Merge branch 'master' into print_warnings_to_stderr

15 files changed, 52 insertions, 47 deletions

diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx
index 4ff37437..dab4b56f 100644
--- a/src/python/gudhi/alpha_complex.pyx
+++ b/src/python/gudhi/alpha_complex.pyx
@@ -26,11 +26,11 @@ __license__ = "GPL v3"
 
 cdef extern from "Alpha_complex_interface.h" namespace "Gudhi":
     cdef cppclass Alpha_complex_interface "Gudhi::alpha_complex::Alpha_complex_interface":
-        Alpha_complex_interface(vector[vector[double]] points)
+        Alpha_complex_interface(vector[vector[double]] points) except +
         # bool from_file is a workaround for cython to find the correct signature
-        Alpha_complex_interface(string off_file, bool from_file)
-        vector[double] get_point(int vertex)
-        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
+        Alpha_complex_interface(string off_file, bool from_file) except +
+        vector[double] get_point(int vertex) except +
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except +
 
 # AlphaComplex python interface
 cdef class AlphaComplex:
@@ -71,7 +71,7 @@ cdef class AlphaComplex:
     def __cinit__(self, points = None, off_file = ''):
         if off_file:
             if os.path.isfile(off_file):
-                self.thisptr = new Alpha_complex_interface(str.encode(off_file), True)
+                self.thisptr = new Alpha_complex_interface(off_file.encode('utf-8'), True)
             else:
                 print("file " + off_file + " not found.")
         else:
@@ -98,8 +98,7 @@ cdef class AlphaComplex:
         :rtype: list of float
         :returns: the point.
         """
-        cdef vector[double] point = self.thisptr.get_point(vertex)
-        return point
+        return self.thisptr.get_point(vertex)
 
     def create_simplex_tree(self, max_alpha_square = float('inf')):
         """
diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index 28913a32..1dd30b4e 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -87,7 +87,7 @@ cdef class CubicalComplex:
         elif ((dimensions is None) and (top_dimensional_cells is None)
             and (perseus_file != '')):
             if os.path.isfile(perseus_file):
-                self.thisptr = new Bitmap_cubical_complex_base_interface(str.encode(perseus_file))
+                self.thisptr = new Bitmap_cubical_complex_base_interface(perseus_file.encode('utf-8'))
             else:
                 print("file " + perseus_file + " not found.", file=sys.stderr)
         else:
diff --git a/src/python/gudhi/euclidean_strong_witness_complex.pyx b/src/python/gudhi/euclidean_strong_witness_complex.pyx
index 9889f92c..aca6084e 100644
--- a/src/python/gudhi/euclidean_strong_witness_complex.pyx
+++ b/src/python/gudhi/euclidean_strong_witness_complex.pyx
@@ -22,9 +22,9 @@ __license__ = "GPL v3"
 cdef extern from "Euclidean_strong_witness_complex_interface.h" namespace "Gudhi":
     cdef cppclass Euclidean_strong_witness_complex_interface "Gudhi::witness_complex::Euclidean_strong_witness_complex_interface":
         Euclidean_strong_witness_complex_interface(vector[vector[double]] landmarks, vector[vector[double]] witnesses)
-        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except +
         void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square,
-            unsigned limit_dimension)
+            unsigned limit_dimension) except +
         vector[double] get_point(unsigned vertex)
 
 # EuclideanStrongWitnessComplex python interface
diff --git a/src/python/gudhi/euclidean_witness_complex.pyx b/src/python/gudhi/euclidean_witness_complex.pyx
index e3ce0e82..fb0c2201 100644
--- a/src/python/gudhi/euclidean_witness_complex.pyx
+++ b/src/python/gudhi/euclidean_witness_complex.pyx
@@ -22,9 +22,9 @@ __license__ = "GPL v3"
 cdef extern from "Euclidean_witness_complex_interface.h" namespace "Gudhi":
     cdef cppclass Euclidean_witness_complex_interface "Gudhi::witness_complex::Euclidean_witness_complex_interface":
         Euclidean_witness_complex_interface(vector[vector[double]] landmarks, vector[vector[double]] witnesses)
-        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except +
         void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square,
-            unsigned limit_dimension)
+            unsigned limit_dimension) except +
         vector[double] get_point(unsigned vertex)
 
 # EuclideanWitnessComplex python interface
diff --git a/src/python/gudhi/nerve_gic.pyx b/src/python/gudhi/nerve_gic.pyx
index 5eb9be0d..022466c5 100644
--- a/src/python/gudhi/nerve_gic.pyx
+++ b/src/python/gudhi/nerve_gic.pyx
@@ -182,7 +182,7 @@ cdef class CoverComplex:
         :returns: Read file status.
         """
         if os.path.isfile(off_file):
-            return self.thisptr.read_point_cloud(str.encode(off_file))
+            return self.thisptr.read_point_cloud(off_file.encode('utf-8'))
         else:
             print("file " + off_file + " not found.", file=sys.stderr)
             return False
@@ -214,7 +214,7 @@ cdef class CoverComplex:
         :type color_file_name: string
         """
         if os.path.isfile(color_file_name):
-            self.thisptr.set_color_from_file(str.encode(color_file_name))
+            self.thisptr.set_color_from_file(color_file_name.encode('utf-8'))
         else:
             print("file " + color_file_name + " not found.", file=sys.stderr)
 
@@ -235,7 +235,7 @@ cdef class CoverComplex:
         :type cover_file_name: string
         """
         if os.path.isfile(cover_file_name):
-            self.thisptr.set_cover_from_file(str.encode(cover_file_name))
+            self.thisptr.set_cover_from_file(cover_file_name.encode('utf-8'))
         else:
             print("file " + cover_file_name + " not found.", file=sys.stderr)
 
@@ -268,7 +268,7 @@ cdef class CoverComplex:
         :type func_file_name: string
         """
         if os.path.isfile(func_file_name):
-            self.thisptr.set_function_from_file(str.encode(func_file_name))
+            self.thisptr.set_function_from_file(func_file_name.encode('utf-8'))
         else:
             print("file " + func_file_name + " not found.", file=sys.stderr)
 
@@ -309,7 +309,7 @@ cdef class CoverComplex:
         :type graph_file_name: string
         """
         if os.path.isfile(graph_file_name):
-            self.thisptr.set_graph_from_file(str.encode(graph_file_name))
+            self.thisptr.set_graph_from_file(graph_file_name.encode('utf-8'))
         else:
             print("file " + graph_file_name + " not found.", file=sys.stderr)
 
@@ -370,7 +370,7 @@ cdef class CoverComplex:
         :param type: either "GIC" or "Nerve".
         :type type: string
         """
-        self.thisptr.set_type(str.encode(type))
+        self.thisptr.set_type(type.encode('utf-8'))
 
     def set_verbose(self, verbose):
         """Specifies whether the program should display information or not.
diff --git a/src/python/gudhi/off_reader.pyx b/src/python/gudhi/off_reader.pyx
index ef8f420a..0a828b83 100644
--- a/src/python/gudhi/off_reader.pyx
+++ b/src/python/gudhi/off_reader.pyx
@@ -28,11 +28,11 @@ def read_points_from_off_file(off_file=''):
     :type off_file: string
 
     :returns:  The point set.
-    :rtype: vector[vector[double]]
+    :rtype: List[List[float]]
     """
     if off_file:
         if os.path.isfile(off_file):
-            return read_points_from_OFF_file(str.encode(off_file))
+            return read_points_from_OFF_file(off_file.encode('utf-8'))
         else:
             print("file " + off_file + " not found.", file=sys.stderr)
             return []
diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx
index 4ec06524..fd08b976 100644
--- a/src/python/gudhi/periodic_cubical_complex.pyx
+++ b/src/python/gudhi/periodic_cubical_complex.pyx
@@ -95,7 +95,7 @@ cdef class PeriodicCubicalComplex:
         elif ((dimensions is None) and (top_dimensional_cells is None)
             and (periodic_dimensions is None) and (perseus_file != '')):
             if os.path.isfile(perseus_file):
-                self.thisptr = new Periodic_cubical_complex_base_interface(str.encode(perseus_file))
+                self.thisptr = new Periodic_cubical_complex_base_interface(perseus_file.encode('utf-8'))
             else:
                 print("file " + perseus_file + " not found.", file=sys.stderr)
         else:
diff --git a/src/python/gudhi/reader_utils.pyx b/src/python/gudhi/reader_utils.pyx
index 345c92f8..fe1c3a2e 100644
--- a/src/python/gudhi/reader_utils.pyx
+++ b/src/python/gudhi/reader_utils.pyx
@@ -34,30 +34,30 @@ def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'):
     :type separator: char
 
     :returns:  The lower triangular matrix.
-    :rtype: vector[vector[double]]
+    :rtype: List[List[float]]
     """
     if csv_file:
         if path.isfile(csv_file):
-            return read_matrix_from_csv_file(str.encode(csv_file), ord(separator[0]))
+            return read_matrix_from_csv_file(csv_file.encode('utf-8'), ord(separator[0]))
     print("file " + csv_file + " not set or not found.")
     return []
 
 def read_persistence_intervals_grouped_by_dimension(persistence_file=''):
     """Reads a file containing persistence intervals.
     Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
-    The return value is an `map[dim, vector[pair[birth, death]]]`
-    where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+    The return value is a `dict(dim, list(tuple(birth, death)))`
+    where `dim` is an `int`, `birth` a `float`, and `death` a `float`.
     Note: the function does not check that birth <= death.
 
     :param persistence_file: A persistence file style name.
     :type persistence_file: string
 
     :returns:  The persistence pairs grouped by dimension.
-    :rtype: map[int, vector[pair[double, double]]]
+    :rtype: Dict[int, List[Tuple[float, float]]]
     """
     if persistence_file:
         if path.isfile(persistence_file):
-            return read_pers_intervals_grouped_by_dimension(str.encode(persistence_file))
+            return read_pers_intervals_grouped_by_dimension(persistence_file.encode('utf-8'))
     print("file " + persistence_file + " not set or not found.")
     return []
 
@@ -80,7 +80,7 @@ def read_persistence_intervals_in_dimension(persistence_file='', only_this_dim=-
     """
     if persistence_file:
         if path.isfile(persistence_file):
-            return np_array(read_pers_intervals_in_dimension(str.encode(
-                persistence_file), only_this_dim))
+            return np_array(read_pers_intervals_in_dimension(persistence_file.encode(
+                'utf-8'), only_this_dim))
     print("file " + persistence_file + " not set or not found.")
     return []
diff --git a/src/python/gudhi/rips_complex.pyx b/src/python/gudhi/rips_complex.pyx
index 722cdcdc..deb8057a 100644
--- a/src/python/gudhi/rips_complex.pyx
+++ b/src/python/gudhi/rips_complex.pyx
@@ -28,7 +28,7 @@ cdef extern from "Rips_complex_interface.h" namespace "Gudhi":
         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)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max) except +
 
 # RipsComplex python interface
 cdef class RipsComplex:
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 1066d44b..96d14079 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -39,7 +39,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         vector[pair[vector[int], double]] get_star(vector[int] simplex)
         vector[pair[vector[int], double]] get_cofaces(vector[int] simplex,
                                                           int dimension)
-        void expansion(int max_dim)
+        void expansion(int max_dim) except +
         void remove_maximal_simplex(vector[int] simplex)
         bool prune_above_filtration(double filtration)
         bool make_filtration_non_decreasing()
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index 85d25492..b18627c4 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -508,7 +508,7 @@ cdef class SimplexTree:
         """
         if self.pcohptr != NULL:
             if persistence_file != '':
-                self.pcohptr.write_output_diagram(str.encode(persistence_file))
+                self.pcohptr.write_output_diagram(persistence_file.encode('utf-8'))
             else:
                 print("persistence_file must be specified")
         else:
diff --git a/src/python/gudhi/strong_witness_complex.pyx b/src/python/gudhi/strong_witness_complex.pyx
index 2c33c3f2..9f89d3ae 100644
--- a/src/python/gudhi/strong_witness_complex.pyx
+++ b/src/python/gudhi/strong_witness_complex.pyx
@@ -22,9 +22,9 @@ __license__ = "MIT"
 cdef extern from "Strong_witness_complex_interface.h" namespace "Gudhi":
     cdef cppclass Strong_witness_complex_interface "Gudhi::witness_complex::Strong_witness_complex_interface":
         Strong_witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table)
-        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except +
         void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square,
-            unsigned limit_dimension)
+            unsigned limit_dimension) except +
 
 # StrongWitnessComplex python interface
 cdef class StrongWitnessComplex:
diff --git a/src/python/gudhi/subsampling.pyx b/src/python/gudhi/subsampling.pyx
index b1812087..f77c6f75 100644
--- a/src/python/gudhi/subsampling.pyx
+++ b/src/python/gudhi/subsampling.pyx
@@ -33,13 +33,15 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi
     The iteration starts with the landmark `starting point`.
 
     :param points: The input point set.
-    :type points: vector[vector[double]].
+    :type points: Iterable[Iterable[float]].
 
     Or
 
     :param off_file: An OFF file style name.
     :type off_file: string
 
+    And in both cases
+
     :param nb_points: Number of points of the subsample.
     :type nb_points: unsigned.
     :param starting_point: The iteration starts with the landmark `starting \
@@ -47,15 +49,15 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi
     index is chosen randomly.
     :type starting_point: unsigned.
     :returns:  The subsample point set.
-    :rtype: vector[vector[double]]
+    :rtype: List[List[float]].
     """
     if off_file:
         if os.path.isfile(off_file):
             if starting_point == '':
-                return subsampling_n_farthest_points_from_file(str.encode(off_file),
+                return subsampling_n_farthest_points_from_file(off_file.encode('utf-8'),
                                                                nb_points)
             else:
-                return subsampling_n_farthest_points_from_file(str.encode(off_file),
+                return subsampling_n_farthest_points_from_file(off_file.encode('utf-8'),
                                                                nb_points,
                                                                starting_point)
         else:
@@ -74,21 +76,23 @@ def pick_n_random_points(points=None, off_file='', nb_points=0):
     """Subsample a point set by picking random vertices.
 
     :param points: The input point set.
-    :type points: vector[vector[double]].
+    :type points: Iterable[Iterable[float]].
 
     Or
 
     :param off_file: An OFF file style name.
     :type off_file: string
 
+    And in both cases
+
     :param nb_points: Number of points of the subsample.
     :type nb_points: unsigned.
     :returns:  The subsample point set.
-    :rtype: vector[vector[double]]
+    :rtype: List[List[float]]
     """
     if off_file:
         if os.path.isfile(off_file):
-            return subsampling_n_random_points_from_file(str.encode(off_file),
+            return subsampling_n_random_points_from_file(off_file.encode('utf-8'),
                 nb_points)
         else:
             print("file " + off_file + " not found.")
@@ -103,22 +107,24 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0):
     between any two points is greater than or equal to min_squared_dist.
 
     :param points: The input point set.
-    :type points: vector[vector[double]].
+    :type points: Iterable[Iterable[float]].
 
     Or
 
     :param off_file: An OFF file style name.
     :type off_file: string
 
+    And in both cases
+
     :param min_squared_dist: Minimum squared distance separating the output \
     points.
     :type min_squared_dist: float.
     :returns:  The subsample point set.
-    :rtype: vector[vector[double]]
+    :rtype: List[List[float]]
     """
     if off_file:
         if os.path.isfile(off_file):
-            return subsampling_sparsify_points_from_file(str.encode(off_file),
+            return subsampling_sparsify_points_from_file(off_file.encode('utf-8'),
                                                          min_squared_dist)
         else:
             print("file " + off_file + " not found.")
diff --git a/src/python/gudhi/tangential_complex.pyx b/src/python/gudhi/tangential_complex.pyx
index 0083033c..6391488c 100644
--- a/src/python/gudhi/tangential_complex.pyx
+++ b/src/python/gudhi/tangential_complex.pyx
@@ -66,7 +66,7 @@ cdef class TangentialComplex:
     def __cinit__(self, intrisic_dim, points=None, off_file=''):
         if off_file:
             if os.path.isfile(off_file):
-                self.thisptr = new Tangential_complex_interface(intrisic_dim, str.encode(off_file), True)
+                self.thisptr = new Tangential_complex_interface(intrisic_dim, off_file.encode('utf-8'), True)
             else:
                 print("file " + off_file + " not found.")
         else:
diff --git a/src/python/gudhi/witness_complex.pyx b/src/python/gudhi/witness_complex.pyx
index b032a5a1..e589d006 100644
--- a/src/python/gudhi/witness_complex.pyx
+++ b/src/python/gudhi/witness_complex.pyx
@@ -22,9 +22,9 @@ __license__ = "MIT"
 cdef extern from "Witness_complex_interface.h" namespace "Gudhi":
     cdef cppclass Witness_complex_interface "Gudhi::witness_complex::Witness_complex_interface":
         Witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table)
-        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except +
         void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square,
-            unsigned limit_dimension)
+            unsigned limit_dimension) except +
 
 # WitnessComplex python interface
 cdef class WitnessComplex: