diff options
author | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2019-09-09 16:03:40 +0200 |
---|---|---|
committer | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2019-09-09 16:03:40 +0200 |
commit | 68753b3c28321e28eedd5829c94234da84e25c8d (patch) | |
tree | 36003a30309b3203b41092ad4d7ee8fa78551452 /src | |
parent | dcbdaa0dc00eb069d1a13575f22c0a2f7d63dcc8 (diff) |
Code review: rename cython as python (make target and directory
Diffstat (limited to 'src')
-rw-r--r-- | src/CMakeLists.txt | 4 | ||||
-rw-r--r-- | src/Doxyfile.in | 2 | ||||
-rw-r--r-- | src/cmake/modules/GUDHI_third_party_libraries.cmake | 20 | ||||
-rw-r--r-- | src/cmake/modules/GUDHI_user_version_target.cmake | 2 | ||||
-rw-r--r-- | src/python/CMakeLists.txt (renamed from src/cython/CMakeLists.txt) | 153 | ||||
-rw-r--r-- | src/python/CONVENTIONS (renamed from src/cython/CONVENTIONS) | 0 | ||||
-rw-r--r-- | src/python/README (renamed from src/cython/README) | 0 | ||||
-rw-r--r-- | src/python/doc/_templates/layout.html (renamed from src/cython/doc/_templates/layout.html) | 0 | ||||
-rw-r--r-- | src/python/doc/alpha_complex_ref.rst (renamed from src/cython/doc/alpha_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/alpha_complex_sum.inc (renamed from src/cython/doc/alpha_complex_sum.inc) | 0 | ||||
-rw-r--r-- | src/python/doc/alpha_complex_user.rst (renamed from src/cython/doc/alpha_complex_user.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/bottleneck_distance_sum.inc (renamed from src/cython/doc/bottleneck_distance_sum.inc) | 0 | ||||
-rw-r--r-- | src/python/doc/bottleneck_distance_user.rst (renamed from src/cython/doc/bottleneck_distance_user.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/citation.rst (renamed from src/cython/doc/citation.rst) | 0 | ||||
-rwxr-xr-x | src/python/doc/conf.py (renamed from src/cython/doc/conf.py) | 0 | ||||
-rw-r--r-- | src/python/doc/cubical_complex_ref.rst (renamed from src/cython/doc/cubical_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/cubical_complex_sum.inc (renamed from src/cython/doc/cubical_complex_sum.inc) | 0 | ||||
-rw-r--r-- | src/python/doc/cubical_complex_user.rst (renamed from src/cython/doc/cubical_complex_user.rst) | 2 | ||||
-rw-r--r-- | src/python/doc/euclidean_strong_witness_complex_ref.rst (renamed from src/cython/doc/euclidean_strong_witness_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/euclidean_witness_complex_ref.rst (renamed from src/cython/doc/euclidean_witness_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/examples.rst (renamed from src/cython/doc/examples.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/fileformats.rst (renamed from src/cython/doc/fileformats.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/img/graphical_tools_representation.png (renamed from src/cython/doc/img/graphical_tools_representation.png) | bin | 10846 -> 10846 bytes | |||
-rw-r--r-- | src/python/doc/index.rst (renamed from src/cython/doc/index.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/installation.rst (renamed from src/cython/doc/installation.rst) | 20 | ||||
-rw-r--r-- | src/python/doc/nerve_gic_complex_ref.rst (renamed from src/cython/doc/nerve_gic_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/nerve_gic_complex_sum.inc (renamed from src/cython/doc/nerve_gic_complex_sum.inc) | 0 | ||||
-rw-r--r-- | src/python/doc/nerve_gic_complex_user.rst (renamed from src/cython/doc/nerve_gic_complex_user.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/periodic_cubical_complex_ref.rst (renamed from src/cython/doc/periodic_cubical_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/persistence_graphical_tools_ref.rst (renamed from src/cython/doc/persistence_graphical_tools_ref.rst) | 1 | ||||
-rw-r--r-- | src/python/doc/persistence_graphical_tools_sum.inc (renamed from src/cython/doc/persistence_graphical_tools_sum.inc) | 0 | ||||
-rw-r--r-- | src/python/doc/persistence_graphical_tools_user.rst (renamed from src/cython/doc/persistence_graphical_tools_user.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/persistent_cohomology_sum.inc (renamed from src/cython/doc/persistent_cohomology_sum.inc) | 0 | ||||
-rw-r--r-- | src/python/doc/persistent_cohomology_user.rst (renamed from src/cython/doc/persistent_cohomology_user.rst) | 0 | ||||
-rwxr-xr-x | src/python/doc/python3-sphinx-build.py (renamed from src/cython/doc/python3-sphinx-build.py) | 0 | ||||
-rw-r--r-- | src/python/doc/reader_utils_ref.rst (renamed from src/cython/doc/reader_utils_ref.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/rips_complex_ref.rst (renamed from src/cython/doc/rips_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/rips_complex_sum.inc (renamed from src/cython/doc/rips_complex_sum.inc) | 0 | ||||
-rw-r--r-- | src/python/doc/rips_complex_user.rst (renamed from src/cython/doc/rips_complex_user.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/simplex_tree_ref.rst (renamed from src/cython/doc/simplex_tree_ref.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/simplex_tree_sum.inc (renamed from src/cython/doc/simplex_tree_sum.inc) | 0 | ||||
-rw-r--r-- | src/python/doc/simplex_tree_user.rst (renamed from src/cython/doc/simplex_tree_user.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/strong_witness_complex_ref.rst (renamed from src/cython/doc/strong_witness_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/tangential_complex_ref.rst (renamed from src/cython/doc/tangential_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/tangential_complex_sum.inc (renamed from src/cython/doc/tangential_complex_sum.inc) | 0 | ||||
-rw-r--r-- | src/python/doc/tangential_complex_user.rst (renamed from src/cython/doc/tangential_complex_user.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/todos.rst (renamed from src/cython/doc/todos.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/witness_complex_ref.rst (renamed from src/cython/doc/witness_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/python/doc/witness_complex_sum.inc (renamed from src/cython/doc/witness_complex_sum.inc) | 0 | ||||
-rw-r--r-- | src/python/doc/witness_complex_user.rst (renamed from src/cython/doc/witness_complex_user.rst) | 0 | ||||
-rwxr-xr-x | src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py (renamed from src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/alpha_complex_from_points_example.py (renamed from src/cython/example/alpha_complex_from_points_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/alpha_rips_persistence_bottleneck_distance.py (renamed from src/cython/example/alpha_rips_persistence_bottleneck_distance.py) | 0 | ||||
-rwxr-xr-x | src/python/example/bottleneck_basic_example.py (renamed from src/cython/example/bottleneck_basic_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/coordinate_graph_induced_complex.py (renamed from src/cython/example/coordinate_graph_induced_complex.py) | 0 | ||||
-rwxr-xr-x | src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py (renamed from src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py (renamed from src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/functional_graph_induced_complex.py (renamed from src/cython/example/functional_graph_induced_complex.py) | 0 | ||||
-rwxr-xr-x | src/python/example/gudhi_graphical_tools_example.py (renamed from src/cython/example/gudhi_graphical_tools_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/nerve_of_a_covering.py (renamed from src/cython/example/nerve_of_a_covering.py) | 0 | ||||
-rwxr-xr-x | src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py (renamed from src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/random_cubical_complex_persistence_example.py (renamed from src/cython/example/random_cubical_complex_persistence_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py (renamed from src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py (renamed from src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/rips_complex_diagram_persistence_from_off_file_example.py (renamed from src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/rips_complex_from_points_example.py (renamed from src/cython/example/rips_complex_from_points_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/rips_persistence_diagram.py (renamed from src/cython/example/rips_persistence_diagram.py) | 0 | ||||
-rwxr-xr-x | src/python/example/simplex_tree_example.py (renamed from src/cython/example/simplex_tree_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/sparse_rips_persistence_diagram.py (renamed from src/cython/example/sparse_rips_persistence_diagram.py) | 0 | ||||
-rwxr-xr-x | src/python/example/tangential_complex_plain_homology_from_off_file_example.py (renamed from src/cython/example/tangential_complex_plain_homology_from_off_file_example.py) | 0 | ||||
-rwxr-xr-x | src/python/example/voronoi_graph_induced_complex.py (renamed from src/cython/example/voronoi_graph_induced_complex.py) | 0 | ||||
-rwxr-xr-x | src/python/example/witness_complex_from_nearest_landmark_table.py (renamed from src/cython/example/witness_complex_from_nearest_landmark_table.py) | 0 | ||||
-rw-r--r-- | src/python/gudhi/__init__.py (renamed from src/cython/gudhi/__init__.py) | 0 | ||||
-rw-r--r-- | src/python/gudhi/__init__.py.in (renamed from src/cython/gudhi/__init__.py.in) | 4 | ||||
-rw-r--r-- | src/python/gudhi/alpha_complex.pyx (renamed from src/cython/gudhi/alpha_complex.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/bottleneck.pyx (renamed from src/cython/gudhi/bottleneck.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/cubical_complex.pyx (renamed from src/cython/gudhi/cubical_complex.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/euclidean_strong_witness_complex.pyx (renamed from src/cython/gudhi/euclidean_strong_witness_complex.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/euclidean_witness_complex.pyx (renamed from src/cython/gudhi/euclidean_witness_complex.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/nerve_gic.pyx (renamed from src/cython/gudhi/nerve_gic.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/off_reader.pyx (renamed from src/cython/gudhi/off_reader.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/periodic_cubical_complex.pyx (renamed from src/cython/gudhi/periodic_cubical_complex.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/persistence_graphical_tools.py (renamed from src/cython/gudhi/persistence_graphical_tools.py) | 0 | ||||
-rw-r--r-- | src/python/gudhi/reader_utils.pyx (renamed from src/cython/gudhi/reader_utils.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/rips_complex.pyx (renamed from src/cython/gudhi/rips_complex.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/simplex_tree.pxd (renamed from src/cython/gudhi/simplex_tree.pxd) | 0 | ||||
-rw-r--r-- | src/python/gudhi/simplex_tree.pyx (renamed from src/cython/gudhi/simplex_tree.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/strong_witness_complex.pyx (renamed from src/cython/gudhi/strong_witness_complex.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/subsampling.pyx (renamed from src/cython/gudhi/subsampling.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/tangential_complex.pyx (renamed from src/cython/gudhi/tangential_complex.pyx) | 0 | ||||
-rw-r--r-- | src/python/gudhi/witness_complex.pyx (renamed from src/cython/gudhi/witness_complex.pyx) | 0 | ||||
-rw-r--r-- | src/python/include/Alpha_complex_interface.h (renamed from src/cython/include/Alpha_complex_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Bottleneck_distance_interface.h (renamed from src/cython/include/Bottleneck_distance_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Cubical_complex_interface.h (renamed from src/cython/include/Cubical_complex_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Euclidean_strong_witness_complex_interface.h (renamed from src/cython/include/Euclidean_strong_witness_complex_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Euclidean_witness_complex_interface.h (renamed from src/cython/include/Euclidean_witness_complex_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Nerve_gic_interface.h (renamed from src/cython/include/Nerve_gic_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Off_reader_interface.h (renamed from src/cython/include/Off_reader_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Persistent_cohomology_interface.h (renamed from src/cython/include/Persistent_cohomology_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Reader_utils_interface.h (renamed from src/cython/include/Reader_utils_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Rips_complex_interface.h (renamed from src/cython/include/Rips_complex_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Simplex_tree_interface.h (renamed from src/cython/include/Simplex_tree_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Strong_witness_complex_interface.h (renamed from src/cython/include/Strong_witness_complex_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Subsampling_interface.h (renamed from src/cython/include/Subsampling_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Tangential_complex_interface.h (renamed from src/cython/include/Tangential_complex_interface.h) | 0 | ||||
-rw-r--r-- | src/python/include/Witness_complex_interface.h (renamed from src/cython/include/Witness_complex_interface.h) | 0 | ||||
-rw-r--r-- | src/python/setup.py.in (renamed from src/cython/setup.py.in) | 14 | ||||
-rwxr-xr-x | src/python/test/test_alpha_complex.py (renamed from src/cython/test/test_alpha_complex.py) | 0 | ||||
-rwxr-xr-x | src/python/test/test_bottleneck_distance.py (renamed from src/cython/test/test_bottleneck_distance.py) | 0 | ||||
-rwxr-xr-x | src/python/test/test_cover_complex.py (renamed from src/cython/test/test_cover_complex.py) | 0 | ||||
-rwxr-xr-x | src/python/test/test_cubical_complex.py (renamed from src/cython/test/test_cubical_complex.py) | 0 | ||||
-rwxr-xr-x | src/python/test/test_euclidean_witness_complex.py (renamed from src/cython/test/test_euclidean_witness_complex.py) | 0 | ||||
-rwxr-xr-x | src/python/test/test_reader_utils.py (renamed from src/cython/test/test_reader_utils.py) | 0 | ||||
-rwxr-xr-x | src/python/test/test_rips_complex.py (renamed from src/cython/test/test_rips_complex.py) | 0 | ||||
-rwxr-xr-x | src/python/test/test_simplex_tree.py (renamed from src/cython/test/test_simplex_tree.py) | 0 | ||||
-rwxr-xr-x | src/python/test/test_subsampling.py (renamed from src/cython/test/test_subsampling.py) | 0 | ||||
-rwxr-xr-x | src/python/test/test_tangential_complex.py (renamed from src/cython/test/test_tangential_complex.py) | 0 | ||||
-rwxr-xr-x | src/python/test/test_witness_complex.py (renamed from src/cython/test/test_witness_complex.py) | 0 |
118 files changed, 111 insertions, 111 deletions
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 40fdcf2b..561aa049 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -10,7 +10,7 @@ set(GUDHI_MODULES "" CACHE INTERNAL "GUDHI_MODULES") set(GUDHI_MISSING_MODULES "" CACHE INTERNAL "GUDHI_MISSING_MODULES") # This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path -set(GUDHI_CYTHON_PATH "cython") +set(GUDHI_PYTHON_PATH "python") # For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH include(GUDHI_third_party_libraries NO_POLICY_SCOPE) @@ -61,7 +61,7 @@ add_subdirectory(GudhUI) if (WITH_GUDHI_PYTHON) # specific for cython module - add_subdirectory(${GUDHI_CYTHON_PATH}) + add_subdirectory(${GUDHI_PYTHON_PATH}) else() message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF") set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python") diff --git a/src/Doxyfile.in b/src/Doxyfile.in index 59f864a0..57775498 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in @@ -784,7 +784,7 @@ EXCLUDE = data/ \ example/ \ GudhUI/ \ cmake/ \ - cython/ \ + python/ \ README.md # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index 1dbddfd9..360a230b 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -101,16 +101,18 @@ function( find_python_module PYTHON_MODULE_NAME ) RESULT_VARIABLE PYTHON_MODULE_RESULT OUTPUT_VARIABLE PYTHON_MODULE_VERSION ERROR_VARIABLE PYTHON_MODULE_ERROR) - message ("PYTHON_MODULE_NAME = ${PYTHON_MODULE_NAME} - - PYTHON_MODULE_RESULT = ${PYTHON_MODULE_RESULT} - - PYTHON_MODULE_VERSION = ${PYTHON_MODULE_VERSION} - - PYTHON_MODULE_ERROR = ${PYTHON_MODULE_ERROR}") if(PYTHON_MODULE_RESULT EQUAL 0) # Remove carriage return string(STRIP ${PYTHON_MODULE_VERSION} PYTHON_MODULE_VERSION) + message ("++ Python module ${PYTHON_MODULE_NAME} - Version ${PYTHON_MODULE_VERSION} found") + set(${PYTHON_MODULE_NAME_UP}_VERSION ${PYTHON_MODULE_VERSION} PARENT_SCOPE) set(${PYTHON_MODULE_NAME_UP}_FOUND TRUE PARENT_SCOPE) else() + message ("PYTHON_MODULE_NAME = ${PYTHON_MODULE_NAME} + - PYTHON_MODULE_RESULT = ${PYTHON_MODULE_RESULT} + - PYTHON_MODULE_VERSION = ${PYTHON_MODULE_VERSION} + - PYTHON_MODULE_ERROR = ${PYTHON_MODULE_ERROR}") unset(${PYTHON_MODULE_NAME_UP}_VERSION PARENT_SCOPE) set(${PYTHON_MODULE_NAME_UP}_FOUND FALSE PARENT_SCOPE) endif() @@ -125,11 +127,11 @@ if( PYTHONINTERP_FOUND ) find_python_module("sphinx") endif() -if(NOT GUDHI_CYTHON_PATH) - message(FATAL_ERROR "ERROR: GUDHI_CYTHON_PATH is not valid.") -endif(NOT GUDHI_CYTHON_PATH) +if(NOT GUDHI_PYTHON_PATH) + message(FATAL_ERROR "ERROR: GUDHI_PYTHON_PATH is not valid.") +endif(NOT GUDHI_PYTHON_PATH) -option(WITH_GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "Build with setting runtime_library_dirs. Usefull when setting rpath is not allowed" ON) +option(WITH_GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS "Build with setting runtime_library_dirs. Usefull when setting rpath is not allowed" ON) if(PYTHONINTERP_FOUND AND CYTHON_FOUND) if(SPHINX_FOUND) @@ -139,7 +141,7 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND) if(NOT SPHINX_PATH) if(PYTHON_VERSION_MAJOR EQUAL 3) # In Python3, just hack sphinx-build if it does not exist - set(SPHINX_PATH "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build.py") + set(SPHINX_PATH "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/${GUDHI_PYTHON_PATH}/doc/python3-sphinx-build.py") endif(PYTHON_VERSION_MAJOR EQUAL 3) endif(NOT SPHINX_PATH) endif(SPHINX_FOUND) diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake index 91eee6b5..f75fb19e 100644 --- a/src/cmake/modules/GUDHI_user_version_target.cmake +++ b/src/cmake/modules/GUDHI_user_version_target.cmake @@ -42,7 +42,7 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/biblio ${GUDHI_USER_VERSION_DIR}/biblio) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${CMAKE_SOURCE_DIR}/src/cython ${GUDHI_USER_VERSION_DIR}/cython) + copy_directory ${CMAKE_SOURCE_DIR}/${GUDHI_PYTHON_PATH} ${GUDHI_USER_VERSION_DIR}/python) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/data ${GUDHI_USER_VERSION_DIR}/data) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E diff --git a/src/cython/CMakeLists.txt b/src/python/CMakeLists.txt index ab20c6e6..9e128d30 100644 --- a/src/cython/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -1,18 +1,18 @@ project(Cython) -function( add_gudhi_cython_lib THE_LIB ) +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 = ${THE_LIB_FILE_NAME}") - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${THE_LIB_FILE_NAME}', " PARENT_SCOPE) + set(GUDHI_PYTHON_LIBRARIES "${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 = ${UNIX_LIB_FILE_NAME}") - set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${UNIX_LIB_FILE_NAME}', " PARENT_SCOPE) + set(GUDHI_PYTHON_LIBRARIES "${GUDHI_PYTHON_LIBRARIES}'${UNIX_LIB_FILE_NAME}', " PARENT_SCOPE) endif(WIN32) endif(EXISTS ${THE_LIB}) -endfunction( add_gudhi_cython_lib ) +endfunction( add_GUDHI_PYTHON_lib ) # THE_TEST is the python test file name (without .py extension) containing tests functions function( add_gudhi_py_test THE_TEST ) @@ -28,27 +28,27 @@ endfunction( add_gudhi_py_test ) # Set gudhi.__debug_info__ # WARNING : to be done before setup.py.in configure_file function( add_gudhi_debug_info DEBUG_INFO ) - set(GUDHI_CYTHON_DEBUG_INFO "${GUDHI_CYTHON_DEBUG_INFO} \"${DEBUG_INFO}\\n\" \\\n" PARENT_SCOPE) + set(GUDHI_PYTHON_DEBUG_INFO "${GUDHI_PYTHON_DEBUG_INFO} \"${DEBUG_INFO}\\n\" \\\n" PARENT_SCOPE) endfunction( add_gudhi_debug_info ) if(PYTHONINTERP_FOUND) if(CYTHON_FOUND) - set(GUDHI_CYTHON_MODULES "${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', ") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'bottleneck', ") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'subsampling', ") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'tangential_complex', ") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'alpha_complex', ") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'euclidean_witness_complex', ") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'euclidean_strong_witness_complex', ") + set(GUDHI_PYTHON_MODULES "${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}") @@ -65,95 +65,94 @@ if(PYTHONINTERP_FOUND) add_gudhi_debug_info("Scipy version ${SCIPY_VERSION}") 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', ") + 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 "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ") # Gudhi and CGAL compilation option if(MSVC) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ") else(MSVC) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ") endif(MSVC) if(CMAKE_COMPILER_IS_GNUCXX) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ") endif(CMAKE_COMPILER_IS_GNUCXX) if (CMAKE_CXX_COMPILER_ID MATCHES Intel) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ") endif(CMAKE_CXX_COMPILER_ID MATCHES Intel) if (DEBUG_TRACES) # For programs to be more verbose - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ") endif() if (EIGEN3_FOUND) add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}") # No problem, even if no CGAL found - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") endif (EIGEN3_FOUND) - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'off_reader', ") - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'simplex_tree', ") - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'rips_complex', ") - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'cubical_complex', ") - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'periodic_cubical_complex', ") - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'reader_utils', ") - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'witness_complex', ") - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'strong_witness_complex', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${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 "${GUDHI_PYTHON_MODULES_TO_COMPILE}'strong_witness_complex', ") if (NOT CGAL_VERSION VERSION_LESS 4.11.0) - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'bottleneck', ") - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'nerve_gic', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'bottleneck', ") + set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'nerve_gic', ") endif () if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'subsampling', ") - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'tangential_complex', ") - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'alpha_complex', ") - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'euclidean_witness_complex', ") - set(GUDHI_CYTHON_MODULES_TO_COMPILE "${GUDHI_CYTHON_MODULES_TO_COMPILE}'euclidean_strong_witness_complex', ") + 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 "${GUDHI_PYTHON_MODULES_TO_COMPILE}'euclidean_strong_witness_complex', ") endif () if(CGAL_FOUND) can_cgal_use_cxx11_thread_local() if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) if(CMAKE_BUILD_TYPE MATCHES Debug) - add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_DEBUG}") + add_GUDHI_PYTHON_lib("${Boost_THREAD_LIBRARY_DEBUG}") else() - add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_RELEASE}") + add_GUDHI_PYTHON_lib("${Boost_THREAD_LIBRARY_RELEASE}") endif() message("** Add Boost ${Boost_LIBRARY_DIRS}") - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") + set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") endif() # Add CGAL compilation args if(CGAL_HEADER_ONLY) add_gudhi_debug_info("CGAL header only version ${CGAL_VERSION}") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") else(CGAL_HEADER_ONLY) add_gudhi_debug_info("CGAL version ${CGAL_VERSION}") - add_gudhi_cython_lib("${CGAL_LIBRARY}") - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") + add_GUDHI_PYTHON_lib("${CGAL_LIBRARY}") + set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") message("** Add CGAL ${CGAL_LIBRARIES_DIR}") # If CGAL is not header only, CGAL library may link with boost system, if(CMAKE_BUILD_TYPE MATCHES Debug) - add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_DEBUG}") + add_GUDHI_PYTHON_lib("${Boost_SYSTEM_LIBRARY_DEBUG}") else() - add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_RELEASE}") + add_GUDHI_PYTHON_lib("${Boost_SYSTEM_LIBRARY_RELEASE}") endif() - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") + set(GUDHI_PYTHON_LIBRARY_DIRS "${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 = ${GMP_LIBRARIES}") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ") - add_gudhi_cython_lib("${GMP_LIBRARIES}") - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${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 = ${GMPXX_LIBRARIES}") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ") - add_gudhi_cython_lib("${GMPXX_LIBRARIES}") - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${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 ${GMPXX_LIBRARIES_DIR}") endif(GMPXX_FOUND) endif(GMP_FOUND) @@ -161,35 +160,35 @@ if(PYTHONINTERP_FOUND) # Specific for Mac if (${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', ") + 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 ${GUDHI_INCLUDE_DIRECTORIES}) - set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ") + set(GUDHI_PYTHON_INCLUDE_DIRS "${GUDHI_PYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ") endforeach() - set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ") + 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 ${TBB_INTERFACE_VERSION} found and used") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ") + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ") if(CMAKE_BUILD_TYPE MATCHES Debug) - add_gudhi_cython_lib("${TBB_DEBUG_LIBRARY}") - add_gudhi_cython_lib("${TBB_MALLOC_DEBUG_LIBRARY}") + add_GUDHI_PYTHON_lib("${TBB_DEBUG_LIBRARY}") + add_GUDHI_PYTHON_lib("${TBB_MALLOC_DEBUG_LIBRARY}") else() - add_gudhi_cython_lib("${TBB_RELEASE_LIBRARY}") - add_gudhi_cython_lib("${TBB_MALLOC_RELEASE_LIBRARY}") + add_GUDHI_PYTHON_lib("${TBB_RELEASE_LIBRARY}") + add_GUDHI_PYTHON_lib("${TBB_MALLOC_RELEASE_LIBRARY}") endif() - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ") + set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ") message("** Add tbb ${TBB_LIBRARY_DIRS}") - set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ") + set(GUDHI_PYTHON_INCLUDE_DIRS "${GUDHI_PYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ") endif() - if(UNIX AND WITH_GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS) - set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}") - endif(UNIX AND WITH_GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS) + 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) @@ -206,7 +205,7 @@ if(PYTHONINTERP_FOUND) 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 + 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)") @@ -381,7 +380,7 @@ if(PYTHONINTERP_FOUND) set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/") # User warning - Sphinx is a static pages generator, and configured to work fine with user_version # Images and biblio warnings because not found on developper version - if (GUDHI_CYTHON_PATH STREQUAL "src/cython") + if (GUDHI_PYTHON_PATH STREQUAL "src/python") set (GUDHI_SPHINX_MESSAGE "${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 diff --git a/src/cython/CONVENTIONS b/src/python/CONVENTIONS index 804e97f3..804e97f3 100644 --- a/src/cython/CONVENTIONS +++ b/src/python/CONVENTIONS diff --git a/src/cython/README b/src/python/README index 7d2c4491..7d2c4491 100644 --- a/src/cython/README +++ b/src/python/README diff --git a/src/cython/doc/_templates/layout.html b/src/python/doc/_templates/layout.html index bc0e9658..bc0e9658 100644 --- a/src/cython/doc/_templates/layout.html +++ b/src/python/doc/_templates/layout.html diff --git a/src/cython/doc/alpha_complex_ref.rst b/src/python/doc/alpha_complex_ref.rst index 7da79543..7da79543 100644 --- a/src/cython/doc/alpha_complex_ref.rst +++ b/src/python/doc/alpha_complex_ref.rst diff --git a/src/cython/doc/alpha_complex_sum.inc b/src/python/doc/alpha_complex_sum.inc index 9049e654..9049e654 100644 --- a/src/cython/doc/alpha_complex_sum.inc +++ b/src/python/doc/alpha_complex_sum.inc diff --git a/src/cython/doc/alpha_complex_user.rst b/src/python/doc/alpha_complex_user.rst index d1e9c7cd..d1e9c7cd 100644 --- a/src/cython/doc/alpha_complex_user.rst +++ b/src/python/doc/alpha_complex_user.rst diff --git a/src/cython/doc/bottleneck_distance_sum.inc b/src/python/doc/bottleneck_distance_sum.inc index 6eb0ac19..6eb0ac19 100644 --- a/src/cython/doc/bottleneck_distance_sum.inc +++ b/src/python/doc/bottleneck_distance_sum.inc diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/python/doc/bottleneck_distance_user.rst index 9435c7f1..9435c7f1 100644 --- a/src/cython/doc/bottleneck_distance_user.rst +++ b/src/python/doc/bottleneck_distance_user.rst diff --git a/src/cython/doc/citation.rst b/src/python/doc/citation.rst index 117eb9dd..117eb9dd 100644 --- a/src/cython/doc/citation.rst +++ b/src/python/doc/citation.rst diff --git a/src/cython/doc/conf.py b/src/python/doc/conf.py index e4c718c3..e4c718c3 100755 --- a/src/cython/doc/conf.py +++ b/src/python/doc/conf.py diff --git a/src/cython/doc/cubical_complex_ref.rst b/src/python/doc/cubical_complex_ref.rst index 1fe9d5fb..1fe9d5fb 100644 --- a/src/cython/doc/cubical_complex_ref.rst +++ b/src/python/doc/cubical_complex_ref.rst diff --git a/src/cython/doc/cubical_complex_sum.inc b/src/python/doc/cubical_complex_sum.inc index f200e695..f200e695 100644 --- a/src/cython/doc/cubical_complex_sum.inc +++ b/src/python/doc/cubical_complex_sum.inc diff --git a/src/cython/doc/cubical_complex_user.rst b/src/python/doc/cubical_complex_user.rst index 19120360..b13b500e 100644 --- a/src/cython/doc/cubical_complex_user.rst +++ b/src/python/doc/cubical_complex_user.rst @@ -158,7 +158,7 @@ the program output is: Examples. --------- -End user programs are available in cython/example/ folder. +End user programs are available in python/example/ folder. Bibliography ============ diff --git a/src/cython/doc/euclidean_strong_witness_complex_ref.rst b/src/python/doc/euclidean_strong_witness_complex_ref.rst index 1a602cd5..1a602cd5 100644 --- a/src/cython/doc/euclidean_strong_witness_complex_ref.rst +++ b/src/python/doc/euclidean_strong_witness_complex_ref.rst diff --git a/src/cython/doc/euclidean_witness_complex_ref.rst b/src/python/doc/euclidean_witness_complex_ref.rst index 28daf965..28daf965 100644 --- a/src/cython/doc/euclidean_witness_complex_ref.rst +++ b/src/python/doc/euclidean_witness_complex_ref.rst diff --git a/src/cython/doc/examples.rst b/src/python/doc/examples.rst index edbc2f72..edbc2f72 100644 --- a/src/cython/doc/examples.rst +++ b/src/python/doc/examples.rst diff --git a/src/cython/doc/fileformats.rst b/src/python/doc/fileformats.rst index 345dfdba..345dfdba 100644 --- a/src/cython/doc/fileformats.rst +++ b/src/python/doc/fileformats.rst diff --git a/src/cython/doc/img/graphical_tools_representation.png b/src/python/doc/img/graphical_tools_representation.png Binary files differindex 9759f7ba..9759f7ba 100644 --- a/src/cython/doc/img/graphical_tools_representation.png +++ b/src/python/doc/img/graphical_tools_representation.png diff --git a/src/cython/doc/index.rst b/src/python/doc/index.rst index e379bc23..e379bc23 100644 --- a/src/cython/doc/index.rst +++ b/src/python/doc/index.rst diff --git a/src/cython/doc/installation.rst b/src/python/doc/installation.rst index 02b889d0..1c672ce3 100644 --- a/src/cython/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -9,14 +9,14 @@ Compiling ********* The library uses c++11 and requires `Boost <https://www.boost.org/>`_ ≥ 1.56.0, `CMake <https://www.cmake.org/>`_ ≥ 3.1 to generate makefiles, and -`Cython <https://www.cython.org/>`_ to compile the GUDHI Python module. +`python <https://www.python.org/>`_ to compile the GUDHI Python module. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. On `Windows <https://wiki.python.org/moin/WindowsCompilers>`_ , only Python 3.5 and 3.6 are available because of the required Visual Studio version. -On other systems, if you have several Python/Cython installed, the version 2.X +On other systems, if you have several Python/python installed, the version 2.X will be used by default, but you can force it by adding :code:`-DPython_ADDITIONAL_VERSIONS=3` to the cmake command. @@ -31,7 +31,7 @@ To build the GUDHI Python module, run the following commands in a terminal: mkdir build cd build/ cmake .. - cd cython + cd python make GUDHI Python module installation @@ -43,13 +43,13 @@ PYTHONPATH: .. code-block:: bash # For windows, you have to set PYTHONPATH environment variable - export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython' + export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/python' Or install it definitely in your Python packages folder: .. code-block:: bash - cd /path-to-gudhi/build/cython + cd /path-to-gudhi/build/python # May require sudo or administrator privileges make install @@ -62,9 +62,9 @@ following command in a terminal: .. code-block:: bash - cd /path-to-gudhi/build/cython + cd /path-to-gudhi/build/python # For windows, you have to set PYTHONPATH environment variable - export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython' + export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/python' make test Debugging issues @@ -86,7 +86,7 @@ You shall have something like: .. code-block:: none Python version 2.7.15 - Cython version 0.26.1 + python version 0.26.1 Eigen3 version 3.1.1 Installed modules are: off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex; persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;alpha_complex; @@ -108,7 +108,7 @@ A complete configuration would be : .. code-block:: none Python version 3.6.5 - Cython version 0.28.2 + python version 0.28.2 Pytest version 3.3.2 Matplotlib version 2.2.2 Numpy version 1.14.5 @@ -135,7 +135,7 @@ Run the following commands in a terminal: .. code-block:: bash - cd /path-to-gudhi/build/cython + cd /path-to-gudhi/build/python make sphinx Optional third-party library diff --git a/src/cython/doc/nerve_gic_complex_ref.rst b/src/python/doc/nerve_gic_complex_ref.rst index abde2e8c..abde2e8c 100644 --- a/src/cython/doc/nerve_gic_complex_ref.rst +++ b/src/python/doc/nerve_gic_complex_ref.rst diff --git a/src/cython/doc/nerve_gic_complex_sum.inc b/src/python/doc/nerve_gic_complex_sum.inc index d633c4ff..d633c4ff 100644 --- a/src/cython/doc/nerve_gic_complex_sum.inc +++ b/src/python/doc/nerve_gic_complex_sum.inc diff --git a/src/cython/doc/nerve_gic_complex_user.rst b/src/python/doc/nerve_gic_complex_user.rst index 9101f45d..9101f45d 100644 --- a/src/cython/doc/nerve_gic_complex_user.rst +++ b/src/python/doc/nerve_gic_complex_user.rst diff --git a/src/cython/doc/periodic_cubical_complex_ref.rst b/src/python/doc/periodic_cubical_complex_ref.rst index 4b831647..4b831647 100644 --- a/src/cython/doc/periodic_cubical_complex_ref.rst +++ b/src/python/doc/periodic_cubical_complex_ref.rst diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/python/doc/persistence_graphical_tools_ref.rst index 54aff4bc..0b0038d9 100644 --- a/src/cython/doc/persistence_graphical_tools_ref.rst +++ b/src/python/doc/persistence_graphical_tools_ref.rst @@ -6,7 +6,6 @@ Persistence graphical tools reference manual ============================================ -.. autofunction:: gudhi.__min_birth_max_death .. autofunction:: gudhi.plot_persistence_barcode .. autofunction:: gudhi.plot_persistence_diagram .. autofunction:: gudhi.plot_persistence_density diff --git a/src/cython/doc/persistence_graphical_tools_sum.inc b/src/python/doc/persistence_graphical_tools_sum.inc index 0cdf8072..0cdf8072 100644 --- a/src/cython/doc/persistence_graphical_tools_sum.inc +++ b/src/python/doc/persistence_graphical_tools_sum.inc diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/python/doc/persistence_graphical_tools_user.rst index b2124fdd..b2124fdd 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/python/doc/persistence_graphical_tools_user.rst diff --git a/src/cython/doc/persistent_cohomology_sum.inc b/src/python/doc/persistent_cohomology_sum.inc index 4d7b077e..4d7b077e 100644 --- a/src/cython/doc/persistent_cohomology_sum.inc +++ b/src/python/doc/persistent_cohomology_sum.inc diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/python/doc/persistent_cohomology_user.rst index de83cda1..de83cda1 100644 --- a/src/cython/doc/persistent_cohomology_user.rst +++ b/src/python/doc/persistent_cohomology_user.rst diff --git a/src/cython/doc/python3-sphinx-build.py b/src/python/doc/python3-sphinx-build.py index 84d158cf..84d158cf 100755 --- a/src/cython/doc/python3-sphinx-build.py +++ b/src/python/doc/python3-sphinx-build.py diff --git a/src/cython/doc/reader_utils_ref.rst b/src/python/doc/reader_utils_ref.rst index f3ecebad..f3ecebad 100644 --- a/src/cython/doc/reader_utils_ref.rst +++ b/src/python/doc/reader_utils_ref.rst diff --git a/src/cython/doc/rips_complex_ref.rst b/src/python/doc/rips_complex_ref.rst index 22b5616c..22b5616c 100644 --- a/src/cython/doc/rips_complex_ref.rst +++ b/src/python/doc/rips_complex_ref.rst diff --git a/src/cython/doc/rips_complex_sum.inc b/src/python/doc/rips_complex_sum.inc index 857c6893..857c6893 100644 --- a/src/cython/doc/rips_complex_sum.inc +++ b/src/python/doc/rips_complex_sum.inc diff --git a/src/cython/doc/rips_complex_user.rst b/src/python/doc/rips_complex_user.rst index 1d340dbe..1d340dbe 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/python/doc/rips_complex_user.rst diff --git a/src/cython/doc/simplex_tree_ref.rst b/src/python/doc/simplex_tree_ref.rst index 9eb8c199..9eb8c199 100644 --- a/src/cython/doc/simplex_tree_ref.rst +++ b/src/python/doc/simplex_tree_ref.rst diff --git a/src/cython/doc/simplex_tree_sum.inc b/src/python/doc/simplex_tree_sum.inc index 5ba58d2b..5ba58d2b 100644 --- a/src/cython/doc/simplex_tree_sum.inc +++ b/src/python/doc/simplex_tree_sum.inc diff --git a/src/cython/doc/simplex_tree_user.rst b/src/python/doc/simplex_tree_user.rst index aebeb29f..aebeb29f 100644 --- a/src/cython/doc/simplex_tree_user.rst +++ b/src/python/doc/simplex_tree_user.rst diff --git a/src/cython/doc/strong_witness_complex_ref.rst b/src/python/doc/strong_witness_complex_ref.rst index d624d711..d624d711 100644 --- a/src/cython/doc/strong_witness_complex_ref.rst +++ b/src/python/doc/strong_witness_complex_ref.rst diff --git a/src/cython/doc/tangential_complex_ref.rst b/src/python/doc/tangential_complex_ref.rst index cdfda082..cdfda082 100644 --- a/src/cython/doc/tangential_complex_ref.rst +++ b/src/python/doc/tangential_complex_ref.rst diff --git a/src/cython/doc/tangential_complex_sum.inc b/src/python/doc/tangential_complex_sum.inc index c8bc1177..c8bc1177 100644 --- a/src/cython/doc/tangential_complex_sum.inc +++ b/src/python/doc/tangential_complex_sum.inc diff --git a/src/cython/doc/tangential_complex_user.rst b/src/python/doc/tangential_complex_user.rst index ebfe1e29..ebfe1e29 100644 --- a/src/cython/doc/tangential_complex_user.rst +++ b/src/python/doc/tangential_complex_user.rst diff --git a/src/cython/doc/todos.rst b/src/python/doc/todos.rst index ca274ced..ca274ced 100644 --- a/src/cython/doc/todos.rst +++ b/src/python/doc/todos.rst diff --git a/src/cython/doc/witness_complex_ref.rst b/src/python/doc/witness_complex_ref.rst index 9987d3fd..9987d3fd 100644 --- a/src/cython/doc/witness_complex_ref.rst +++ b/src/python/doc/witness_complex_ref.rst diff --git a/src/cython/doc/witness_complex_sum.inc b/src/python/doc/witness_complex_sum.inc index 2be8b220..2be8b220 100644 --- a/src/cython/doc/witness_complex_sum.inc +++ b/src/python/doc/witness_complex_sum.inc diff --git a/src/cython/doc/witness_complex_user.rst b/src/python/doc/witness_complex_user.rst index 40e94134..40e94134 100644 --- a/src/cython/doc/witness_complex_user.rst +++ b/src/python/doc/witness_complex_user.rst diff --git a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py index b8f283b3..b8f283b3 100755 --- a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py diff --git a/src/cython/example/alpha_complex_from_points_example.py b/src/python/example/alpha_complex_from_points_example.py index a746998c..a746998c 100755 --- a/src/cython/example/alpha_complex_from_points_example.py +++ b/src/python/example/alpha_complex_from_points_example.py diff --git a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py b/src/python/example/alpha_rips_persistence_bottleneck_distance.py index 086307ee..086307ee 100755 --- a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py +++ b/src/python/example/alpha_rips_persistence_bottleneck_distance.py diff --git a/src/cython/example/bottleneck_basic_example.py b/src/python/example/bottleneck_basic_example.py index 392d2a6e..392d2a6e 100755 --- a/src/cython/example/bottleneck_basic_example.py +++ b/src/python/example/bottleneck_basic_example.py diff --git a/src/cython/example/coordinate_graph_induced_complex.py b/src/python/example/coordinate_graph_induced_complex.py index e32141b4..e32141b4 100755 --- a/src/cython/example/coordinate_graph_induced_complex.py +++ b/src/python/example/coordinate_graph_induced_complex.py diff --git a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index 610ba44f..610ba44f 100755 --- a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index 7587b732..7587b732 100755 --- a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py diff --git a/src/cython/example/functional_graph_induced_complex.py b/src/python/example/functional_graph_induced_complex.py index 8b645040..8b645040 100755 --- a/src/cython/example/functional_graph_induced_complex.py +++ b/src/python/example/functional_graph_induced_complex.py diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/python/example/gudhi_graphical_tools_example.py index 3b0ca54d..3b0ca54d 100755 --- a/src/cython/example/gudhi_graphical_tools_example.py +++ b/src/python/example/gudhi_graphical_tools_example.py diff --git a/src/cython/example/nerve_of_a_covering.py b/src/python/example/nerve_of_a_covering.py index 3c8e0f90..3c8e0f90 100755 --- a/src/cython/example/nerve_of_a_covering.py +++ b/src/python/example/nerve_of_a_covering.py diff --git a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index 9cb855cd..9cb855cd 100755 --- a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py diff --git a/src/cython/example/random_cubical_complex_persistence_example.py b/src/python/example/random_cubical_complex_persistence_example.py index da0eb177..da0eb177 100755 --- a/src/cython/example/random_cubical_complex_persistence_example.py +++ b/src/python/example/random_cubical_complex_persistence_example.py diff --git a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py index 3571580b..3571580b 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py index 0b9a9ba9..0b9a9ba9 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py index 2b335bba..2b335bba 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py diff --git a/src/cython/example/rips_complex_from_points_example.py b/src/python/example/rips_complex_from_points_example.py index 59d8a261..59d8a261 100755 --- a/src/cython/example/rips_complex_from_points_example.py +++ b/src/python/example/rips_complex_from_points_example.py diff --git a/src/cython/example/rips_persistence_diagram.py b/src/python/example/rips_persistence_diagram.py index f5897d7b..f5897d7b 100755 --- a/src/cython/example/rips_persistence_diagram.py +++ b/src/python/example/rips_persistence_diagram.py diff --git a/src/cython/example/simplex_tree_example.py b/src/python/example/simplex_tree_example.py index 30de00da..30de00da 100755 --- a/src/cython/example/simplex_tree_example.py +++ b/src/python/example/simplex_tree_example.py diff --git a/src/cython/example/sparse_rips_persistence_diagram.py b/src/python/example/sparse_rips_persistence_diagram.py index 671d5e34..671d5e34 100755 --- a/src/cython/example/sparse_rips_persistence_diagram.py +++ b/src/python/example/sparse_rips_persistence_diagram.py diff --git a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py index 456bc9eb..456bc9eb 100755 --- a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py diff --git a/src/cython/example/voronoi_graph_induced_complex.py b/src/python/example/voronoi_graph_induced_complex.py index 38be6c92..38be6c92 100755 --- a/src/cython/example/voronoi_graph_induced_complex.py +++ b/src/python/example/voronoi_graph_induced_complex.py diff --git a/src/cython/example/witness_complex_from_nearest_landmark_table.py b/src/python/example/witness_complex_from_nearest_landmark_table.py index c04a82b2..c04a82b2 100755 --- a/src/cython/example/witness_complex_from_nearest_landmark_table.py +++ b/src/python/example/witness_complex_from_nearest_landmark_table.py diff --git a/src/cython/gudhi/__init__.py b/src/python/gudhi/__init__.py index fde749eb..fde749eb 100644 --- a/src/cython/gudhi/__init__.py +++ b/src/python/gudhi/__init__.py diff --git a/src/cython/gudhi/__init__.py.in b/src/python/gudhi/__init__.py.in index b2d2d3d7..947aa3c9 100644 --- a/src/cython/gudhi/__init__.py.in +++ b/src/python/gudhi/__init__.py.in @@ -16,12 +16,12 @@ __license__ = "https://gudhi.inria.fr/licensing/" __version__ = "@GUDHI_VERSION@" # This variable is used by doctest to find files __root_source_dir__ = "@CMAKE_SOURCE_DIR@" -__debug_info__ = @GUDHI_CYTHON_DEBUG_INFO@ +__debug_info__ = @GUDHI_PYTHON_DEBUG_INFO@ from sys import exc_info from importlib import import_module -__all__ = [@GUDHI_CYTHON_MODULES@] +__all__ = [@GUDHI_PYTHON_MODULES@] __available_modules__ = '' __missing_modules__ = '' diff --git a/src/cython/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx index 6d6309db..6d6309db 100644 --- a/src/cython/gudhi/alpha_complex.pyx +++ b/src/python/gudhi/alpha_complex.pyx diff --git a/src/cython/gudhi/bottleneck.pyx b/src/python/gudhi/bottleneck.pyx index 4b378cbc..4b378cbc 100644 --- a/src/cython/gudhi/bottleneck.pyx +++ b/src/python/gudhi/bottleneck.pyx diff --git a/src/cython/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx index 0dc133d1..0dc133d1 100644 --- a/src/cython/gudhi/cubical_complex.pyx +++ b/src/python/gudhi/cubical_complex.pyx diff --git a/src/cython/gudhi/euclidean_strong_witness_complex.pyx b/src/python/gudhi/euclidean_strong_witness_complex.pyx index 5d6e4fb9..5d6e4fb9 100644 --- a/src/cython/gudhi/euclidean_strong_witness_complex.pyx +++ b/src/python/gudhi/euclidean_strong_witness_complex.pyx diff --git a/src/cython/gudhi/euclidean_witness_complex.pyx b/src/python/gudhi/euclidean_witness_complex.pyx index 2531919b..2531919b 100644 --- a/src/cython/gudhi/euclidean_witness_complex.pyx +++ b/src/python/gudhi/euclidean_witness_complex.pyx diff --git a/src/cython/gudhi/nerve_gic.pyx b/src/python/gudhi/nerve_gic.pyx index 2b230b8c..2b230b8c 100644 --- a/src/cython/gudhi/nerve_gic.pyx +++ b/src/python/gudhi/nerve_gic.pyx diff --git a/src/cython/gudhi/off_reader.pyx b/src/python/gudhi/off_reader.pyx index 9efd97ff..9efd97ff 100644 --- a/src/cython/gudhi/off_reader.pyx +++ b/src/python/gudhi/off_reader.pyx diff --git a/src/cython/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx index 724fadd4..724fadd4 100644 --- a/src/cython/gudhi/periodic_cubical_complex.pyx +++ b/src/python/gudhi/periodic_cubical_complex.pyx diff --git a/src/cython/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py index 181bc8ea..181bc8ea 100644 --- a/src/cython/gudhi/persistence_graphical_tools.py +++ b/src/python/gudhi/persistence_graphical_tools.py diff --git a/src/cython/gudhi/reader_utils.pyx b/src/python/gudhi/reader_utils.pyx index 147fae71..147fae71 100644 --- a/src/cython/gudhi/reader_utils.pyx +++ b/src/python/gudhi/reader_utils.pyx diff --git a/src/cython/gudhi/rips_complex.pyx b/src/python/gudhi/rips_complex.pyx index f2cd6a8d..f2cd6a8d 100644 --- a/src/cython/gudhi/rips_complex.pyx +++ b/src/python/gudhi/rips_complex.pyx diff --git a/src/cython/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index 5f86cfe2..5f86cfe2 100644 --- a/src/cython/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd diff --git a/src/cython/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 9f490271..9f490271 100644 --- a/src/cython/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx diff --git a/src/cython/gudhi/strong_witness_complex.pyx b/src/python/gudhi/strong_witness_complex.pyx index e757abea..e757abea 100644 --- a/src/cython/gudhi/strong_witness_complex.pyx +++ b/src/python/gudhi/strong_witness_complex.pyx diff --git a/src/cython/gudhi/subsampling.pyx b/src/python/gudhi/subsampling.pyx index 1135c1fb..1135c1fb 100644 --- a/src/cython/gudhi/subsampling.pyx +++ b/src/python/gudhi/subsampling.pyx diff --git a/src/cython/gudhi/tangential_complex.pyx b/src/python/gudhi/tangential_complex.pyx index 3a945fe2..3a945fe2 100644 --- a/src/cython/gudhi/tangential_complex.pyx +++ b/src/python/gudhi/tangential_complex.pyx diff --git a/src/cython/gudhi/witness_complex.pyx b/src/python/gudhi/witness_complex.pyx index baa70b7a..baa70b7a 100644 --- a/src/cython/gudhi/witness_complex.pyx +++ b/src/python/gudhi/witness_complex.pyx diff --git a/src/cython/include/Alpha_complex_interface.h b/src/python/include/Alpha_complex_interface.h index 1199b741..1199b741 100644 --- a/src/cython/include/Alpha_complex_interface.h +++ b/src/python/include/Alpha_complex_interface.h diff --git a/src/cython/include/Bottleneck_distance_interface.h b/src/python/include/Bottleneck_distance_interface.h index 22c9a97a..22c9a97a 100644 --- a/src/cython/include/Bottleneck_distance_interface.h +++ b/src/python/include/Bottleneck_distance_interface.h diff --git a/src/cython/include/Cubical_complex_interface.h b/src/python/include/Cubical_complex_interface.h index 7d32914c..7d32914c 100644 --- a/src/cython/include/Cubical_complex_interface.h +++ b/src/python/include/Cubical_complex_interface.h diff --git a/src/cython/include/Euclidean_strong_witness_complex_interface.h b/src/python/include/Euclidean_strong_witness_complex_interface.h index 90bd54ac..90bd54ac 100644 --- a/src/cython/include/Euclidean_strong_witness_complex_interface.h +++ b/src/python/include/Euclidean_strong_witness_complex_interface.h diff --git a/src/cython/include/Euclidean_witness_complex_interface.h b/src/python/include/Euclidean_witness_complex_interface.h index 0c01a741..0c01a741 100644 --- a/src/cython/include/Euclidean_witness_complex_interface.h +++ b/src/python/include/Euclidean_witness_complex_interface.h diff --git a/src/cython/include/Nerve_gic_interface.h b/src/python/include/Nerve_gic_interface.h index 729b39fb..729b39fb 100644 --- a/src/cython/include/Nerve_gic_interface.h +++ b/src/python/include/Nerve_gic_interface.h diff --git a/src/cython/include/Off_reader_interface.h b/src/python/include/Off_reader_interface.h index 4b3643be..4b3643be 100644 --- a/src/cython/include/Off_reader_interface.h +++ b/src/python/include/Off_reader_interface.h diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/python/include/Persistent_cohomology_interface.h index 64e2ddc8..64e2ddc8 100644 --- a/src/cython/include/Persistent_cohomology_interface.h +++ b/src/python/include/Persistent_cohomology_interface.h diff --git a/src/cython/include/Reader_utils_interface.h b/src/python/include/Reader_utils_interface.h index 5bddf9ce..5bddf9ce 100644 --- a/src/cython/include/Reader_utils_interface.h +++ b/src/python/include/Reader_utils_interface.h diff --git a/src/cython/include/Rips_complex_interface.h b/src/python/include/Rips_complex_interface.h index f818a2ed..f818a2ed 100644 --- a/src/cython/include/Rips_complex_interface.h +++ b/src/python/include/Rips_complex_interface.h diff --git a/src/cython/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h index c15a44a5..c15a44a5 100644 --- a/src/cython/include/Simplex_tree_interface.h +++ b/src/python/include/Simplex_tree_interface.h diff --git a/src/cython/include/Strong_witness_complex_interface.h b/src/python/include/Strong_witness_complex_interface.h index 4c333da8..4c333da8 100644 --- a/src/cython/include/Strong_witness_complex_interface.h +++ b/src/python/include/Strong_witness_complex_interface.h diff --git a/src/cython/include/Subsampling_interface.h b/src/python/include/Subsampling_interface.h index bc390485..bc390485 100644 --- a/src/cython/include/Subsampling_interface.h +++ b/src/python/include/Subsampling_interface.h diff --git a/src/cython/include/Tangential_complex_interface.h b/src/python/include/Tangential_complex_interface.h index 7c3f2789..7c3f2789 100644 --- a/src/cython/include/Tangential_complex_interface.h +++ b/src/python/include/Tangential_complex_interface.h diff --git a/src/cython/include/Witness_complex_interface.h b/src/python/include/Witness_complex_interface.h index 609277d6..609277d6 100644 --- a/src/cython/include/Witness_complex_interface.h +++ b/src/python/include/Witness_complex_interface.h diff --git a/src/cython/setup.py.in b/src/python/setup.py.in index 974dfb7a..3f1d4424 100644 --- a/src/cython/setup.py.in +++ b/src/python/setup.py.in @@ -16,15 +16,15 @@ __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" -modules = [@GUDHI_CYTHON_MODULES_TO_COMPILE@] +modules = [@GUDHI_PYTHON_MODULES_TO_COMPILE@] source_dir='@CMAKE_CURRENT_SOURCE_DIR@/gudhi/' -extra_compile_args=[@GUDHI_CYTHON_EXTRA_COMPILE_ARGS@] -extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@] -libraries=[@GUDHI_CYTHON_LIBRARIES@] -library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@] -include_dirs = [numpy_get_include(), '@CMAKE_CURRENT_SOURCE_DIR@/gudhi/', @GUDHI_CYTHON_INCLUDE_DIRS@] -runtime_library_dirs=[@GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS@] +extra_compile_args=[@GUDHI_PYTHON_EXTRA_COMPILE_ARGS@] +extra_link_args=[@GUDHI_PYTHON_EXTRA_LINK_ARGS@] +libraries=[@GUDHI_PYTHON_LIBRARIES@] +library_dirs=[@GUDHI_PYTHON_LIBRARY_DIRS@] +include_dirs = [numpy_get_include(), '@CMAKE_CURRENT_SOURCE_DIR@/gudhi/', @GUDHI_PYTHON_INCLUDE_DIRS@] +runtime_library_dirs=[@GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS@] # Create ext_modules list from module list ext_modules = [] diff --git a/src/cython/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py index 24f8bf53..24f8bf53 100755 --- a/src/cython/test/test_alpha_complex.py +++ b/src/python/test/test_alpha_complex.py diff --git a/src/cython/test/test_bottleneck_distance.py b/src/python/test/test_bottleneck_distance.py index f5f019b9..f5f019b9 100755 --- a/src/cython/test/test_bottleneck_distance.py +++ b/src/python/test/test_bottleneck_distance.py diff --git a/src/cython/test/test_cover_complex.py b/src/python/test/test_cover_complex.py index 8cd12272..8cd12272 100755 --- a/src/cython/test/test_cover_complex.py +++ b/src/python/test/test_cover_complex.py diff --git a/src/cython/test/test_cubical_complex.py b/src/python/test/test_cubical_complex.py index 68f54fbe..68f54fbe 100755 --- a/src/cython/test/test_cubical_complex.py +++ b/src/python/test/test_cubical_complex.py diff --git a/src/cython/test/test_euclidean_witness_complex.py b/src/python/test/test_euclidean_witness_complex.py index f5eae5fa..f5eae5fa 100755 --- a/src/cython/test/test_euclidean_witness_complex.py +++ b/src/python/test/test_euclidean_witness_complex.py diff --git a/src/cython/test/test_reader_utils.py b/src/python/test/test_reader_utils.py index 4c7b32c2..4c7b32c2 100755 --- a/src/cython/test/test_reader_utils.py +++ b/src/python/test/test_reader_utils.py diff --git a/src/cython/test/test_rips_complex.py b/src/python/test/test_rips_complex.py index d55ae22f..d55ae22f 100755 --- a/src/cython/test/test_rips_complex.py +++ b/src/python/test/test_rips_complex.py diff --git a/src/cython/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index 8d8971c1..8d8971c1 100755 --- a/src/cython/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py diff --git a/src/cython/test/test_subsampling.py b/src/python/test/test_subsampling.py index c816e203..c816e203 100755 --- a/src/cython/test/test_subsampling.py +++ b/src/python/test/test_subsampling.py diff --git a/src/cython/test/test_tangential_complex.py b/src/python/test/test_tangential_complex.py index 0f828d8e..0f828d8e 100755 --- a/src/cython/test/test_tangential_complex.py +++ b/src/python/test/test_tangential_complex.py diff --git a/src/cython/test/test_witness_complex.py b/src/python/test/test_witness_complex.py index 36ced635..36ced635 100755 --- a/src/cython/test/test_witness_complex.py +++ b/src/python/test/test_witness_complex.py |