Move cython/src/* in cython/

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1436 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 8f971ef16ef6df597d5d3667db0eecbca94233b2

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