First version that compiles the simplex_tree module

3 files changed, 15 insertions, 12 deletions

diff --git a/src/cython/gudhi/simplex_tree.pxd b/src/cython/gudhi/simplex_tree.pxd
index 25051295..5f86cfe2 100644
--- a/src/cython/gudhi/simplex_tree.pxd
+++ b/src/cython/gudhi/simplex_tree.pxd
@@ -44,3 +44,13 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         void remove_maximal_simplex(vector[int] simplex)
         bool prune_above_filtration(double filtration)
         bool make_filtration_non_decreasing()
+
+cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
+    cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>":
+        Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * st, bool persistence_dim_max)
+        vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence)
+        vector[int] betti_numbers()
+        vector[int] persistent_betti_numbers(double from_value, double to_value)
+        vector[pair[double,double]] intervals_in_dimension(int dimension)
+        void write_output_diagram(string diagram_file_name)
+        vector[pair[vector[int], vector[int]]] persistence_pairs()
diff --git a/src/cython/gudhi/simplex_tree.pyx b/src/cython/gudhi/simplex_tree.pyx
index e5f9e9d1..604328e9 100644
--- a/src/cython/gudhi/simplex_tree.pyx
+++ b/src/cython/gudhi/simplex_tree.pyx
@@ -1,5 +1,6 @@
 from libc.stdint cimport intptr_t
 from numpy import array as np_array
+from simplex_tree cimport *
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
     See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
@@ -15,16 +16,6 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
 
-cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
-    cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>":
-        Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * st, bool persistence_dim_max)
-        vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence)
-        vector[int] betti_numbers()
-        vector[int] persistent_betti_numbers(double from_value, double to_value)
-        vector[pair[double,double]] intervals_in_dimension(int dimension)
-        void write_output_diagram(string diagram_file_name)
-        vector[pair[vector[int], vector[int]]] persistence_pairs()
-
 # SimplexTree python interface
 cdef class SimplexTree:
     """The simplex tree is an efficient and flexible data structure for
diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in
index 454be9af..f158f6cb 100644
--- a/src/cython/setup.py.in
+++ b/src/cython/setup.py.in
@@ -18,23 +18,25 @@ __license__ = "MIT"
 
 simplextree = Extension(
     "gudhi.simplextree",
-    sources = ['@CMAKE_CURRENT_SOURCE_DIR@/cython/simplex_tree.pyx',],
+    sources = ['@CMAKE_CURRENT_SOURCE_DIR@/gudhi/simplex_tree.pyx',],
     language = 'c++',
     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(), @GUDHI_CYTHON_INCLUDE_DIRS@],
+    include_dirs = [numpy_get_include(), '@CMAKE_CURRENT_SOURCE_DIR@/gudhi/', @GUDHI_CYTHON_INCLUDE_DIRS@],
     runtime_library_dirs=[@GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS@],
 )
 
 setup(
     name = 'gudhi',
+    packages=["gudhi",],
     author='GUDHI Editorial Board',
     author_email='gudhi-contact@lists.gforge.inria.fr',
     version='@GUDHI_VERSION@',
     url='http://gudhi.gforge.inria.fr/',
     ext_modules = cythonize(simplextree),
+#    cmdclass = {'build_ext': build_ext},
     install_requires = ['cython','numpy >= 1.9',],
     setup_requires = ['numpy >= 1.9',],
 )