From b5510c0c362cd2bef79d82fd9809e654aea73957 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Mon, 16 Dec 2019 23:10:24 +0100
Subject: Add numpy ndarray to init a cubical and a periodic one

---
 src/python/gudhi/cubical_complex.pyx | 27 +++++++++++++++++++++------
 1 file changed, 21 insertions(+), 6 deletions(-)

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

diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index 011c407c..2ec0146a 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -5,7 +5,7 @@ from libcpp.string cimport string
 from libcpp cimport bool
 import os
 
-from numpy import array as np_array
+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.
@@ -47,7 +47,7 @@ cdef class CubicalComplex:
 
     # Fake constructor that does nothing but documenting the constructor
     def __init__(self, dimensions=None, top_dimensional_cells=None,
-                  perseus_file=''):
+                 numpy_array=None, perseus_file=''):
         """CubicalComplex constructor from dimensions and
         top_dimensional_cells or from a Perseus-style file name.
 
@@ -58,16 +58,31 @@ cdef class CubicalComplex:
 
         Or
 
+        :param numpy_array: Filtration values in a d-array.
+        :type numpy_array: numpy ndarray
+
+        Or
+
         :param perseus_file: A Perseus-style file name.
         :type perseus_file: string
         """
 
     # The real cython constructor
     def __cinit__(self, dimensions=None, top_dimensional_cells=None,
-                  perseus_file=''):
-        if (dimensions is not None) and (top_dimensional_cells is not None) and (perseus_file == ''):
+                  numpy_array=None, perseus_file=''):
+        if ((dimensions is not None) and (top_dimensional_cells is not None)
+            and (numpy_array is None) and (perseus_file == '')):
             self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
-        elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file != ''):
+        elif ((dimensions is None) and (top_dimensional_cells is None)
+            and (numpy_array is not None) and (perseus_file == '')):
+            if isinstance(numpy_array, np.ndarray):
+                dimensions = list(numpy_array.shape)
+                top_dimensional_cells = numpy_array.flatten().tolist()
+                self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
+            else:
+                print("numpy_array is not an instance of ndarray. It is a " + type(numpy_array))
+        elif ((dimensions is None) and (top_dimensional_cells is None)
+            and (numpy_array is None) and (perseus_file != '')):
             if os.path.isfile(perseus_file):
                 self.thisptr = new Bitmap_cubical_complex_base_interface(str.encode(perseus_file))
             else:
@@ -184,4 +199,4 @@ cdef class CubicalComplex:
         else:
             print("intervals_in_dim function requires persistence function"
                   " to be launched first.")
-        return np_array(intervals_result)
+        return np.array(intervals_result)
-- 
cgit v1.2.3


From b63be266effe24646823acc59fe397021bb13a3e Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Wed, 18 Dec 2019 10:44:17 +0100
Subject: Reuse top_dimensional_cells instead of numpy_array argument to create
 a cubical

---
 src/python/doc/cubical_complex_user.rst       |  2 +-
 src/python/gudhi/cubical_complex.pyx          | 25 ++++++++++---------
 src/python/gudhi/periodic_cubical_complex.pyx | 35 +++++++++++++--------------
 src/python/test/test_cubical_complex.py       | 12 ++++-----
 4 files changed, 37 insertions(+), 37 deletions(-)

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

diff --git a/src/python/doc/cubical_complex_user.rst b/src/python/doc/cubical_complex_user.rst
index 21806038..d56c8789 100644
--- a/src/python/doc/cubical_complex_user.rst
+++ b/src/python/doc/cubical_complex_user.rst
@@ -143,7 +143,7 @@ Or it can be defined as follows:
 
     from gudhi import PeriodicCubicalComplex as pcc
     from numpy import array as np_array
-    periodic_cc = pcc(numpy_array = np_array([[0, 0, 0], [0, 1, 0], [0, 0, 0]]),
+    periodic_cc = pcc(top_dimensional_cells = np_array([[0, 0, 0], [0, 1, 0], [0, 0, 0]]),
          periodic_dimensions=[True, False])
     result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \
         repr(periodic_cc.num_simplices()) + ' simplices.'
diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index 2ec0146a..1aa1164c 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -47,7 +47,7 @@ cdef class CubicalComplex:
 
     # Fake constructor that does nothing but documenting the constructor
     def __init__(self, dimensions=None, top_dimensional_cells=None,
-                 numpy_array=None, perseus_file=''):
+                 perseus_file=''):
         """CubicalComplex constructor from dimensions and
         top_dimensional_cells or from a Perseus-style file name.
 
@@ -58,8 +58,9 @@ cdef class CubicalComplex:
 
         Or
 
-        :param numpy_array: Filtration values in a d-array.
-        :type numpy_array: numpy ndarray
+        :param top_dimensional_cells: A multidimensional array of cells
+            filtration values.
+        :type top_dimensional_cells: numpy ndarray
 
         Or
 
@@ -69,20 +70,20 @@ cdef class CubicalComplex:
 
     # The real cython constructor
     def __cinit__(self, dimensions=None, top_dimensional_cells=None,
-                  numpy_array=None, perseus_file=''):
+                  perseus_file=''):
         if ((dimensions is not None) and (top_dimensional_cells is not None)
-            and (numpy_array is None) and (perseus_file == '')):
+            and (perseus_file == '')):
             self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
-        elif ((dimensions is None) and (top_dimensional_cells is None)
-            and (numpy_array is not None) and (perseus_file == '')):
-            if isinstance(numpy_array, np.ndarray):
-                dimensions = list(numpy_array.shape)
-                top_dimensional_cells = numpy_array.flatten().tolist()
+        elif ((dimensions is None) and (top_dimensional_cells is not None)
+            and (perseus_file == '')):
+            if isinstance(top_dimensional_cells, np.ndarray):
+                dimensions = list(top_dimensional_cells.shape)
+                top_dimensional_cells = top_dimensional_cells.flatten().tolist()
                 self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
             else:
-                print("numpy_array is not an instance of ndarray. It is a " + type(numpy_array))
+                print("top_dimensional_cells is not an instance of ndarray. It is a " + type(top_dimensional_cells))
         elif ((dimensions is None) and (top_dimensional_cells is None)
-            and (numpy_array is None) and (perseus_file != '')):
+            and (perseus_file != '')):
             if os.path.isfile(perseus_file):
                 self.thisptr = new Bitmap_cubical_complex_base_interface(str.encode(perseus_file))
             else:
diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx
index 8318b7d3..e623058a 100644
--- a/src/python/gudhi/periodic_cubical_complex.pyx
+++ b/src/python/gudhi/periodic_cubical_complex.pyx
@@ -47,7 +47,7 @@ cdef class PeriodicCubicalComplex:
 
     # Fake constructor that does nothing but documenting the constructor
     def __init__(self, dimensions=None, top_dimensional_cells=None,
-                 numpy_array=None, periodic_dimensions=None, perseus_file=''):
+                 periodic_dimensions=None, perseus_file=''):
         """PeriodicCubicalComplex constructor from dimensions and
         top_dimensional_cells or from a Perseus-style file name.
 
@@ -60,8 +60,9 @@ cdef class PeriodicCubicalComplex:
 
         Or
 
-        :param numpy_array: Filtration values in a d-array.
-        :type numpy_array: numpy ndarray
+        :param top_dimensional_cells: A multidimensional array of cells
+            filtration values.
+        :type top_dimensional_cells: numpy ndarray
         :param periodic_dimensions: A list of top dimensional cells periodicity value.
         :type periodic_dimensions: list of boolean
 
@@ -73,35 +74,33 @@ cdef class PeriodicCubicalComplex:
 
     # The real cython constructor
     def __cinit__(self, dimensions=None, top_dimensional_cells=None,
-                  numpy_array=None, periodic_dimensions=None,
-                  perseus_file=''):
+                  periodic_dimensions=None, perseus_file=''):
         if ((dimensions is not None) and (top_dimensional_cells is not None)
-            and (numpy_array is None) and (periodic_dimensions is not None)
-            and (perseus_file == '')):
+            and (periodic_dimensions is not None) and (perseus_file == '')):
             self.thisptr = new Periodic_cubical_complex_base_interface(dimensions,
                                                                        top_dimensional_cells,
                                                                        periodic_dimensions)
-        elif ((dimensions is None) and (top_dimensional_cells is None)
-            and (numpy_array is not None) and (periodic_dimensions is not None)
-            and (perseus_file == '')):
-            if isinstance(numpy_array, np.ndarray):
-                dimensions = list(numpy_array.shape)
-                top_dimensional_cells = numpy_array.flatten().tolist()
+        elif ((dimensions is None) and (top_dimensional_cells is not None)
+            and (periodic_dimensions is not None) and (perseus_file == '')):
+            if isinstance(top_dimensional_cells, np.ndarray):
+                dimensions = list(top_dimensional_cells.shape)
+                top_dimensional_cells = top_dimensional_cells.flatten().tolist()
                 self.thisptr = new Periodic_cubical_complex_base_interface(dimensions,
                                                                            top_dimensional_cells,
                                                                            periodic_dimensions)
             else:
-                print("numpy_array is not an instance of ndarray. It is a " + type(numpy_array))
+                print("top_dimensional_cells is not an instance of ndarray. It is a " + type(top_dimensional_cells))
         elif ((dimensions is None) and (top_dimensional_cells is None)
-            and (numpy_array is None) and (periodic_dimensions is None)
-            and (perseus_file != '')):
+            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))
             else:
                 print("file " + perseus_file + " not found.")
         else:
-            print("CubicalComplex can be constructed from dimensions and "
-              "top_dimensional_cells or from a Perseus-style file name.")
+            print("CubicalComplex can be constructed from dimensions, "
+              "top_dimensional_cells and periodic_dimensions, or from "
+              "top_dimensional_cells and periodic_dimensions or from "
+              "a Perseus-style file name.")
 
     def __dealloc__(self):
         if self.thisptr != NULL:
diff --git a/src/python/test/test_cubical_complex.py b/src/python/test/test_cubical_complex.py
index a37d7821..6d4e0309 100755
--- a/src/python/test/test_cubical_complex.py
+++ b/src/python/test/test_cubical_complex.py
@@ -77,9 +77,9 @@ def test_simple_constructor_from_top_cells():
 
 def test_simple_constructor_from_numpy_array():
     cub = CubicalComplex(
-        numpy_array=np.array([[1, 2, 3],
-                              [4, 5, 6],
-                              [7, 8, 9]])
+        top_dimensional_cells=np.array([[1, 2, 3],
+                                        [4, 5, 6],
+                                        [7, 8, 9]])
     )
     simple_constructor(cub)
 
@@ -103,9 +103,9 @@ def test_user_case_simple_constructor_from_top_cells():
 
 def test_user_case_simple_constructor_from_numpy_array():
     cub = CubicalComplex(
-        numpy_array=np.array([[float("inf"), 0.0, 0.0],
-                              [0.0, 1.0, 0.0],
-                              [0.0, 0.0, 0.0]])
+        top_dimensional_cells=np.array([[float("inf"), 0.0, 0.0],
+                                        [0.0, 1.0, 0.0],
+                                        [0.0, 0.0, 0.0]])
     )
     user_case_simple_constructor(cub)
 
-- 
cgit v1.2.3


From 32a9c5e4df26e59f5f376e54c05c7bec92012cff Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Wed, 18 Dec 2019 10:57:31 +0100
Subject: use ravel instead of flatten (that makes a copy) and no more
 converting to a list

---
 src/python/gudhi/cubical_complex.pyx          | 4 ++--
 src/python/gudhi/periodic_cubical_complex.pyx | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

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

diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index 1aa1164c..756a9dab 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -77,8 +77,8 @@ cdef class CubicalComplex:
         elif ((dimensions is None) and (top_dimensional_cells is not None)
             and (perseus_file == '')):
             if isinstance(top_dimensional_cells, np.ndarray):
-                dimensions = list(top_dimensional_cells.shape)
-                top_dimensional_cells = top_dimensional_cells.flatten().tolist()
+                dimensions = top_dimensional_cells.shape
+                top_dimensional_cells = top_dimensional_cells.ravel(order='C')
                 self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
             else:
                 print("top_dimensional_cells is not an instance of ndarray. It is a " + type(top_dimensional_cells))
diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx
index e623058a..c3d64123 100644
--- a/src/python/gudhi/periodic_cubical_complex.pyx
+++ b/src/python/gudhi/periodic_cubical_complex.pyx
@@ -83,8 +83,8 @@ cdef class PeriodicCubicalComplex:
         elif ((dimensions is None) and (top_dimensional_cells is not None)
             and (periodic_dimensions is not None) and (perseus_file == '')):
             if isinstance(top_dimensional_cells, np.ndarray):
-                dimensions = list(top_dimensional_cells.shape)
-                top_dimensional_cells = top_dimensional_cells.flatten().tolist()
+                dimensions = top_dimensional_cells.shape
+                top_dimensional_cells = top_dimensional_cells.ravel(order='C')
                 self.thisptr = new Periodic_cubical_complex_base_interface(dimensions,
                                                                            top_dimensional_cells,
                                                                            periodic_dimensions)
-- 
cgit v1.2.3


From ba406558f707f55b638be92d197ae3039595b29a Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Fri, 20 Dec 2019 16:57:36 +0100
Subject: Fix dimension cell linearization and test connected sublevel sets

---
 src/python/gudhi/cubical_complex.pyx          |  2 +-
 src/python/gudhi/periodic_cubical_complex.pyx |  2 +-
 src/python/test/test_cubical_complex.py       | 28 ++++++++++++++++++++++++++-
 3 files changed, 29 insertions(+), 3 deletions(-)

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

diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index 756a9dab..04b22921 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -78,7 +78,7 @@ cdef class CubicalComplex:
             and (perseus_file == '')):
             if isinstance(top_dimensional_cells, np.ndarray):
                 dimensions = top_dimensional_cells.shape
-                top_dimensional_cells = top_dimensional_cells.ravel(order='C')
+                top_dimensional_cells = top_dimensional_cells.ravel(order='F')
                 self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
             else:
                 print("top_dimensional_cells is not an instance of ndarray. It is a " + type(top_dimensional_cells))
diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx
index c3d64123..1d6f1e59 100644
--- a/src/python/gudhi/periodic_cubical_complex.pyx
+++ b/src/python/gudhi/periodic_cubical_complex.pyx
@@ -84,7 +84,7 @@ cdef class PeriodicCubicalComplex:
             and (periodic_dimensions is not None) and (perseus_file == '')):
             if isinstance(top_dimensional_cells, np.ndarray):
                 dimensions = top_dimensional_cells.shape
-                top_dimensional_cells = top_dimensional_cells.ravel(order='C')
+                top_dimensional_cells = top_dimensional_cells.ravel(order='F')
                 self.thisptr = new Periodic_cubical_complex_base_interface(dimensions,
                                                                            top_dimensional_cells,
                                                                            periodic_dimensions)
diff --git a/src/python/test/test_cubical_complex.py b/src/python/test/test_cubical_complex.py
index 6d4e0309..121da12a 100755
--- a/src/python/test/test_cubical_complex.py
+++ b/src/python/test/test_cubical_complex.py
@@ -1,4 +1,4 @@
-from gudhi import CubicalComplex
+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.
@@ -121,3 +121,29 @@ def test_dimension_file_constructor():
     assert cub.__is_persistence_defined() == True
     assert cub.betti_numbers() == [1, 0, 0]
     assert cub.persistent_betti_numbers(0, 1000) == [1, 0, 0]
+
+def test_connected_sublevel_sets():
+    array_cells = np.array([[3, 3], [2, 2], [4, 4]])
+    linear_cells = [3, 3, 2, 2, 4, 4]
+    dimensions = [2, 3]
+    periodic_dimensions = [False, False]
+    # with a numpy array version
+    cub = CubicalComplex(top_dimensional_cells = array_cells)
+    assert cub.persistence() == [(0, (2.0, float("inf")))]
+    assert cub.betti_numbers() == [1, 0, 0]
+    # with vector of dimensions
+    cub = CubicalComplex(dimensions = dimensions,
+                         top_dimensional_cells = linear_cells)
+    assert cub.persistence() == [(0, (2.0, float("inf")))]
+    assert cub.betti_numbers() == [1, 0, 0]
+    # periodic with a numpy array version
+    cub = PeriodicCubicalComplex(top_dimensional_cells = array_cells,
+                                periodic_dimensions = periodic_dimensions)
+    assert cub.persistence() == [(0, (2.0, float("inf")))]
+    assert cub.betti_numbers() == [1, 0, 0]
+    # periodic with vector of dimensions
+    cub = PeriodicCubicalComplex(dimensions = dimensions,
+                                 top_dimensional_cells = linear_cells,
+                                 periodic_dimensions = periodic_dimensions)
+    assert cub.persistence() == [(0, (2.0, float("inf")))]
+    assert cub.betti_numbers() == [1, 0, 0]
-- 
cgit v1.2.3


From d832d3585bf47c48f28d861469730fc47f4956c8 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Tue, 7 Jan 2020 12:24:45 +0100
Subject: Code review: less strict with numpy arrays for cubical ctors. Also
 accept lists

---
 src/python/gudhi/cubical_complex.pyx          | 14 +++++++-------
 src/python/gudhi/periodic_cubical_complex.pyx | 18 +++++++++---------
 2 files changed, 16 insertions(+), 16 deletions(-)

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

diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index 04b22921..63911478 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -60,7 +60,7 @@ cdef class CubicalComplex:
 
         :param top_dimensional_cells: A multidimensional array of cells
             filtration values.
-        :type top_dimensional_cells: numpy ndarray
+        :type top_dimensional_cells: numpy ndarray or list of list of double
 
         Or
 
@@ -76,12 +76,12 @@ cdef class CubicalComplex:
             self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
         elif ((dimensions is None) and (top_dimensional_cells is not None)
             and (perseus_file == '')):
-            if isinstance(top_dimensional_cells, np.ndarray):
-                dimensions = top_dimensional_cells.shape
-                top_dimensional_cells = top_dimensional_cells.ravel(order='F')
-                self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
-            else:
-                print("top_dimensional_cells is not an instance of ndarray. It is a " + type(top_dimensional_cells))
+            top_dimensional_cells = np.array(top_dimensional_cells,
+                                             copy = False,
+                                             order = 'F')
+            dimensions = top_dimensional_cells.shape
+            top_dimensional_cells = top_dimensional_cells.ravel(order='F')
+            self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
         elif ((dimensions is None) and (top_dimensional_cells is None)
             and (perseus_file != '')):
             if os.path.isfile(perseus_file):
diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx
index 1d6f1e59..3c0f529b 100644
--- a/src/python/gudhi/periodic_cubical_complex.pyx
+++ b/src/python/gudhi/periodic_cubical_complex.pyx
@@ -62,7 +62,7 @@ cdef class PeriodicCubicalComplex:
 
         :param top_dimensional_cells: A multidimensional array of cells
             filtration values.
-        :type top_dimensional_cells: numpy ndarray
+        :type top_dimensional_cells: numpy ndarray or list of list of double
         :param periodic_dimensions: A list of top dimensional cells periodicity value.
         :type periodic_dimensions: list of boolean
 
@@ -82,14 +82,14 @@ cdef class PeriodicCubicalComplex:
                                                                        periodic_dimensions)
         elif ((dimensions is None) and (top_dimensional_cells is not None)
             and (periodic_dimensions is not None) and (perseus_file == '')):
-            if isinstance(top_dimensional_cells, np.ndarray):
-                dimensions = top_dimensional_cells.shape
-                top_dimensional_cells = top_dimensional_cells.ravel(order='F')
-                self.thisptr = new Periodic_cubical_complex_base_interface(dimensions,
-                                                                           top_dimensional_cells,
-                                                                           periodic_dimensions)
-            else:
-                print("top_dimensional_cells is not an instance of ndarray. It is a " + type(top_dimensional_cells))
+            top_dimensional_cells = np.array(top_dimensional_cells,
+                                             copy = False,
+                                             order = 'F')
+            dimensions = top_dimensional_cells.shape
+            top_dimensional_cells = top_dimensional_cells.ravel(order='F')
+            self.thisptr = new Periodic_cubical_complex_base_interface(dimensions,
+                                                                       top_dimensional_cells,
+                                                                       periodic_dimensions)
         elif ((dimensions is None) and (top_dimensional_cells is None)
             and (periodic_dimensions is None) and (perseus_file != '')):
             if os.path.isfile(perseus_file):
-- 
cgit v1.2.3


From 6a7a7b6d6d81946dd903f68f525389ab2fd51f71 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Tue, 7 Jan 2020 13:31:18 +0100
Subject: Doc review: anything convertible to a numpy ndarray

---
 src/python/gudhi/cubical_complex.pyx          | 2 +-
 src/python/gudhi/periodic_cubical_complex.pyx | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

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

diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index 63911478..b7047d4f 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -60,7 +60,7 @@ cdef class CubicalComplex:
 
         :param top_dimensional_cells: A multidimensional array of cells
             filtration values.
-        :type top_dimensional_cells: numpy ndarray or list of list of double
+        :type top_dimensional_cells: anything convertible to a numpy ndarray
 
         Or
 
diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx
index 3c0f529b..eb96ab5f 100644
--- a/src/python/gudhi/periodic_cubical_complex.pyx
+++ b/src/python/gudhi/periodic_cubical_complex.pyx
@@ -62,7 +62,7 @@ cdef class PeriodicCubicalComplex:
 
         :param top_dimensional_cells: A multidimensional array of cells
             filtration values.
-        :type top_dimensional_cells: numpy ndarray or list of list of double
+        :type top_dimensional_cells: anything convertible to a numpy ndarray
         :param periodic_dimensions: A list of top dimensional cells periodicity value.
         :type periodic_dimensions: list of boolean
 
-- 
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/cubical_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/cubical_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:
-- 
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