diff options
-rw-r--r-- | src/cython/CMakeLists.txt | 25 | ||||
-rw-r--r-- | src/cython/cython/alpha_complex.pyx (renamed from src/cython/src/cython/alpha_complex.pyx) | 0 | ||||
-rw-r--r-- | src/cython/cython/cubical_complex.pyx (renamed from src/cython/src/cython/cubical_complex.pyx) | 0 | ||||
-rw-r--r-- | src/cython/cython/mini_simplex_tree.pyx (renamed from src/cython/src/cython/mini_simplex_tree.pyx) | 0 | ||||
-rw-r--r-- | src/cython/cython/periodic_cubical_complex.pyx (renamed from src/cython/src/cython/periodic_cubical_complex.pyx) | 0 | ||||
-rwxr-xr-x | src/cython/cython/persistence_graphical_tools.py (renamed from src/cython/src/cython/persistence_graphical_tools.py) | 0 | ||||
-rw-r--r-- | src/cython/cython/rips_complex.pyx (renamed from src/cython/src/cython/rips_complex.pyx) | 0 | ||||
-rw-r--r-- | src/cython/cython/simplex_tree.pyx (renamed from src/cython/src/cython/simplex_tree.pyx) | 0 | ||||
-rw-r--r-- | src/cython/cython/witness_complex.pyx (renamed from src/cython/src/cython/witness_complex.pyx) | 0 | ||||
-rw-r--r-- | src/cython/doc/Makefile (renamed from src/cython/src/doc/Makefile) | 0 | ||||
-rw-r--r-- | src/cython/doc/alpha_complex_ref.rst (renamed from src/cython/src/doc/alpha_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/alpha_complex_sum.rst (renamed from src/cython/src/doc/alpha_complex_sum.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/alpha_complex_user.rst (renamed from src/cython/src/doc/alpha_complex_user.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/biblio.rst (renamed from src/cython/src/doc/biblio.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/cgal_citation.rst (renamed from src/cython/src/doc/cgal_citation.rst) | 0 | ||||
-rwxr-xr-x | src/cython/doc/conf.py (renamed from src/cython/src/doc/conf.py) | 0 | ||||
-rw-r--r-- | src/cython/doc/cubical_complex_ref.rst (renamed from src/cython/src/doc/cubical_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/cubical_complex_sum.rst (renamed from src/cython/src/doc/cubical_complex_sum.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/cubical_complex_user.rst (renamed from src/cython/src/doc/cubical_complex_user.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/index.rst (renamed from src/cython/src/doc/index.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/make.bat (renamed from src/cython/src/doc/make.bat) | 0 | ||||
-rw-r--r-- | src/cython/doc/periodic_cubical_complex_ref.rst (renamed from src/cython/src/doc/periodic_cubical_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/persistent_cohomology_sum.rst (renamed from src/cython/src/doc/persistent_cohomology_sum.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/persistent_cohomology_user.rst (renamed from src/cython/src/doc/persistent_cohomology_user.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/simplex_tree_ref.rst (renamed from src/cython/src/doc/simplex_tree_ref.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/simplex_tree_sum.rst (renamed from src/cython/src/doc/simplex_tree_sum.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/simplex_tree_user.rst (renamed from src/cython/src/doc/simplex_tree_user.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/witness_complex_ref.rst (renamed from src/cython/src/doc/witness_complex_ref.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/witness_complex_sum.rst (renamed from src/cython/src/doc/witness_complex_sum.rst) | 0 | ||||
-rw-r--r-- | src/cython/doc/witness_complex_user.rst (renamed from src/cython/src/doc/witness_complex_user.rst) | 0 | ||||
-rw-r--r-- | src/cython/gudhi.pyx.in | 14 | ||||
-rw-r--r-- | src/cython/include/Alpha_complex_interface.h (renamed from src/cython/src/include/Alpha_complex_interface.h) | 0 | ||||
-rw-r--r-- | src/cython/include/Cubical_complex_interface.h (renamed from src/cython/src/include/Cubical_complex_interface.h) | 0 | ||||
-rw-r--r-- | src/cython/include/Persistent_cohomology_interface.h (renamed from src/cython/src/include/Persistent_cohomology_interface.h) | 0 | ||||
-rw-r--r-- | src/cython/include/Simplex_tree_interface.h (renamed from src/cython/src/include/Simplex_tree_interface.h) | 0 | ||||
-rw-r--r-- | src/cython/include/Witness_complex_interface.h (renamed from src/cython/src/include/Witness_complex_interface.h) | 0 |
36 files changed, 20 insertions, 19 deletions
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index bb90ad5b..823d5bb6 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -26,9 +26,10 @@ if(PYTHON_PATH AND CYTHON_PATH) set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${EIGEN3_INCLUDE_DIR}', ") endif (EIGEN3_FOUND) - # Copy recursively src and test repositories before packages finding + # Copy recursively include, cython and test repositories before packages finding # Some tests files are removed in case some packages are not found - file(COPY src DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + file(COPY include DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + file(COPY cython DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) if (CGAL_FOUND) @@ -48,7 +49,7 @@ if(PYTHON_PATH AND CYTHON_PATH) endif(GMPXX_FOUND) endif(GMP_FOUND) - set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'src/cython/alpha_complex.pyx'") + set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'") else (NOT CGAL_VERSION VERSION_LESS 4.7.0) # Remove alpha complex unitary tests file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py) @@ -60,7 +61,7 @@ if(PYTHON_PATH AND CYTHON_PATH) foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES}) set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ") endforeach() - set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/src/include', ") + set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ") # Generate cythonize_gudhi.py file to cythonize Gudhi configure_file(cythonize_gudhi.py.in "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" @ONLY) @@ -88,27 +89,27 @@ if(PYTHON_PATH AND CYTHON_PATH) # Documentation generation is available through sphinx find_program( SPHINX_PATH sphinx-build ) if(SPHINX_PATH) - file(COPY src/doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) # Developper version file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png") - file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/src/doc/img") + file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") # User version file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png") - file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/src/doc/img") + file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img") # Biblio file(GLOB GUDHI_BIB_FILES "${CMAKE_SOURCE_DIR}/biblio/*.bib") - file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/src/doc/") + file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") # Cubical complex perseus doc example file(GLOB GUDHI_CUBICAL_PERSEUS_FILES "${CMAKE_SOURCE_DIR}/data/bitmap/*cubicalcomplexdoc.txt") - file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/src/doc/") - file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/src/doc/") + file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") + file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/") if (UNIX) add_custom_target(html - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/src/doc + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc COMMAND make html && make doctest) else (UNIX) add_custom_target(html - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/src/doc + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc COMMAND make.bat html) endif (UNIX) endif(SPHINX_PATH) diff --git a/src/cython/src/cython/alpha_complex.pyx b/src/cython/cython/alpha_complex.pyx index 44da8c9d..44da8c9d 100644 --- a/src/cython/src/cython/alpha_complex.pyx +++ b/src/cython/cython/alpha_complex.pyx diff --git a/src/cython/src/cython/cubical_complex.pyx b/src/cython/cython/cubical_complex.pyx index 3441b2e9..3441b2e9 100644 --- a/src/cython/src/cython/cubical_complex.pyx +++ b/src/cython/cython/cubical_complex.pyx diff --git a/src/cython/src/cython/mini_simplex_tree.pyx b/src/cython/cython/mini_simplex_tree.pyx index 3ba7e853..3ba7e853 100644 --- a/src/cython/src/cython/mini_simplex_tree.pyx +++ b/src/cython/cython/mini_simplex_tree.pyx diff --git a/src/cython/src/cython/periodic_cubical_complex.pyx b/src/cython/cython/periodic_cubical_complex.pyx index d56eb5b1..d56eb5b1 100644 --- a/src/cython/src/cython/periodic_cubical_complex.pyx +++ b/src/cython/cython/periodic_cubical_complex.pyx diff --git a/src/cython/src/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 247e119e..247e119e 100755 --- a/src/cython/src/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py diff --git a/src/cython/src/cython/rips_complex.pyx b/src/cython/cython/rips_complex.pyx index ee4c34b0..ee4c34b0 100644 --- a/src/cython/src/cython/rips_complex.pyx +++ b/src/cython/cython/rips_complex.pyx diff --git a/src/cython/src/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx index bf91e812..bf91e812 100644 --- a/src/cython/src/cython/simplex_tree.pyx +++ b/src/cython/cython/simplex_tree.pyx diff --git a/src/cython/src/cython/witness_complex.pyx b/src/cython/cython/witness_complex.pyx index 835244cf..835244cf 100644 --- a/src/cython/src/cython/witness_complex.pyx +++ b/src/cython/cython/witness_complex.pyx diff --git a/src/cython/src/doc/Makefile b/src/cython/doc/Makefile index fc353a37..fc353a37 100644 --- a/src/cython/src/doc/Makefile +++ b/src/cython/doc/Makefile diff --git a/src/cython/src/doc/alpha_complex_ref.rst b/src/cython/doc/alpha_complex_ref.rst index 6a122b09..6a122b09 100644 --- a/src/cython/src/doc/alpha_complex_ref.rst +++ b/src/cython/doc/alpha_complex_ref.rst diff --git a/src/cython/src/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst index b608050e..b608050e 100644 --- a/src/cython/src/doc/alpha_complex_sum.rst +++ b/src/cython/doc/alpha_complex_sum.rst diff --git a/src/cython/src/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst index b6b6e550..b6b6e550 100644 --- a/src/cython/src/doc/alpha_complex_user.rst +++ b/src/cython/doc/alpha_complex_user.rst diff --git a/src/cython/src/doc/biblio.rst b/src/cython/doc/biblio.rst index b8e733ed..b8e733ed 100644 --- a/src/cython/src/doc/biblio.rst +++ b/src/cython/doc/biblio.rst diff --git a/src/cython/src/doc/cgal_citation.rst b/src/cython/doc/cgal_citation.rst index bbc4ef9e..bbc4ef9e 100644 --- a/src/cython/src/doc/cgal_citation.rst +++ b/src/cython/doc/cgal_citation.rst diff --git a/src/cython/src/doc/conf.py b/src/cython/doc/conf.py index bc138025..bc138025 100755 --- a/src/cython/src/doc/conf.py +++ b/src/cython/doc/conf.py diff --git a/src/cython/src/doc/cubical_complex_ref.rst b/src/cython/doc/cubical_complex_ref.rst index 84aa4223..84aa4223 100644 --- a/src/cython/src/doc/cubical_complex_ref.rst +++ b/src/cython/doc/cubical_complex_ref.rst diff --git a/src/cython/src/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.rst index 4008a1fd..4008a1fd 100644 --- a/src/cython/src/doc/cubical_complex_sum.rst +++ b/src/cython/doc/cubical_complex_sum.rst diff --git a/src/cython/src/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst index 2cd85c0a..2cd85c0a 100644 --- a/src/cython/src/doc/cubical_complex_user.rst +++ b/src/cython/doc/cubical_complex_user.rst diff --git a/src/cython/src/doc/index.rst b/src/cython/doc/index.rst index 5245d69d..5245d69d 100644 --- a/src/cython/src/doc/index.rst +++ b/src/cython/doc/index.rst diff --git a/src/cython/src/doc/make.bat b/src/cython/doc/make.bat index 656c0105..656c0105 100644 --- a/src/cython/src/doc/make.bat +++ b/src/cython/doc/make.bat diff --git a/src/cython/src/doc/periodic_cubical_complex_ref.rst b/src/cython/doc/periodic_cubical_complex_ref.rst index c6190a1b..c6190a1b 100644 --- a/src/cython/src/doc/periodic_cubical_complex_ref.rst +++ b/src/cython/doc/periodic_cubical_complex_ref.rst diff --git a/src/cython/src/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.rst index 081399a5..081399a5 100644 --- a/src/cython/src/doc/persistent_cohomology_sum.rst +++ b/src/cython/doc/persistent_cohomology_sum.rst diff --git a/src/cython/src/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst index 33b19ce2..33b19ce2 100644 --- a/src/cython/src/doc/persistent_cohomology_user.rst +++ b/src/cython/doc/persistent_cohomology_user.rst diff --git a/src/cython/src/doc/simplex_tree_ref.rst b/src/cython/doc/simplex_tree_ref.rst index 6d196843..6d196843 100644 --- a/src/cython/src/doc/simplex_tree_ref.rst +++ b/src/cython/doc/simplex_tree_ref.rst diff --git a/src/cython/src/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.rst index ffdb2cf4..ffdb2cf4 100644 --- a/src/cython/src/doc/simplex_tree_sum.rst +++ b/src/cython/doc/simplex_tree_sum.rst diff --git a/src/cython/src/doc/simplex_tree_user.rst b/src/cython/doc/simplex_tree_user.rst index 3a00f1ac..3a00f1ac 100644 --- a/src/cython/src/doc/simplex_tree_user.rst +++ b/src/cython/doc/simplex_tree_user.rst diff --git a/src/cython/src/doc/witness_complex_ref.rst b/src/cython/doc/witness_complex_ref.rst index c78760cb..c78760cb 100644 --- a/src/cython/src/doc/witness_complex_ref.rst +++ b/src/cython/doc/witness_complex_ref.rst diff --git a/src/cython/src/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.rst index 0d65d420..0d65d420 100644 --- a/src/cython/src/doc/witness_complex_sum.rst +++ b/src/cython/doc/witness_complex_sum.rst diff --git a/src/cython/src/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst index 604c7357..604c7357 100644 --- a/src/cython/src/doc/witness_complex_user.rst +++ b/src/cython/doc/witness_complex_user.rst diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in index 5f7809d6..1b8a669b 100644 --- a/src/cython/gudhi.pyx.in +++ b/src/cython/gudhi.pyx.in @@ -24,11 +24,11 @@ __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 INRIA Saclay (France)" __license__ = "GPL v3" -include "src/cython/simplex_tree.pyx" -include "src/cython/mini_simplex_tree.pyx" -include "src/cython/rips_complex.pyx" -include "src/cython/cubical_complex.pyx" -include "src/cython/periodic_cubical_complex.pyx" -include "src/cython/persistence_graphical_tools.py" -include "src/cython/witness_complex.pyx" +include "cython/simplex_tree.pyx" +include "cython/mini_simplex_tree.pyx" +include "cython/rips_complex.pyx" +include "cython/cubical_complex.pyx" +include "cython/periodic_cubical_complex.pyx" +include "cython/persistence_graphical_tools.py" +include "cython/witness_complex.pyx" @GUDHI_CYTHON_ALPHA_COMPLEX@ diff --git a/src/cython/src/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h index e2e6d100..e2e6d100 100644 --- a/src/cython/src/include/Alpha_complex_interface.h +++ b/src/cython/include/Alpha_complex_interface.h diff --git a/src/cython/src/include/Cubical_complex_interface.h b/src/cython/include/Cubical_complex_interface.h index 5d17ff6b..5d17ff6b 100644 --- a/src/cython/src/include/Cubical_complex_interface.h +++ b/src/cython/include/Cubical_complex_interface.h diff --git a/src/cython/src/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h index 58421799..58421799 100644 --- a/src/cython/src/include/Persistent_cohomology_interface.h +++ b/src/cython/include/Persistent_cohomology_interface.h diff --git a/src/cython/src/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h index 9aee630b..9aee630b 100644 --- a/src/cython/src/include/Simplex_tree_interface.h +++ b/src/cython/include/Simplex_tree_interface.h diff --git a/src/cython/src/include/Witness_complex_interface.h b/src/cython/include/Witness_complex_interface.h index bdfea91f..bdfea91f 100644 --- a/src/cython/src/include/Witness_complex_interface.h +++ b/src/cython/include/Witness_complex_interface.h |