From 68753b3c28321e28eedd5829c94234da84e25c8d Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Mon, 9 Sep 2019 16:03:40 +0200
Subject: Code review: rename cython as python (make target and directory

---
 src/python/gudhi/rips_complex.pyx | 103 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 103 insertions(+)
 create mode 100644 src/python/gudhi/rips_complex.pyx

(limited to 'src/python/gudhi/rips_complex.pyx')

diff --git a/src/python/gudhi/rips_complex.pyx b/src/python/gudhi/rips_complex.pyx
new file mode 100644
index 00000000..f2cd6a8d
--- /dev/null
+++ b/src/python/gudhi/rips_complex.pyx
@@ -0,0 +1,103 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libcpp.string cimport string
+from libcpp cimport bool
+from libc.stdint cimport intptr_t
+
+from gudhi.simplex_tree cimport *
+from gudhi.simplex_tree import SimplexTree
+
+""" 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.
+    Author(s):       Vincent Rouvreau
+
+    Copyright (C) 2016 Inria
+
+    Modification(s):
+      - YYYY/MM Author: Description of the modification
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 Inria"
+__license__ = "MIT"
+
+cdef extern from "Rips_complex_interface.h" namespace "Gudhi":
+    cdef cppclass Rips_complex_interface "Gudhi::rips_complex::Rips_complex_interface":
+        Rips_complex_interface()
+        void init_points(vector[vector[double]] values, double threshold)
+        void init_matrix(vector[vector[double]] values, double threshold)
+        void init_points_sparse(vector[vector[double]] values, double threshold, double sparse)
+        void init_matrix_sparse(vector[vector[double]] values, double threshold, double sparse)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max)
+
+# RipsComplex python interface
+cdef class RipsComplex:
+    """The data structure is a one skeleton graph, or Rips graph, containing
+    edges when the edge length is less or equal to a given threshold. Edge
+    length is computed from a user given point cloud with a given distance
+    function, or a distance matrix.
+    """
+
+    cdef Rips_complex_interface thisref
+
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self, points=None, distance_matrix=None,
+                 max_edge_length=float('inf'), sparse=None):
+        """RipsComplex constructor.
+
+        :param max_edge_length: Rips value.
+        :type max_edge_length: float
+
+        :param points: A list of points in d-Dimension.
+        :type points: list of list of double
+
+        Or
+
+        :param distance_matrix: A distance matrix (full square or lower
+            triangular).
+        :type points: list of list of double
+
+        And in both cases
+
+        :param sparse: If this is not None, it switches to building a sparse
+            Rips and represents the approximation parameter epsilon.
+        :type sparse: float
+        """
+
+    # The real cython constructor
+    def __cinit__(self, points=None, distance_matrix=None,
+                  max_edge_length=float('inf'), sparse=None):
+        if sparse is not None:
+          if distance_matrix is not None:
+              self.thisref.init_matrix_sparse(distance_matrix,
+                                              max_edge_length,
+                                              sparse)
+          else:
+              if points is None:
+                  # Empty Rips construction
+                  points=[]
+              self.thisref.init_points_sparse(points, max_edge_length, sparse)
+        else:
+          if distance_matrix is not None:
+              self.thisref.init_matrix(distance_matrix, max_edge_length)
+          else:
+              if points is None:
+                  # Empty Rips construction
+                  points=[]
+              self.thisref.init_points(points, max_edge_length)
+
+
+    def create_simplex_tree(self, max_dimension=1):
+        """
+        :param max_dimension: graph expansion for rips until this given maximal
+            dimension.
+        :type max_dimension: int
+        :returns: A simplex tree created from the Delaunay Triangulation.
+        :rtype: SimplexTree
+        """
+        stree = SimplexTree()
+        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
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