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-rw-r--r--CMakeLists.txt6
-rw-r--r--src/CMakeLists.txt8
-rw-r--r--src/cmake/modules/GUDHI_third_party_libraries.txt46
-rw-r--r--src/cython/CMakeLists.txt41
-rw-r--r--src/cython/example/CMakeLists.txt84
-rwxr-xr-xsrc/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py2
-rwxr-xr-xsrc/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py2
7 files changed, 140 insertions, 49 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 18cd0ca2..f95407b7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -16,6 +16,8 @@ enable_testing()
include("${CMAKE_MODULE_PATH}/GUDHI_user_version_target.txt")
# For "make doxygen"
include("${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt")
+# This variable is used by Cython CMakeLists.txt to know its path
+set(GUDHI_CYTHON_PATH "src/cython")
# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
include("${CMAKE_MODULE_PATH}/GUDHI_third_party_libraries.txt")
@@ -87,6 +89,6 @@ add_subdirectory(data/points/generator)
add_subdirectory(src/GudhUI)
-# This variable is used by Cython CMakeLists.txt to know its path
-set(GUDHI_CYTHON_PATH "src/cython")
+# specific for cython module
add_subdirectory(${GUDHI_CYTHON_PATH})
+add_subdirectory(${GUDHI_CYTHON_PATH}/example)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 4fa73662..48d433bf 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -13,6 +13,8 @@ list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/")
set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
include(${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt)
+# This variable is used by Cython CMakeLists.txt to know its path
+set(GUDHI_CYTHON_PATH "cython")
# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
include("${CMAKE_MODULE_PATH}/GUDHI_third_party_libraries.txt")
@@ -56,13 +58,11 @@ add_subdirectory(example/Bottleneck_distance)
# data points generator
add_subdirectory(data/points/generator)
-# Please let GudhUI in last compilation position as QT is known to modify CMAKE_CXX_FLAGS
-# GudhUI
add_subdirectory(GudhUI)
-# This variable is used by Cython CMakeLists.txt to know its path
-set(GUDHI_CYTHON_PATH "cython")
+# specific for cython module
add_subdirectory(${GUDHI_CYTHON_PATH})
+add_subdirectory(${GUDHI_CYTHON_PATH}/example)
#---------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.txt b/src/cmake/modules/GUDHI_third_party_libraries.txt
index 1974f70f..2ddc9f1f 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.txt
+++ b/src/cmake/modules/GUDHI_third_party_libraries.txt
@@ -105,3 +105,49 @@ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
+
+macro( find_the_lib placeholder THE_LIBS )
+ set (THE_LIB_WE_FOUND "NO")
+ foreach(THE_LIB ${THE_LIBS})
+ if(EXISTS ${THE_LIB})
+ get_filename_component(THE_LIB_WE ${THE_LIB} NAME_WE)
+ if (NOT THE_LIB_WE_FOUND)
+ set (THE_LIB_WE_FOUND "YES")
+ set(returnValue "${THE_LIB_WE}")
+ endif(NOT THE_LIB_WE_FOUND)
+ endif(EXISTS ${THE_LIB})
+ endforeach(THE_LIB ${THE_LIBS})
+endmacro( find_the_lib )
+
+# Find the correct Python interpreter.
+# Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance.
+if(PYTHON_EXECUTABLE)
+ if(NOT EXISTS "${PYTHON_EXECUTABLE}")
+ message(FATAL_ERROR "ERROR: ${PYTHON_EXECUTABLE} does not exist.")
+ endif(NOT EXISTS "${PYTHON_EXECUTABLE}")
+endif(PYTHON_EXECUTABLE)
+find_package(PythonInterp)
+
+if(NOT GUDHI_CYTHON_PATH)
+ message(FATAL_ERROR "ERROR: GUDHI_CYTHON_PATH is not valid.")
+endif(NOT GUDHI_CYTHON_PATH)
+
+if(PYTHONINTERP_FOUND)
+ # Default found version 2
+ if(PYTHON_VERSION_MAJOR EQUAL 2)
+ FIND_PROGRAM(CYTHON_PATH cython)
+ # Unitary tests are available through py.test
+ find_program( PYTEST_PATH py.test )
+ # Documentation generation is available through sphinx
+ find_program( SPHINX_PATH sphinx-build )
+ elseif(PYTHON_VERSION_MAJOR EQUAL 3)
+ FIND_PROGRAM(CYTHON_PATH cython3)
+ # Unitary tests are available through py.test
+ find_program( PYTEST_PATH py.test )
+ # Documentation generation is available through sphinx
+ set(SPHINX_PATH "${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+ else()
+ message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
+ endif(PYTHON_VERSION_MAJOR EQUAL 2)
+endif(PYTHONINTERP_FOUND)
+
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 233a557e..da55fb9b 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -1,47 +1,6 @@
cmake_minimum_required(VERSION 2.8)
project(Cython)
-macro( find_the_lib placeholder THE_LIBS )
- set (THE_LIB_WE_FOUND "NO")
- foreach(THE_LIB ${THE_LIBS})
- if(EXISTS ${THE_LIB})
- get_filename_component(THE_LIB_WE ${THE_LIB} NAME_WE)
- if (NOT THE_LIB_WE_FOUND)
- set (THE_LIB_WE_FOUND "YES")
- set(returnValue "${THE_LIB_WE}")
- endif(NOT THE_LIB_WE_FOUND)
- endif(EXISTS ${THE_LIB})
- endforeach(THE_LIB ${THE_LIBS})
-endmacro( find_the_lib )
-
-# Find the correct Python interpreter.
-# Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance.
-if(PYTHON_EXECUTABLE)
- if(NOT EXISTS "${PYTHON_EXECUTABLE}")
- message(FATAL_ERROR "ERROR: ${PYTHON_EXECUTABLE} does not exist.")
- endif(NOT EXISTS "${PYTHON_EXECUTABLE}")
-endif(PYTHON_EXECUTABLE)
-find_package(PythonInterp)
-
-if(PYTHONINTERP_FOUND)
- # Default found version 2
- if(PYTHON_VERSION_MAJOR EQUAL 2)
- FIND_PROGRAM(CYTHON_PATH cython)
- # Unitary tests are available through py.test
- find_program( PYTEST_PATH py.test )
- # Documentation generation is available through sphinx
- find_program( SPHINX_PATH sphinx-build )
- elseif(PYTHON_VERSION_MAJOR EQUAL 3)
- FIND_PROGRAM(CYTHON_PATH cython3)
- # Unitary tests are available through py.test
- find_program( PYTEST_PATH py.test )
- # Documentation generation is available through sphinx
- set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build")
- else()
- message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
- endif(PYTHON_VERSION_MAJOR EQUAL 2)
-endif(PYTHONINTERP_FOUND)
-
if(CYTHON_PATH)
message("${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_PATH} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}")
diff --git a/src/cython/example/CMakeLists.txt b/src/cython/example/CMakeLists.txt
new file mode 100644
index 00000000..d55b39aa
--- /dev/null
+++ b/src/cython/example/CMakeLists.txt
@@ -0,0 +1,84 @@
+cmake_minimum_required(VERSION 2.8)
+project(Cython_examples)
+
+if(CYTHON_PATH)
+ # Test examples
+ add_test(NAME alpha_complex_from_points_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_from_points_example.py")
+ set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
+ set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+ -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
+ set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME bottleneck_basic_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/bottleneck_basic_example.py")
+ set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+ set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+ set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
+ --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
+ set_tests_properties(periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME random_cubical_complex_persistence_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/random_cubical_complex_persistence_example.py"
+ 10 10 10)
+ set_tests_properties(random_cubical_complex_persistence_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
+ set_tests_properties(rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3)
+ set_tests_properties(rips_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME rips_complex_from_points_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_from_points_example.py)
+ set_tests_properties(rips_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME simplex_tree_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/simplex_tree_example.py)
+ set_tests_properties(simplex_tree_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+ set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+ add_test(NAME witness_complex_from_nearest_landmark_table_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/witness_complex_from_nearest_landmark_table.py)
+ set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+endif(CYTHON_PATH)
diff --git a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
index 2474fc87..2371c36c 100755
--- a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
@@ -32,7 +32,7 @@ __license__ = "GPL v3"
parser = argparse.ArgumentParser(description='EuclideanStrongWitnessComplex creation from '
'points read in a OFF file.',
epilog='Example: '
- 'example/witness_complex_diagram_persistence_from_off_file_example.py '
+ 'example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py '
'-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2'
'- Constructs a strong witness complex with the '
'points from the given OFF file.')
diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
index 5a75417b..5748aa8a 100755
--- a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -32,7 +32,7 @@ __license__ = "GPL v3"
parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation from '
'points read in a OFF file.',
epilog='Example: '
- 'example/witness_complex_diagram_persistence_from_off_file_example.py '
+ 'example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py '
'-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2'
'- Constructs a weak witness complex with the '
'points from the given OFF file.')
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-06 16:10:20 +0000