From c3414741af6ef98703ba9414803aff5a2d08777d Mon Sep 17 00:00:00 2001
From: Marc Glisse <marc.glisse@inria.fr>
Date: Sat, 16 Nov 2019 06:34:54 +0100
Subject: More 'is' to '=='

---
 src/python/gudhi/alpha_complex.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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

diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx
index 6d6309db..a85c47c8 100644
--- a/src/python/gudhi/alpha_complex.pyx
+++ b/src/python/gudhi/alpha_complex.pyx
@@ -68,7 +68,7 @@ cdef class AlphaComplex:
 
     # The real cython constructor
     def __cinit__(self, points=None, off_file=''):
-        if off_file is not '':
+        if off_file:
             if os.path.isfile(off_file):
                 self.thisptr = new Alpha_complex_interface(str.encode(off_file), True)
             else:
-- 
cgit v1.2.3


From 63616eba3031334d8e2c267e54f9aa4a801baeff Mon Sep 17 00:00:00 2001
From: Marc Glisse <marc.glisse@inria.fr>
Date: Thu, 14 Nov 2019 13:13:38 +0100
Subject: Make the license a comment instead of a string

I think this interacts better with sphinx automodule
---
 src/python/gudhi/__init__.py.in                       | 17 ++++++++---------
 src/python/gudhi/alpha_complex.pyx                    | 17 ++++++++---------
 src/python/gudhi/bottleneck.pyx                       | 17 ++++++++---------
 src/python/gudhi/cubical_complex.pyx                  | 17 ++++++++---------
 src/python/gudhi/euclidean_strong_witness_complex.pyx | 17 ++++++++---------
 src/python/gudhi/euclidean_witness_complex.pyx        | 17 ++++++++---------
 src/python/gudhi/nerve_gic.pyx                        | 17 ++++++++---------
 src/python/gudhi/off_reader.pyx                       | 17 ++++++++---------
 src/python/gudhi/periodic_cubical_complex.pyx         | 17 ++++++++---------
 src/python/gudhi/persistence_graphical_tools.py       | 17 ++++++++---------
 src/python/gudhi/reader_utils.pyx                     | 17 ++++++++---------
 src/python/gudhi/rips_complex.pyx                     | 17 ++++++++---------
 src/python/gudhi/simplex_tree.pyx                     | 17 ++++++++---------
 src/python/gudhi/strong_witness_complex.pyx           | 17 ++++++++---------
 src/python/gudhi/subsampling.pyx                      | 17 ++++++++---------
 src/python/gudhi/tangential_complex.pyx               | 17 ++++++++---------
 src/python/gudhi/wasserstein.py                       | 17 ++++++++---------
 src/python/gudhi/witness_complex.pyx                  | 17 ++++++++---------
 18 files changed, 144 insertions(+), 162 deletions(-)

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

diff --git a/src/python/gudhi/__init__.py.in b/src/python/gudhi/__init__.py.in
index 02888fff..0c462b02 100644
--- a/src/python/gudhi/__init__.py.in
+++ b/src/python/gudhi/__init__.py.in
@@ -1,14 +1,13 @@
 from importlib import import_module
 
-"""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
-"""
+# 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__ = "GUDHI Editorial Board"
 __copyright__ = "Copyright (C) 2016 Inria"
diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx
index a85c47c8..8f2c98d5 100644
--- a/src/python/gudhi/alpha_complex.pyx
+++ b/src/python/gudhi/alpha_complex.pyx
@@ -9,15 +9,14 @@ import os
 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
-"""
+# 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"
diff --git a/src/python/gudhi/bottleneck.pyx b/src/python/gudhi/bottleneck.pyx
index 4b378cbc..c2361024 100644
--- a/src/python/gudhi/bottleneck.pyx
+++ b/src/python/gudhi/bottleneck.pyx
@@ -3,15 +3,14 @@ from libcpp.vector cimport vector
 from libcpp.utility cimport pair
 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.
-    Author(s):       Vincent Rouvreau
-
-    Copyright (C) 2016 Inria
-
-    Modification(s):
-      - YYYY/MM Author: Description of the modification
-"""
+# 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"
diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index 579c942b..011c407c 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -7,15 +7,14 @@ import os
 
 from numpy import array as np_array
 
-""" 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
-"""
+# 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"
diff --git a/src/python/gudhi/euclidean_strong_witness_complex.pyx b/src/python/gudhi/euclidean_strong_witness_complex.pyx
index 0e5b544a..e3f451f0 100644
--- a/src/python/gudhi/euclidean_strong_witness_complex.pyx
+++ b/src/python/gudhi/euclidean_strong_witness_complex.pyx
@@ -6,15 +6,14 @@ 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
-"""
+# 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"
diff --git a/src/python/gudhi/euclidean_witness_complex.pyx b/src/python/gudhi/euclidean_witness_complex.pyx
index 86d2d996..84a8ea1a 100644
--- a/src/python/gudhi/euclidean_witness_complex.pyx
+++ b/src/python/gudhi/euclidean_witness_complex.pyx
@@ -6,15 +6,14 @@ 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
-"""
+# 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"
diff --git a/src/python/gudhi/nerve_gic.pyx b/src/python/gudhi/nerve_gic.pyx
index 2b230b8c..acb78564 100644
--- a/src/python/gudhi/nerve_gic.pyx
+++ b/src/python/gudhi/nerve_gic.pyx
@@ -9,15 +9,14 @@ 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) 2018 Inria
-
-    Modification(s):
-      - YYYY/MM Author: Description of the modification
-"""
+# 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
+#
+# Modification(s):
+#   - YYYY/MM Author: Description of the modification
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2018 Inria"
diff --git a/src/python/gudhi/off_reader.pyx b/src/python/gudhi/off_reader.pyx
index 27a89870..225e981c 100644
--- a/src/python/gudhi/off_reader.pyx
+++ b/src/python/gudhi/off_reader.pyx
@@ -3,15 +3,14 @@ from libcpp.vector cimport vector
 from libcpp.string cimport string
 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.
-    Author(s):       Vincent Rouvreau
-
-    Copyright (C) 2016 Inria
-
-    Modification(s):
-      - YYYY/MM Author: Description of the modification
-"""
+# 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"
diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx
index 88223afb..c89055db 100644
--- a/src/python/gudhi/periodic_cubical_complex.pyx
+++ b/src/python/gudhi/periodic_cubical_complex.pyx
@@ -7,15 +7,14 @@ import os
 
 from numpy import array as np_array
 
-""" 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
-"""
+# 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"
diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py
index 181bc8ea..43a00459 100644
--- a/src/python/gudhi/persistence_graphical_tools.py
+++ b/src/python/gudhi/persistence_graphical_tools.py
@@ -5,15 +5,14 @@ import numpy as np
 from gudhi.reader_utils import read_persistence_intervals_in_dimension
 from gudhi.reader_utils import read_persistence_intervals_grouped_by_dimension
 
-""" 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, Bertrand Michel
-
-    Copyright (C) 2016 Inria
-
-    Modification(s):
-      - YYYY/MM Author: Description of the modification
-"""
+# 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, Bertrand Michel
+#
+# Copyright (C) 2016 Inria
+#
+# Modification(s):
+#   - YYYY/MM Author: Description of the modification
 
 __author__ = "Vincent Rouvreau, Bertrand Michel"
 __copyright__ = "Copyright (C) 2016 Inria"
diff --git a/src/python/gudhi/reader_utils.pyx b/src/python/gudhi/reader_utils.pyx
index b266c783..6994c4f9 100644
--- a/src/python/gudhi/reader_utils.pyx
+++ b/src/python/gudhi/reader_utils.pyx
@@ -7,15 +7,14 @@ from libcpp.pair cimport pair
 from os import path
 from numpy import array as np_array
 
-""" 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) 2017 Inria
-
-    Modification(s):
-      - YYYY/MM Author: Description of the modification
-"""
+# 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) 2017 Inria
+#
+# Modification(s):
+#   - YYYY/MM Author: Description of the modification
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2017 Inria"
diff --git a/src/python/gudhi/rips_complex.pyx b/src/python/gudhi/rips_complex.pyx
index f2cd6a8d..cbbbab0d 100644
--- a/src/python/gudhi/rips_complex.pyx
+++ b/src/python/gudhi/rips_complex.pyx
@@ -8,15 +8,14 @@ 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
-"""
+# 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"
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index 90ddf6dd..ade3bf6c 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -2,15 +2,14 @@ from libc.stdint cimport intptr_t
 from numpy import array as np_array
 cimport simplex_tree
 
-""" 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
-"""
+# 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"
diff --git a/src/python/gudhi/strong_witness_complex.pyx b/src/python/gudhi/strong_witness_complex.pyx
index e35ba6ad..66d49b49 100644
--- a/src/python/gudhi/strong_witness_complex.pyx
+++ b/src/python/gudhi/strong_witness_complex.pyx
@@ -6,15 +6,14 @@ 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
-"""
+# 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"
diff --git a/src/python/gudhi/subsampling.pyx b/src/python/gudhi/subsampling.pyx
index e622ac99..e0cd1348 100644
--- a/src/python/gudhi/subsampling.pyx
+++ b/src/python/gudhi/subsampling.pyx
@@ -4,15 +4,14 @@ from libcpp.string cimport string
 from libcpp cimport bool
 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.
-    Author(s):       Vincent Rouvreau
-
-    Copyright (C) 2016 Inria
-
-    Modification(s):
-      - YYYY/MM Author: Description of the modification
-"""
+# 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"
diff --git a/src/python/gudhi/tangential_complex.pyx b/src/python/gudhi/tangential_complex.pyx
index 9ef15567..b7678f4d 100644
--- a/src/python/gudhi/tangential_complex.pyx
+++ b/src/python/gudhi/tangential_complex.pyx
@@ -9,15 +9,14 @@ import os
 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
-"""
+# 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"
diff --git a/src/python/gudhi/wasserstein.py b/src/python/gudhi/wasserstein.py
index eba7c6d5..d8a3104c 100644
--- a/src/python/gudhi/wasserstein.py
+++ b/src/python/gudhi/wasserstein.py
@@ -5,15 +5,14 @@ try:
 except ImportError:
     print("POT (Python Optimal Transport) package is not installed. Try to run $ conda install -c conda-forge pot ; or $ pip install POT")
 
-""" 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):       Theo Lacombe
-
-    Copyright (C) 2019 Inria
-
-    Modification(s):
-      - YYYY/MM Author: Description of the modification
-"""
+# 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):       Theo Lacombe
+#
+# Copyright (C) 2019 Inria
+#
+# Modification(s):
+#   - YYYY/MM Author: Description of the modification
 
 def _proj_on_diag(X):
     '''
diff --git a/src/python/gudhi/witness_complex.pyx b/src/python/gudhi/witness_complex.pyx
index c19ccf2b..153fc615 100644
--- a/src/python/gudhi/witness_complex.pyx
+++ b/src/python/gudhi/witness_complex.pyx
@@ -6,15 +6,14 @@ 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
-"""
+# 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"
-- 
cgit v1.2.3


From 9fc45aafa4588b86ccd903b9173a8cdf48db68a1 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Thu, 5 Dec 2019 16:01:45 +0100
Subject: Add MPFR dependency for python module. Use Epeck_d by default for
 Alpha complex. Add boolean exact version mechanism

---
 src/cmake/modules/FindMPFR.cmake                   | 51 ++++++++++++++++++
 .../modules/GUDHI_third_party_libraries.cmake      |  2 +
 src/python/CMakeLists.txt                          | 61 +++++++++++++---------
 src/python/gudhi/alpha_complex.pyx                 | 13 +++--
 src/python/include/Alpha_complex_interface.h       |  9 ++--
 5 files changed, 102 insertions(+), 34 deletions(-)
 create mode 100644 src/cmake/modules/FindMPFR.cmake

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

diff --git a/src/cmake/modules/FindMPFR.cmake b/src/cmake/modules/FindMPFR.cmake
new file mode 100644
index 00000000..6c963272
--- /dev/null
+++ b/src/cmake/modules/FindMPFR.cmake
@@ -0,0 +1,51 @@
+# Try to find the MPFR libraries
+# MPFR_FOUND - system has MPFR lib
+# MPFR_INCLUDE_DIR - the MPFR include directory
+# MPFR_LIBRARIES_DIR - Directory where the MPFR libraries are located
+# MPFR_LIBRARIES - the MPFR libraries
+
+# TODO: support MacOSX
+
+include(FindPackageHandleStandardArgs)
+
+if(MPFR_INCLUDE_DIR)
+  set(MPFR_in_cache TRUE)
+else()
+  set(MPFR_in_cache FALSE)
+endif()
+if(NOT MPFR_LIBRARIES)
+  set(MPFR_in_cache FALSE)
+endif()
+
+# Is it already configured?
+if (MPFR_in_cache)
+  set(MPFR_FOUND TRUE)
+else()
+  find_path(MPFR_INCLUDE_DIR
+            NAMES mpfr.h
+            HINTS ENV MPFR_INC_DIR
+                  ENV MPFR_DIR
+                  ${CGAL_INSTALLATION_PACKAGE_DIR}/auxiliary/gmp/include
+            PATH_SUFFIXES include
+  	        DOC "The directory containing the MPFR header files"
+           )
+
+  find_library(MPFR_LIBRARIES NAMES mpfr libmpfr-4 libmpfr-1
+    HINTS ENV MPFR_LIB_DIR
+          ENV MPFR_DIR
+          ${CGAL_INSTALLATION_PACKAGE_DIR}/auxiliary/gmp/lib
+    PATH_SUFFIXES lib
+    DOC "Path to the MPFR library"
+    )
+
+  if ( MPFR_LIBRARIES )
+    get_filename_component(MPFR_LIBRARIES_DIR ${MPFR_LIBRARIES} PATH CACHE )
+  endif()
+
+  # Attempt to load a user-defined configuration for MPFR if couldn't be found
+  if ( NOT MPFR_INCLUDE_DIR OR NOT MPFR_LIBRARIES_DIR )
+    include( MPFRConfig OPTIONAL )
+  endif()
+
+  find_package_handle_standard_args(MPFR "DEFAULT_MSG" MPFR_LIBRARIES MPFR_INCLUDE_DIR)
+endif()
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 24a34150..d8c7a428 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -6,6 +6,8 @@ if(NOT Boost_FOUND)
   message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
 endif(NOT Boost_FOUND)
 
+find_package(MPFR)
+
 find_package(GMP)
 if(GMP_FOUND)
   INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 9af85eac..13a8a909 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -114,9 +114,9 @@ if(PYTHONINTERP_FOUND)
       set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'nerve_gic', ")
     endif ()
     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+      set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'alpha_complex', ")
       set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'subsampling', ")
       set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'tangential_complex', ")
-      set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'alpha_complex', ")
       set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'euclidean_witness_complex', ")
       set(GUDHI_PYTHON_MODULES_TO_COMPILE "${GUDHI_PYTHON_MODULES_TO_COMPILE}'euclidean_strong_witness_complex', ")
     endif ()
@@ -162,10 +162,17 @@ if(PYTHONINTERP_FOUND)
           set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
           add_GUDHI_PYTHON_lib("${GMPXX_LIBRARIES}")
           set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
-        message("** Add gmpxx ${GMPXX_LIBRARIES_DIR}")
+          message("** Add gmpxx ${GMPXX_LIBRARIES_DIR}")
         endif(GMPXX_FOUND)
       endif(GMP_FOUND)
-    endif(CGAL_FOUND)
+      if(MPFR_FOUND)
+        add_gudhi_debug_info("MPFR_LIBRARIES = ${MPFR_LIBRARIES}")
+        set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_MPFR', ")
+        add_GUDHI_PYTHON_lib("${MPFR_LIBRARIES}")
+        set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${MPFR_LIBRARIES_DIR}', ")
+        message("** Add mpfr ${MPFR_LIBRARIES}")
+      endif(MPFR_FOUND)
+endif(CGAL_FOUND)
 
     # Specific for Mac
     if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
@@ -223,13 +230,14 @@ if(PYTHONINTERP_FOUND)
 
     # Test examples
     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
-      # Bottleneck and Alpha
-      add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
-               -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
-
+      if (MPFR_FOUND)
+        # Bottleneck and Alpha
+        add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+                 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
+      endif(MPFR_FOUND)
       if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
         # Tangential
         add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
@@ -300,22 +308,23 @@ if(PYTHONINTERP_FOUND)
     endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
 
     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
-      # Alpha
-      add_test(NAME alpha_complex_from_points_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
-
-      if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
-        add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
-               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
-      endif()
-
-      add_gudhi_py_test(test_alpha_complex)
-
+      if (MPFR_FOUND)
+        # Alpha
+        add_test(NAME alpha_complex_from_points_example_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
+  
+        if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+          add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
+        endif()
+  
+        add_gudhi_py_test(test_alpha_complex)
+      endif(MPFR_FOUND)
     endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
 
     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx
index 8f2c98d5..abac6e7b 100644
--- a/src/python/gudhi/alpha_complex.pyx
+++ b/src/python/gudhi/alpha_complex.pyx
@@ -28,7 +28,7 @@ cdef extern from "Alpha_complex_interface.h" namespace "Gudhi":
         # 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)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, bool exact_version)
 
 # AlphaComplex python interface
 cdef class AlphaComplex:
@@ -66,7 +66,7 @@ cdef class AlphaComplex:
         """
 
     # The real cython constructor
-    def __cinit__(self, points=None, off_file=''):
+    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)
@@ -99,17 +99,22 @@ cdef class AlphaComplex:
         cdef vector[double] point = self.thisptr.get_point(vertex)
         return point
 
-    def create_simplex_tree(self, max_alpha_square=float('inf')):
+    def create_simplex_tree(self, max_alpha_square = float('inf'),
+                            exact_version = False):
         """
         :param max_alpha_square: The maximum alpha square threshold the
             simplices shall not exceed. Default is set to infinity, and
             there is very little point using anything else since it does
             not save time.
         :type max_alpha_square: float
+        :param exact_version: Exact computation version. Default is false
+            which means Safe version is used.
+        :type exact_version: bool
         :returns: A simplex tree created from the Delaunay Triangulation.
         :rtype: SimplexTree
         """
         stree = SimplexTree()
         cdef intptr_t stree_int_ptr=stree.thisptr
-        self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr, max_alpha_square)
+        self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr,
+                                         max_alpha_square, exact_version)
         return stree
diff --git a/src/python/include/Alpha_complex_interface.h b/src/python/include/Alpha_complex_interface.h
index 96353cc4..a7621f2b 100644
--- a/src/python/include/Alpha_complex_interface.h
+++ b/src/python/include/Alpha_complex_interface.h
@@ -13,6 +13,7 @@
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Alpha_complex.h>
+#include <CGAL/Epeck_d.h>
 #include <CGAL/Epick_d.h>
 
 #include <boost/range/adaptor/transformed.hpp>
@@ -28,7 +29,7 @@ namespace Gudhi {
 namespace alpha_complex {
 
 class Alpha_complex_interface {
-  using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+  using Dynamic_kernel = CGAL::Epeck_d< CGAL::Dynamic_dimension_tag >;
   using Point_d = Dynamic_kernel::Point_d;
 
  public:
@@ -51,7 +52,7 @@ class Alpha_complex_interface {
     std::vector<double> vd;
     try {
       Point_d const& ph = alpha_complex_->get_point(vh);
-      for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++)
+      for (auto coord = ph.cartesian_begin(); coord != ph.cartesian_end(); coord++)
         vd.push_back(CGAL::to_double(*coord));
     } catch (std::out_of_range const&) {
       // std::out_of_range is thrown in case not found. Other exceptions must be re-thrown
@@ -59,8 +60,8 @@ class Alpha_complex_interface {
     return vd;
   }
 
-  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square) {
-    alpha_complex_->create_complex(*simplex_tree, max_alpha_square);
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square, bool exact_version) {
+    alpha_complex_->create_complex(*simplex_tree, max_alpha_square, exact_version);
     simplex_tree->initialize_filtration();
   }
 
-- 
cgit v1.2.3


From 6142e146e92801cafe1438bf487f3ecafa502177 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Thu, 5 Dec 2019 17:57:19 +0100
Subject: nicer doc presentation

---
 src/python/gudhi/alpha_complex.pyx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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

diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx
index abac6e7b..bfb9783a 100644
--- a/src/python/gudhi/alpha_complex.pyx
+++ b/src/python/gudhi/alpha_complex.pyx
@@ -107,8 +107,8 @@ cdef class AlphaComplex:
             there is very little point using anything else since it does
             not save time.
         :type max_alpha_square: float
-        :param exact_version: Exact computation version. Default is false
-            which means Safe version is used.
+        :param exact_version: :code:`EXACT` computation version if set.
+            Default is false which means :code:`SAFE` version is used.
         :type exact_version: bool
         :returns: A simplex tree created from the Delaunay Triangulation.
         :rtype: SimplexTree
-- 
cgit v1.2.3


From 490a5774601e344bb732de5eab2a8cf6d5a7e81f Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Mon, 16 Dec 2019 13:38:58 +0100
Subject: Rollback exact version mechanism

---
 src/python/gudhi/alpha_complex.pyx           | 11 +++--------
 src/python/include/Alpha_complex_interface.h |  4 ++--
 src/python/test/test_alpha_complex.py        | 12 +++---------
 3 files changed, 8 insertions(+), 19 deletions(-)

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

diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx
index bfb9783a..24e36bea 100644
--- a/src/python/gudhi/alpha_complex.pyx
+++ b/src/python/gudhi/alpha_complex.pyx
@@ -28,7 +28,7 @@ cdef extern from "Alpha_complex_interface.h" namespace "Gudhi":
         # 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, bool exact_version)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
 
 # AlphaComplex python interface
 cdef class AlphaComplex:
@@ -99,22 +99,17 @@ cdef class AlphaComplex:
         cdef vector[double] point = self.thisptr.get_point(vertex)
         return point
 
-    def create_simplex_tree(self, max_alpha_square = float('inf'),
-                            exact_version = False):
+    def create_simplex_tree(self, max_alpha_square = float('inf')):
         """
         :param max_alpha_square: The maximum alpha square threshold the
             simplices shall not exceed. Default is set to infinity, and
             there is very little point using anything else since it does
             not save time.
         :type max_alpha_square: float
-        :param exact_version: :code:`EXACT` computation version if set.
-            Default is false which means :code:`SAFE` version is used.
-        :type exact_version: bool
         :returns: A simplex tree created from the Delaunay Triangulation.
         :rtype: SimplexTree
         """
         stree = SimplexTree()
         cdef intptr_t stree_int_ptr=stree.thisptr
-        self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr,
-                                         max_alpha_square, exact_version)
+        self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr, max_alpha_square)
         return stree
diff --git a/src/python/include/Alpha_complex_interface.h b/src/python/include/Alpha_complex_interface.h
index a7621f2b..e9bbadb0 100644
--- a/src/python/include/Alpha_complex_interface.h
+++ b/src/python/include/Alpha_complex_interface.h
@@ -60,8 +60,8 @@ class Alpha_complex_interface {
     return vd;
   }
 
-  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square, bool exact_version) {
-    alpha_complex_->create_complex(*simplex_tree, max_alpha_square, exact_version);
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square) {
+    alpha_complex_->create_complex(*simplex_tree, max_alpha_square);
     simplex_tree->initialize_filtration();
   }
 
diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py
index ab84daaa..9b27fff2 100755
--- a/src/python/test/test_alpha_complex.py
+++ b/src/python/test/test_alpha_complex.py
@@ -93,7 +93,7 @@ def test_filtered_alpha():
     assert simplex_tree.get_star([0]) == [([0], 0.0), ([0, 1], 0.25), ([0, 2], 0.25)]
     assert simplex_tree.get_cofaces([0], 1) == [([0, 1], 0.25), ([0, 2], 0.25)]
 
-def alpha_persistence_comparison(exact_version):
+def test_safe_alpha_persistence_comparison():
     #generate periodic signal
     time = np.arange(0, 10, 1)
     signal = [math.sin(x) for x in time]
@@ -106,10 +106,10 @@ def alpha_persistence_comparison(exact_version):
     
     #build alpha complex and simplex tree
     alpha_complex1 = AlphaComplex(points=embedding1)
-    simplex_tree1 = alpha_complex1.create_simplex_tree(exact_version = exact_version)
+    simplex_tree1 = alpha_complex1.create_simplex_tree()
     
     alpha_complex2 = AlphaComplex(points=embedding2)
-    simplex_tree2 = alpha_complex2.create_simplex_tree(exact_version = exact_version)
+    simplex_tree2 = alpha_complex2.create_simplex_tree()
     
     diag1 = simplex_tree1.persistence()
     diag2 = simplex_tree2.persistence()
@@ -117,9 +117,3 @@ def alpha_persistence_comparison(exact_version):
     for (first_p, second_p) in itertools.zip_longest(diag1, diag2):
         assert first_p[0] == pytest.approx(second_p[0])
         assert first_p[1] == pytest.approx(second_p[1])
-
-def test_exact_alpha_version():
-    alpha_persistence_comparison(exact_version = True)
-
-def test_safe_alpha_version():
-    alpha_persistence_comparison(exact_version = False)
-- 
cgit v1.2.3


From 8f5cb043bf78b8f008b67e292668543a899e6795 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Fri, 10 Jan 2020 19:43:04 +0100
Subject: Reorder import and docstrings. Modify test_representations

---
 src/python/gudhi/__init__.py.in                       |  8 +++-----
 src/python/gudhi/alpha_complex.pyx                    | 18 +++++++++---------
 src/python/gudhi/bottleneck.pyx                       | 10 +++++-----
 src/python/gudhi/cubical_complex.pyx                  | 18 +++++++++---------
 src/python/gudhi/euclidean_strong_witness_complex.pyx | 16 ++++++++--------
 src/python/gudhi/euclidean_witness_complex.pyx        | 16 ++++++++--------
 src/python/gudhi/nerve_gic.pyx                        | 18 +++++++++---------
 src/python/gudhi/off_reader.pyx                       | 10 +++++-----
 src/python/gudhi/periodic_cubical_complex.pyx         | 18 +++++++++---------
 src/python/gudhi/persistence_graphical_tools.py       | 14 +++++++-------
 src/python/gudhi/reader_utils.pyx                     | 18 +++++++++---------
 src/python/gudhi/rips_complex.pyx                     | 18 +++++++++---------
 src/python/gudhi/simplex_tree.pxd                     | 19 +++++++++----------
 src/python/gudhi/simplex_tree.pyx                     |  8 ++++----
 src/python/gudhi/strong_witness_complex.pyx           | 16 ++++++++--------
 src/python/gudhi/subsampling.pyx                      | 12 ++++++------
 src/python/gudhi/tangential_complex.pyx               | 18 +++++++++---------
 src/python/gudhi/wasserstein.py                       | 14 +++++++-------
 src/python/gudhi/witness_complex.pyx                  | 16 ++++++++--------
 src/python/setup.py.in                                |  8 ++++----
 src/python/test/test_alpha_complex.py                 | 12 ++++++------
 src/python/test/test_bottleneck_distance.py           |  4 ++--
 src/python/test/test_cover_complex.py                 |  4 ++--
 src/python/test/test_cubical_complex.py               |  6 +++---
 src/python/test/test_euclidean_witness_complex.py     |  4 ++--
 src/python/test/test_reader_utils.py                  |  6 +++---
 src/python/test/test_representations.py               | 15 ++++++++-------
 src/python/test/test_rips_complex.py                  |  6 +++---
 src/python/test/test_simplex_tree.py                  |  4 ++--
 src/python/test/test_subsampling.py                   |  4 ++--
 src/python/test/test_tangential_complex.py            |  4 ++--
 src/python/test/test_wasserstein_distance.py          |  6 +++---
 src/python/test/test_witness_complex.py               |  4 ++--
 33 files changed, 185 insertions(+), 187 deletions(-)

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

diff --git a/src/python/gudhi/__init__.py.in b/src/python/gudhi/__init__.py.in
index 0c462b02..79e12fbc 100644
--- a/src/python/gudhi/__init__.py.in
+++ b/src/python/gudhi/__init__.py.in
@@ -1,5 +1,3 @@
-from importlib import import_module
-
 # 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
@@ -9,6 +7,9 @@ from importlib import import_module
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from importlib import import_module
+from sys import exc_info
+
 __author__ = "GUDHI Editorial Board"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "https://gudhi.inria.fr/licensing/"
@@ -17,9 +18,6 @@ __version__ = "@GUDHI_VERSION@"
 __root_source_dir__ = "@CMAKE_SOURCE_DIR@"
 __debug_info__ = @GUDHI_PYTHON_DEBUG_INFO@
 
-from sys import exc_info
-from importlib import import_module
-
 __all__ = [@GUDHI_PYTHON_MODULES@ @GUDHI_PYTHON_MODULES_EXTRA@]
 
 __available_modules = ''
diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx
index 24e36bea..db11416c 100644
--- a/src/python/gudhi/alpha_complex.pyx
+++ b/src/python/gudhi/alpha_complex.pyx
@@ -1,3 +1,12 @@
+# 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
+
 from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
@@ -9,15 +18,6 @@ import os
 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__ = "GPL v3"
diff --git a/src/python/gudhi/bottleneck.pyx b/src/python/gudhi/bottleneck.pyx
index c2361024..af011e88 100644
--- a/src/python/gudhi/bottleneck.pyx
+++ b/src/python/gudhi/bottleneck.pyx
@@ -1,8 +1,3 @@
-from cython cimport numeric
-from libcpp.vector cimport vector
-from libcpp.utility cimport pair
-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.
 # Author(s):       Vincent Rouvreau
@@ -12,6 +7,11 @@ import os
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+import os
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index b7047d4f..92ff6411 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -1,12 +1,3 @@
-from cython cimport numeric
-from libcpp.vector cimport vector
-from libcpp.utility cimport pair
-from libcpp.string cimport string
-from libcpp cimport bool
-import os
-
-import numpy as np
-
 # 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
@@ -16,6 +7,15 @@ import numpy as np
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libcpp.string cimport string
+from libcpp cimport bool
+import os
+
+import numpy as np
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/gudhi/euclidean_strong_witness_complex.pyx b/src/python/gudhi/euclidean_strong_witness_complex.pyx
index e3f451f0..9889f92c 100644
--- a/src/python/gudhi/euclidean_strong_witness_complex.pyx
+++ b/src/python/gudhi/euclidean_strong_witness_complex.pyx
@@ -1,11 +1,3 @@
-from cython cimport numeric
-from libcpp.vector cimport vector
-from libcpp.utility cimport pair
-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
@@ -15,6 +7,14 @@ from gudhi.simplex_tree import SimplexTree
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libc.stdint cimport intptr_t
+
+from gudhi.simplex_tree cimport *
+from gudhi.simplex_tree import SimplexTree
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
diff --git a/src/python/gudhi/euclidean_witness_complex.pyx b/src/python/gudhi/euclidean_witness_complex.pyx
index 84a8ea1a..e3ce0e82 100644
--- a/src/python/gudhi/euclidean_witness_complex.pyx
+++ b/src/python/gudhi/euclidean_witness_complex.pyx
@@ -1,11 +1,3 @@
-from cython cimport numeric
-from libcpp.vector cimport vector
-from libcpp.utility cimport pair
-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
@@ -15,6 +7,14 @@ from gudhi.simplex_tree import SimplexTree
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libc.stdint cimport intptr_t
+
+from gudhi.simplex_tree cimport *
+from gudhi.simplex_tree import SimplexTree
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
diff --git a/src/python/gudhi/nerve_gic.pyx b/src/python/gudhi/nerve_gic.pyx
index acb78564..68c06432 100644
--- a/src/python/gudhi/nerve_gic.pyx
+++ b/src/python/gudhi/nerve_gic.pyx
@@ -1,3 +1,12 @@
+# 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
+#
+# Modification(s):
+#   - YYYY/MM Author: Description of the modification
+
 from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
@@ -9,15 +18,6 @@ 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) 2018 Inria
-#
-# Modification(s):
-#   - YYYY/MM Author: Description of the modification
-
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2018 Inria"
 __license__ = "GPL v3"
diff --git a/src/python/gudhi/off_reader.pyx b/src/python/gudhi/off_reader.pyx
index 225e981c..54a275e2 100644
--- a/src/python/gudhi/off_reader.pyx
+++ b/src/python/gudhi/off_reader.pyx
@@ -1,8 +1,3 @@
-from cython cimport numeric
-from libcpp.vector cimport vector
-from libcpp.string cimport string
-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.
 # Author(s):       Vincent Rouvreau
@@ -12,6 +7,11 @@ import os
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.string cimport string
+import os
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx
index eb96ab5f..b5dece10 100644
--- a/src/python/gudhi/periodic_cubical_complex.pyx
+++ b/src/python/gudhi/periodic_cubical_complex.pyx
@@ -1,12 +1,3 @@
-from cython cimport numeric
-from libcpp.vector cimport vector
-from libcpp.utility cimport pair
-from libcpp.string cimport string
-from libcpp cimport bool
-import os
-
-import numpy as np
-
 # 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
@@ -16,6 +7,15 @@ import numpy as np
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libcpp.string cimport string
+from libcpp cimport bool
+import os
+
+import numpy as np
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py
index 7d232c85..246280de 100644
--- a/src/python/gudhi/persistence_graphical_tools.py
+++ b/src/python/gudhi/persistence_graphical_tools.py
@@ -1,10 +1,3 @@
-from os import path
-from math import isfinite
-import numpy as np
-
-from gudhi.reader_utils import read_persistence_intervals_in_dimension
-from gudhi.reader_utils import read_persistence_intervals_grouped_by_dimension
-
 # 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, Bertrand Michel
@@ -14,6 +7,13 @@ from gudhi.reader_utils import read_persistence_intervals_grouped_by_dimension
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from os import path
+from math import isfinite
+import numpy as np
+
+from gudhi.reader_utils import read_persistence_intervals_in_dimension
+from gudhi.reader_utils import read_persistence_intervals_grouped_by_dimension
+
 __author__ = "Vincent Rouvreau, Bertrand Michel"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/gudhi/reader_utils.pyx b/src/python/gudhi/reader_utils.pyx
index 6994c4f9..345c92f8 100644
--- a/src/python/gudhi/reader_utils.pyx
+++ b/src/python/gudhi/reader_utils.pyx
@@ -1,12 +1,3 @@
-from cython cimport numeric
-from libcpp.vector cimport vector
-from libcpp.string cimport string
-from libcpp.map cimport map
-from libcpp.pair cimport pair
-
-from os import path
-from numpy import array as np_array
-
 # 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
@@ -16,6 +7,15 @@ from numpy import array as np_array
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.string cimport string
+from libcpp.map cimport map
+from libcpp.pair cimport pair
+
+from os import path
+from numpy import array as np_array
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2017 Inria"
 __license__ = "MIT"
diff --git a/src/python/gudhi/rips_complex.pyx b/src/python/gudhi/rips_complex.pyx
index cbbbab0d..722cdcdc 100644
--- a/src/python/gudhi/rips_complex.pyx
+++ b/src/python/gudhi/rips_complex.pyx
@@ -1,3 +1,12 @@
+# 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
+
 from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
@@ -8,15 +17,6 @@ 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"
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 5f86cfe2..1066d44b 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -1,19 +1,18 @@
+# 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
+
 from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
 from libcpp cimport bool
 from libcpp.string cimport string
 
-""" 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"
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index 4a3cd9bc..85d25492 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -1,7 +1,3 @@
-from libc.stdint cimport intptr_t
-from numpy import array as np_array
-cimport simplex_tree
-
 # 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
@@ -11,6 +7,10 @@ cimport simplex_tree
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from libc.stdint cimport intptr_t
+from numpy import array as np_array
+cimport simplex_tree
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/gudhi/strong_witness_complex.pyx b/src/python/gudhi/strong_witness_complex.pyx
index 66d49b49..2c33c3f2 100644
--- a/src/python/gudhi/strong_witness_complex.pyx
+++ b/src/python/gudhi/strong_witness_complex.pyx
@@ -1,11 +1,3 @@
-from cython cimport numeric
-from libcpp.vector cimport vector
-from libcpp.utility cimport pair
-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
@@ -15,6 +7,14 @@ from gudhi.simplex_tree import SimplexTree
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libc.stdint cimport intptr_t
+
+from gudhi.simplex_tree cimport *
+from gudhi.simplex_tree import SimplexTree
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/gudhi/subsampling.pyx b/src/python/gudhi/subsampling.pyx
index e0cd1348..b1812087 100644
--- a/src/python/gudhi/subsampling.pyx
+++ b/src/python/gudhi/subsampling.pyx
@@ -1,9 +1,3 @@
-from cython cimport numeric
-from libcpp.vector cimport vector
-from libcpp.string cimport string
-from libcpp cimport bool
-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.
 # Author(s):       Vincent Rouvreau
@@ -13,6 +7,12 @@ import os
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.string cimport string
+from libcpp cimport bool
+import os
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
diff --git a/src/python/gudhi/tangential_complex.pyx b/src/python/gudhi/tangential_complex.pyx
index f4c8b079..0083033c 100644
--- a/src/python/gudhi/tangential_complex.pyx
+++ b/src/python/gudhi/tangential_complex.pyx
@@ -1,3 +1,12 @@
+# 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
+
 from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
@@ -9,15 +18,6 @@ import os
 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__ = "GPL v3"
diff --git a/src/python/gudhi/wasserstein.py b/src/python/gudhi/wasserstein.py
index d8a3104c..1906eeb1 100644
--- a/src/python/gudhi/wasserstein.py
+++ b/src/python/gudhi/wasserstein.py
@@ -1,10 +1,3 @@
-import numpy as np
-import scipy.spatial.distance as sc
-try:
-    import ot
-except ImportError:
-    print("POT (Python Optimal Transport) package is not installed. Try to run $ conda install -c conda-forge pot ; or $ pip install POT")
-
 # 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):       Theo Lacombe
@@ -14,6 +7,13 @@ except ImportError:
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+import numpy as np
+import scipy.spatial.distance as sc
+try:
+    import ot
+except ImportError:
+    print("POT (Python Optimal Transport) package is not installed. Try to run $ conda install -c conda-forge pot ; or $ pip install POT")
+
 def _proj_on_diag(X):
     '''
     :param X: (n x 2) array encoding the points of a persistent diagram.
diff --git a/src/python/gudhi/witness_complex.pyx b/src/python/gudhi/witness_complex.pyx
index 153fc615..b032a5a1 100644
--- a/src/python/gudhi/witness_complex.pyx
+++ b/src/python/gudhi/witness_complex.pyx
@@ -1,11 +1,3 @@
-from cython cimport numeric
-from libcpp.vector cimport vector
-from libcpp.utility cimport pair
-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
@@ -15,6 +7,14 @@ from gudhi.simplex_tree import SimplexTree
 # Modification(s):
 #   - YYYY/MM Author: Description of the modification
 
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libc.stdint cimport intptr_t
+
+from gudhi.simplex_tree cimport *
+from gudhi.simplex_tree import SimplexTree
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index 3f1d4424..24d05025 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -1,7 +1,3 @@
-from setuptools import setup, Extension
-from Cython.Build import cythonize
-from numpy import get_include as numpy_get_include
-
 """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
@@ -12,6 +8,10 @@ from numpy import get_include as numpy_get_include
      - YYYY/MM Author: Description of the modification
 """
 
+from setuptools import setup, Extension
+from Cython.Build import cythonize
+from numpy import get_include as numpy_get_include
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016  Inria"
 __license__ = "MIT"
diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py
index 9b27fff2..712a50b6 100755
--- a/src/python/test/test_alpha_complex.py
+++ b/src/python/test/test_alpha_complex.py
@@ -1,9 +1,3 @@
-from gudhi import AlphaComplex, SimplexTree
-import math
-import numpy as np
-import itertools
-import pytest
-
 """ 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
@@ -14,6 +8,12 @@ import pytest
       - YYYY/MM Author: Description of the modification
 """
 
+from gudhi import AlphaComplex, SimplexTree
+import math
+import numpy as np
+import itertools
+import pytest
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/test/test_bottleneck_distance.py b/src/python/test/test_bottleneck_distance.py
index f5f019b9..70b2abad 100755
--- a/src/python/test/test_bottleneck_distance.py
+++ b/src/python/test/test_bottleneck_distance.py
@@ -1,5 +1,3 @@
-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.
     Author(s):       Vincent Rouvreau
@@ -10,6 +8,8 @@ import gudhi
       - YYYY/MM Author: Description of the modification
 """
 
+import gudhi
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/test/test_cover_complex.py b/src/python/test/test_cover_complex.py
index 8cd12272..32bc5a26 100755
--- a/src/python/test/test_cover_complex.py
+++ b/src/python/test/test_cover_complex.py
@@ -1,5 +1,3 @@
-from gudhi import CoverComplex
-
 """ 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
@@ -10,6 +8,8 @@ from gudhi import CoverComplex
       - YYYY/MM Author: Description of the modification
 """
 
+from gudhi import CoverComplex
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2018 Inria"
 __license__ = "MIT"
diff --git a/src/python/test/test_cubical_complex.py b/src/python/test/test_cubical_complex.py
index 121da12a..8c1b2600 100755
--- a/src/python/test/test_cubical_complex.py
+++ b/src/python/test/test_cubical_complex.py
@@ -1,6 +1,3 @@
-from gudhi import CubicalComplex, PeriodicCubicalComplex
-import numpy as np
-
 """ 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
@@ -11,6 +8,9 @@ import numpy as np
       - YYYY/MM Author: Description of the modification
 """
 
+from gudhi import CubicalComplex, PeriodicCubicalComplex
+import numpy as np
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/test/test_euclidean_witness_complex.py b/src/python/test/test_euclidean_witness_complex.py
index f5eae5fa..c18d2484 100755
--- a/src/python/test/test_euclidean_witness_complex.py
+++ b/src/python/test/test_euclidean_witness_complex.py
@@ -1,5 +1,3 @@
-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.
     Author(s):       Vincent Rouvreau
@@ -10,6 +8,8 @@ import gudhi
       - YYYY/MM Author: Description of the modification
 """
 
+import gudhi
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/test/test_reader_utils.py b/src/python/test/test_reader_utils.py
index 4c7b32c2..90da6651 100755
--- a/src/python/test/test_reader_utils.py
+++ b/src/python/test/test_reader_utils.py
@@ -1,6 +1,3 @@
-import gudhi
-import numpy as np
-
 """ 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
@@ -11,6 +8,9 @@ import numpy as np
       - YYYY/MM Author: Description of the modification
 """
 
+import gudhi
+import numpy as np
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2017 Inria"
 __license__ = "MIT"
diff --git a/src/python/test/test_representations.py b/src/python/test/test_representations.py
index 4ff65f98..dba7f952 100755
--- a/src/python/test/test_representations.py
+++ b/src/python/test/test_representations.py
@@ -1,11 +1,12 @@
 import os
 import sys
 import matplotlib.pyplot as plt
-# Disable graphics for testing purposes
-plt.show = lambda:None
-here = os.path.dirname(os.path.realpath(__file__))
-sys.path.append(here + "/../example")
-import diagram_vectorizations_distances_kernels
-# pytest is unhappy if there are 0 tests
-def test_nothing():
+
+def test_representations_examples():
+    # Disable graphics for testing purposes
+    plt.show = lambda:None
+    here = os.path.dirname(os.path.realpath(__file__))
+    sys.path.append(here + "/../example")
+    import diagram_vectorizations_distances_kernels
+
     return None
diff --git a/src/python/test/test_rips_complex.py b/src/python/test/test_rips_complex.py
index d55ae22f..b02a68e1 100755
--- a/src/python/test/test_rips_complex.py
+++ b/src/python/test/test_rips_complex.py
@@ -1,6 +1,3 @@
-from gudhi import RipsComplex
-from math import sqrt
-
 """ 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
@@ -11,6 +8,9 @@ from math import sqrt
       - YYYY/MM Author: Description of the modification
 """
 
+from gudhi import RipsComplex
+from math import sqrt
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py
index 8d8971c1..1822c43b 100755
--- a/src/python/test/test_simplex_tree.py
+++ b/src/python/test/test_simplex_tree.py
@@ -1,5 +1,3 @@
-from gudhi 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
@@ -10,6 +8,8 @@ from gudhi import SimplexTree
       - YYYY/MM Author: Description of the modification
 """
 
+from gudhi import SimplexTree
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/test/test_subsampling.py b/src/python/test/test_subsampling.py
index c816e203..fe0985fa 100755
--- a/src/python/test/test_subsampling.py
+++ b/src/python/test/test_subsampling.py
@@ -1,5 +1,3 @@
-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.
     Author(s):       Vincent Rouvreau
@@ -10,6 +8,8 @@ import gudhi
       - YYYY/MM Author: Description of the modification
 """
 
+import gudhi
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/test/test_tangential_complex.py b/src/python/test/test_tangential_complex.py
index 0f828d8e..e650e99c 100755
--- a/src/python/test/test_tangential_complex.py
+++ b/src/python/test/test_tangential_complex.py
@@ -1,5 +1,3 @@
-from gudhi import TangentialComplex, 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
@@ -10,6 +8,8 @@ from gudhi import TangentialComplex, SimplexTree
       - YYYY/MM Author: Description of the modification
 """
 
+from gudhi import TangentialComplex, SimplexTree
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
diff --git a/src/python/test/test_wasserstein_distance.py b/src/python/test/test_wasserstein_distance.py
index a6bf9901..bb59b3c2 100755
--- a/src/python/test/test_wasserstein_distance.py
+++ b/src/python/test/test_wasserstein_distance.py
@@ -1,6 +1,3 @@
-from gudhi.wasserstein import wasserstein_distance
-import numpy as np
-
 """ 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):       Theo Lacombe
@@ -11,6 +8,9 @@ import numpy as np
       - YYYY/MM Author: Description of the modification
 """
 
+from gudhi.wasserstein import wasserstein_distance
+import numpy as np
+
 __author__ = "Theo Lacombe"
 __copyright__ = "Copyright (C) 2019 Inria"
 __license__ = "MIT"
diff --git a/src/python/test/test_witness_complex.py b/src/python/test/test_witness_complex.py
index 36ced635..7baf18c9 100755
--- a/src/python/test/test_witness_complex.py
+++ b/src/python/test/test_witness_complex.py
@@ -1,5 +1,3 @@
-from gudhi import WitnessComplex, StrongWitnessComplex, 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
@@ -10,6 +8,8 @@ from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree
       - YYYY/MM Author: Description of the modification
 """
 
+from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
-- 
cgit v1.2.3


From d747facccbe835be1384e569cf3d6e4c335c0364 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Wed, 15 Jan 2020 10:23:58 +0100
Subject: In python2,  does not work.  is ok for Python 2 and 3

---
 src/python/gudhi/alpha_complex.pyx            |  2 +-
 src/python/gudhi/cubical_complex.pyx          |  2 +-
 src/python/gudhi/nerve_gic.pyx                | 12 ++++++------
 src/python/gudhi/off_reader.pyx               |  2 +-
 src/python/gudhi/periodic_cubical_complex.pyx |  2 +-
 src/python/gudhi/reader_utils.pyx             |  8 ++++----
 src/python/gudhi/simplex_tree.pyx             |  2 +-
 src/python/gudhi/subsampling.pyx              |  8 ++++----
 src/python/gudhi/tangential_complex.pyx       |  2 +-
 9 files changed, 20 insertions(+), 20 deletions(-)

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

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:
-- 
cgit v1.2.3