Merge master

18 files changed, 411 insertions, 55 deletions

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 4b04c487..63a2e006 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -330,9 +330,9 @@ if(PYTHONINTERP_FOUND)
                   if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0)
                     set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
                     # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
-                    # Images and biblio warnings because not found on developper version
+                    # Images and biblio warnings because not found on developer version
                     if (GUDHI_PYTHON_PATH STREQUAL "src/python")
-                      set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
+                      set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developer version. Images and biblio will miss")
                     endif()
                     # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
                     add_custom_target(sphinx
@@ -485,7 +485,7 @@ if(PYTHONINTERP_FOUND)
       add_gudhi_py_test(test_euclidean_witness_complex)
 
       # Datasets generators
-      add_gudhi_py_test(test_datasets_generators) # TODO separate full python datasets generators in another test file independant from CGAL ?
+      add_gudhi_py_test(test_datasets_generators) # TODO separate full python datasets generators in another test file independent from CGAL ?
 
     endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
 
@@ -597,6 +597,11 @@ if(PYTHONINTERP_FOUND)
       add_gudhi_py_test(test_dtm_rips_complex)
     endif()
 
+    # Fetch remote datasets
+    if(WITH_GUDHI_REMOTE_TEST)
+      add_gudhi_py_test(test_remote_datasets)
+    endif()
+
     # sklearn
     if(SKLEARN_FOUND)
       add_gudhi_py_test(test_sklearn_cubical_persistence)
diff --git a/src/python/doc/datasets_generators.inc b/src/python/doc/datasets.inc
index 8d169275..95a87678 100644
--- a/src/python/doc/datasets_generators.inc
+++ b/src/python/doc/datasets.inc
@@ -2,7 +2,7 @@
    :widths: 30 40 30
 
    +-----------------------------------+--------------------------------------------+--------------------------------------------------------------------------------------+
-   | .. figure::                       | Datasets generators (points).              | :Authors: Hind Montassif                                                             |
+   | .. figure::                       | Datasets either generated or fetched.      | :Authors: Hind Montassif                                                             |
    |     img/sphere_3d.png             |                                            |                                                                                      |
    |                                   |                                            | :Since: GUDHI 3.5.0                                                                  |
    |                                   |                                            |                                                                                      |
@@ -10,5 +10,5 @@
    |                                   |                                            |                                                                                      |
    |                                   |                                            | :Requires: `CGAL <installation.html#cgal>`_                                          |
    +-----------------------------------+--------------------------------------------+--------------------------------------------------------------------------------------+
-   | * :doc:`datasets_generators`                                                                                                                                          |
+   | * :doc:`datasets`                                                                                                                                                     |
    +-----------------------------------+-----------------------------------------------------------------------------------------------------------------------------------+
diff --git a/src/python/doc/datasets_generators.rst b/src/python/doc/datasets.rst
index 260c3882..2d11a19d 100644
--- a/src/python/doc/datasets_generators.rst
+++ b/src/python/doc/datasets.rst
@@ -3,12 +3,14 @@
 
 .. To get rid of WARNING: document isn't included in any toctree
 
-===========================
-Datasets generators manual
-===========================
+================
+Datasets manual
+================
 
-We provide the generation of different customizable datasets to use as inputs for Gudhi complexes and data structures.
+Datasets generators
+===================
 
+We provide the generation of different customizable datasets to use as inputs for Gudhi complexes and data structures.
 
 Points generators
 ------------------
@@ -103,3 +105,29 @@ Example
 
 
 .. autofunction:: gudhi.datasets.generators.points.torus
+
+
+Fetching datasets
+=================
+
+We provide some ready-to-use datasets that are not available by default when getting GUDHI, and need to be fetched explicitly.
+
+By **default**, the fetched datasets directory is set to a folder named **'gudhi_data'** in the **user home folder**.
+Alternatively, it can be set using the **'GUDHI_DATA'** environment variable.
+
+.. autofunction:: gudhi.datasets.remote.fetch_bunny
+
+.. figure:: ./img/bunny.png
+     :figclass: align-center
+
+     3D Stanford bunny with 35947 vertices.
+
+
+.. autofunction:: gudhi.datasets.remote.fetch_spiral_2d
+
+.. figure:: ./img/spiral_2d.png
+     :figclass: align-center
+
+     2D spiral with 114562 vertices.
+
+.. autofunction:: gudhi.datasets.remote.clear_data_home
diff --git a/src/python/doc/img/bunny.png b/src/python/doc/img/bunny.png
new file mode 100644
index 00000000..769aa530
--- /dev/null
+++ b/src/python/doc/img/bunny.png
diff --git a/src/python/doc/img/spiral_2d.png b/src/python/doc/img/spiral_2d.png
new file mode 100644
index 00000000..abd247cd
--- /dev/null
+++ b/src/python/doc/img/spiral_2d.png
diff --git a/src/python/doc/index.rst b/src/python/doc/index.rst
index 2d7921ae..35f4ba46 100644
--- a/src/python/doc/index.rst
+++ b/src/python/doc/index.rst
@@ -92,7 +92,7 @@ Clustering
 
 .. include:: clustering.inc
 
-Datasets generators
-*******************
+Datasets
+********
 
-.. include:: datasets_generators.inc
+.. include:: datasets.inc
diff --git a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
index ea2eb7e1..0b35dbc5 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
@@ -40,7 +40,7 @@ parser.add_argument(
 args = parser.parse_args()
 
 if not (-1.0 < args.min_edge_correlation < 1.0):
-    print("Wrong value of the treshold corelation (should be between -1 and 1).")
+    print("Wrong value of the threshold corelation (should be between -1 and 1).")
     sys.exit(1)
 
 print("#####################################################################")
diff --git a/src/python/gudhi/datasets/remote.py b/src/python/gudhi/datasets/remote.py
new file mode 100644
index 00000000..f6d3fe56
--- /dev/null
+++ b/src/python/gudhi/datasets/remote.py
@@ -0,0 +1,223 @@
+# 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):       Hind Montassif
+#
+# Copyright (C) 2021 Inria
+#
+# Modification(s):
+#   - YYYY/MM Author: Description of the modification
+
+from os.path import join, split, exists, expanduser
+from os import makedirs, remove, environ
+
+from urllib.request import urlretrieve
+import hashlib
+import shutil
+
+import numpy as np
+
+def _get_data_home(data_home = None):
+    """
+    Return the path of the remote datasets directory.
+    This folder is used to store remotely fetched datasets.
+    By default the datasets directory is set to a folder named 'gudhi_data' in the user home folder.
+    Alternatively, it can be set by the 'GUDHI_DATA' environment variable.
+    The '~' symbol is expanded to the user home folder.
+    If the folder does not already exist, it is automatically created.
+
+    Parameters
+    ----------
+    data_home : string
+        The path to remote datasets directory.
+        Default is `None`, meaning that the data home directory will be set to "~/gudhi_data",
+        if the 'GUDHI_DATA' environment variable does not exist.
+
+    Returns
+    -------
+    data_home: string
+        The path to remote datasets directory.
+    """
+    if data_home is None:
+        data_home = environ.get("GUDHI_DATA", join("~", "gudhi_data"))
+    data_home = expanduser(data_home)
+    makedirs(data_home, exist_ok=True)
+    return data_home
+
+
+def clear_data_home(data_home = None):
+    """
+    Delete the data home cache directory and all its content.
+
+    Parameters
+    ----------
+    data_home : string, default is None.
+        The path to remote datasets directory.
+        If `None` and the 'GUDHI_DATA' environment variable does not exist,
+        the default directory to be removed is set to "~/gudhi_data".
+    """
+    data_home = _get_data_home(data_home)
+    shutil.rmtree(data_home)
+
+def _checksum_sha256(file_path):
+    """
+    Compute the file checksum using sha256.
+
+    Parameters
+    ----------
+    file_path: string
+        Full path of the created file including filename.
+
+    Returns
+    -------
+        The hex digest of file_path.
+    """
+    sha256_hash = hashlib.sha256()
+    chunk_size = 4096
+    with open(file_path,"rb") as f:
+        # Read and update hash string value in blocks of 4K
+        while True:
+            buffer = f.read(chunk_size)
+            if not buffer:
+                break
+            sha256_hash.update(buffer)
+    return sha256_hash.hexdigest()
+
+def _fetch_remote(url, file_path, file_checksum = None):
+    """
+    Fetch the wanted dataset from the given url and save it in file_path.
+
+    Parameters
+    ----------
+    url : string
+        The url to fetch the dataset from.
+    file_path : string
+        Full path of the downloaded file including filename.
+    file_checksum : string
+        The file checksum using sha256 to check against the one computed on the downloaded file.
+        Default is 'None', which means the checksum is not checked.
+
+    Raises
+    ------
+    IOError
+        If the computed SHA256 checksum of file does not match the one given by the user.
+    """
+
+    # Get the file
+    urlretrieve(url, file_path)
+
+    if file_checksum is not None:
+        checksum = _checksum_sha256(file_path)
+        if file_checksum != checksum:
+            # Remove file and raise error
+            remove(file_path)
+            raise IOError("{} has a SHA256 checksum : {}, "
+                        "different from expected : {}."
+                        "The file may be corrupted or the given url may be wrong !".format(file_path, checksum, file_checksum))
+
+def _get_archive_path(file_path, label):
+    """
+    Get archive path based on file_path given by user and label.
+
+    Parameters
+    ----------
+    file_path: string
+        Full path of the file to get including filename, or None.
+    label: string
+        Label used along with 'data_home' to get archive path, in case 'file_path' is None.
+
+    Returns
+    -------
+        Full path of archive including filename.
+    """
+    if file_path is None:
+        archive_path = join(_get_data_home(), label)
+        dirname = split(archive_path)[0]
+        makedirs(dirname, exist_ok=True)
+    else:
+        archive_path = file_path
+        dirname = split(archive_path)[0]
+        makedirs(dirname, exist_ok=True)
+
+    return archive_path
+
+def fetch_spiral_2d(file_path = None):
+    """
+    Load the spiral_2d dataset.
+
+    Note that if the dataset already exists in the target location, it is not downloaded again,
+    and the corresponding array is returned from cache.
+
+    Parameters
+    ----------
+    file_path : string
+        Full path of the downloaded file including filename.
+
+        Default is None, meaning that it's set to "data_home/points/spiral_2d/spiral_2d.npy".
+
+        The "data_home" directory is set by default to "~/gudhi_data",
+        unless the 'GUDHI_DATA' environment variable is set.
+
+    Returns
+    -------
+    points: numpy array
+        Array of shape (114562, 2).
+    """
+    file_url = "https://raw.githubusercontent.com/GUDHI/gudhi-data/main/points/spiral_2d/spiral_2d.npy"
+    file_checksum = '2226024da76c073dd2f24b884baefbfd14928b52296df41ad2d9b9dc170f2401'
+
+    archive_path = _get_archive_path(file_path, "points/spiral_2d/spiral_2d.npy")
+
+    if not exists(archive_path):
+        _fetch_remote(file_url, archive_path, file_checksum)
+
+    return np.load(archive_path, mmap_mode='r')
+
+def fetch_bunny(file_path = None, accept_license = False):
+    """
+    Load the Stanford bunny dataset.
+
+    This dataset contains 35947 vertices.
+
+    Note that if the dataset already exists in the target location, it is not downloaded again,
+    and the corresponding array is returned from cache.
+
+    Parameters
+    ----------
+    file_path : string
+        Full path of the downloaded file including filename.
+
+        Default is None, meaning that it's set to "data_home/points/bunny/bunny.npy".
+        In this case, the LICENSE file would be downloaded as "data_home/points/bunny/bunny.LICENSE".
+
+        The "data_home" directory is set by default to "~/gudhi_data",
+        unless the 'GUDHI_DATA' environment variable is set.
+
+    accept_license : boolean
+        Flag to specify if user accepts the file LICENSE and prevents from printing the corresponding license terms.
+
+        Default is False.
+
+    Returns
+    -------
+    points: numpy array
+        Array of shape (35947, 3).
+    """
+
+    file_url = "https://raw.githubusercontent.com/GUDHI/gudhi-data/main/points/bunny/bunny.npy"
+    file_checksum = 'f382482fd89df8d6444152dc8fd454444fe597581b193fd139725a85af4a6c6e'
+    license_url = "https://raw.githubusercontent.com/GUDHI/gudhi-data/main/points/bunny/bunny.LICENSE"
+    license_checksum = 'b763dbe1b2fc6015d05cbf7bcc686412a2eb100a1f2220296e3b4a644c69633a'
+
+    archive_path = _get_archive_path(file_path, "points/bunny/bunny.npy")
+
+    if not exists(archive_path):
+        _fetch_remote(file_url, archive_path, file_checksum)
+        license_path = join(split(archive_path)[0], "bunny.LICENSE")
+        _fetch_remote(license_url, license_path, license_checksum)
+        # Print license terms unless accept_license is set to True
+        if not accept_license:
+            if exists(license_path):
+                with open(license_path, 'r') as f:
+                    print(f.read())
+
+    return np.load(archive_path, mmap_mode='r')
diff --git a/src/python/gudhi/hera/wasserstein.cc b/src/python/gudhi/hera/wasserstein.cc
index 1a21f02f..fa0cf8aa 100644
--- a/src/python/gudhi/hera/wasserstein.cc
+++ b/src/python/gudhi/hera/wasserstein.cc
@@ -29,7 +29,7 @@ double wasserstein_distance(
   if(std::isinf(internal_p)) internal_p = hera::get_infinity<double>();
   params.internal_p = internal_p;
   params.delta = delta;
-  // The extra parameters are purposedly not exposed for now.
+  // The extra parameters are purposely not exposed for now.
   return hera::wasserstein_dist(diag1, diag2, params);
 }
 
diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py
index 7ed11360..21275cdd 100644
--- a/src/python/gudhi/persistence_graphical_tools.py
+++ b/src/python/gudhi/persistence_graphical_tools.py
@@ -332,7 +332,7 @@ def plot_persistence_diagram(
             axes.plot([axis_start, axis_end], [infinity, infinity], linewidth=1.0, color="k", alpha=alpha)
             # Infinity label
             yt = axes.get_yticks()
-            yt = yt[np.where(yt < axis_end)]  # to avoid ploting ticklabel higher than infinity
+            yt = yt[np.where(yt < axis_end)]  # to avoid plotting ticklabel higher than infinity
             yt = np.append(yt, infinity)
             ytl = ["%.3f" % e for e in yt]  # to avoid float precision error
             ytl[-1] = r"$+\infty$"
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 4f229663..5642f82d 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -63,7 +63,6 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         bool prune_above_filtration(double filtration) nogil
         bool make_filtration_non_decreasing() nogil
         void compute_extended_filtration() nogil
-        vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(vector[pair[int, pair[double, double]]] dgm, double min_persistence) nogil
         Simplex_tree_interface_full_featured* collapse_edges(int nb_collapse_iteration) nogil except +
         void reset_filtration(double filtration, int dimension) nogil
         bint operator==(Simplex_tree_interface_full_featured) nogil
@@ -81,7 +80,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         void expansion_with_blockers_callback(int dimension, blocker_func_t user_func, void *user_data)
 
 cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
-    cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>":
+    cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>>":
         Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * st, bool persistence_dim_max) nogil
         void compute_persistence(int homology_coeff_field, double min_persistence) nogil except +
         vector[pair[int, pair[double, double]]] get_persistence() nogil
@@ -92,3 +91,4 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
         vector[pair[vector[int], vector[int]]] persistence_pairs() nogil
         pair[vector[vector[int]], vector[vector[int]]] lower_star_generators() nogil
         pair[vector[vector[int]], vector[vector[int]]] flag_generators() nogil
+        vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(double min_persistence) nogil
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index 2c53a872..521a7763 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -474,8 +474,7 @@ cdef class SimplexTree:
             del self.pcohptr
         self.pcohptr = new Simplex_tree_persistence_interface(self.get_ptr(), False)
         self.pcohptr.compute_persistence(homology_coeff_field, -1.)
-        persistence_result = self.pcohptr.get_persistence()
-        return self.get_ptr().compute_extended_persistence_subdiagrams(persistence_result, min_persistence)
+        return self.pcohptr.compute_extended_persistence_subdiagrams(min_persistence)
 
     def expansion_with_blocker(self, max_dim, blocker_func):
         """Expands the Simplex_tree containing only a graph. Simplices corresponding to cliques in the graph are added
diff --git a/src/python/gudhi/wasserstein/barycenter.py b/src/python/gudhi/wasserstein/barycenter.py
index d67bcde7..bb6e641e 100644
--- a/src/python/gudhi/wasserstein/barycenter.py
+++ b/src/python/gudhi/wasserstein/barycenter.py
@@ -37,7 +37,7 @@ def lagrangian_barycenter(pdiagset, init=None, verbose=False):
     :param init: The initial value for barycenter estimate.
         If ``None``, init is made on a random diagram from the dataset.
         Otherwise, it can be an ``int`` (then initialization is made on ``pdiagset[init]``)
-        or a `(n x 2)` ``numpy.array`` enconding a persistence diagram with `n` points.
+        or a `(n x 2)` ``numpy.array`` encoding a persistence diagram with `n` points.
     :type init: ``int``, or (n x 2) ``np.array``
     :param verbose: if ``True``, returns additional information about the barycenter.
     :type verbose: boolean
@@ -45,7 +45,7 @@ def lagrangian_barycenter(pdiagset, init=None, verbose=False):
         (local minimum of the energy function).
         If ``pdiagset`` is empty, returns ``None``.
         If verbose, returns a couple ``(Y, log)`` where ``Y`` is the barycenter estimate,
-        and ``log`` is a ``dict`` that contains additional informations:
+        and ``log`` is a ``dict`` that contains additional information:
 
         - `"groupings"`, a list of list of pairs ``(i,j)``. Namely, ``G[k] = [...(i, j)...]``, where ``(i,j)`` indicates that `pdiagset[k][i]`` is matched to ``Y[j]`` if ``i = -1`` or ``j = -1``, it means they represent the diagonal.
 
@@ -73,7 +73,7 @@ def lagrangian_barycenter(pdiagset, init=None, verbose=False):
 
     nb_iter = 0
 
-    converged = False  # stoping criterion
+    converged = False  # stopping criterion
     while not converged:
         nb_iter += 1
         K = len(Y)  # current nb of points in Y (some might be on diagonal)
diff --git a/src/python/include/Persistent_cohomology_interface.h b/src/python/include/Persistent_cohomology_interface.h
index e5a3dfba..945378a0 100644
--- a/src/python/include/Persistent_cohomology_interface.h
+++ b/src/python/include/Persistent_cohomology_interface.h
@@ -12,6 +12,8 @@
 #define INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_
 
 #include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Simplex_tree.h>  // for Extended_simplex_type
+
 
 #include <cstdlib>
 #include <vector>
@@ -223,6 +225,44 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
     return out;
   }
 
+  using Filtration_value = typename FilteredComplex::Filtration_value;
+  using Birth_death = std::pair<Filtration_value, Filtration_value>;
+  using Persistence_subdiagrams = std::vector<std::vector<std::pair<int, Birth_death>>>;
+
+  Persistence_subdiagrams compute_extended_persistence_subdiagrams(Filtration_value min_persistence){
+    Persistence_subdiagrams pers_subs(4);
+    auto const& persistent_pairs = Base::get_persistent_pairs();
+    for (auto pair : persistent_pairs) {
+      std::pair<Filtration_value, Extended_simplex_type> px = stptr_->decode_extended_filtration(stptr_->filtration(get<0>(pair)),
+                                                                                                        stptr_->efd);
+      std::pair<Filtration_value, Extended_simplex_type> py = stptr_->decode_extended_filtration(stptr_->filtration(get<1>(pair)),
+                                                                                                        stptr_->efd);
+      std::pair<int, Birth_death> pd_point = std::make_pair(stptr_->dimension(get<0>(pair)),
+                                                            std::make_pair(px.first, py.first));
+      if(std::abs(px.first - py.first) > min_persistence){
+        //Ordinary
+        if (px.second == Extended_simplex_type::UP && py.second == Extended_simplex_type::UP){
+          pers_subs[0].push_back(pd_point);
+        }
+        // Relative
+        else if (px.second == Extended_simplex_type::DOWN && py.second == Extended_simplex_type::DOWN){
+          pers_subs[1].push_back(pd_point);
+        }
+        else{
+          // Extended+
+          if (px.first < py.first){
+            pers_subs[2].push_back(pd_point);
+          }
+          //Extended-
+          else{
+            pers_subs[3].push_back(pd_point);
+          }
+        }
+      }
+    }
+    return pers_subs;
+  }
+
  private:
   // A copy
   FilteredComplex* stptr_;
diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h
index 7f9b0067..3848c5ad 100644
--- a/src/python/include/Simplex_tree_interface.h
+++ b/src/python/include/Simplex_tree_interface.h
@@ -132,36 +132,6 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     return;
   }
 
-  std::vector<std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>> compute_extended_persistence_subdiagrams(const std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>& dgm, Filtration_value min_persistence){
-    std::vector<std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>> new_dgm(4);
-    for (unsigned int i = 0; i < dgm.size(); i++){
-      std::pair<Filtration_value, Extended_simplex_type> px = this->decode_extended_filtration(dgm[i].second.first, this->efd);
-      std::pair<Filtration_value, Extended_simplex_type> py = this->decode_extended_filtration(dgm[i].second.second, this->efd);
-      std::pair<int, std::pair<Filtration_value, Filtration_value>> pd_point = std::make_pair(dgm[i].first, std::make_pair(px.first, py.first));
-      if(std::abs(px.first - py.first) > min_persistence){
-        //Ordinary
-        if (px.second == Extended_simplex_type::UP && py.second == Extended_simplex_type::UP){
-          new_dgm[0].push_back(pd_point);
-        }
-        // Relative
-        else if (px.second == Extended_simplex_type::DOWN && py.second == Extended_simplex_type::DOWN){
-          new_dgm[1].push_back(pd_point);
-        }
-        else{
-          // Extended+
-          if (px.first < py.first){
-            new_dgm[2].push_back(pd_point);
-          }
-          //Extended-
-          else{
-            new_dgm[3].push_back(pd_point);
-          }
-        }
-      }
-    }
-    return new_dgm;
-  }
-
   Simplex_tree_interface* collapse_edges(int nb_collapse_iteration) {
     using Filtered_edge = std::tuple<Vertex_handle, Vertex_handle, Filtration_value>;
     std::vector<Filtered_edge> edges;
diff --git a/src/python/test/test_remote_datasets.py b/src/python/test/test_remote_datasets.py
new file mode 100644
index 00000000..e5d2de82
--- /dev/null
+++ b/src/python/test/test_remote_datasets.py
@@ -0,0 +1,87 @@
+# 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):       Hind Montassif
+#
+# Copyright (C) 2021 Inria
+#
+# Modification(s):
+#   - YYYY/MM Author: Description of the modification
+
+from gudhi.datasets import remote
+
+import shutil
+import io
+import sys
+import pytest
+
+from os.path import isdir, expanduser, exists
+from os import remove, environ
+
+def test_data_home():
+    # Test _get_data_home and clear_data_home on new empty folder
+    empty_data_home = remote._get_data_home(data_home="empty_folder_for_test")
+    assert isdir(empty_data_home)
+
+    remote.clear_data_home(data_home=empty_data_home)
+    assert not isdir(empty_data_home)
+
+def test_fetch_remote():
+    # Test fetch with a wrong checksum
+    with pytest.raises(OSError):
+        remote._fetch_remote("https://raw.githubusercontent.com/GUDHI/gudhi-data/main/points/spiral_2d/spiral_2d.npy", "tmp_spiral_2d.npy", file_checksum = 'XXXXXXXXXX')
+    assert not exists("tmp_spiral_2d.npy")
+
+def _get_bunny_license_print(accept_license = False):
+    capturedOutput = io.StringIO()
+    # Redirect stdout
+    sys.stdout = capturedOutput
+
+    bunny_arr = remote.fetch_bunny("./tmp_for_test/bunny.npy", accept_license)
+    assert bunny_arr.shape == (35947, 3)
+    del bunny_arr
+    remove("./tmp_for_test/bunny.npy")
+
+    # Reset redirect
+    sys.stdout = sys.__stdout__
+    return capturedOutput
+
+def test_print_bunny_license():
+    # Test not printing bunny.npy LICENSE when accept_license = True
+    assert "" == _get_bunny_license_print(accept_license = True).getvalue()
+    # Test printing bunny.LICENSE file when fetching bunny.npy with accept_license = False (default)
+    with open("./tmp_for_test/bunny.LICENSE") as f:
+        assert f.read().rstrip("\n") == _get_bunny_license_print().getvalue().rstrip("\n")
+    shutil.rmtree("./tmp_for_test")
+
+def test_fetch_remote_datasets_wrapped():
+    # Test fetch_spiral_2d and fetch_bunny wrapping functions with data directory different from default (twice, to test case of already fetched files)
+    # Default case is not tested because it would fail in case the user sets the 'GUDHI_DATA' environment variable locally
+    for i in range(2):
+        spiral_2d_arr = remote.fetch_spiral_2d("./another_fetch_folder_for_test/spiral_2d.npy")
+        assert spiral_2d_arr.shape == (114562, 2)
+
+        bunny_arr = remote.fetch_bunny("./another_fetch_folder_for_test/bunny.npy")
+        assert bunny_arr.shape == (35947, 3)
+
+    # Check that the directory was created
+    assert isdir("./another_fetch_folder_for_test")
+    # Check downloaded files
+    assert exists("./another_fetch_folder_for_test/spiral_2d.npy")
+    assert exists("./another_fetch_folder_for_test/bunny.npy")
+    assert exists("./another_fetch_folder_for_test/bunny.LICENSE")
+
+    # Remove test folders
+    del spiral_2d_arr
+    del bunny_arr
+    shutil.rmtree("./another_fetch_folder_for_test")
+
+def test_gudhi_data_env():
+    # Set environment variable "GUDHI_DATA"
+    environ["GUDHI_DATA"] = "./test_folder_from_env_var"
+    bunny_arr = remote.fetch_bunny()
+    assert bunny_arr.shape == (35947, 3)
+    assert exists("./test_folder_from_env_var/points/bunny/bunny.npy")
+    assert exists("./test_folder_from_env_var/points/bunny/bunny.LICENSE")
+    # Remove test folder
+    del bunny_arr
+    shutil.rmtree("./test_folder_from_env_var")
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py
index 688f4fd6..54bafed5 100755
--- a/src/python/test/test_simplex_tree.py
+++ b/src/python/test/test_simplex_tree.py
@@ -320,6 +320,10 @@ def test_extend_filtration():
     ]
 
     dgms = st.extended_persistence(min_persistence=-1.)
+    assert len(dgms) == 4
+    # Sort by (death-birth) descending - we are only interested in those with the longest life span
+    for idx in range(4):
+        dgms[idx] = sorted(dgms[idx], key=lambda x:(-abs(x[1][0]-x[1][1])))
 
     assert dgms[0][0][1][0] == pytest.approx(2.)
     assert dgms[0][0][1][1] == pytest.approx(3.)
@@ -528,7 +532,7 @@ def test_expansion_with_blocker():
 
     def blocker(simplex):
         try:
-            # Block all simplices that countains vertex 6
+            # Block all simplices that contain vertex 6
             simplex.index(6)
             print(simplex, ' is blocked')
             return True
diff --git a/src/python/test/test_subsampling.py b/src/python/test/test_subsampling.py
index 4019852e..3431f372 100755
--- a/src/python/test/test_subsampling.py
+++ b/src/python/test/test_subsampling.py
@@ -91,7 +91,7 @@ def test_simple_choose_n_farthest_points_randomed():
     assert gudhi.choose_n_farthest_points(points=[], nb_points=1) == []
     assert gudhi.choose_n_farthest_points(points=point_set, nb_points=0) == []
 
-    # Go furter than point set on purpose
+    # Go further than point set on purpose
     for iter in range(1, 10):
         sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=iter)
         for sub in sub_set:
@@ -117,7 +117,7 @@ def test_simple_pick_n_random_points():
     assert gudhi.pick_n_random_points(points=[], nb_points=1) == []
     assert gudhi.pick_n_random_points(points=point_set, nb_points=0) == []
 
-    # Go furter than point set on purpose
+    # Go further than point set on purpose
     for iter in range(1, 10):
         sub_set = gudhi.pick_n_random_points(points=point_set, nb_points=iter)
         for sub in sub_set: