Merge remote-tracking branch 'origin/master' into gen2

16 files changed, 140 insertions, 81 deletions

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 22af3ec9..f00966a5 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -128,16 +128,6 @@ if(PYTHONINTERP_FOUND)
     endif ()
 
     if(CGAL_FOUND)
-      can_cgal_use_cxx11_thread_local()
-      if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
-        if(CMAKE_BUILD_TYPE MATCHES Debug)
-          add_GUDHI_PYTHON_lib("${Boost_THREAD_LIBRARY_DEBUG}")
-        else()
-          add_GUDHI_PYTHON_lib("${Boost_THREAD_LIBRARY_RELEASE}")
-        endif()
-        message("** Add Boost ${Boost_LIBRARY_DIRS}")
-        set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
-      endif()
       # Add CGAL compilation args
       if(CGAL_HEADER_ONLY)
         add_gudhi_debug_info("CGAL header only version ${CGAL_VERSION}")
diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
index 4079a469..727af4fa 100755
--- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
@@ -1,11 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
 import gudhi
 
-""" 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.
+""" 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
@@ -41,7 +45,7 @@ args = parser.parse_args()
 with open(args.file, "r") as f:
     first_line = f.readline()
     if (first_line == "OFF\n") or (first_line == "nOFF\n"):
-        print("#####################################################################")
+        print("##############################################################")
         print("AlphaComplex creation from points read in a OFF file")
 
         message = "AlphaComplex with max_edge_length=" + repr(args.max_alpha_square)
@@ -64,6 +68,7 @@ with open(args.file, "r") as f:
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
-        print(args.file, "is not a valid OFF file")
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                args.file)
 
     f.close()
diff --git a/src/python/example/alpha_rips_persistence_bottleneck_distance.py b/src/python/example/alpha_rips_persistence_bottleneck_distance.py
index d5c33ec8..f156826d 100755
--- a/src/python/example/alpha_rips_persistence_bottleneck_distance.py
+++ b/src/python/example/alpha_rips_persistence_bottleneck_distance.py
@@ -3,9 +3,13 @@
 import gudhi
 import argparse
 import math
+import errno
+import os
 
-""" 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.
+""" 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
@@ -36,7 +40,7 @@ with open(args.file, "r") as f:
     first_line = f.readline()
     if (first_line == "OFF\n") or (first_line == "nOFF\n"):
         point_cloud = gudhi.read_points_from_off_file(off_file=args.file)
-        print("#####################################################################")
+        print("##############################################################")
         print("RipsComplex creation from points read in a OFF file")
 
         message = "RipsComplex with max_edge_length=" + repr(args.threshold)
@@ -46,14 +50,15 @@ with open(args.file, "r") as f:
             points=point_cloud, max_edge_length=args.threshold
         )
 
-        rips_stree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
+        rips_stree = rips_complex.create_simplex_tree(
+            max_dimension=args.max_dimension)
 
         message = "Number of simplices=" + repr(rips_stree.num_simplices())
         print(message)
 
         rips_diag = rips_stree.persistence()
 
-        print("#####################################################################")
+        print("##############################################################")
         print("AlphaComplex creation from points read in a OFF file")
 
         message = "AlphaComplex with max_edge_length=" + repr(args.threshold)
@@ -93,13 +98,13 @@ with open(args.file, "r") as f:
             print(message)
             max_b_distance = max(bottleneck_distance, max_b_distance)
 
-        print(
-            "================================================================================"
-        )
+        print("==============================================================")
         message = "Bottleneck distance is " + repr(max_b_distance)
         print(message)
 
     else:
-        print(args.file, "is not a valid OFF file")
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                args.file)
+
 
     f.close()
diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
index 4903667e..e1e572df 100755
--- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
@@ -1,11 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
 import gudhi
 
-""" 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.
+""" 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
@@ -44,8 +48,9 @@ args = parser.parse_args()
 with open(args.file, "r") as f:
     first_line = f.readline()
     if (first_line == "OFF\n") or (first_line == "nOFF\n"):
-        print("#####################################################################")
-        print("EuclideanStrongWitnessComplex creation from points read in a OFF file")
+        print("##############################################################")
+        print("EuclideanStrongWitnessComplex creation from points read "\
+            "in a OFF file")
 
         witnesses = gudhi.read_points_from_off_file(off_file=args.file)
         landmarks = gudhi.pick_n_random_points(
@@ -64,7 +69,8 @@ with open(args.file, "r") as f:
             witnesses=witnesses, landmarks=landmarks
         )
         simplex_tree = witness_complex.create_simplex_tree(
-            max_alpha_square=args.max_alpha_square, limit_dimension=args.limit_dimension
+            max_alpha_square=args.max_alpha_square,
+            limit_dimension=args.limit_dimension
         )
 
         message = "Number of simplices=" + repr(simplex_tree.num_simplices())
@@ -79,6 +85,7 @@ with open(args.file, "r") as f:
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
-        print(args.file, "is not a valid OFF file")
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                args.file)
 
     f.close()
diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
index 339a8577..58cb2bb5 100755
--- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -1,11 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
 import gudhi
 
-""" 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.
+""" 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
@@ -78,6 +82,7 @@ with open(args.file, "r") as f:
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
-        print(args.file, "is not a valid OFF file")
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                args.file)
 
     f.close()
diff --git a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
index c692e66f..499171df 100755
--- a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
+++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
@@ -2,10 +2,14 @@
 
 import argparse
 import matplotlib.pyplot as plot
+import errno
+import os
 import gudhi
 
-""" 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.
+""" 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
@@ -57,9 +61,10 @@ parser.add_argument(
 args = parser.parse_args()
 
 if is_file_perseus(args.file):
-    print("#####################################################################")
+    print("##################################################################")
     print("PeriodicCubicalComplex creation")
-    periodic_cubical_complex = gudhi.PeriodicCubicalComplex(perseus_file=args.file)
+    periodic_cubical_complex = gudhi.PeriodicCubicalComplex(
+        perseus_file=args.file)
 
     print("persistence(homology_coeff_field=3, min_persistence=0)=")
     diag = periodic_cubical_complex.persistence(
@@ -73,4 +78,5 @@ if is_file_perseus(args.file):
         gudhi.plot_persistence_barcode(diag)
         plot.show()
 else:
-    print(args.file, "is not a valid perseus style file")
+    raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                            args.file)
diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
index c757aca7..6f992508 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
@@ -1,11 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
 import gudhi
 
-""" 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.
+""" 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
@@ -42,10 +46,11 @@ args = parser.parse_args()
 with open(args.file, "r") as f:
     first_line = f.readline()
     if (first_line == "OFF\n") or (first_line == "nOFF\n"):
-        print("#####################################################################")
+        print("##############################################################")
         print("RipsComplex creation from points read in a OFF file")
 
-        message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
+        message = "RipsComplex with max_edge_length=" + \
+            repr(args.max_edge_length)
         print(message)
 
         point_cloud = gudhi.read_points_from_off_file(off_file=args.file)
@@ -68,6 +73,7 @@ with open(args.file, "r") as f:
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
-        print(args.file, "is not a valid OFF file")
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                args.file)
 
     f.close()
diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
index f0df2189..85bade4a 100755
--- a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
+++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
@@ -1,11 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
 import gudhi
 
-""" 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.
+""" 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
@@ -19,7 +23,7 @@ __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
 
 parser = argparse.ArgumentParser(
-    description="TangentialComplex creation from " "points read in a OFF file.",
+    description="TangentialComplex creation from points read in a OFF file.",
     epilog="Example: "
     "example/tangential_complex_plain_homology_from_off_file_example.py "
     "-f ../data/points/tore3D_300.off -i 3"
@@ -41,10 +45,11 @@ args = parser.parse_args()
 with open(args.file, "r") as f:
     first_line = f.readline()
     if (first_line == "OFF\n") or (first_line == "nOFF\n"):
-        print("#####################################################################")
+        print("##############################################################")
         print("TangentialComplex creation from points read in a OFF file")
 
-        tc = gudhi.TangentialComplex(intrisic_dim=args.intrisic_dim, off_file=args.file)
+        tc = gudhi.TangentialComplex(intrisic_dim=args.intrisic_dim,
+            off_file=args.file)
         tc.compute_tangential_complex()
         st = tc.create_simplex_tree()
 
@@ -60,6 +65,7 @@ with open(args.file, "r") as f:
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
-        print(args.file, "is not a valid OFF file")
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                args.file)
 
     f.close()
diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx
index fff3e920..e04dc652 100644
--- a/src/python/gudhi/alpha_complex.pyx
+++ b/src/python/gudhi/alpha_complex.pyx
@@ -1,5 +1,7 @@
-# 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.
+# 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
@@ -7,6 +9,7 @@
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from __future__ import print_function
 from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
@@ -69,7 +72,8 @@ 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(off_file.encode('utf-8'), 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 cbeda014..d5ad1266 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -1,5 +1,7 @@
-# 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.
+# 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
@@ -7,12 +9,15 @@
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from __future__ import print_function
 from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
 from libcpp.string cimport string
 from libcpp cimport bool
+import errno
 import os
+import sys
 
 import numpy as np
 
@@ -87,10 +92,12 @@ cdef class CubicalComplex:
             if os.path.isfile(perseus_file):
                 self.thisptr = new Bitmap_cubical_complex_base_interface(perseus_file.encode('utf-8'))
             else:
-                print("file " + perseus_file + " not found.")
+                raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                        perseus_file)
         else:
             print("CubicalComplex can be constructed from dimensions and "
-              "top_dimensional_cells or from a Perseus-style file name.")
+                "top_dimensional_cells or from a Perseus-style file name.",
+                file=sys.stderr)
 
     def __dealloc__(self):
         if self.thisptr != NULL:
@@ -199,5 +206,5 @@ cdef class CubicalComplex:
             intervals_result = self.pcohptr.intervals_in_dimension(dimension)
         else:
             print("intervals_in_dim function requires persistence function"
-                  " to be launched first.")
+                  " to be launched first.", file=sys.stderr)
         return np.array(intervals_result)
diff --git a/src/python/gudhi/nerve_gic.pyx b/src/python/gudhi/nerve_gic.pyx
index 45cc8eba..9c89b239 100644
--- a/src/python/gudhi/nerve_gic.pyx
+++ b/src/python/gudhi/nerve_gic.pyx
@@ -1,5 +1,7 @@
-# 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.
+# 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) 2018 Inria
@@ -7,11 +9,13 @@
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from __future__ import print_function
 from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
 from libcpp.string cimport string
 from libcpp cimport bool
+import errno
 import os
 from libc.stdint cimport intptr_t
 
@@ -96,7 +100,8 @@ cdef class CoverComplex:
         return self.thisptr != NULL
 
     def set_point_cloud_from_range(self, cloud):
-        """ Reads and stores the input point cloud from a vector stored in memory.
+        """ Reads and stores the input point cloud from a vector stored in
+        memory.
 
         :param cloud: Input vector containing the point cloud.
         :type cloud: vector[vector[double]]
@@ -104,7 +109,8 @@ cdef class CoverComplex:
         return self.thisptr.set_point_cloud_from_range(cloud)
 
     def set_distances_from_range(self, distance_matrix):
-        """ Reads and stores the input distance matrix from a vector stored in memory.
+        """ Reads and stores the input distance matrix from a vector stored in
+        memory.
 
         :param distance_matrix: Input vector containing the distance matrix.
         :type distance_matrix: vector[vector[double]]
@@ -163,7 +169,8 @@ cdef class CoverComplex:
         """
         stree = SimplexTree()
         cdef intptr_t stree_int_ptr=stree.thisptr
-        self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr)
+        self.thisptr.create_simplex_tree(
+            <Simplex_tree_interface_full_featured*>stree_int_ptr)
         return stree
 
     def find_simplices(self):
@@ -182,8 +189,8 @@ cdef class CoverComplex:
         if os.path.isfile(off_file):
             return self.thisptr.read_point_cloud(off_file.encode('utf-8'))
         else:
-            print("file " + off_file + " not found.")
-            return False
+            raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                    off_file)
 
     def set_automatic_resolution(self):
         """Computes the optimal length of intervals (i.e. the smallest interval
@@ -214,7 +221,8 @@ cdef class CoverComplex:
         if os.path.isfile(color_file_name):
             self.thisptr.set_color_from_file(color_file_name.encode('utf-8'))
         else:
-            print("file " + color_file_name + " not found.")
+            raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                    color_file_name)
 
     def set_color_from_range(self, color):
         """Computes the function used to color the nodes of the simplicial
@@ -235,7 +243,8 @@ cdef class CoverComplex:
         if os.path.isfile(cover_file_name):
             self.thisptr.set_cover_from_file(cover_file_name.encode('utf-8'))
         else:
-            print("file " + cover_file_name + " not found.")
+            raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                    cover_file_name)
 
     def set_cover_from_function(self):
         """Creates a cover C from the preimages of the function f.
@@ -268,7 +277,8 @@ cdef class CoverComplex:
         if os.path.isfile(func_file_name):
             self.thisptr.set_function_from_file(func_file_name.encode('utf-8'))
         else:
-            print("file " + func_file_name + " not found.")
+            raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                    func_file_name)
 
     def set_function_from_range(self, function):
         """Creates the function f from a vector stored in memory.
@@ -302,14 +312,15 @@ cdef class CoverComplex:
         """Creates a graph G from a file containing the edges.
 
         :param graph_file_name: Name of the input graph file. The graph file
-            contains one edge per line, each edge being represented by the IDs of
-            its two nodes.
+            contains one edge per line, each edge being represented by the IDs
+            of its two nodes.
         :type graph_file_name: string
         """
         if os.path.isfile(graph_file_name):
             self.thisptr.set_graph_from_file(graph_file_name.encode('utf-8'))
         else:
-            print("file " + graph_file_name + " not found.")
+            raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                    graph_file_name)
 
     def set_graph_from_OFF(self):
         """Creates a graph G from the triangulation given by the input OFF
diff --git a/src/python/gudhi/off_reader.pyx b/src/python/gudhi/off_reader.pyx
index 7e6d9d80..a3200704 100644
--- a/src/python/gudhi/off_reader.pyx
+++ b/src/python/gudhi/off_reader.pyx
@@ -1,5 +1,7 @@
-# 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.
+# 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
@@ -7,9 +9,11 @@
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from __future__ import print_function
 from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.string cimport string
+import errno
 import os
 
 __author__ = "Vincent Rouvreau"
@@ -32,6 +36,6 @@ def read_points_from_off_file(off_file=''):
         if os.path.isfile(off_file):
             return read_points_from_OFF_file(off_file.encode('utf-8'))
         else:
-            print("file " + off_file + " not found.")
-            return []
+            raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                    off_file)
 
diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx
index 37f76201..fd08b976 100644
--- a/src/python/gudhi/periodic_cubical_complex.pyx
+++ b/src/python/gudhi/periodic_cubical_complex.pyx
@@ -7,11 +7,13 @@
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from __future__ import print_function
 from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
 from libcpp.string cimport string
 from libcpp cimport bool
+import sys
 import os
 
 import numpy as np
@@ -95,12 +97,12 @@ cdef class PeriodicCubicalComplex:
             if os.path.isfile(perseus_file):
                 self.thisptr = new Periodic_cubical_complex_base_interface(perseus_file.encode('utf-8'))
             else:
-                print("file " + perseus_file + " not found.")
+                print("file " + perseus_file + " not found.", file=sys.stderr)
         else:
             print("CubicalComplex can be constructed from dimensions, "
               "top_dimensional_cells and periodic_dimensions, or from "
               "top_dimensional_cells and periodic_dimensions or from "
-              "a Perseus-style file name.")
+              "a Perseus-style file name.", file=sys.stderr)
 
     def __dealloc__(self):
         if self.thisptr != NULL:
@@ -209,5 +211,5 @@ cdef class PeriodicCubicalComplex:
             intervals_result = self.pcohptr.intervals_in_dimension(dimension)
         else:
             print("intervals_in_dim function requires persistence function"
-                  " to be launched first.")
+                  " to be launched first.", file=sys.stderr)
         return np.array(intervals_result)
diff --git a/src/python/test/test_cover_complex.py b/src/python/test/test_cover_complex.py
index 32bc5a26..260f6a5c 100755
--- a/src/python/test/test_cover_complex.py
+++ b/src/python/test/test_cover_complex.py
@@ -9,6 +9,7 @@
 """
 
 from gudhi import CoverComplex
+import pytest
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2018 Inria"
@@ -24,7 +25,8 @@ def test_empty_constructor():
 def test_non_existing_file_read():
     # Try to open a non existing file
     cover = CoverComplex()
-    assert cover.read_point_cloud("pouetpouettralala.toubiloubabdou") == False
+    with pytest.raises(FileNotFoundError):
+        cover.read_point_cloud("pouetpouettralala.toubiloubabdou")
 
 
 def test_files_creation():
diff --git a/src/python/test/test_cubical_complex.py b/src/python/test/test_cubical_complex.py
index 8c1b2600..fce4875c 100755
--- a/src/python/test/test_cubical_complex.py
+++ b/src/python/test/test_cubical_complex.py
@@ -10,6 +10,7 @@
 
 from gudhi import CubicalComplex, PeriodicCubicalComplex
 import numpy as np
+import pytest
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
@@ -25,9 +26,8 @@ def test_empty_constructor():
 
 def test_non_existing_perseus_file_constructor():
     # Try to open a non existing file
-    cub = CubicalComplex(perseus_file="pouetpouettralala.toubiloubabdou")
-    assert cub.__is_defined() == False
-    assert cub.__is_persistence_defined() == False
+    with pytest.raises(FileNotFoundError):
+        cub = CubicalComplex(perseus_file="pouetpouettralala.toubiloubabdou")
 
 
 def test_dimension_or_perseus_file_constructor():
diff --git a/src/python/test/test_subsampling.py b/src/python/test/test_subsampling.py
index fe0985fa..31f64e32 100755
--- a/src/python/test/test_subsampling.py
+++ b/src/python/test/test_subsampling.py
@@ -120,7 +120,6 @@ def test_simple_pick_n_random_points():
     # Go furter than point set on purpose
     for iter in range(1, 10):
         sub_set = gudhi.pick_n_random_points(points=point_set, nb_points=iter)
-        print(5)
         for sub in sub_set:
             found = False
             for point in point_set: