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

48 files changed, 394 insertions, 293 deletions

diff --git a/src/python/doc/alpha_complex_sum.inc b/src/python/doc/alpha_complex_sum.inc
index c5ba9dc7..a1184663 100644
--- a/src/python/doc/alpha_complex_sum.inc
+++ b/src/python/doc/alpha_complex_sum.inc
@@ -9,9 +9,9 @@
    |                                                                | circumradius of the simplex if the circumsphere is empty (the simplex  | :Copyright: MIT (`GPL v3 </licensing/>`_)                                                                                   |
    |                                                                | is then said to be Gabriel), and as the minimum of the filtration      |                                                                                                                             |
    |                                                                | values of the codimension 1 cofaces that make it not Gabriel           | :Requires: `Eigen <installation.html#eigen>`__ :math:`\geq` 3.1.0 and `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 |
-   |                                                                | otherwise. All simplices that have a filtration value strictly         |                                                                                                                             |
-   |                                                                | greater than a given alpha squared value are not inserted into the     |                                                                                                                             |
-   |                                                                | complex.                                                               |                                                                                                                             |
+   |                                                                | otherwise. All simplices that have a filtration value                  |                                                                                                                             |
+   |                                                                | :math:`> \alpha^2` are removed from the Delaunay complex               |                                                                                                                             |
+   |                                                                | when creating the simplicial complex if it is specified.               |                                                                                                                             |
    |                                                                |                                                                        |                                                                                                                             |
    |                                                                | This package requires having CGAL version 4.7 or higher (4.8.1 is      |                                                                                                                             |
    |                                                                | advised for better performance).                                       |                                                                                                                             |
diff --git a/src/python/doc/alpha_complex_user.rst b/src/python/doc/alpha_complex_user.rst
index b7e69e12..60319e84 100644
--- a/src/python/doc/alpha_complex_user.rst
+++ b/src/python/doc/alpha_complex_user.rst
@@ -16,7 +16,8 @@ Definition
 
 Remarks
 ^^^^^^^
-When an :math:`\alpha`-complex is constructed with an infinite value of :math:`\alpha`, the complex is a Delaunay complex (with special filtration values).
+When an :math:`\alpha`-complex is constructed with an infinite value of :math:`\alpha^2`,
+the complex is a Delaunay complex (with special filtration values).
 
 Example from points
 -------------------
@@ -137,19 +138,20 @@ sets the filtration value (0 in case of a vertex - propagation will have no effe
 Non decreasing filtration values
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-As the squared radii computed by CGAL are an approximation, it might happen that these alpha squared values do not
-quite define a proper filtration (i.e. non-decreasing with respect to inclusion).
+As the squared radii computed by CGAL are an approximation, it might happen that these
+:math:`\alpha^2` values do not quite define a proper filtration (i.e. non-decreasing with
+respect to inclusion).
 We fix that up by calling :func:`~gudhi.SimplexTree.make_filtration_non_decreasing` (cf.
 `C++ version <http://gudhi.gforge.inria.fr/doc/latest/index.html>`_).
 
 Prune above given filtration value
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The simplex tree is pruned from the given maximum alpha squared value (cf.
+The simplex tree is pruned from the given maximum :math:`\alpha^2` value (cf.
 :func:`~gudhi.SimplexTree.prune_above_filtration`). Note that this does not provide any kind
 of speed-up, since we always first build the full filtered complex, so it is recommended not to use
 :paramref:`~gudhi.AlphaComplex.create_simplex_tree.max_alpha_square`.
-In the following example, a threshold of 59 is used.
+In the following example, a threshold of :math:`\alpha^2 = 32.0` is used.
 
 
 Example from OFF file
@@ -166,7 +168,7 @@ Then, it is asked to display information about the alpha complex:
     import gudhi
     alpha_complex = gudhi.AlphaComplex(off_file=gudhi.__root_source_dir__ + \
         '/data/points/alphacomplexdoc.off')
-    simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=59.0)
+    simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=32.0)
     result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
@@ -179,7 +181,7 @@ the program output is:
 
 .. testoutput::
 
-   Alpha complex is of dimension 2 - 23 simplices - 7 vertices.
+   Alpha complex is of dimension 2 - 20 simplices - 7 vertices.
    [0] -> 0.00
    [1] -> 0.00
    [2] -> 0.00
@@ -200,9 +202,6 @@ the program output is:
    [4, 6] -> 22.74
    [4, 5, 6] -> 22.74
    [3, 6] -> 30.25
-   [2, 6] -> 36.50
-   [2, 3, 6] -> 36.50
-   [2, 4, 6] -> 37.24
 
 CGAL citations
 ==============
diff --git a/src/python/doc/cubical_complex_user.rst b/src/python/doc/cubical_complex_user.rst
index b13b500e..56cf0170 100644
--- a/src/python/doc/cubical_complex_user.rst
+++ b/src/python/doc/cubical_complex_user.rst
@@ -142,8 +142,7 @@ Or it can be defined as follows:
 .. testcode::
 
     from gudhi import PeriodicCubicalComplex as pcc
-    periodic_cc = pcc(dimensions=[3,3],
-         top_dimensional_cells= [0, 0, 0, 0, 1, 0, 0, 0, 0],
+    periodic_cc = pcc(top_dimensional_cells = [[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/doc/installation.rst b/src/python/doc/installation.rst
index 50a697c7..40f3f44b 100644
--- a/src/python/doc/installation.rst
+++ b/src/python/doc/installation.rst
@@ -257,6 +257,13 @@ The :doc:`Wasserstein distance </wasserstein_distance_user>`
 module requires `POT <https://pot.readthedocs.io/>`_, a library that provides
 several solvers for optimization problems related to Optimal Transport.
 
+Scikit-learn
+============
+
+The :doc:`persistence representations </representations>` module require
+`scikit-learn <https://scikit-learn.org/>`_, a Python-based ecosystem of
+open-source software for machine learning.
+
 SciPy
 =====
 
diff --git a/src/python/doc/persistence_graphical_tools_user.rst b/src/python/doc/persistence_graphical_tools_user.rst
index f41a926b..80002db6 100644
--- a/src/python/doc/persistence_graphical_tools_user.rst
+++ b/src/python/doc/persistence_graphical_tools_user.rst
@@ -24,7 +24,7 @@ This function can display the persistence result as a barcode:
     import gudhi
 
     off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off'
-    point_cloud = gudhi.read_off(off_file=off_file)
+    point_cloud = gudhi.read_points_from_off_file(off_file=off_file)
 
     rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.7)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
diff --git a/src/python/doc/point_cloud.rst b/src/python/doc/point_cloud.rst
index 6a74d253..d668428a 100644
--- a/src/python/doc/point_cloud.rst
+++ b/src/python/doc/point_cloud.rst
@@ -9,7 +9,7 @@ Point cloud utilities manual
 File Readers
 ------------
 
-.. autofunction:: gudhi.read_off
+.. autofunction:: gudhi.read_points_from_off_file
 
 .. autofunction:: gudhi.read_lower_triangular_matrix_from_csv_file
 
diff --git a/src/python/doc/rips_complex_user.rst b/src/python/doc/rips_complex_user.rst
index a8659542..a27573e8 100644
--- a/src/python/doc/rips_complex_user.rst
+++ b/src/python/doc/rips_complex_user.rst
@@ -136,7 +136,8 @@ Finally, it is asked to display information about the Rips complex.
 .. testcode::
 
     import gudhi
-    point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/alphacomplexdoc.off')
+    off_file = gudhi.__root_source_dir__ + '/data/points/alphacomplexdoc.off'
+    point_cloud = gudhi.read_points_from_off_file(off_file = off_file)
     rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=12.0)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
     result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
diff --git a/src/python/doc/wasserstein_distance_sum.inc b/src/python/doc/wasserstein_distance_sum.inc
index ffd4d312..a97f428d 100644
--- a/src/python/doc/wasserstein_distance_sum.inc
+++ b/src/python/doc/wasserstein_distance_sum.inc
@@ -2,12 +2,12 @@
    :widths: 30 50 20
 
    +-----------------------------------------------------------------+----------------------------------------------------------------------+------------------------------------------------------------------+
-   | .. figure::                                                     | The p-Wasserstein distance measures the similarity between two       | :Author: Theo Lacombe                                            |
+   | .. figure::                                                     | The q-Wasserstein distance measures the similarity between two       | :Author: Theo Lacombe                                            |
    |      ../../doc/Bottleneck_distance/perturb_pd.png               | persistence diagrams. It's the minimum value c that can be achieved  |                                                                  |
    |      :figclass: align-center                                    | by a perfect matching between the points of the two diagrams (+ all  | :Introduced in: GUDHI 3.1.0                                      |
    |                                                                 | diagonal points), where the value of a matching is defined as the    |                                                                  |
-   |      Wasserstein distance is the p-th root of the sum of the    | p-th root of the sum of all edge lengths to the power p. Edge lengths| :Copyright: MIT                                                  |
-   |      edge lengths to the power p.                               | are measured in norm q, for :math:`1 \leq q \leq \infty`.            |                                                                  |
+   |      Wasserstein distance is the q-th root of the sum of the    | q-th root of the sum of all edge lengths to the power q. Edge lengths| :Copyright: MIT                                                  |
+   |      edge lengths to the power q.                               | are measured in norm p, for :math:`1 \leq p \leq \infty`.            |                                                                  |
    |                                                                 |                                                                      | :Requires: Python Optimal Transport (POT) :math:`\geq` 0.5.1     |
    +-----------------------------------------------------------------+----------------------------------------------------------------------+------------------------------------------------------------------+
    | * :doc:`wasserstein_distance_user`                              |                                                                                                                                         |
diff --git a/src/python/doc/wasserstein_distance_user.rst b/src/python/doc/wasserstein_distance_user.rst
index a049cfb5..32999a0c 100644
--- a/src/python/doc/wasserstein_distance_user.rst
+++ b/src/python/doc/wasserstein_distance_user.rst
@@ -30,7 +30,7 @@ Note that persistence diagrams must be submitted as (n x 2) numpy arrays and mus
     diag1 = np.array([[2.7, 3.7],[9.6, 14.],[34.2, 34.974]])
     diag2 = np.array([[2.8, 4.45],[9.5, 14.1]])
 
-    message = "Wasserstein distance value = " + '%.2f' % gudhi.wasserstein.wasserstein_distance(diag1, diag2, q=2., p=1.)
+    message = "Wasserstein distance value = " + '%.2f' % gudhi.wasserstein.wasserstein_distance(diag1, diag2, order=1., internal_p=2.)
     print(message)
 
 The output is:
diff --git a/src/python/doc/witness_complex_user.rst b/src/python/doc/witness_complex_user.rst
index 45ba5b3b..7087fa98 100644
--- a/src/python/doc/witness_complex_user.rst
+++ b/src/python/doc/witness_complex_user.rst
@@ -101,7 +101,7 @@ Let's start with a simple example, which reads an off point file and computes a
             print("#####################################################################")
             print("EuclideanWitnessComplex creation from points read in a OFF file")
 
-            witnesses = gudhi.read_off(off_file=args.file)
+            witnesses = gudhi.read_points_from_off_file(off_file=args.file)
             landmarks = gudhi.pick_n_random_points(points=witnesses, nb_points=args.number_of_landmarks)
 
             message = "EuclideanWitnessComplex with max_edge_length=" + repr(args.max_alpha_square) + \
diff --git a/src/python/example/alpha_rips_persistence_bottleneck_distance.py b/src/python/example/alpha_rips_persistence_bottleneck_distance.py
index 086307ee..d5c33ec8 100755
--- a/src/python/example/alpha_rips_persistence_bottleneck_distance.py
+++ b/src/python/example/alpha_rips_persistence_bottleneck_distance.py
@@ -35,7 +35,7 @@ args = parser.parse_args()
 with open(args.file, "r") as f:
     first_line = f.readline()
     if (first_line == "OFF\n") or (first_line == "nOFF\n"):
-        point_cloud = gudhi.read_off(off_file=args.file)
+        point_cloud = gudhi.read_points_from_off_file(off_file=args.file)
         print("#####################################################################")
         print("RipsComplex creation from points read in a OFF file")
 
diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
index 0eedd140..4903667e 100755
--- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
@@ -47,7 +47,7 @@ with open(args.file, "r") as f:
         print("#####################################################################")
         print("EuclideanStrongWitnessComplex creation from points read in a OFF file")
 
-        witnesses = gudhi.read_off(off_file=args.file)
+        witnesses = gudhi.read_points_from_off_file(off_file=args.file)
         landmarks = gudhi.pick_n_random_points(
             points=witnesses, nb_points=args.number_of_landmarks
         )
diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
index 1fe55737..339a8577 100755
--- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -46,7 +46,7 @@ with open(args.file, "r") as f:
         print("#####################################################################")
         print("EuclideanWitnessComplex creation from points read in a OFF file")
 
-        witnesses = gudhi.read_off(off_file=args.file)
+        witnesses = gudhi.read_points_from_off_file(off_file=args.file)
         landmarks = gudhi.pick_n_random_points(
             points=witnesses, nb_points=args.number_of_landmarks
         )
diff --git a/src/python/example/plot_rips_complex.py b/src/python/example/plot_rips_complex.py
index 1c878db1..214a3c0a 100755
--- a/src/python/example/plot_rips_complex.py
+++ b/src/python/example/plot_rips_complex.py
@@ -2,7 +2,7 @@
 
 import numpy as np
 import gudhi
-points = np.array(gudhi.read_off('../../data/points/Kl.off'))
+points = np.array(gudhi.read_points_from_off_file('../../data/points/Kl.off'))
 rc = gudhi.RipsComplex(points=points, max_edge_length=.2)
 st = rc.create_simplex_tree(max_dimension=2)
 # We are only going to plot the triangles
diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
index b9074cf9..c757aca7 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
@@ -48,7 +48,7 @@ with open(args.file, "r") as f:
         message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
         print(message)
 
-        point_cloud = gudhi.read_off(off_file=args.file)
+        point_cloud = gudhi.read_points_from_off_file(off_file=args.file)
         rips_complex = gudhi.RipsComplex(
             points=point_cloud, max_edge_length=args.max_edge_length
         )
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..f3ca3dd5 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"
@@ -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/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 011c407c..cbeda014 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
-
-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.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"
@@ -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=''):
+                 perseus_file=''):
         """CubicalComplex constructor from dimensions and
         top_dimensional_cells or from a Perseus-style file name.
 
@@ -58,6 +58,12 @@ cdef class CubicalComplex:
 
         Or
 
+        :param top_dimensional_cells: A multidimensional array of cells
+            filtration values.
+        :type top_dimensional_cells: anything convertible to a numpy ndarray
+
+        Or
+
         :param perseus_file: A Perseus-style file name.
         :type perseus_file: string
         """
@@ -65,11 +71,21 @@ cdef class CubicalComplex:
     # 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 == ''):
+        if ((dimensions is not None) and (top_dimensional_cells is not 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 not None)
+            and (perseus_file == '')):
+            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 != ''):
+        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:
@@ -184,4 +200,4 @@ 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)
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..382e71c5 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"
@@ -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 3a31eba6..7e6d9d80 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"
@@ -19,7 +19,7 @@ __license__ = "MIT"
 cdef extern from "Off_reader_interface.h" namespace "Gudhi":
     vector[vector[double]] read_points_from_OFF_file(string off_file)
 
-def read_off(off_file=''):
+def read_points_from_off_file(off_file=''):
     """Read points from OFF file.
 
     :param off_file: An OFF file style name.
@@ -30,7 +30,7 @@ def read_off(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 c89055db..37f76201 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
-
-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.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"
@@ -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,
-                  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.
 
@@ -60,6 +60,14 @@ cdef class PeriodicCubicalComplex:
 
         Or
 
+        :param top_dimensional_cells: A multidimensional array of cells
+            filtration values.
+        :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
+
+        Or
+
         :param perseus_file: A Perseus-style file name.
         :type perseus_file: string
         """
@@ -67,16 +75,32 @@ cdef class PeriodicCubicalComplex:
     # The real cython constructor
     def __cinit__(self, dimensions=None, top_dimensional_cells=None,
                   periodic_dimensions=None, perseus_file=''):
-        if (dimensions is not None) and (top_dimensional_cells is not None) 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 (periodic_dimensions is None) and (perseus_file != ''):
+        if ((dimensions is not None) and (top_dimensional_cells is not None)
+            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 not None)
+            and (periodic_dimensions is not None) and (perseus_file == '')):
+            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):
-                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:
-            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:
@@ -186,4 +210,4 @@ cdef class PeriodicCubicalComplex:
         else:
             print("intervals_in_dim function requires persistence function"
                   " to be launched first.")
-        return np_array(intervals_result)
+        return np.array(intervals_result)
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 9ced6bca..fe1c3a2e 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"
@@ -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/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..b18627c4 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"
@@ -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/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 f50f4b0c..4c84cb03 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"
@@ -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 f4c8b079..6391488c 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"
@@ -66,7 +66,7 @@ cdef class TangentialComplex:
     def __cinit__(self, intrisic_dim, points=None, off_file=''):
         if off_file:
             if os.path.isfile(off_file):
-                self.thisptr = new Tangential_complex_interface(intrisic_dim, str.encode(off_file), True)
+                self.thisptr = new Tangential_complex_interface(intrisic_dim, off_file.encode('utf-8'), True)
             else:
                 print("file " + off_file + " not found.")
         else:
diff --git a/src/python/gudhi/wasserstein.py b/src/python/gudhi/wasserstein.py
index d8a3104c..db5ddff2 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.
@@ -23,26 +23,26 @@ def _proj_on_diag(X):
     return np.array([Z , Z]).T
 
 
-def _build_dist_matrix(X, Y, p=2., q=2.):
+def _build_dist_matrix(X, Y, order=2., internal_p=2.):
     '''
     :param X: (n x 2) numpy.array encoding the (points of the) first diagram.
     :param Y: (m x 2) numpy.array encoding the second diagram.
-    :param q: Ground metric (i.e. norm l_q).
-    :param p: exponent for the Wasserstein metric.
+    :param internal_p: Ground metric (i.e. norm l_p).
+    :param order: exponent for the Wasserstein metric.
     :returns: (n+1) x (m+1) np.array encoding the cost matrix C. 
                 For 1 <= i <= n, 1 <= j <= m, C[i,j] encodes the distance between X[i] and Y[j], while C[i, m+1] (resp. C[n+1, j]) encodes the distance (to the p) between X[i] (resp Y[j]) and its orthogonal proj onto the diagonal.
                 note also that C[n+1, m+1] = 0  (it costs nothing to move from the diagonal to the diagonal).
     '''
     Xdiag = _proj_on_diag(X)
     Ydiag = _proj_on_diag(Y)
-    if np.isinf(q):
-        C = sc.cdist(X,Y, metric='chebyshev')**p
-        Cxd = np.linalg.norm(X - Xdiag, ord=q, axis=1)**p
-        Cdy = np.linalg.norm(Y - Ydiag, ord=q, axis=1)**p
+    if np.isinf(internal_p):
+        C = sc.cdist(X,Y, metric='chebyshev')**order
+        Cxd = np.linalg.norm(X - Xdiag, ord=internal_p, axis=1)**order
+        Cdy = np.linalg.norm(Y - Ydiag, ord=internal_p, axis=1)**order
     else:
-        C = sc.cdist(X,Y, metric='minkowski', p=q)**p
-        Cxd = np.linalg.norm(X - Xdiag, ord=q, axis=1)**p
-        Cdy = np.linalg.norm(Y - Ydiag, ord=q, axis=1)**p
+        C = sc.cdist(X,Y, metric='minkowski', p=internal_p)**order
+        Cxd = np.linalg.norm(X - Xdiag, ord=internal_p, axis=1)**order
+        Cdy = np.linalg.norm(Y - Ydiag, ord=internal_p, axis=1)**order
     Cf = np.hstack((C, Cxd[:,None]))
     Cdy = np.append(Cdy, 0)
 
@@ -51,24 +51,24 @@ def _build_dist_matrix(X, Y, p=2., q=2.):
     return Cf
 
 
-def _perstot(X, p, q):
+def _perstot(X, order, internal_p):
     '''
     :param X: (n x 2) numpy.array (points of a given diagram).
-    :param q: Ground metric on the (upper-half) plane (i.e. norm l_q in R^2); Default value is 2 (Euclidean norm).
-    :param p: exponent for Wasserstein; Default value is 2.
+    :param internal_p: Ground metric on the (upper-half) plane (i.e. norm l_p in R^2); Default value is 2 (Euclidean norm).
+    :param order: exponent for Wasserstein. Default value is 2.
     :returns: float, the total persistence of the diagram (that is, its distance to the empty diagram).    
     '''
     Xdiag = _proj_on_diag(X)
-    return (np.sum(np.linalg.norm(X - Xdiag, ord=q, axis=1)**p))**(1./p)
+    return (np.sum(np.linalg.norm(X - Xdiag, ord=internal_p, axis=1)**order))**(1./order)
 
 
-def wasserstein_distance(X, Y, p=2., q=2.):
+def wasserstein_distance(X, Y, order=2., internal_p=2.):
     '''
     :param X: (n x 2) numpy.array encoding the (finite points of the) first diagram. Must not contain essential points (i.e. with infinite coordinate).
     :param Y: (m x 2) numpy.array encoding the second diagram.
-    :param q: Ground metric on the (upper-half) plane (i.e. norm l_q in R^2); Default value is 2 (euclidean norm).
-    :param p: exponent for Wasserstein; Default value is 2.
-    :returns: the p-Wasserstein distance (1 <= p < infinity) with respect to the q-norm as ground metric.
+    :param internal_p: Ground metric on the (upper-half) plane (i.e. norm l_p in R^2); Default value is 2 (euclidean norm).
+    :param order: exponent for Wasserstein; Default value is 2.
+    :returns: the Wasserstein distance of order q (1 <= q < infinity) between persistence diagrams with respect to the internal_p-norm as ground metric.
     :rtype: float
     '''
     n = len(X)
@@ -79,20 +79,19 @@ def wasserstein_distance(X, Y, p=2., q=2.):
         if Y.size == 0:
             return 0.
         else:
-            return _perstot(Y, p, q)
+            return _perstot(Y, order, internal_p)
     elif Y.size == 0:
-        return _perstot(X, p, q)
+        return _perstot(X, order, internal_p)
 
-    M = _build_dist_matrix(X, Y, p=p, q=q)
+    M = _build_dist_matrix(X, Y, order=order, internal_p=internal_p)
     a = np.full(n+1, 1. / (n + m) )  # weight vector of the input diagram. Uniform here.
     a[-1] = a[-1] * m                # normalized so that we have a probability measure, required by POT
     b = np.full(m+1, 1. / (n + m) )  # weight vector of the input diagram. Uniform here.
     b[-1] = b[-1] * n                # so that we have a probability measure, required by POT
 
     # Comptuation of the otcost using the ot.emd2 library.
-    # Note: it is the squared Wasserstein distance.
+    # Note: it is the Wasserstein distance to the power q.
     # The default numItermax=100000 is not sufficient for some examples with 5000 points, what is a good value?
     ot_cost = (n+m) * ot.emd2(a, b, M, numItermax=2000000)
 
-    return ot_cost ** (1./p)
-
+    return ot_cost ** (1./order)
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..9c2124f4 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 +8,11 @@ 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
+import sys
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016  Inria"
 __license__ = "MIT"
@@ -38,7 +39,8 @@ for module in modules:
         libraries=libraries,
         library_dirs=library_dirs,
         include_dirs=include_dirs,
-        runtime_library_dirs=runtime_library_dirs,))
+        runtime_library_dirs=runtime_library_dirs,
+        cython_directives = {'language_level': str(sys.version_info[0])},))
 
 setup(
     name = 'gudhi',
diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py
index 9b27fff2..0d9e9e45 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 +8,17 @@ import pytest
       - YYYY/MM Author: Description of the modification
 """
 
+from gudhi import AlphaComplex, SimplexTree
+import math
+import numpy as np
+import pytest
+try:
+    # python3
+    from itertools import zip_longest
+except ImportError:
+    # python2
+    from itertools import izip_longest as zip_longest
+
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
@@ -114,6 +119,6 @@ def test_safe_alpha_persistence_comparison():
     diag1 = simplex_tree1.persistence()
     diag2 = simplex_tree2.persistence()
 
-    for (first_p, second_p) in itertools.zip_longest(diag1, diag2):
+    for (first_p, second_p) in zip_longest(diag1, diag2):
         assert first_p[0] == pytest.approx(second_p[0])
         assert first_p[1] == pytest.approx(second_p[1])
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 68f54fbe..8c1b2600 100755
--- a/src/python/test/test_cubical_complex.py
+++ b/src/python/test/test_cubical_complex.py
@@ -1,5 +1,3 @@
-from gudhi import CubicalComplex
-
 """ 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 +8,9 @@ from gudhi import CubicalComplex
       - 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"
@@ -56,7 +57,7 @@ def test_dimension_or_perseus_file_constructor():
     assert cub.__is_persistence_defined() == False
 
 
-def test_dimension_simple_constructor():
+def simple_constructor(cub):
     cub = CubicalComplex(
         dimensions=[3, 3], top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9]
     )
@@ -67,12 +68,22 @@ def test_dimension_simple_constructor():
     assert cub.betti_numbers() == [1, 0, 0]
     assert cub.persistent_betti_numbers(0, 1000) == [0, 0, 0]
 
-
-def test_user_case_simple_constructor():
+def test_simple_constructor_from_top_cells():
     cub = CubicalComplex(
         dimensions=[3, 3],
-        top_dimensional_cells=[float("inf"), 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
+        top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9],
     )
+    simple_constructor(cub)
+
+def test_simple_constructor_from_numpy_array():
+    cub = CubicalComplex(
+        top_dimensional_cells=np.array([[1, 2, 3],
+                                        [4, 5, 6],
+                                        [7, 8, 9]])
+    )
+    simple_constructor(cub)
+
+def user_case_simple_constructor(cub):
     assert cub.__is_defined() == True
     assert cub.__is_persistence_defined() == False
     assert cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float("inf")))]
@@ -83,6 +94,20 @@ def test_user_case_simple_constructor():
     )
     assert other_cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float("inf")))]
 
+def test_user_case_simple_constructor_from_top_cells():
+    cub = CubicalComplex(
+        dimensions=[3, 3],
+        top_dimensional_cells=[float("inf"), 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
+    )
+    user_case_simple_constructor(cub)
+
+def test_user_case_simple_constructor_from_numpy_array():
+    cub = CubicalComplex(
+        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)
 
 def test_dimension_file_constructor():
     # Create test file
@@ -96,3 +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]
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..43dda77e 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"
@@ -23,26 +23,26 @@ def test_basic_wasserstein():
     diag4 = np.array([[0, 3], [4, 8]])
     emptydiag = np.array([[]])
 
-    assert wasserstein_distance(emptydiag, emptydiag, q=2., p=1.) == 0.
-    assert wasserstein_distance(emptydiag, emptydiag, q=np.inf, p=1.) == 0.
-    assert wasserstein_distance(emptydiag, emptydiag, q=np.inf, p=2.) == 0.
-    assert wasserstein_distance(emptydiag, emptydiag, q=2., p=2.) == 0.
+    assert wasserstein_distance(emptydiag, emptydiag, internal_p=2.,     order=1.) == 0.
+    assert wasserstein_distance(emptydiag, emptydiag, internal_p=np.inf, order=1.) == 0.
+    assert wasserstein_distance(emptydiag, emptydiag, internal_p=np.inf, order=2.) == 0.
+    assert wasserstein_distance(emptydiag, emptydiag, internal_p=2.,     order=2.) == 0.
 
-    assert wasserstein_distance(diag3, emptydiag, q=np.inf, p=1.) == 2.
-    assert wasserstein_distance(diag3, emptydiag, q=1., p=1.) == 4.
+    assert wasserstein_distance(diag3, emptydiag, internal_p=np.inf,     order=1.) == 2.
+    assert wasserstein_distance(diag3, emptydiag, internal_p=1.,         order=1.) == 4.
 
-    assert wasserstein_distance(diag4, emptydiag, q=1., p=2.) == 5.  # thank you Pythagorician triplets
-    assert wasserstein_distance(diag4, emptydiag, q=np.inf, p=2.) == 2.5
-    assert wasserstein_distance(diag4, emptydiag, q=2., p=2.) == 3.5355339059327378
+    assert wasserstein_distance(diag4, emptydiag, internal_p=1.,     order=2.) == 5.  # thank you Pythagorician triplets
+    assert wasserstein_distance(diag4, emptydiag, internal_p=np.inf, order=2.) == 2.5
+    assert wasserstein_distance(diag4, emptydiag, internal_p=2.,     order=2.) == 3.5355339059327378
 
-    assert wasserstein_distance(diag1, diag2, q=2., p=1.) == 1.4453593023967701
-    assert wasserstein_distance(diag1, diag2, q=2.35, p=1.74) == 0.9772734057168739
+    assert wasserstein_distance(diag1, diag2, internal_p=2.,   order=1.)   == 1.4453593023967701
+    assert wasserstein_distance(diag1, diag2, internal_p=2.35, order=1.74) == 0.9772734057168739
 
-    assert wasserstein_distance(diag1, emptydiag, q=2.35, p=1.7863) == 3.141592214572228
+    assert wasserstein_distance(diag1, emptydiag, internal_p=2.35, order=1.7863) == 3.141592214572228
 
-    assert wasserstein_distance(diag3, diag4, q=1., p=1.) == 3.
-    assert wasserstein_distance(diag3, diag4, q=np.inf, p=1.) == 3.  # no diag matching here
-    assert wasserstein_distance(diag3, diag4, q=np.inf, p=2.) == np.sqrt(5)
-    assert wasserstein_distance(diag3, diag4, q=1., p=2.) == np.sqrt(5)
-    assert wasserstein_distance(diag3, diag4, q=4.5, p=2.) == np.sqrt(5)
+    assert wasserstein_distance(diag3, diag4, internal_p=1.,     order=1.) == 3.
+    assert wasserstein_distance(diag3, diag4, internal_p=np.inf, order=1.) == 3.  # no diag matching here
+    assert wasserstein_distance(diag3, diag4, internal_p=np.inf, order=2.) == np.sqrt(5)
+    assert wasserstein_distance(diag3, diag4, internal_p=1.,     order=2.) == np.sqrt(5)
+    assert wasserstein_distance(diag3, diag4, internal_p=4.5,    order=2.) == np.sqrt(5)
 
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"