From 45917ecf17acacfede909994d7b3a78fc18355da Mon Sep 17 00:00:00 2001
From: Hind <hind.montassif@gmail.com>
Date: Thu, 22 Apr 2021 17:08:17 +0200
Subject: Add random points generator on sphere in python, with an example

---
 .../alpha_complex_from_generated_points_example.py | 52 ++++++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 src/python/example/alpha_complex_from_generated_points_example.py

(limited to 'src/python/example')

diff --git a/src/python/example/alpha_complex_from_generated_points_example.py b/src/python/example/alpha_complex_from_generated_points_example.py
new file mode 100644
index 00000000..7a07ed42
--- /dev/null
+++ b/src/python/example/alpha_complex_from_generated_points_example.py
@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+
+from gudhi import random_point_generators
+from gudhi import AlphaComplex, SimplexTree
+from gudhi import plot_persistence_barcode, plot_persistence_diagram
+
+import matplotlib.pyplot as plt
+
+
+""" 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
+"""
+
+__author__ = "Hind Montassif"
+__copyright__ = "Copyright (C) 2021 Inria"
+__license__ = "MIT"
+
+print("#####################################################################")
+print("AlphaComplex creation from generated points")
+
+
+# Generate a circle: 50 points; dim 2; radius 1
+points = random_point_generators.generate_points_on_sphere_d(50, 2, 1)
+
+# Plot the generated points (to uncomment if wished)
+#plt.scatter(points[:,0], points[:,1])
+#plt.show()
+
+# Create an alpha complex
+alpha_complex = AlphaComplex(points=points)
+simplex_tree = alpha_complex.create_simplex_tree()
+
+result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
+    repr(simplex_tree.num_simplices()) + ' simplices - ' + \
+    repr(simplex_tree.num_vertices()) + ' vertices.'
+print(result_str)
+
+
+# Compute the persistence
+diag = simplex_tree.persistence()
+
+# Plot the barcode and diagram (to uncomment if wished)
+#plot_persistence_barcode(diag)
+#plt.show()
+#plot_persistence_diagram(diag)
+#plt.show()
-- 
cgit v1.2.3


From 7573e67c8c6c1bb3cd21fd8b9ffb8aa0168eb7f7 Mon Sep 17 00:00:00 2001
From: Hind <hind.montassif@gmail.com>
Date: Tue, 27 Apr 2021 15:13:25 +0200
Subject: Remove the commented graphic part from the example (to be added to
 tutorial notebooks)

---
 .../alpha_complex_from_generated_points_example.py     | 18 +-----------------
 1 file changed, 1 insertion(+), 17 deletions(-)

(limited to 'src/python/example')

diff --git a/src/python/example/alpha_complex_from_generated_points_example.py b/src/python/example/alpha_complex_from_generated_points_example.py
index 7a07ed42..c2562d8a 100644
--- a/src/python/example/alpha_complex_from_generated_points_example.py
+++ b/src/python/example/alpha_complex_from_generated_points_example.py
@@ -1,10 +1,7 @@
 #!/usr/bin/env python
 
 from gudhi import random_point_generators
-from gudhi import AlphaComplex, SimplexTree
-from gudhi import plot_persistence_barcode, plot_persistence_diagram
-
-import matplotlib.pyplot as plt
+from gudhi import AlphaComplex
 
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
@@ -28,10 +25,6 @@ print("AlphaComplex creation from generated points")
 # Generate a circle: 50 points; dim 2; radius 1
 points = random_point_generators.generate_points_on_sphere_d(50, 2, 1)
 
-# Plot the generated points (to uncomment if wished)
-#plt.scatter(points[:,0], points[:,1])
-#plt.show()
-
 # Create an alpha complex
 alpha_complex = AlphaComplex(points=points)
 simplex_tree = alpha_complex.create_simplex_tree()
@@ -41,12 +34,3 @@ result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) +
     repr(simplex_tree.num_vertices()) + ' vertices.'
 print(result_str)
 
-
-# Compute the persistence
-diag = simplex_tree.persistence()
-
-# Plot the barcode and diagram (to uncomment if wished)
-#plot_persistence_barcode(diag)
-#plt.show()
-#plot_persistence_diagram(diag)
-#plt.show()
-- 
cgit v1.2.3


From df9daf64aa7623ac188a5842a90162d65a54b07e Mon Sep 17 00:00:00 2001
From: Hind <hind.montassif@gmail.com>
Date: Tue, 27 Apr 2021 18:01:00 +0200
Subject: Rename and reorganize point generators module

---
 src/python/CMakeLists.txt                          | 10 ++--
 .../alpha_complex_from_generated_points_example.py | 36 -------------
 ...plex_from_generated_points_on_sphere_example.py | 36 +++++++++++++
 src/python/gudhi/datasets/generators/__init__.py   |  0
 src/python/gudhi/datasets/generators/sphere.cc     | 61 ++++++++++++++++++++++
 src/python/gudhi/random_point_generators.cc        | 61 ----------------------
 6 files changed, 103 insertions(+), 101 deletions(-)
 delete mode 100644 src/python/example/alpha_complex_from_generated_points_example.py
 create mode 100644 src/python/example/alpha_complex_from_generated_points_on_sphere_example.py
 create mode 100644 src/python/gudhi/datasets/generators/__init__.py
 create mode 100644 src/python/gudhi/datasets/generators/sphere.cc
 delete mode 100644 src/python/gudhi/random_point_generators.cc

(limited to 'src/python/example')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 87f10a1a..bcdd0741 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -46,7 +46,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'bottleneck', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'hera', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'clustering', ")
-    set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'random_point_generators', ")
+    set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'datasets/generators', ")
   endif()
   if(CYTHON_FOUND)
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_reader', ")
@@ -152,7 +152,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/wasserstein', ")
     set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/bottleneck', ")
     if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
-      set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'random_point_generators', ")
+      set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'datasets/generators/sphere', ")
       set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'bottleneck', ")
       set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ")
     endif ()
@@ -264,6 +264,8 @@ if(PYTHONINTERP_FOUND)
     file(COPY "gudhi/weighted_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/dtm_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/hera/__init__.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/hera")
+    file(COPY "gudhi/datasets/generators/__init__.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/datasets/generators")
+
 
     # Some files for pip package
     file(COPY "introduction.rst" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
@@ -427,10 +429,10 @@ if(PYTHONINTERP_FOUND)
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
                COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
-      add_test(NAME alpha_complex_from_generated_points_example_py_test
+      add_test(NAME alpha_complex_from_generated_points_on_sphere_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
                COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_generated_points_example.py")
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_generated_points_on_sphere_example.py")
       add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
diff --git a/src/python/example/alpha_complex_from_generated_points_example.py b/src/python/example/alpha_complex_from_generated_points_example.py
deleted file mode 100644
index c2562d8a..00000000
--- a/src/python/example/alpha_complex_from_generated_points_example.py
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env python
-
-from gudhi import random_point_generators
-from gudhi import AlphaComplex
-
-
-""" 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
-"""
-
-__author__ = "Hind Montassif"
-__copyright__ = "Copyright (C) 2021 Inria"
-__license__ = "MIT"
-
-print("#####################################################################")
-print("AlphaComplex creation from generated points")
-
-
-# Generate a circle: 50 points; dim 2; radius 1
-points = random_point_generators.generate_points_on_sphere_d(50, 2, 1)
-
-# Create an alpha complex
-alpha_complex = AlphaComplex(points=points)
-simplex_tree = alpha_complex.create_simplex_tree()
-
-result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
-    repr(simplex_tree.num_simplices()) + ' simplices - ' + \
-    repr(simplex_tree.num_vertices()) + ' vertices.'
-print(result_str)
-
diff --git a/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py b/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py
new file mode 100644
index 00000000..2de9ec08
--- /dev/null
+++ b/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py
@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+
+from gudhi.datasets.generators import sphere
+from gudhi import AlphaComplex
+
+
+""" 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
+"""
+
+__author__ = "Hind Montassif"
+__copyright__ = "Copyright (C) 2021 Inria"
+__license__ = "MIT"
+
+print("#####################################################################")
+print("AlphaComplex creation from generated points on sphere")
+
+
+# Generate a circle: 50 points; dim 2; radius 1
+points = sphere.generate_random_points(50, 2, 1)
+
+# Create an alpha complex
+alpha_complex = AlphaComplex(points=points)
+simplex_tree = alpha_complex.create_simplex_tree()
+
+result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
+    repr(simplex_tree.num_simplices()) + ' simplices - ' + \
+    repr(simplex_tree.num_vertices()) + ' vertices.'
+print(result_str)
+
diff --git a/src/python/gudhi/datasets/generators/__init__.py b/src/python/gudhi/datasets/generators/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/python/gudhi/datasets/generators/sphere.cc b/src/python/gudhi/datasets/generators/sphere.cc
new file mode 100644
index 00000000..79392ef0
--- /dev/null
+++ b/src/python/gudhi/datasets/generators/sphere.cc
@@ -0,0 +1,61 @@
+/*    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
+ */
+
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+
+#include <gudhi/random_point_generators.h>
+#include <gudhi/Debug_utils.h>
+
+#include <CGAL/Epick_d.h>
+
+namespace py = pybind11;
+
+
+typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kern;
+
+py::array_t<double> generate_points_on_sphere(size_t num_points, int dim, double radius) {
+
+    py::array_t<double> points({num_points, (size_t)dim});
+
+    py::buffer_info buf = points.request();
+    double *ptr = static_cast<double *>(buf.ptr);
+
+    GUDHI_CHECK(num_points == buf.shape[0], "Py array first dimension not matching num_points on sphere");
+    GUDHI_CHECK(dim == buf.shape[1], "Py array second dimension not matching the ambient space dimension");
+
+
+    py::gil_scoped_release release;
+    auto points_generated = Gudhi::generate_points_on_sphere_d<Kern>(num_points, dim, radius);
+
+    for (size_t i = 0; i < num_points; i++)
+        for (int j = 0; j < dim; j++)
+            ptr[i*dim+j] = points_generated[i][j];
+
+    return points;
+}
+
+PYBIND11_MODULE(sphere, m) {
+      m.attr("__license__") = "LGPL v3";
+      m.def("generate_random_points", &generate_points_on_sphere,
+          py::arg("num_points"), py::arg("dim"), py::arg("radius") = 1,
+          R"pbdoc(
+    Generate random i.i.d. points uniformly on a (d-1)-sphere in R^d
+
+    :param num_points: The number of points to be generated.
+    :type num_points: unsigned integer
+    :param dim: The dimension.
+    :type dim: integer
+    :param radius: The radius.
+    :type radius: float
+    :rtype: numpy array of float
+    :returns: the generated points on a sphere.
+    )pbdoc");
+}
diff --git a/src/python/gudhi/random_point_generators.cc b/src/python/gudhi/random_point_generators.cc
deleted file mode 100644
index 6eb40429..00000000
--- a/src/python/gudhi/random_point_generators.cc
+++ /dev/null
@@ -1,61 +0,0 @@
-/*    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
- */
-
-#include <pybind11/pybind11.h>
-#include <pybind11/numpy.h>
-
-#include <gudhi/random_point_generators.h>
-#include <gudhi/Debug_utils.h>
-
-#include <CGAL/Epick_d.h>
-
-namespace py = pybind11;
-
-
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kern;
-
-py::array_t<double> generate_points_on_sphere(size_t num_points, int dim, double radius) {
-
-    py::array_t<double> points({num_points, (size_t)dim});
-
-    py::buffer_info buf = points.request();
-    double *ptr = static_cast<double *>(buf.ptr);
-
-    GUDHI_CHECK(num_points == buf.shape[0], "Py array first dimension not matching num_points on sphere");
-    GUDHI_CHECK(dim == buf.shape[1], "Py array second dimension not matching the ambient space dimension");
-
-
-    py::gil_scoped_release release;
-    auto points_generated = Gudhi::generate_points_on_sphere_d<Kern>(num_points, dim, radius);
-
-    for (size_t i = 0; i < num_points; i++)
-        for (int j = 0; j < dim; j++)
-            ptr[i*dim+j] = points_generated[i][j];
-
-    return points;
-}
-
-PYBIND11_MODULE(random_point_generators, m) {
-      m.attr("__license__") = "LGPL v3";
-      m.def("generate_points_on_sphere_d", &generate_points_on_sphere,
-          py::arg("num_points"), py::arg("dim"), py::arg("radius") = 1,
-          R"pbdoc(
-    Generate random i.i.d. points uniformly on a (d-1)-sphere in R^d
-
-    :param num_points: The number of points to be generated.
-    :type num_points: unsigned integer
-    :param dim: The dimension.
-    :type dim: integer
-    :param radius: The radius.
-    :type radius: float
-    :rtype: numpy array of float
-    :returns: the generated points on a sphere.
-    )pbdoc");
-}
-- 
cgit v1.2.3


From d68ddc94bd82c48a4433ae0b3b1b3f10c167ed0b Mon Sep 17 00:00:00 2001
From: Hind <hind.montassif@gmail.com>
Date: Wed, 28 Apr 2021 14:05:03 +0200
Subject: Add points (dataset type) before the underlying model (sphere) as a
 module

---
 src/python/CMakeLists.txt                          |  6 +--
 ...plex_from_generated_points_on_sphere_example.py |  2 +-
 src/python/gudhi/datasets/generators/__init__.py   |  0
 .../gudhi/datasets/generators/points/__init__.py   |  0
 .../gudhi/datasets/generators/points/sphere.cc     | 61 ++++++++++++++++++++++
 src/python/gudhi/datasets/generators/sphere.cc     | 61 ----------------------
 6 files changed, 65 insertions(+), 65 deletions(-)
 delete mode 100644 src/python/gudhi/datasets/generators/__init__.py
 create mode 100644 src/python/gudhi/datasets/generators/points/__init__.py
 create mode 100644 src/python/gudhi/datasets/generators/points/sphere.cc
 delete mode 100644 src/python/gudhi/datasets/generators/sphere.cc

(limited to 'src/python/example')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index bcdd0741..ef9dc3ab 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -46,7 +46,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'bottleneck', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'hera', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'clustering', ")
-    set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'datasets/generators', ")
+    set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'datasets/generators/points', ")
   endif()
   if(CYTHON_FOUND)
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_reader', ")
@@ -152,7 +152,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/wasserstein', ")
     set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/bottleneck', ")
     if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
-      set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'datasets/generators/sphere', ")
+      set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'datasets/generators/points/sphere', ")
       set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'bottleneck', ")
       set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ")
     endif ()
@@ -264,7 +264,7 @@ if(PYTHONINTERP_FOUND)
     file(COPY "gudhi/weighted_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/dtm_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/hera/__init__.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/hera")
-    file(COPY "gudhi/datasets/generators/__init__.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/datasets/generators")
+    file(COPY "gudhi/datasets/generators/points/__init__.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/datasets/generators/points")
 
 
     # Some files for pip package
diff --git a/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py b/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py
index 2de9ec08..2b023bbe 100644
--- a/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py
+++ b/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-from gudhi.datasets.generators import sphere
+from gudhi.datasets.generators.points import sphere
 from gudhi import AlphaComplex
 
 
diff --git a/src/python/gudhi/datasets/generators/__init__.py b/src/python/gudhi/datasets/generators/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/src/python/gudhi/datasets/generators/points/__init__.py b/src/python/gudhi/datasets/generators/points/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/python/gudhi/datasets/generators/points/sphere.cc b/src/python/gudhi/datasets/generators/points/sphere.cc
new file mode 100644
index 00000000..79392ef0
--- /dev/null
+++ b/src/python/gudhi/datasets/generators/points/sphere.cc
@@ -0,0 +1,61 @@
+/*    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
+ */
+
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+
+#include <gudhi/random_point_generators.h>
+#include <gudhi/Debug_utils.h>
+
+#include <CGAL/Epick_d.h>
+
+namespace py = pybind11;
+
+
+typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kern;
+
+py::array_t<double> generate_points_on_sphere(size_t num_points, int dim, double radius) {
+
+    py::array_t<double> points({num_points, (size_t)dim});
+
+    py::buffer_info buf = points.request();
+    double *ptr = static_cast<double *>(buf.ptr);
+
+    GUDHI_CHECK(num_points == buf.shape[0], "Py array first dimension not matching num_points on sphere");
+    GUDHI_CHECK(dim == buf.shape[1], "Py array second dimension not matching the ambient space dimension");
+
+
+    py::gil_scoped_release release;
+    auto points_generated = Gudhi::generate_points_on_sphere_d<Kern>(num_points, dim, radius);
+
+    for (size_t i = 0; i < num_points; i++)
+        for (int j = 0; j < dim; j++)
+            ptr[i*dim+j] = points_generated[i][j];
+
+    return points;
+}
+
+PYBIND11_MODULE(sphere, m) {
+      m.attr("__license__") = "LGPL v3";
+      m.def("generate_random_points", &generate_points_on_sphere,
+          py::arg("num_points"), py::arg("dim"), py::arg("radius") = 1,
+          R"pbdoc(
+    Generate random i.i.d. points uniformly on a (d-1)-sphere in R^d
+
+    :param num_points: The number of points to be generated.
+    :type num_points: unsigned integer
+    :param dim: The dimension.
+    :type dim: integer
+    :param radius: The radius.
+    :type radius: float
+    :rtype: numpy array of float
+    :returns: the generated points on a sphere.
+    )pbdoc");
+}
diff --git a/src/python/gudhi/datasets/generators/sphere.cc b/src/python/gudhi/datasets/generators/sphere.cc
deleted file mode 100644
index 79392ef0..00000000
--- a/src/python/gudhi/datasets/generators/sphere.cc
+++ /dev/null
@@ -1,61 +0,0 @@
-/*    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
- */
-
-#include <pybind11/pybind11.h>
-#include <pybind11/numpy.h>
-
-#include <gudhi/random_point_generators.h>
-#include <gudhi/Debug_utils.h>
-
-#include <CGAL/Epick_d.h>
-
-namespace py = pybind11;
-
-
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kern;
-
-py::array_t<double> generate_points_on_sphere(size_t num_points, int dim, double radius) {
-
-    py::array_t<double> points({num_points, (size_t)dim});
-
-    py::buffer_info buf = points.request();
-    double *ptr = static_cast<double *>(buf.ptr);
-
-    GUDHI_CHECK(num_points == buf.shape[0], "Py array first dimension not matching num_points on sphere");
-    GUDHI_CHECK(dim == buf.shape[1], "Py array second dimension not matching the ambient space dimension");
-
-
-    py::gil_scoped_release release;
-    auto points_generated = Gudhi::generate_points_on_sphere_d<Kern>(num_points, dim, radius);
-
-    for (size_t i = 0; i < num_points; i++)
-        for (int j = 0; j < dim; j++)
-            ptr[i*dim+j] = points_generated[i][j];
-
-    return points;
-}
-
-PYBIND11_MODULE(sphere, m) {
-      m.attr("__license__") = "LGPL v3";
-      m.def("generate_random_points", &generate_points_on_sphere,
-          py::arg("num_points"), py::arg("dim"), py::arg("radius") = 1,
-          R"pbdoc(
-    Generate random i.i.d. points uniformly on a (d-1)-sphere in R^d
-
-    :param num_points: The number of points to be generated.
-    :type num_points: unsigned integer
-    :param dim: The dimension.
-    :type dim: integer
-    :param radius: The radius.
-    :type radius: float
-    :rtype: numpy array of float
-    :returns: the generated points on a sphere.
-    )pbdoc");
-}
-- 
cgit v1.2.3


From 2b694f9beae0e5fa78ae5b8923e7f2905c58777f Mon Sep 17 00:00:00 2001
From: Hind Montassif <hind.montassif@gmail.com>
Date: Wed, 5 May 2021 13:58:30 +0200
Subject: Add __init__ files at every level in modules Remove last modules
 level and add sample type argument Rename num_points to n_samples

---
 src/python/CMakeLists.txt                          |  7 +--
 ...plex_from_generated_points_on_sphere_example.py |  7 +--
 src/python/gudhi/datasets/__init__.py              |  0
 src/python/gudhi/datasets/generators/__init__.py   |  0
 src/python/gudhi/datasets/generators/points.cc     | 68 ++++++++++++++++++++++
 .../gudhi/datasets/generators/points/__init__.py   |  0
 .../gudhi/datasets/generators/points/sphere.cc     | 61 -------------------
 7 files changed, 74 insertions(+), 69 deletions(-)
 create mode 100644 src/python/gudhi/datasets/__init__.py
 create mode 100644 src/python/gudhi/datasets/generators/__init__.py
 create mode 100644 src/python/gudhi/datasets/generators/points.cc
 delete mode 100644 src/python/gudhi/datasets/generators/points/__init__.py
 delete mode 100644 src/python/gudhi/datasets/generators/points/sphere.cc

(limited to 'src/python/example')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index ef9dc3ab..8dd4ea5d 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -46,7 +46,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'bottleneck', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'hera', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'clustering', ")
-    set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'datasets/generators/points', ")
+    set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'datasets', ")
   endif()
   if(CYTHON_FOUND)
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_reader', ")
@@ -152,7 +152,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/wasserstein', ")
     set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/bottleneck', ")
     if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
-      set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'datasets/generators/points/sphere', ")
+      set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'datasets/generators/points', ")
       set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'bottleneck', ")
       set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ")
     endif ()
@@ -264,8 +264,7 @@ if(PYTHONINTERP_FOUND)
     file(COPY "gudhi/weighted_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/dtm_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/hera/__init__.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/hera")
-    file(COPY "gudhi/datasets/generators/points/__init__.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/datasets/generators/points")
-
+    file(COPY "gudhi/datasets" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi" FILES_MATCHING PATTERN "*.py")
 
     # Some files for pip package
     file(COPY "introduction.rst" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
diff --git a/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py b/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py
index 2b023bbe..e73584d3 100644
--- a/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py
+++ b/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-from gudhi.datasets.generators.points import sphere
+from gudhi.datasets.generators import points
 from gudhi import AlphaComplex
 
 
@@ -22,11 +22,10 @@ print("#####################################################################")
 print("AlphaComplex creation from generated points on sphere")
 
 
-# Generate a circle: 50 points; dim 2; radius 1
-points = sphere.generate_random_points(50, 2, 1)
+gen_points = points.sphere(n_samples = 50, dim = 2, radius = 1, sample = "random")
 
 # Create an alpha complex
-alpha_complex = AlphaComplex(points=points)
+alpha_complex = AlphaComplex(points = gen_points)
 simplex_tree = alpha_complex.create_simplex_tree()
 
 result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
diff --git a/src/python/gudhi/datasets/__init__.py b/src/python/gudhi/datasets/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/python/gudhi/datasets/generators/__init__.py b/src/python/gudhi/datasets/generators/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/python/gudhi/datasets/generators/points.cc b/src/python/gudhi/datasets/generators/points.cc
new file mode 100644
index 00000000..f02c7d73
--- /dev/null
+++ b/src/python/gudhi/datasets/generators/points.cc
@@ -0,0 +1,68 @@
+/*    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
+ */
+
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+
+#include <gudhi/random_point_generators.h>
+#include <gudhi/Debug_utils.h>
+
+#include <CGAL/Epick_d.h>
+
+namespace py = pybind11;
+
+
+typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kern;
+
+py::array_t<double> generate_points_on_sphere(size_t n_samples, int dim, double radius, std::string sample) {
+    
+    if (sample != "random") {
+        throw pybind11::value_error("sample type is not supported");
+    }
+
+    py::array_t<double> points({n_samples, (size_t)dim});
+
+    py::buffer_info buf = points.request();
+    double *ptr = static_cast<double *>(buf.ptr);
+
+    GUDHI_CHECK(n_samples == buf.shape[0], "Py array first dimension not matching n_samples on sphere");
+    GUDHI_CHECK(dim == buf.shape[1], "Py array second dimension not matching the ambient space dimension");
+
+
+    py::gil_scoped_release release;
+    auto points_generated = Gudhi::generate_points_on_sphere_d<Kern>(n_samples, dim, radius);
+
+    for (size_t i = 0; i < n_samples; i++)
+        for (int j = 0; j < dim; j++)
+            ptr[i*dim+j] = points_generated[i][j];
+
+    return points;
+}
+
+PYBIND11_MODULE(points, m) {
+      m.attr("__license__") = "LGPL v3";
+      m.def("sphere", &generate_points_on_sphere,
+          py::arg("n_samples"), py::arg("dim"),
+          py::arg("radius") = 1, py::arg("sample") = "random",
+          R"pbdoc(
+    Generate random i.i.d. points uniformly on a (d-1)-sphere in R^d
+
+    :param n_samples: The number of points to be generated.
+    :type n_samples: integer
+    :param dim: The ambient dimension d.
+    :type dim: integer
+    :param radius: The radius.
+    :type radius: float
+    :param sample: The sample type.
+    :type sample: string
+    :rtype: numpy array of float
+    :returns: the generated points on a sphere.
+    )pbdoc");
+}
diff --git a/src/python/gudhi/datasets/generators/points/__init__.py b/src/python/gudhi/datasets/generators/points/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/src/python/gudhi/datasets/generators/points/sphere.cc b/src/python/gudhi/datasets/generators/points/sphere.cc
deleted file mode 100644
index 79392ef0..00000000
--- a/src/python/gudhi/datasets/generators/points/sphere.cc
+++ /dev/null
@@ -1,61 +0,0 @@
-/*    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
- */
-
-#include <pybind11/pybind11.h>
-#include <pybind11/numpy.h>
-
-#include <gudhi/random_point_generators.h>
-#include <gudhi/Debug_utils.h>
-
-#include <CGAL/Epick_d.h>
-
-namespace py = pybind11;
-
-
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kern;
-
-py::array_t<double> generate_points_on_sphere(size_t num_points, int dim, double radius) {
-
-    py::array_t<double> points({num_points, (size_t)dim});
-
-    py::buffer_info buf = points.request();
-    double *ptr = static_cast<double *>(buf.ptr);
-
-    GUDHI_CHECK(num_points == buf.shape[0], "Py array first dimension not matching num_points on sphere");
-    GUDHI_CHECK(dim == buf.shape[1], "Py array second dimension not matching the ambient space dimension");
-
-
-    py::gil_scoped_release release;
-    auto points_generated = Gudhi::generate_points_on_sphere_d<Kern>(num_points, dim, radius);
-
-    for (size_t i = 0; i < num_points; i++)
-        for (int j = 0; j < dim; j++)
-            ptr[i*dim+j] = points_generated[i][j];
-
-    return points;
-}
-
-PYBIND11_MODULE(sphere, m) {
-      m.attr("__license__") = "LGPL v3";
-      m.def("generate_random_points", &generate_points_on_sphere,
-          py::arg("num_points"), py::arg("dim"), py::arg("radius") = 1,
-          R"pbdoc(
-    Generate random i.i.d. points uniformly on a (d-1)-sphere in R^d
-
-    :param num_points: The number of points to be generated.
-    :type num_points: unsigned integer
-    :param dim: The dimension.
-    :type dim: integer
-    :param radius: The radius.
-    :type radius: float
-    :rtype: numpy array of float
-    :returns: the generated points on a sphere.
-    )pbdoc");
-}
-- 
cgit v1.2.3


From 62510e70009ff2fc65028b88b56886fb53743e51 Mon Sep 17 00:00:00 2001
From: Hind Montassif <hind.montassif@gmail.com>
Date: Mon, 10 May 2021 10:58:36 +0200
Subject: Rename dim to ambient_dim for sphere (to be consistent with dim in
 torus)

---
 ..._complex_from_generated_points_on_sphere_example.py |  2 +-
 src/python/gudhi/datasets/generators/points.cc         | 18 +++++++++---------
 2 files changed, 10 insertions(+), 10 deletions(-)

(limited to 'src/python/example')

diff --git a/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py b/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py
index e73584d3..267e6436 100644
--- a/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py
+++ b/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py
@@ -22,7 +22,7 @@ print("#####################################################################")
 print("AlphaComplex creation from generated points on sphere")
 
 
-gen_points = points.sphere(n_samples = 50, dim = 2, radius = 1, sample = "random")
+gen_points = points.sphere(n_samples = 50, ambient_dim = 2, radius = 1, sample = "random")
 
 # Create an alpha complex
 alpha_complex = AlphaComplex(points = gen_points)
diff --git a/src/python/gudhi/datasets/generators/points.cc b/src/python/gudhi/datasets/generators/points.cc
index f02c7d73..e2626b09 100644
--- a/src/python/gudhi/datasets/generators/points.cc
+++ b/src/python/gudhi/datasets/generators/points.cc
@@ -21,27 +21,27 @@ namespace py = pybind11;
 
 typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kern;
 
-py::array_t<double> generate_points_on_sphere(size_t n_samples, int dim, double radius, std::string sample) {
+py::array_t<double> generate_points_on_sphere(size_t n_samples, int ambient_dim, double radius, std::string sample) {
     
     if (sample != "random") {
         throw pybind11::value_error("sample type is not supported");
     }
 
-    py::array_t<double> points({n_samples, (size_t)dim});
+    py::array_t<double> points({n_samples, (size_t)ambient_dim});
 
     py::buffer_info buf = points.request();
     double *ptr = static_cast<double *>(buf.ptr);
 
     GUDHI_CHECK(n_samples == buf.shape[0], "Py array first dimension not matching n_samples on sphere");
-    GUDHI_CHECK(dim == buf.shape[1], "Py array second dimension not matching the ambient space dimension");
+    GUDHI_CHECK(ambient_dim == buf.shape[1], "Py array second dimension not matching the ambient space dimension");
 
 
     py::gil_scoped_release release;
-    auto points_generated = Gudhi::generate_points_on_sphere_d<Kern>(n_samples, dim, radius);
+    auto points_generated = Gudhi::generate_points_on_sphere_d<Kern>(n_samples, ambient_dim, radius);
 
     for (size_t i = 0; i < n_samples; i++)
-        for (int j = 0; j < dim; j++)
-            ptr[i*dim+j] = points_generated[i][j];
+        for (int j = 0; j < ambient_dim; j++)
+            ptr[i*ambient_dim+j] = points_generated[i][j];
 
     return points;
 }
@@ -49,15 +49,15 @@ py::array_t<double> generate_points_on_sphere(size_t n_samples, int dim, double
 PYBIND11_MODULE(points, m) {
       m.attr("__license__") = "LGPL v3";
       m.def("sphere", &generate_points_on_sphere,
-          py::arg("n_samples"), py::arg("dim"),
+          py::arg("n_samples"), py::arg("ambient_dim"),
           py::arg("radius") = 1, py::arg("sample") = "random",
           R"pbdoc(
     Generate random i.i.d. points uniformly on a (d-1)-sphere in R^d
 
     :param n_samples: The number of points to be generated.
     :type n_samples: integer
-    :param dim: The ambient dimension d.
-    :type dim: integer
+    :param ambient_dim: The ambient dimension d.
+    :type ambient_dim: integer
     :param radius: The radius.
     :type radius: float
     :param sample: The sample type.
-- 
cgit v1.2.3


From a571f198535b5ab5751eb55693371e9348aa1804 Mon Sep 17 00:00:00 2001
From: Hind-M <hind.montassif@gmail.com>
Date: Fri, 21 May 2021 17:32:43 +0200
Subject: Fix issue #489 RipsComplex out of bounds access

---
 ...ips_complex_diagram_persistence_from_distance_matrix_file_example.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'src/python/example')

diff --git a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
index 236d085d..9320d904 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -44,7 +44,7 @@ print("RipsComplex creation from distance matrix read in a csv file")
 message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
 print(message)
 
-distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file)
+distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file, separator=',')
 rips_complex = gudhi.RipsComplex(
     distance_matrix=distance_matrix, max_edge_length=args.max_edge_length
 )
-- 
cgit v1.2.3


From 8b3c55502718e4c184d828151ee6f75fd2cfc9eb Mon Sep 17 00:00:00 2001
From: Hind-M <hind.montassif@gmail.com>
Date: Tue, 25 May 2021 18:01:54 +0200
Subject: Add a separator argument that goes with the
 rips_complex_diagram_persistence_from_distance_matrix_file_example input file
 Specify explicitly the separator when using a specific input file

---
 src/common/test/test_distance_matrix_reader.cpp                      | 2 +-
 src/python/CMakeLists.txt                                            | 2 +-
 ..._complex_diagram_persistence_from_distance_matrix_file_example.py | 5 +++--
 src/python/test/test_reader_utils.py                                 | 2 +-
 4 files changed, 6 insertions(+), 5 deletions(-)

(limited to 'src/python/example')

diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp
index 73be8104..92e899b8 100644
--- a/src/common/test/test_distance_matrix_reader.cpp
+++ b/src/common/test/test_distance_matrix_reader.cpp
@@ -57,7 +57,7 @@ BOOST_AUTO_TEST_CASE( full_square_distance_matrix )
 {
   Distance_matrix from_full_square;
   // Read full_square_distance_matrix.csv file where the separator is the default one ';'
-  from_full_square = Gudhi::read_lower_triangular_matrix_from_csv_file<double>("full_square_distance_matrix.csv");
+  from_full_square = Gudhi::read_lower_triangular_matrix_from_csv_file<double>("full_square_distance_matrix.csv", ';');
   for (auto& i : from_full_square) {
     for (auto j : i) {
       std::clog << j << " ";
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index a1440cbc..bc9a3b7b 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -457,7 +457,7 @@ if(PYTHONINTERP_FOUND)
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -s , -e 12.0 -d 3)
 
     add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
diff --git a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
index 9320d904..8a9cc857 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -21,11 +21,12 @@ parser = argparse.ArgumentParser(
     description="RipsComplex creation from " "a distance matrix read in a csv file.",
     epilog="Example: "
     "example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py "
-    "-f ../data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3"
+    "-f ../data/distance_matrix/lower_triangular_distance_matrix.csv -s , -e 12.0 -d 3"
     "- Constructs a Rips complex with the "
     "distance matrix from the given csv file.",
 )
 parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-s", "--separator", type=str, required=True)
 parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
 parser.add_argument("-b", "--band", type=float, default=0.0)
@@ -44,7 +45,7 @@ print("RipsComplex creation from distance matrix read in a csv file")
 message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
 print(message)
 
-distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file, separator=',')
+distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file, separator=args.separator)
 rips_complex = gudhi.RipsComplex(
     distance_matrix=distance_matrix, max_edge_length=args.max_edge_length
 )
diff --git a/src/python/test/test_reader_utils.py b/src/python/test/test_reader_utils.py
index 90da6651..e96e0569 100755
--- a/src/python/test/test_reader_utils.py
+++ b/src/python/test/test_reader_utils.py
@@ -30,7 +30,7 @@ def test_full_square_distance_matrix_csv_file():
     test_file.write("0;1;2;3;\n1;0;4;5;\n2;4;0;6;\n3;5;6;0;")
     test_file.close()
     matrix = gudhi.read_lower_triangular_matrix_from_csv_file(
-        csv_file="full_square_distance_matrix.csv"
+        csv_file="full_square_distance_matrix.csv", separator=";"
     )
     assert matrix == [[], [1.0], [2.0, 4.0], [3.0, 5.0, 6.0]]
 
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