Merge pull request #202 from VincentRouvreau/cython_language_level_not_set

Cython language level not set

11 files changed, 30 insertions, 23 deletions

diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx
index db11416c..f3ca3dd5 100644
--- a/src/python/gudhi/alpha_complex.pyx
+++ b/src/python/gudhi/alpha_complex.pyx
@@ -69,7 +69,7 @@ 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:
diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index 92ff6411..cbeda014 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -85,7 +85,7 @@ 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.")
         else:
diff --git a/src/python/gudhi/nerve_gic.pyx b/src/python/gudhi/nerve_gic.pyx
index 68c06432..382e71c5 100644
--- a/src/python/gudhi/nerve_gic.pyx
+++ b/src/python/gudhi/nerve_gic.pyx
@@ -180,7 +180,7 @@ 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.")
             return False
@@ -212,7 +212,7 @@ 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.")
 
@@ -233,7 +233,7 @@ 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.")
 
@@ -266,7 +266,7 @@ 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.")
 
@@ -307,7 +307,7 @@ 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.")
 
@@ -368,7 +368,7 @@ 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 58f05db8..a0d5bf25 100644
--- a/src/python/gudhi/off_reader.pyx
+++ b/src/python/gudhi/off_reader.pyx
@@ -30,7 +30,7 @@ def read_points_from_off_file(off_file=''):
     """
     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.")
             return []
diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx
index b5dece10..37f76201 100644
--- a/src/python/gudhi/periodic_cubical_complex.pyx
+++ b/src/python/gudhi/periodic_cubical_complex.pyx
@@ -93,7 +93,7 @@ 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.")
         else:
diff --git a/src/python/gudhi/reader_utils.pyx b/src/python/gudhi/reader_utils.pyx
index 345c92f8..d6033b86 100644
--- a/src/python/gudhi/reader_utils.pyx
+++ b/src/python/gudhi/reader_utils.pyx
@@ -38,7 +38,7 @@ def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'):
     """
     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 []
 
@@ -57,7 +57,7 @@ def read_persistence_intervals_grouped_by_dimension(persistence_file=''):
     """
     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/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/subsampling.pyx b/src/python/gudhi/subsampling.pyx
index b1812087..c501d16b 100644
--- a/src/python/gudhi/subsampling.pyx
+++ b/src/python/gudhi/subsampling.pyx
@@ -52,10 +52,10 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi
     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:
@@ -88,7 +88,7 @@ def pick_n_random_points(points=None, off_file='', nb_points=0):
     """
     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.")
@@ -118,7 +118,7 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0):
     """
     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/setup.py.in b/src/python/setup.py.in
index 24d05025..9c2124f4 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -11,6 +11,7 @@
 from setuptools import setup, Extension
 from Cython.Build import cythonize
 from numpy import get_include as numpy_get_include
+import sys
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016  Inria"
@@ -38,7 +39,8 @@ for module in modules:
         libraries=libraries,
         library_dirs=library_dirs,
         include_dirs=include_dirs,
-        runtime_library_dirs=runtime_library_dirs,))
+        runtime_library_dirs=runtime_library_dirs,
+        cython_directives = {'language_level': str(sys.version_info[0])},))
 
 setup(
     name = 'gudhi',
diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py
index 712a50b6..0d9e9e45 100755
--- a/src/python/test/test_alpha_complex.py
+++ b/src/python/test/test_alpha_complex.py
@@ -11,8 +11,13 @@
 from gudhi import AlphaComplex, SimplexTree
 import math
 import numpy as np
-import itertools
 import pytest
+try:
+    # python3
+    from itertools import zip_longest
+except ImportError:
+    # python2
+    from itertools import izip_longest as zip_longest
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
@@ -114,6 +119,6 @@ def test_safe_alpha_persistence_comparison():
     diag1 = simplex_tree1.persistence()
     diag2 = simplex_tree2.persistence()
 
-    for (first_p, second_p) in itertools.zip_longest(diag1, diag2):
+    for (first_p, second_p) in zip_longest(diag1, diag2):
         assert first_p[0] == pytest.approx(second_p[0])
         assert first_p[1] == pytest.approx(second_p[1])