Use exceptions uinstead of error message for non existing files

10 files changed, 98 insertions, 58 deletions

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 6afaf533..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
@@ -1,12 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
-import sys
 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
@@ -42,7 +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)
@@ -65,6 +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", file=sys.stderr)
+        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 7b4aa3e7..f156826d 100755
--- a/src/python/example/alpha_rips_persistence_bottleneck_distance.py
+++ b/src/python/example/alpha_rips_persistence_bottleneck_distance.py
@@ -3,10 +3,13 @@
 import gudhi
 import argparse
 import math
-import sys
+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
@@ -37,7 +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)
@@ -47,14 +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)
@@ -94,13 +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", file=sys.stderr)
+        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 f61d692b..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
@@ -1,12 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
-import sys
 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
@@ -45,8 +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(
@@ -65,7 +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())
@@ -80,6 +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", file=sys.stderr)
+        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 aaa03dad..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
@@ -1,12 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
-import sys
 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
@@ -79,6 +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", file=sys.stderr)
+        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 97bfd49f..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
@@ -2,11 +2,14 @@
 
 import argparse
 import matplotlib.pyplot as plot
-import sys
+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
@@ -58,9 +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(
@@ -74,4 +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", file=sys.stderr)
+    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 5d8f057b..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
@@ -1,12 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
-import sys
 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
@@ -43,10 +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)
@@ -69,6 +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", file=sys.stderr)
+        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 77ac2ea7..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
@@ -1,12 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
-import sys
 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
@@ -20,7 +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"
@@ -42,10 +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()
 
@@ -61,6 +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", file=sys.stderr)
+        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 dab4b56f..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
@@ -14,7 +16,6 @@ from libcpp.utility cimport pair
 from libcpp.string cimport string
 from libcpp cimport bool
 from libc.stdint cimport intptr_t
-import sys
 import os
 
 from gudhi.simplex_tree cimport *
@@ -71,7 +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 1dd30b4e..463bd4ee 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
@@ -13,7 +15,7 @@ from libcpp.vector cimport vector
 from libcpp.utility cimport pair
 from libcpp.string cimport string
 from libcpp cimport bool
-import sys
+import errno
 import os
 
 import numpy as np
@@ -89,7 +91,8 @@ 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.", file=sys.stderr)
+                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.",
diff --git a/src/python/gudhi/off_reader.pyx b/src/python/gudhi/off_reader.pyx
index 0a828b83..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
@@ -11,7 +13,7 @@ from __future__ import print_function
 from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.string cimport string
-import sys
+import errno
 import os
 
 __author__ = "Vincent Rouvreau"
@@ -34,6 +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.", file=sys.stderr)
-            return []
+            raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                    off_file)