake_minimum_required(VERSION 2.8)
project(Cython)
FIND_PROGRAM( PYTHON_PATH python )
FIND_PROGRAM( CYTHON_PATH cython )
if(PYTHON_PATH AND CYTHON_PATH)
find_package(Boost REQUIRED COMPONENTS system REQUIRED)
if(NOT Boost_FOUND)
message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.")
else(NOT Boost_FOUND)
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_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${Boost_INCLUDE_DIRS}', ")
set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'boost_system', ")
set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
# Gudhi and CGAL compilation option
if(MSVC)
set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${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 ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
if (DEBUG_TRACES)
# For programs to be more verbose
set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ")
endif()
find_package(Eigen3 3.1.0)
if (EIGEN3_FOUND)
# No problem, even if no CGAL found
set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${EIGEN3_INCLUDE_DIR}', ")
endif (EIGEN3_FOUND)
# Copy recursively include, cython and test repositories before packages finding
# Some tests 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 test DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
if (CGAL_FOUND)
if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
# If CGAL_VERSION >= 4.8.1, include subsampling
# CGAL things are done in CGAL_VERSION >= 4.8.0
set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'")
else (NOT CGAL_VERSION VERSION_LESS 4.8.1)
# Remove alpha complex unitary tests
file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py)
endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
# If CGAL_VERSION >= 4.8.0, include alpha and tangential complex
set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL', ")
set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
# GMP and GMPXX are not required, but if present, CGAL will link with them.
if(GMP_FOUND)
set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ")
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', ")
set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
endif(GMPXX_FOUND)
endif(GMP_FOUND)
set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'")
set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'")
else (NOT CGAL_VERSION VERSION_LESS 4.8.0)
# Remove alpha complex unitary tests
file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py)
file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_tangential_complex.py)
endif (NOT CGAL_VERSION VERSION_LESS 4.8.0)
endif (CGAL_FOUND)
# 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', ")
# Generate cythonize_gudhi.py file to cythonize Gudhi
configure_file(cythonize_gudhi.py.in "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" @ONLY)
# Generate gudhi.pyx - Gudhi cython file
configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY)
add_custom_command(
OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMAND python "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace")
add_custom_target(cythonize_gudhi ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/gudhi.so to your PYTHONPATH before using examples")
# Unitary tests are available through py.test
find_program( PYTEST_PATH py.test )
if(PYTEST_PATH)
add_test(
NAME gudhi_cython_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMAND ${PYTEST_PATH})
set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
endif(PYTEST_PATH)
# Documentation generation is available through sphinx
find_program( SPHINX_PATH sphinx-build )
if(SPHINX_PATH)
file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
# Developper version
file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png")
file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
# User version
file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png")
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/")
# 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 (UNIX)
add_custom_target(html
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
COMMAND make html && make doctest)
else (UNIX)
add_custom_target(html
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
COMMAND make.bat html)
endif (UNIX)
endif(SPHINX_PATH)
endif(NOT Boost_FOUND)
endif(PYTHON_PATH AND CYTHON_PATH)
|
