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authorVincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com>2019-09-10 11:23:03 +0200
committerGitHub <noreply@github.com>2019-09-10 11:23:03 +0200
commit9d5ddcac38d43c9df813c0ca4a37b7dc48c68913 (patch)
treed6e893623f5c621a2bd356bc053d7c0d71aa9234
parentf510a7e607b46ba8cc118cd787ff9b0b8bff091f (diff)
parent2a313b489f1412f7e9d65681cea622d88828cba3 (diff)
Merge pull request #91 from VincentRouvreau/split_gudhi_python_in_modules
Split gudhi python in modules
-rw-r--r--.appveyor.yml2
-rw-r--r--.circleci/config.yml2
-rw-r--r--.gitignore16
-rw-r--r--CMakeLists.txt4
-rw-r--r--src/CMakeLists.txt4
-rw-r--r--src/Doxyfile.in2
-rw-r--r--src/cmake/modules/GUDHI_third_party_libraries.cmake20
-rw-r--r--src/cmake/modules/GUDHI_user_version_target.cmake2
-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-xsrc/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)bin10846 -> 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)14
-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-xsrc/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-xsrc/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-xsrc/python/example/alpha_complex_from_points_example.py (renamed from src/cython/example/alpha_complex_from_points_example.py)0
-rwxr-xr-xsrc/python/example/alpha_rips_persistence_bottleneck_distance.py (renamed from src/cython/example/alpha_rips_persistence_bottleneck_distance.py)0
-rwxr-xr-xsrc/python/example/bottleneck_basic_example.py (renamed from src/cython/example/bottleneck_basic_example.py)0
-rwxr-xr-xsrc/python/example/coordinate_graph_induced_complex.py (renamed from src/cython/example/coordinate_graph_induced_complex.py)0
-rwxr-xr-xsrc/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-xsrc/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-xsrc/python/example/functional_graph_induced_complex.py (renamed from src/cython/example/functional_graph_induced_complex.py)0
-rwxr-xr-xsrc/python/example/gudhi_graphical_tools_example.py (renamed from src/cython/example/gudhi_graphical_tools_example.py)0
-rwxr-xr-xsrc/python/example/nerve_of_a_covering.py (renamed from src/cython/example/nerve_of_a_covering.py)0
-rwxr-xr-xsrc/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-xsrc/python/example/random_cubical_complex_persistence_example.py (renamed from src/cython/example/random_cubical_complex_persistence_example.py)0
-rwxr-xr-xsrc/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-xsrc/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-xsrc/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-xsrc/python/example/rips_complex_from_points_example.py (renamed from src/cython/example/rips_complex_from_points_example.py)0
-rwxr-xr-xsrc/python/example/rips_persistence_diagram.py (renamed from src/cython/example/rips_persistence_diagram.py)0
-rwxr-xr-xsrc/python/example/simplex_tree_example.py (renamed from src/cython/example/simplex_tree_example.py)0
-rwxr-xr-xsrc/python/example/sparse_rips_persistence_diagram.py (renamed from src/cython/example/sparse_rips_persistence_diagram.py)0
-rwxr-xr-xsrc/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-xsrc/python/example/voronoi_graph_induced_complex.py (renamed from src/cython/example/voronoi_graph_induced_complex.py)0
-rwxr-xr-xsrc/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)3
-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)7
-rw-r--r--src/python/gudhi/euclidean_witness_complex.pyx (renamed from src/cython/gudhi/euclidean_witness_complex.pyx)7
-rw-r--r--src/python/gudhi/nerve_gic.pyx (renamed from src/cython/gudhi/nerve_gic.pyx)3
-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)5
-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)3
-rw-r--r--src/python/gudhi/strong_witness_complex.pyx (renamed from src/cython/gudhi/strong_witness_complex.pyx)6
-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)3
-rw-r--r--src/python/gudhi/witness_complex.pyx (renamed from src/cython/gudhi/witness_complex.pyx)6
-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)16
-rwxr-xr-xsrc/python/test/test_alpha_complex.py (renamed from src/cython/test/test_alpha_complex.py)0
-rwxr-xr-xsrc/python/test/test_bottleneck_distance.py (renamed from src/cython/test/test_bottleneck_distance.py)0
-rwxr-xr-xsrc/python/test/test_cover_complex.py (renamed from src/cython/test/test_cover_complex.py)0
-rwxr-xr-xsrc/python/test/test_cubical_complex.py (renamed from src/cython/test/test_cubical_complex.py)0
-rwxr-xr-xsrc/python/test/test_euclidean_witness_complex.py (renamed from src/cython/test/test_euclidean_witness_complex.py)0
-rwxr-xr-xsrc/python/test/test_reader_utils.py (renamed from src/cython/test/test_reader_utils.py)0
-rwxr-xr-xsrc/python/test/test_rips_complex.py (renamed from src/cython/test/test_rips_complex.py)0
-rwxr-xr-xsrc/python/test/test_simplex_tree.py (renamed from src/cython/test/test_simplex_tree.py)0
-rwxr-xr-xsrc/python/test/test_subsampling.py (renamed from src/cython/test/test_subsampling.py)0
-rwxr-xr-xsrc/python/test/test_tangential_complex.py (renamed from src/cython/test/test_tangential_complex.py)0
-rwxr-xr-xsrc/python/test/test_witness_complex.py (renamed from src/cython/test/test_witness_complex.py)0
122 files changed, 135 insertions, 150 deletions
diff --git a/.appveyor.yml b/.appveyor.yml
index ab943fb7..5f9c4ef9 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -54,7 +54,7 @@ build_script:
- cd build
- cmake -G "Visual Studio 15 2017 Win64" %CMAKE_FLAGS% -DCMAKE_TOOLCHAIN_FILE=c:/Tools/vcpkg/scripts/buildsystems/vcpkg.cmake ..
- if [%target%]==[Python] (
- cd src/cython &
+ cd src/python &
MSBuild Cython.sln /m /p:Configuration=Release /p:Platform=x64 &
ctest -j 1 -C Release
) else (
diff --git a/.circleci/config.yml b/.circleci/config.yml
index b9f0376e..52cb3d45 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -56,7 +56,7 @@ jobs:
cd build;
cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..;
make all test sphinx;
- cp -R cython/sphinx /tmp/sphinx;
+ cp -R python/sphinx /tmp/sphinx;
- store_artifacts:
path: /tmp/sphinx
diff --git a/.gitignore b/.gitignore
index 31efc180..6aab7337 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,21 +2,7 @@
build/
# Generated by Cython
-src/cython/gudhi/simplex_tree.cpp
-src/cython/gudhi/alpha_complex.cpp
-src/cython/gudhi/bottleneck.cpp
-src/cython/gudhi/cubical_complex.cpp
-src/cython/gudhi/euclidean_strong_witness_complex.cpp
-src/cython/gudhi/off_reader.cpp
-src/cython/gudhi/periodic_cubical_complex.cpp
-src/cython/gudhi/reader_utils.cpp
-src/cython/gudhi/rips_complex.cpp
-src/cython/gudhi/subsampling.cpp
-src/cython/gudhi/euclidean_witness_complex.cpp
-src/cython/gudhi/nerve_gic.cpp
-src/cython/gudhi/strong_witness_complex.cpp
-src/cython/gudhi/tangential_complex.cpp
-src/cython/gudhi/witness_complex.cpp
+src/python/gudhi/*.cpp
# Generated by tests
data/points/COIL_database/lucky_cat.off_dist
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 9b97947f..5dcc6803 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -11,7 +11,7 @@ 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 "src/cython")
+set(GUDHI_PYTHON_PATH "src/python")
# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
include(GUDHI_third_party_libraries NO_POLICY_SCOPE)
@@ -54,7 +54,7 @@ add_subdirectory(src/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 ${GUDHI_MISSING_MODULES} "python")
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 40fdcf2b..561aa049 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -10,7 +10,7 @@ set(GUDHI_MODULES "" CACHE INTERNAL "GUDHI_MODULES")
set(GUDHI_MISSING_MODULES "" CACHE INTERNAL "GUDHI_MISSING_MODULES")
# This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path
-set(GUDHI_CYTHON_PATH "cython")
+set(GUDHI_PYTHON_PATH "python")
# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
include(GUDHI_third_party_libraries NO_POLICY_SCOPE)
@@ -61,7 +61,7 @@ add_subdirectory(GudhUI)
if (WITH_GUDHI_PYTHON)
# specific for cython module
- add_subdirectory(${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 fe64fb3d..fe64fb3d 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 c5ba9dc7..c5ba9dc7 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 f9662a6d..f9662a6d 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
index 9759f7ba..9759f7ba 100644
--- a/src/cython/doc/img/graphical_tools_representation.png
+++ b/src/python/doc/img/graphical_tools_representation.png
Binary files differ
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 15f383c2..d8b6f861 100644
--- a/src/cython/doc/installation.rst
+++ b/src/python/doc/installation.rst
@@ -22,7 +22,7 @@ Studio 2015.
On `Windows <https://wiki.python.org/moin/WindowsCompilers>`_ , only Python
≥ 3.5 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.
@@ -37,7 +37,7 @@ 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
@@ -49,13 +49,13 @@ 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
@@ -68,9 +68,9 @@ 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
@@ -146,7 +146,7 @@ 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 3f6b960d..3f6b960d 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 d84aa433..d84aa433 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 71b65a71..71b65a71 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 88ef3b1b..6d6309db 100644
--- a/src/cython/gudhi/alpha_complex.pyx
+++ b/src/python/gudhi/alpha_complex.pyx
@@ -112,6 +112,5 @@ cdef class AlphaComplex:
"""
stree = SimplexTree()
cdef intptr_t stree_int_ptr=stree.thisptr
- cdef Simplex_tree_interface_full_featured* stree_ptr = <Simplex_tree_interface_full_featured*>stree_int_ptr
- self.thisptr.create_simplex_tree(stree_ptr, max_alpha_square)
+ self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr, max_alpha_square)
return stree
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 465635c4..5d6e4fb9 100644
--- a/src/cython/gudhi/euclidean_strong_witness_complex.pyx
+++ b/src/python/gudhi/euclidean_strong_witness_complex.pyx
@@ -71,11 +71,12 @@ cdef class EuclideanStrongWitnessComplex:
"""
stree = SimplexTree()
cdef intptr_t stree_int_ptr=stree.thisptr
- cdef Simplex_tree_interface_full_featured* stree_ptr = <Simplex_tree_interface_full_featured*>stree_int_ptr
if limit_dimension is not -1:
- self.thisptr.create_simplex_tree(stree_ptr, max_alpha_square, limit_dimension)
+ self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr,
+ max_alpha_square, limit_dimension)
else:
- self.thisptr.create_simplex_tree(stree_ptr, max_alpha_square)
+ self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr,
+ max_alpha_square)
return stree
def get_point(self, vertex):
diff --git a/src/cython/gudhi/euclidean_witness_complex.pyx b/src/python/gudhi/euclidean_witness_complex.pyx
index 92d54eb5..2531919b 100644
--- a/src/cython/gudhi/euclidean_witness_complex.pyx
+++ b/src/python/gudhi/euclidean_witness_complex.pyx
@@ -71,11 +71,12 @@ cdef class EuclideanWitnessComplex:
"""
stree = SimplexTree()
cdef intptr_t stree_int_ptr=stree.thisptr
- cdef Simplex_tree_interface_full_featured* stree_ptr = <Simplex_tree_interface_full_featured*>stree_int_ptr
if limit_dimension is not -1:
- self.thisptr.create_simplex_tree(stree_ptr, max_alpha_square, limit_dimension)
+ self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr,
+ max_alpha_square, limit_dimension)
else:
- self.thisptr.create_simplex_tree(stree_ptr, max_alpha_square)
+ self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr,
+ max_alpha_square)
return stree
def get_point(self, vertex):
diff --git a/src/cython/gudhi/nerve_gic.pyx b/src/python/gudhi/nerve_gic.pyx
index 9fec626f..2b230b8c 100644
--- a/src/cython/gudhi/nerve_gic.pyx
+++ b/src/python/gudhi/nerve_gic.pyx
@@ -164,8 +164,7 @@ cdef class CoverComplex:
"""
stree = SimplexTree()
cdef intptr_t stree_int_ptr=stree.thisptr
- cdef Simplex_tree_interface_full_featured* stree_ptr = <Simplex_tree_interface_full_featured*>stree_int_ptr
- self.thisptr.create_simplex_tree(stree_ptr)
+ self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr)
return stree
def find_simplices(self):
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 1a6c8571..f2cd6a8d 100644
--- a/src/cython/gudhi/rips_complex.pyx
+++ b/src/python/gudhi/rips_complex.pyx
@@ -97,6 +97,7 @@ cdef class RipsComplex:
:rtype: SimplexTree
"""
stree = SimplexTree()
- cdef intptr_t stree_ptr=stree.thisptr
- self.thisref.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_ptr, max_dimension)
+ cdef intptr_t stree_int_ptr=stree.thisptr
+ self.thisref.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr,
+ max_dimension)
return stree
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 51134681..9f490271 100644
--- a/src/cython/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -44,8 +44,7 @@ cdef class SimplexTree:
# The real cython constructor
def __cinit__(self):
- cdef Simplex_tree_interface_full_featured* ptr = new Simplex_tree_interface_full_featured()
- self.thisptr = <intptr_t>ptr
+ self.thisptr = <intptr_t>(new Simplex_tree_interface_full_featured())
def __dealloc__(self):
cdef Simplex_tree_interface_full_featured* ptr = self.get_ptr()
diff --git a/src/cython/gudhi/strong_witness_complex.pyx b/src/python/gudhi/strong_witness_complex.pyx
index 4e3d1b67..e757abea 100644
--- a/src/cython/gudhi/strong_witness_complex.pyx
+++ b/src/python/gudhi/strong_witness_complex.pyx
@@ -69,10 +69,10 @@ cdef class StrongWitnessComplex:
"""
stree = SimplexTree()
cdef intptr_t stree_int_ptr=stree.thisptr
- cdef Simplex_tree_interface_full_featured* stree_ptr = <Simplex_tree_interface_full_featured*>stree_int_ptr
if limit_dimension is not -1:
- self.thisptr.create_simplex_tree(stree_ptr,
+ self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr,
max_alpha_square, limit_dimension)
else:
- self.thisptr.create_simplex_tree(stree_ptr, max_alpha_square)
+ self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr,
+ max_alpha_square)
return stree
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 9eb22115..3a945fe2 100644
--- a/src/cython/gudhi/tangential_complex.pyx
+++ b/src/python/gudhi/tangential_complex.pyx
@@ -144,8 +144,7 @@ cdef class TangentialComplex:
"""
stree = SimplexTree()
cdef intptr_t stree_int_ptr=stree.thisptr
- cdef Simplex_tree_interface_full_featured* stree_ptr = <Simplex_tree_interface_full_featured*>stree_int_ptr
- self.thisptr.create_simplex_tree(stree_ptr)
+ self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr)
return stree
def fix_inconsistencies_using_perturbation(self, max_perturb, time_limit=-1.0):
diff --git a/src/cython/gudhi/witness_complex.pyx b/src/python/gudhi/witness_complex.pyx
index c859877d..baa70b7a 100644
--- a/src/cython/gudhi/witness_complex.pyx
+++ b/src/python/gudhi/witness_complex.pyx
@@ -69,10 +69,10 @@ cdef class WitnessComplex:
"""
stree = SimplexTree()
cdef intptr_t stree_int_ptr=stree.thisptr
- cdef Simplex_tree_interface_full_featured* stree_ptr = <Simplex_tree_interface_full_featured*>stree_int_ptr
if limit_dimension is not -1:
- self.thisptr.create_simplex_tree(stree_ptr,
+ self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr,
max_alpha_square, limit_dimension)
else:
- self.thisptr.create_simplex_tree(stree_ptr, max_alpha_square)
+ self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr,
+ max_alpha_square)
return stree
diff --git a/src/cython/include/Alpha_complex_interface.h b/src/python/include/Alpha_complex_interface.h
index b3553d32..b3553d32 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 a4f3eaf1..a4f3eaf1 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 648598e1..648598e1 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 c1c72737..c1c72737 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 5d7dbdc2..5d7dbdc2 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 5e7f8ae6..5e7f8ae6 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 e6e1f931..e6e1f931 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 8c79e6f3..8c79e6f3 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 5f0deb87..5f0deb87 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 a66b0e5b..a66b0e5b 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 06f31341..06f31341 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 cda5b514..cda5b514 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 cdda851f..cdda851f 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 698226cc..698226cc 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 45e14253..45e14253 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 fd4307e3..3f1d4424 100644
--- a/src/cython/setup.py.in
+++ b/src/python/setup.py.in
@@ -1,4 +1,4 @@
-from distutils.core import setup, Extension
+from setuptools import setup, Extension
from Cython.Build import cythonize
from numpy import get_include as numpy_get_include
@@ -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