From 68b6e3f3d641cd4a1e86f08bff96e417cc17ac59 Mon Sep 17 00:00:00 2001
From: takeshimeonerespect <m.takenouchi@fujitsu.com>
Date: Fri, 31 Jan 2020 08:08:43 +0100
Subject: timedelay added on fork

---
 src/python/CMakeLists.txt                 |  5 +++
 src/python/doc/point_cloud.rst            |  7 ++++
 src/python/gudhi/point_cloud/timedelay.py | 56 +++++++++++++++++++++++++++++++
 src/python/test/test_point_cloud.py       | 35 +++++++++++++++++++
 4 files changed, 103 insertions(+)
 create mode 100644 src/python/gudhi/point_cloud/timedelay.py
 create mode 100755 src/python/test/test_point_cloud.py

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index b558d4c4..b23ec8a9 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -52,6 +52,7 @@ if(PYTHONINTERP_FOUND)
     # Modules that should not be auto-imported in __init__.py
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'representations', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'wasserstein', ")
+    set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'point_cloud', ")
 
     add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}")
     add_gudhi_debug_info("Cython version ${CYTHON_VERSION}")
@@ -221,6 +222,7 @@ endif(CGAL_FOUND)
     file(COPY "gudhi/persistence_graphical_tools.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/representations" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/")
     file(COPY "gudhi/wasserstein.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
+    file(COPY "gudhi/point_cloud" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
 
     add_custom_command(
         OUTPUT gudhi.so
@@ -399,6 +401,9 @@ endif(CGAL_FOUND)
       add_gudhi_py_test(test_representations)
     endif()
 
+    # Point cloud
+    add_gudhi_py_test(test_point_cloud)
+
     # Documentation generation is available through sphinx - requires all modules
     if(SPHINX_PATH)
       if(MATPLOTLIB_FOUND)
diff --git a/src/python/doc/point_cloud.rst b/src/python/doc/point_cloud.rst
index d668428a..55c74ff3 100644
--- a/src/python/doc/point_cloud.rst
+++ b/src/python/doc/point_cloud.rst
@@ -20,3 +20,10 @@ Subsampling
    :members:
    :special-members:
    :show-inheritance:
+
+TimeDelayEmbedding
+------------------
+
+.. autoclass:: gudhi.point_cloud.timedelay.TimeDelayEmbedding
+   :members:
+
diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
new file mode 100644
index 00000000..5c7ba542
--- /dev/null
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -0,0 +1,56 @@
+import numpy as np
+
+class TimeDelayEmbedding:
+    """Point cloud transformation class.
+
+    Embeds time-series data in the R^d according to Takens' Embedding Theorem
+    and obtains the coordinates of each point.
+
+    Parameters
+    ----------
+    dim : int, optional (default=3)
+        `d` of R^d to be embedded.
+
+    delay : int, optional (default=1)
+        Time-Delay embedding.
+
+    skip : int, optional (default=1)
+        How often to skip embedded points.
+
+    """
+    def __init__(self, dim=3, delay=1, skip=1):
+        self._dim = dim
+        self._delay = delay
+        self._skip = skip
+
+    def __call__(self, *args, **kwargs):
+        return self.transform(*args, **kwargs)
+
+    def _transform(self, ts):
+        """Guts of transform method."""
+        return ts[
+            np.add.outer(
+                np.arange(0, len(ts)-self._delay*(self._dim-1), self._skip),
+                np.arange(0, self._dim*self._delay, self._delay))
+        ]
+
+    def transform(self, ts):
+        """Transform method.
+
+        Parameters
+        ----------
+        ts : list[float] or list[list[float]]
+            A single or multiple time-series data.
+
+        Returns
+        -------
+        point clouds : list[list[float, float, float]] or list[list[list[float, float, float]]]
+            Makes point cloud every a single time-series data.
+        """
+        ndts = np.array(ts)
+        if ndts.ndim == 1:
+            # for single.
+            return self._transform(ndts).tolist()
+        else:
+            # for multiple.
+            return np.apply_along_axis(self._transform, 1, ndts).tolist()
diff --git a/src/python/test/test_point_cloud.py b/src/python/test/test_point_cloud.py
new file mode 100755
index 00000000..2ee0c1fb
--- /dev/null
+++ b/src/python/test/test_point_cloud.py
@@ -0,0 +1,35 @@
+from gudhi.point_cloud.timedelay import TimeDelayEmbedding
+
+def test_normal():
+    # Sample array
+    ts = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+    # Normal case.
+    prep = TimeDelayEmbedding()
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 2, 3])
+    assert (attractor[1] == [2, 3, 4])
+    assert (attractor[2] == [3, 4, 5])
+    assert (attractor[3] == [4, 5, 6])
+    assert (attractor[4] == [5, 6, 7])
+    assert (attractor[5] == [6, 7, 8])
+    assert (attractor[6] == [7, 8, 9])
+    assert (attractor[7] == [8, 9, 10])
+    # Delay = 3
+    prep = TimeDelayEmbedding(delay=3)
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 4, 7])
+    assert (attractor[1] == [2, 5, 8])
+    assert (attractor[2] == [3, 6, 9])
+    assert (attractor[3] == [4, 7, 10])
+    # Skip = 3
+    prep = TimeDelayEmbedding(skip=3)
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 2, 3])
+    assert (attractor[1] == [4, 5, 6])
+    assert (attractor[2] == [7, 8, 9])
+    # Delay = 2 / Skip = 2
+    prep = TimeDelayEmbedding(delay=2, skip=2)
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 3, 5])
+    assert (attractor[1] == [3, 5, 7])
+    assert (attractor[2] == [5, 7, 9])
-- 
cgit v1.2.3


From d6afaa8300daa6204282a7d34df6bea33ea59fd2 Mon Sep 17 00:00:00 2001
From: takeshimeonerespect
 <58589594+takeshimeonerespect@users.noreply.github.com>
Date: Mon, 3 Feb 2020 14:13:52 +0900
Subject: Update timedelay.py

---
 src/python/gudhi/point_cloud/timedelay.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
index 5c7ba542..f283916d 100644
--- a/src/python/gudhi/point_cloud/timedelay.py
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -1,3 +1,11 @@
+# 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):       Martin Royer, Yuichi Ike, Masatoshi Takenouchi
+#
+# Copyright (C) 2020 Inria, Copyright (C) 2020 Fujitsu Laboratories Ltd.
+# Modification(s):
+#   - YYYY/MM Author: Description of the modification
+
 import numpy as np
 
 class TimeDelayEmbedding:
-- 
cgit v1.2.3


From eded147ffffe5b7143cad19ecd134fb7a63991a3 Mon Sep 17 00:00:00 2001
From: takenouchi <m.takenouchi@fujitsu.com>
Date: Tue, 4 Feb 2020 14:08:19 +0900
Subject: change a file name

---
 src/python/test/test_time_delay.py | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100755 src/python/test/test_time_delay.py

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
new file mode 100755
index 00000000..2ee0c1fb
--- /dev/null
+++ b/src/python/test/test_time_delay.py
@@ -0,0 +1,35 @@
+from gudhi.point_cloud.timedelay import TimeDelayEmbedding
+
+def test_normal():
+    # Sample array
+    ts = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+    # Normal case.
+    prep = TimeDelayEmbedding()
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 2, 3])
+    assert (attractor[1] == [2, 3, 4])
+    assert (attractor[2] == [3, 4, 5])
+    assert (attractor[3] == [4, 5, 6])
+    assert (attractor[4] == [5, 6, 7])
+    assert (attractor[5] == [6, 7, 8])
+    assert (attractor[6] == [7, 8, 9])
+    assert (attractor[7] == [8, 9, 10])
+    # Delay = 3
+    prep = TimeDelayEmbedding(delay=3)
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 4, 7])
+    assert (attractor[1] == [2, 5, 8])
+    assert (attractor[2] == [3, 6, 9])
+    assert (attractor[3] == [4, 7, 10])
+    # Skip = 3
+    prep = TimeDelayEmbedding(skip=3)
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 2, 3])
+    assert (attractor[1] == [4, 5, 6])
+    assert (attractor[2] == [7, 8, 9])
+    # Delay = 2 / Skip = 2
+    prep = TimeDelayEmbedding(delay=2, skip=2)
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 3, 5])
+    assert (attractor[1] == [3, 5, 7])
+    assert (attractor[2] == [5, 7, 9])
-- 
cgit v1.2.3


From 5ddb724824798fe194a66285e29ea4c5cc2713e2 Mon Sep 17 00:00:00 2001
From: takeshimeonerespect <m.takenouchi@fujitsu.com>
Date: Tue, 4 Feb 2020 14:24:27 +0900
Subject: Delete test_point_cloud.py

---
 src/python/test/test_point_cloud.py | 35 -----------------------------------
 1 file changed, 35 deletions(-)
 delete mode 100755 src/python/test/test_point_cloud.py

diff --git a/src/python/test/test_point_cloud.py b/src/python/test/test_point_cloud.py
deleted file mode 100755
index 2ee0c1fb..00000000
--- a/src/python/test/test_point_cloud.py
+++ /dev/null
@@ -1,35 +0,0 @@
-from gudhi.point_cloud.timedelay import TimeDelayEmbedding
-
-def test_normal():
-    # Sample array
-    ts = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
-    # Normal case.
-    prep = TimeDelayEmbedding()
-    attractor = prep(ts)
-    assert (attractor[0] == [1, 2, 3])
-    assert (attractor[1] == [2, 3, 4])
-    assert (attractor[2] == [3, 4, 5])
-    assert (attractor[3] == [4, 5, 6])
-    assert (attractor[4] == [5, 6, 7])
-    assert (attractor[5] == [6, 7, 8])
-    assert (attractor[6] == [7, 8, 9])
-    assert (attractor[7] == [8, 9, 10])
-    # Delay = 3
-    prep = TimeDelayEmbedding(delay=3)
-    attractor = prep(ts)
-    assert (attractor[0] == [1, 4, 7])
-    assert (attractor[1] == [2, 5, 8])
-    assert (attractor[2] == [3, 6, 9])
-    assert (attractor[3] == [4, 7, 10])
-    # Skip = 3
-    prep = TimeDelayEmbedding(skip=3)
-    attractor = prep(ts)
-    assert (attractor[0] == [1, 2, 3])
-    assert (attractor[1] == [4, 5, 6])
-    assert (attractor[2] == [7, 8, 9])
-    # Delay = 2 / Skip = 2
-    prep = TimeDelayEmbedding(delay=2, skip=2)
-    attractor = prep(ts)
-    assert (attractor[0] == [1, 3, 5])
-    assert (attractor[1] == [3, 5, 7])
-    assert (attractor[2] == [5, 7, 9])
-- 
cgit v1.2.3


From 596355344e6205d02110e38a0cb7e0a94e8dbd27 Mon Sep 17 00:00:00 2001
From: takenouchi <m.takenouchi@fujitsu.com>
Date: Thu, 6 Feb 2020 16:00:47 +0900
Subject: modify CMakeLists.txt

---
 src/python/CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index b23ec8a9..798e2907 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -401,8 +401,8 @@ endif(CGAL_FOUND)
       add_gudhi_py_test(test_representations)
     endif()
 
-    # Point cloud
-    add_gudhi_py_test(test_point_cloud)
+    # Time Delay
+    add_gudhi_py_test(test_time_delay)
 
     # Documentation generation is available through sphinx - requires all modules
     if(SPHINX_PATH)
-- 
cgit v1.2.3


From a6a4f375822cf3e2ca1866d78472e4350140ddbc Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 11:02:56 +0900
Subject: Add __init__.py

---
 src/python/gudhi/point_cloud/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 src/python/gudhi/point_cloud/__init__.py

diff --git a/src/python/gudhi/point_cloud/__init__.py b/src/python/gudhi/point_cloud/__init__.py
new file mode 100644
index 00000000..e69de29b
-- 
cgit v1.2.3


From 9cc9e1cf3cd9ea42908324d410ef68fa12e8e832 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 11:08:50 +0900
Subject: Update timedelay.py

---
 src/python/gudhi/point_cloud/timedelay.py | 66 ++++++++++++++++++++++---------
 1 file changed, 48 insertions(+), 18 deletions(-)

diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
index f283916d..d899da67 100644
--- a/src/python/gudhi/point_cloud/timedelay.py
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -10,30 +10,55 @@ import numpy as np
 
 class TimeDelayEmbedding:
     """Point cloud transformation class.
-
     Embeds time-series data in the R^d according to Takens' Embedding Theorem
     and obtains the coordinates of each point.
-
     Parameters
     ----------
     dim : int, optional (default=3)
         `d` of R^d to be embedded.
-
     delay : int, optional (default=1)
         Time-Delay embedding.
-
     skip : int, optional (default=1)
         How often to skip embedded points.
-
+        Given delay=3 and skip=2, an point cloud which is obtained by embedding 
+        a single time-series data into R^3 is as follows.
+        
+    .. code-block:: none
+    
+    time-series = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+    point clouds = [[1, 4, 7], 
+                    [3, 6, 9]]
+                   
     """
     def __init__(self, dim=3, delay=1, skip=1):
         self._dim = dim
         self._delay = delay
         self._skip = skip
 
-    def __call__(self, *args, **kwargs):
-        return self.transform(*args, **kwargs)
+    def __call__(self, ts):
+        """Transform method for single time-series data.
+        Parameters
+        ----------
+        ts : list[float]
+            A single time-series data.
+        Returns
+        -------
+        point clouds : list[list[float, float, float]]
+            Makes point cloud every a single time-series data.
+        Raises
+        -------
+        TypeError
+            If the parameter's type does not match the desired type.
+        """
+        ndts = np.array(ts)
+        if ndts.ndim == 1:
+            return self._transform(ndts)
+        else:
+            raise TypeError("Expects 1-dimensional array.")
 
+    def fit(self, ts, y=None):
+        return self
+    
     def _transform(self, ts):
         """Guts of transform method."""
         return ts[
@@ -43,22 +68,27 @@ class TimeDelayEmbedding:
         ]
 
     def transform(self, ts):
-        """Transform method.
-
+        """Transform method for multiple time-series data.
         Parameters
         ----------
-        ts : list[float] or list[list[float]]
-            A single or multiple time-series data.
-
+        ts : list[list[float]]
+            Multiple time-series data.
+        Attributes
+        ----------
+        ndts : 
+             The ndts means that all time series need to have exactly 
+             the same size. 
         Returns
         -------
-        point clouds : list[list[float, float, float]] or list[list[list[float, float, float]]]
+        point clouds : list[list[list[float, float, float]]]
             Makes point cloud every a single time-series data.
+        Raises
+        -------
+        TypeError
+            If the parameter's type does not match the desired type.
         """
         ndts = np.array(ts)
-        if ndts.ndim == 1:
-            # for single.
-            return self._transform(ndts).tolist()
+        if ndts.ndim == 2:
+            return np.apply_along_axis(self._transform, 1, ndts)
         else:
-            # for multiple.
-            return np.apply_along_axis(self._transform, 1, ndts).tolist()
+            raise TypeError("Expects 2-dimensional array.")
-- 
cgit v1.2.3


From 2253fd03bb49aea455309f6d633a6edeb2362d79 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 17:52:07 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index 2ee0c1fb..d2ffbf40 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -6,30 +6,30 @@ def test_normal():
     # Normal case.
     prep = TimeDelayEmbedding()
     attractor = prep(ts)
-    assert (attractor[0] == [1, 2, 3])
-    assert (attractor[1] == [2, 3, 4])
-    assert (attractor[2] == [3, 4, 5])
-    assert (attractor[3] == [4, 5, 6])
-    assert (attractor[4] == [5, 6, 7])
-    assert (attractor[5] == [6, 7, 8])
-    assert (attractor[6] == [7, 8, 9])
-    assert (attractor[7] == [8, 9, 10])
+    assert (attractor[0] == np.array[1, 2, 3])
+    assert (attractor[1] == np.array[2, 3, 4])
+    assert (attractor[2] == np.array[3, 4, 5])
+    assert (attractor[3] == np.array[4, 5, 6])
+    assert (attractor[4] == np.array[5, 6, 7])
+    assert (attractor[5] == np.array[6, 7, 8])
+    assert (attractor[6] == np.array[7, 8, 9])
+    assert (attractor[7] == np.array[8, 9, 10])
     # Delay = 3
     prep = TimeDelayEmbedding(delay=3)
     attractor = prep(ts)
-    assert (attractor[0] == [1, 4, 7])
-    assert (attractor[1] == [2, 5, 8])
-    assert (attractor[2] == [3, 6, 9])
-    assert (attractor[3] == [4, 7, 10])
+    assert (attractor[0] == np.array[1, 4, 7])
+    assert (attractor[1] == np.array[2, 5, 8])
+    assert (attractor[2] == np.array[3, 6, 9])
+    assert (attractor[3] == np.array[4, 7, 10])
     # Skip = 3
     prep = TimeDelayEmbedding(skip=3)
     attractor = prep(ts)
-    assert (attractor[0] == [1, 2, 3])
-    assert (attractor[1] == [4, 5, 6])
-    assert (attractor[2] == [7, 8, 9])
+    assert (attractor[0] == np.array[1, 2, 3])
+    assert (attractor[1] == np.array[4, 5, 6])
+    assert (attractor[2] == np.array[7, 8, 9])
     # Delay = 2 / Skip = 2
     prep = TimeDelayEmbedding(delay=2, skip=2)
     attractor = prep(ts)
-    assert (attractor[0] == [1, 3, 5])
-    assert (attractor[1] == [3, 5, 7])
-    assert (attractor[2] == [5, 7, 9])
+    assert (attractor[0] == np.array[1, 3, 5])
+    assert (attractor[1] == np.array[3, 5, 7])
+    assert (attractor[2] == np.array[5, 7, 9])
-- 
cgit v1.2.3


From f58a4120b70487aede3cb4e81fbb15171e34fa37 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 18:24:18 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index d2ffbf40..1cdf56f9 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -6,30 +6,30 @@ def test_normal():
     # Normal case.
     prep = TimeDelayEmbedding()
     attractor = prep(ts)
-    assert (attractor[0] == np.array[1, 2, 3])
-    assert (attractor[1] == np.array[2, 3, 4])
-    assert (attractor[2] == np.array[3, 4, 5])
-    assert (attractor[3] == np.array[4, 5, 6])
-    assert (attractor[4] == np.array[5, 6, 7])
-    assert (attractor[5] == np.array[6, 7, 8])
-    assert (attractor[6] == np.array[7, 8, 9])
-    assert (attractor[7] == np.array[8, 9, 10])
+    assert (attractor[0] == np.array([1, 2, 3]))
+    assert (attractor[1] == np.array([2, 3, 4]))
+    assert (attractor[2] == np.array([3, 4, 5]))
+    assert (attractor[3] == np.array([4, 5, 6]))
+    assert (attractor[4] == np.array([5, 6, 7]))
+    assert (attractor[5] == np.array([6, 7, 8]))
+    assert (attractor[6] == np.array([7, 8, 9]))
+    assert (attractor[7] == np.array([8, 9, 10]))
     # Delay = 3
     prep = TimeDelayEmbedding(delay=3)
     attractor = prep(ts)
-    assert (attractor[0] == np.array[1, 4, 7])
-    assert (attractor[1] == np.array[2, 5, 8])
-    assert (attractor[2] == np.array[3, 6, 9])
-    assert (attractor[3] == np.array[4, 7, 10])
+    assert (attractor[0] == np.array([1, 4, 7]))
+    assert (attractor[1] == np.array([2, 5, 8]))
+    assert (attractor[2] == np.array([3, 6, 9]))
+    assert (attractor[3] == np.array([4, 7, 10]))
     # Skip = 3
     prep = TimeDelayEmbedding(skip=3)
     attractor = prep(ts)
-    assert (attractor[0] == np.array[1, 2, 3])
-    assert (attractor[1] == np.array[4, 5, 6])
-    assert (attractor[2] == np.array[7, 8, 9])
+    assert (attractor[0] == np.array([1, 2, 3]))
+    assert (attractor[1] == np.array([4, 5, 6]))
+    assert (attractor[2] == np.array([7, 8, 9]))
     # Delay = 2 / Skip = 2
     prep = TimeDelayEmbedding(delay=2, skip=2)
     attractor = prep(ts)
-    assert (attractor[0] == np.array[1, 3, 5])
-    assert (attractor[1] == np.array[3, 5, 7])
-    assert (attractor[2] == np.array[5, 7, 9])
+    assert (attractor[0] == np.array([1, 3, 5]))
+    assert (attractor[1] == np.array([3, 5, 7]))
+    assert (attractor[2] == np.array([5, 7, 9]))
-- 
cgit v1.2.3


From 1c0f48fb26bb2e606dfe0a22e62618357686e2c2 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 18:49:27 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index 1cdf56f9..3b586ad2 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -1,4 +1,5 @@
 from gudhi.point_cloud.timedelay import TimeDelayEmbedding
+import numpy as np
 
 def test_normal():
     # Sample array
-- 
cgit v1.2.3


From 39873c0cf43ca7352dddeab8c1cc6a3fc40a2e58 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 19:08:50 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index 3b586ad2..7b6562a5 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -7,7 +7,8 @@ def test_normal():
     # Normal case.
     prep = TimeDelayEmbedding()
     attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 2, 3]))
+    assert (attractor[0] == np.array([1, 2, 3])
+            print(attractor[0].all()))
     assert (attractor[1] == np.array([2, 3, 4]))
     assert (attractor[2] == np.array([3, 4, 5]))
     assert (attractor[3] == np.array([4, 5, 6]))
-- 
cgit v1.2.3


From 7c6966ee9821aaeb60d282616445a47071ac1fee Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 19:20:25 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 37 ++++++++++++++++++-------------------
 1 file changed, 18 insertions(+), 19 deletions(-)

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index 7b6562a5..f652fc88 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -7,31 +7,30 @@ def test_normal():
     # Normal case.
     prep = TimeDelayEmbedding()
     attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 2, 3])
-            print(attractor[0].all()))
-    assert (attractor[1] == np.array([2, 3, 4]))
-    assert (attractor[2] == np.array([3, 4, 5]))
-    assert (attractor[3] == np.array([4, 5, 6]))
-    assert (attractor[4] == np.array([5, 6, 7]))
-    assert (attractor[5] == np.array([6, 7, 8]))
-    assert (attractor[6] == np.array([7, 8, 9]))
-    assert (attractor[7] == np.array([8, 9, 10]))
+    assert (attractor[0].all() == np.array([1, 2, 3]))
+    assert (attractor[1].all() == np.array([2, 3, 4]))
+    assert (attractor[2].all() == np.array([3, 4, 5]))
+    assert (attractor[3].all() == np.array([4, 5, 6]))
+    assert (attractor[4].all() == np.array([5, 6, 7]))
+    assert (attractor[5].all() == np.array([6, 7, 8]))
+    assert (attractor[6].all() == np.array([7, 8, 9]))
+    assert (attractor[7].all() == np.array([8, 9, 10]))
     # Delay = 3
     prep = TimeDelayEmbedding(delay=3)
     attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 4, 7]))
-    assert (attractor[1] == np.array([2, 5, 8]))
-    assert (attractor[2] == np.array([3, 6, 9]))
-    assert (attractor[3] == np.array([4, 7, 10]))
+    assert (attractor[0].all() == np.array([1, 4, 7]))
+    assert (attractor[1].all() == np.array([2, 5, 8]))
+    assert (attractor[2].all() == np.array([3, 6, 9]))
+    assert (attractor[3].all() == np.array([4, 7, 10]))
     # Skip = 3
     prep = TimeDelayEmbedding(skip=3)
     attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 2, 3]))
-    assert (attractor[1] == np.array([4, 5, 6]))
-    assert (attractor[2] == np.array([7, 8, 9]))
+    assert (attractor[0].all() == np.array([1, 2, 3]))
+    assert (attractor[1].all() == np.array([4, 5, 6]))
+    assert (attractor[2].all() == np.array([7, 8, 9]))
     # Delay = 2 / Skip = 2
     prep = TimeDelayEmbedding(delay=2, skip=2)
     attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 3, 5]))
-    assert (attractor[1] == np.array([3, 5, 7]))
-    assert (attractor[2] == np.array([5, 7, 9]))
+    assert (attractor[0].all() == np.array([1, 3, 5]))
+    assert (attractor[1].all() == np.array([3, 5, 7]))
+    assert (attractor[2].all() == np.array([5, 7, 9]))
-- 
cgit v1.2.3


From 5023aa0ff30474a96783152844e7fb0ed52e0c98 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 20:25:14 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index f652fc88..5464a185 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -7,30 +7,30 @@ def test_normal():
     # Normal case.
     prep = TimeDelayEmbedding()
     attractor = prep(ts)
-    assert (attractor[0].all() == np.array([1, 2, 3]))
-    assert (attractor[1].all() == np.array([2, 3, 4]))
-    assert (attractor[2].all() == np.array([3, 4, 5]))
-    assert (attractor[3].all() == np.array([4, 5, 6]))
-    assert (attractor[4].all() == np.array([5, 6, 7]))
-    assert (attractor[5].all() == np.array([6, 7, 8]))
-    assert (attractor[6].all() == np.array([7, 8, 9]))
-    assert (attractor[7].all() == np.array([8, 9, 10]))
+    assert (attractor[0] == np.array([1, 2, 3])).all()
+    assert (attractor[1] == np.array([2, 3, 4])).all()
+    assert (attractor[2] == np.array([3, 4, 5])).all()
+    assert (attractor[3] == np.array([4, 5, 6])).all()
+    assert (attractor[4] == np.array([5, 6, 7])).all()
+    assert (attractor[5] == np.array([6, 7, 8])).all()
+    assert (attractor[6] == np.array([7, 8, 9])).all()
+    assert (attractor[7] == np.array([8, 9, 10])).all()
     # Delay = 3
     prep = TimeDelayEmbedding(delay=3)
     attractor = prep(ts)
-    assert (attractor[0].all() == np.array([1, 4, 7]))
-    assert (attractor[1].all() == np.array([2, 5, 8]))
-    assert (attractor[2].all() == np.array([3, 6, 9]))
-    assert (attractor[3].all() == np.array([4, 7, 10]))
+    assert (attractor[0] == np.array([1, 4, 7])).all()
+    assert (attractor[1] == np.array([2, 5, 8])).all()
+    assert (attractor[2] == np.array([3, 6, 9])).all()
+    assert (attractor[3] == np.array([4, 7, 10])).all()
     # Skip = 3
     prep = TimeDelayEmbedding(skip=3)
     attractor = prep(ts)
-    assert (attractor[0].all() == np.array([1, 2, 3]))
-    assert (attractor[1].all() == np.array([4, 5, 6]))
-    assert (attractor[2].all() == np.array([7, 8, 9]))
+    assert (attractor[0] == np.array([1, 2, 3])).all()
+    assert (attractor[1] == np.array([4, 5, 6])).all()
+    assert (attractor[2] == np.array([7, 8, 9])).all()
     # Delay = 2 / Skip = 2
     prep = TimeDelayEmbedding(delay=2, skip=2)
     attractor = prep(ts)
-    assert (attractor[0].all() == np.array([1, 3, 5]))
-    assert (attractor[1].all() == np.array([3, 5, 7]))
-    assert (attractor[2].all() == np.array([5, 7, 9]))
+    assert (attractor[0] == np.array([1, 3, 5])).all()
+    assert (attractor[1] == np.array([3, 5, 7])).all()
+    assert (attractor[2] == np.array([5, 7, 9])).all()
-- 
cgit v1.2.3


From 80d84e5d8f9a24de745d23f7d721ea3e62217ff4 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Wed, 19 Feb 2020 12:32:00 +0900
Subject: Update timedelay.py

---
 src/python/gudhi/point_cloud/timedelay.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
index d899da67..6ad87cdc 100644
--- a/src/python/gudhi/point_cloud/timedelay.py
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -43,7 +43,7 @@ class TimeDelayEmbedding:
             A single time-series data.
         Returns
         -------
-        point clouds : list[list[float, float, float]]
+        point clouds : list of n x 2 numpy arrays
             Makes point cloud every a single time-series data.
         Raises
         -------
@@ -80,7 +80,7 @@ class TimeDelayEmbedding:
              the same size. 
         Returns
         -------
-        point clouds : list[list[list[float, float, float]]]
+        point clouds : list of n x 3 numpy arrays
             Makes point cloud every a single time-series data.
         Raises
         -------
-- 
cgit v1.2.3


From 88964b4ff10798d6d9c3d0a342c004ee6b8b1496 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Tue, 25 Feb 2020 13:21:55 +0900
Subject: Update timedelay.py

---
 src/python/gudhi/point_cloud/timedelay.py | 89 +++++++++++++++----------------
 1 file changed, 44 insertions(+), 45 deletions(-)

diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
index 6ad87cdc..d7a1dab7 100644
--- a/src/python/gudhi/point_cloud/timedelay.py
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -8,10 +8,12 @@
 
 import numpy as np
 
+
 class TimeDelayEmbedding:
     """Point cloud transformation class.
     Embeds time-series data in the R^d according to Takens' Embedding Theorem
     and obtains the coordinates of each point.
+
     Parameters
     ----------
     dim : int, optional (default=3)
@@ -20,16 +22,27 @@ class TimeDelayEmbedding:
         Time-Delay embedding.
     skip : int, optional (default=1)
         How often to skip embedded points.
-        Given delay=3 and skip=2, an point cloud which is obtained by embedding 
-        a single time-series data into R^3 is as follows.
-        
-    .. code-block:: none
-    
-    time-series = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
-    point clouds = [[1, 4, 7], 
-                    [3, 6, 9]]
-                   
+
+    Example
+    -------
+
+    Given delay=3 and skip=2, a point cloud which is obtained by embedding
+    a scalar time-series into R^3 is as follows::
+
+        time-series = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+        point cloud = [[1, 4, 7],
+                       [3, 6, 9]]
+
+    Given delay=1 and skip=1, a point cloud which is obtained by embedding
+    a 2D vector time-series data into R^4 is as follows::
+
+        time-series = [[0, 1], [2, 3], [4, 5], [6, 7], [8, 9]]
+        point cloud = [[0, 1, 2, 3],
+                       [2, 3, 4, 5],
+                       [4, 5, 6, 7],
+                       [6, 7, 8, 9]]
     """
+
     def __init__(self, dim=3, delay=1, skip=1):
         self._dim = dim
         self._delay = delay
@@ -39,56 +52,42 @@ class TimeDelayEmbedding:
         """Transform method for single time-series data.
         Parameters
         ----------
-        ts : list[float]
-            A single time-series data.
+        ts : Iterable[float] or Iterable[Iterable[float]]
+            A single time-series data, with scalar or vector values.
+
         Returns
         -------
-        point clouds : list of n x 2 numpy arrays
-            Makes point cloud every a single time-series data.
-        Raises
-        -------
-        TypeError
-            If the parameter's type does not match the desired type.
+        point cloud : n x dim numpy arrays
+            Makes point cloud from a single time-series data.
         """
-        ndts = np.array(ts)
-        if ndts.ndim == 1:
-            return self._transform(ndts)
-        else:
-            raise TypeError("Expects 1-dimensional array.")
+        return self._transform(np.array(ts))
 
     def fit(self, ts, y=None):
         return self
     
     def _transform(self, ts):
         """Guts of transform method."""
-        return ts[
-            np.add.outer(
-                np.arange(0, len(ts)-self._delay*(self._dim-1), self._skip),
-                np.arange(0, self._dim*self._delay, self._delay))
-        ]
+        if ts.ndim == 1:
+            repeat = self._dim
+        else:
+            assert self._dim % ts.shape[1] == 0
+            repeat = self._dim // ts.shape[1]
+        end = len(ts) - self._delay * (repeat - 1)
+        short = np.arange(0, end, self._skip)
+        vertical = np.arange(0, repeat * self._delay, self._delay)
+        return ts[np.add.outer(short, vertical)].reshape(len(short), -1)
 
     def transform(self, ts):
         """Transform method for multiple time-series data.
+
         Parameters
         ----------
-        ts : list[list[float]]
-            Multiple time-series data.
-        Attributes
-        ----------
-        ndts : 
-             The ndts means that all time series need to have exactly 
-             the same size. 
+        ts : Iterable[Iterable[float]] or Iterable[Iterable[Iterable[float]]]
+            Multiple time-series data, with scalar or vector values.
+
         Returns
         -------
-        point clouds : list of n x 3 numpy arrays
-            Makes point cloud every a single time-series data.
-        Raises
-        -------
-        TypeError
-            If the parameter's type does not match the desired type.
+        point clouds : list of n x dim numpy arrays
+            Makes point cloud from each time-series data.
         """
-        ndts = np.array(ts)
-        if ndts.ndim == 2:
-            return np.apply_along_axis(self._transform, 1, ndts)
-        else:
-            raise TypeError("Expects 2-dimensional array.")
+        return [self._transform(np.array(s)) for s in ts]
-- 
cgit v1.2.3


From 66c96498b994fea1fcaa6877121023410f4209f9 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Tue, 25 Feb 2020 13:24:48 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 51 ++++++++++++++++++++++----------------
 1 file changed, 29 insertions(+), 22 deletions(-)

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index 5464a185..1ead9bca 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -1,36 +1,43 @@
 from gudhi.point_cloud.timedelay import TimeDelayEmbedding
 import numpy as np
 
+
 def test_normal():
     # Sample array
     ts = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
     # Normal case.
     prep = TimeDelayEmbedding()
-    attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 2, 3])).all()
-    assert (attractor[1] == np.array([2, 3, 4])).all()
-    assert (attractor[2] == np.array([3, 4, 5])).all()
-    assert (attractor[3] == np.array([4, 5, 6])).all()
-    assert (attractor[4] == np.array([5, 6, 7])).all()
-    assert (attractor[5] == np.array([6, 7, 8])).all()
-    assert (attractor[6] == np.array([7, 8, 9])).all()
-    assert (attractor[7] == np.array([8, 9, 10])).all()
+    pointclouds = prep(ts)
+    assert (pointclouds[0] == np.array([1, 2, 3])).all()
+    assert (pointclouds[1] == np.array([2, 3, 4])).all()
+    assert (pointclouds[2] == np.array([3, 4, 5])).all()
+    assert (pointclouds[3] == np.array([4, 5, 6])).all()
+    assert (pointclouds[4] == np.array([5, 6, 7])).all()
+    assert (pointclouds[5] == np.array([6, 7, 8])).all()
+    assert (pointclouds[6] == np.array([7, 8, 9])).all()
+    assert (pointclouds[7] == np.array([8, 9, 10])).all()
     # Delay = 3
     prep = TimeDelayEmbedding(delay=3)
-    attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 4, 7])).all()
-    assert (attractor[1] == np.array([2, 5, 8])).all()
-    assert (attractor[2] == np.array([3, 6, 9])).all()
-    assert (attractor[3] == np.array([4, 7, 10])).all()
+    pointclouds = prep(ts)
+    assert (pointclouds[0] == np.array([1, 4, 7])).all()
+    assert (pointclouds[1] == np.array([2, 5, 8])).all()
+    assert (pointclouds[2] == np.array([3, 6, 9])).all()
+    assert (pointclouds[3] == np.array([4, 7, 10])).all()
     # Skip = 3
     prep = TimeDelayEmbedding(skip=3)
-    attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 2, 3])).all()
-    assert (attractor[1] == np.array([4, 5, 6])).all()
-    assert (attractor[2] == np.array([7, 8, 9])).all()
+    pointclouds = prep(ts)
+    assert (pointclouds[0] == np.array([1, 2, 3])).all()
+    assert (pointclouds[1] == np.array([4, 5, 6])).all()
+    assert (pointclouds[2] == np.array([7, 8, 9])).all()
     # Delay = 2 / Skip = 2
     prep = TimeDelayEmbedding(delay=2, skip=2)
-    attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 3, 5])).all()
-    assert (attractor[1] == np.array([3, 5, 7])).all()
-    assert (attractor[2] == np.array([5, 7, 9])).all()
+    pointclouds = prep(ts)
+    assert (pointclouds[0] == np.array([1, 3, 5])).all()
+    assert (pointclouds[1] == np.array([3, 5, 7])).all()
+    assert (pointclouds[2] == np.array([5, 7, 9])).all()
+
+    # Vector series
+    ts = np.arange(0, 10).reshape(-1, 2)
+    prep = TimeDelayEmbedding(dim=4)
+    prep.fit([ts])
+    assert (prep.transform([ts])[0] == [[0, 1, 2, 3], [2, 3, 4, 5], [4, 5, 6, 7], [6, 7, 8, 9]]).all()
-- 
cgit v1.2.3


From a74ec878560bbe5fa340b2650ca9c16471b685af Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Tue, 25 Feb 2020 13:27:03 +0900
Subject: Update point_cloud.rst

---
 src/python/doc/point_cloud.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/python/doc/point_cloud.rst b/src/python/doc/point_cloud.rst
index 55c74ff3..c0d4b303 100644
--- a/src/python/doc/point_cloud.rst
+++ b/src/python/doc/point_cloud.rst
@@ -26,4 +26,5 @@ TimeDelayEmbedding
 
 .. autoclass:: gudhi.point_cloud.timedelay.TimeDelayEmbedding
    :members:
+   :special-members: __call__
 
-- 
cgit v1.2.3


From f25d0f86fcd4ac9ab2939b2919d7a66df8b21269 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Tue, 25 Feb 2020 16:35:41 +0900
Subject: Update timedelay.py

---
 src/python/gudhi/point_cloud/timedelay.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
index d7a1dab7..576f4386 100644
--- a/src/python/gudhi/point_cloud/timedelay.py
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -50,6 +50,7 @@ class TimeDelayEmbedding:
 
     def __call__(self, ts):
         """Transform method for single time-series data.
+
         Parameters
         ----------
         ts : Iterable[float] or Iterable[Iterable[float]]
-- 
cgit v1.2.3


From 2c1edeb7fd241c8718a22618438b482704703b4a Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Tue, 25 Feb 2020 17:46:28 +0900
Subject: Update timedelay.py

---
 src/python/gudhi/point_cloud/timedelay.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
index 576f4386..f01df442 100644
--- a/src/python/gudhi/point_cloud/timedelay.py
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -11,8 +11,9 @@ import numpy as np
 
 class TimeDelayEmbedding:
     """Point cloud transformation class.
-    Embeds time-series data in the R^d according to Takens' Embedding Theorem
-    and obtains the coordinates of each point.
+    Embeds time-series data in the R^d according to [Takens' Embedding Theorem]
+    (https://en.wikipedia.org/wiki/Takens%27s_theorem) and obtains the 
+    coordinates of each point.
 
     Parameters
     ----------
-- 
cgit v1.2.3


From 73194242e1c8012c1320a7581a382a3b2b59eb09 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Tue, 3 Mar 2020 16:30:22 +0100
Subject: Fix #172 and add a proper comment on the modification

---
 src/Simplex_tree/include/gudhi/Simplex_tree.h | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 76608008..5110819f 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -1347,7 +1347,9 @@ class Simplex_tree {
                                                               });
 
       Filtration_value max_filt_border_value = filtration(*max_border);
-      if (simplex.second.filtration() < max_filt_border_value) {
+      // Replacing if(f<max) with if(!(f>=max)) would mean that if f is NaN, we replace it with the max of the children.
+      // That seems more useful than keeping NaN.
+      if (!(simplex.second.filtration() >= max_filt_border_value)) {
         // Store the filtration modification information
         modified = true;
         simplex.second.assign_filtration(max_filt_border_value);
-- 
cgit v1.2.3


From 5b5e9fce6a80151f29f98dde67f5e4150edb9a5b Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Thu, 5 Mar 2020 10:03:26 +0100
Subject: Add some tests and documentation for NaN management in
 make_filtration_non_decreasing Simplex tree method

---
 src/Simplex_tree/include/gudhi/Simplex_tree.h      |   2 +
 src/Simplex_tree/test/CMakeLists.txt               |   6 +
 ...ee_make_filtration_non_decreasing_unit_test.cpp | 148 +++++++++++++++++++++
 src/Simplex_tree/test/simplex_tree_unit_test.cpp   |  84 ------------
 4 files changed, 156 insertions(+), 84 deletions(-)
 create mode 100644 src/Simplex_tree/test/simplex_tree_make_filtration_non_decreasing_unit_test.cpp

diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 5110819f..7b39a500 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -1317,6 +1317,8 @@ class Simplex_tree {
    * \post Some simplex tree functions require the filtration to be valid. `make_filtration_non_decreasing()`
    * function is not launching `initialize_filtration()` but returns the filtration modification information. If the
    * complex has changed , please call `initialize_filtration()` to recompute it.
+   * 
+   * If a simplex has a `NaN` filtration value, it is considered lower than any other defined filtration value.
    */
   bool make_filtration_non_decreasing() {
     bool modified = false;
diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt
index 8b9163f5..cf2b0153 100644
--- a/src/Simplex_tree/test/CMakeLists.txt
+++ b/src/Simplex_tree/test/CMakeLists.txt
@@ -28,3 +28,9 @@ if (TBB_FOUND)
   target_link_libraries(Simplex_tree_ctor_and_move_test_unit ${TBB_LIBRARIES})
 endif()
 gudhi_add_boost_test(Simplex_tree_ctor_and_move_test_unit)
+
+add_executable ( Simplex_tree_make_filtration_non_decreasing_test_unit simplex_tree_make_filtration_non_decreasing_unit_test.cpp )
+if (TBB_FOUND)
+  target_link_libraries(Simplex_tree_make_filtration_non_decreasing_test_unit ${TBB_LIBRARIES})
+endif()
+gudhi_add_boost_test(Simplex_tree_make_filtration_non_decreasing_test_unit)
diff --git a/src/Simplex_tree/test/simplex_tree_make_filtration_non_decreasing_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_make_filtration_non_decreasing_unit_test.cpp
new file mode 100644
index 00000000..a8130e25
--- /dev/null
+++ b/src/Simplex_tree/test/simplex_tree_make_filtration_non_decreasing_unit_test.cpp
@@ -0,0 +1,148 @@
+/*    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) 2020 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#include <iostream>
+#include <limits>  // for NaN
+#include <cmath>  // for isNaN
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "simplex_tree_make_filtration_non_decreasing"
+#include <boost/test/unit_test.hpp>
+#include <boost/mpl/list.hpp>
+
+//  ^
+// /!\ Nothing else from Simplex_tree shall be included to test includes are well defined.
+#include "gudhi/Simplex_tree.h"
+
+using namespace Gudhi;
+
+typedef boost::mpl::list<Simplex_tree<>, Simplex_tree<Simplex_tree_options_fast_persistence>> list_of_tested_variants;
+
+BOOST_AUTO_TEST_CASE_TEMPLATE(make_filtration_non_decreasing, typeST, list_of_tested_variants) {
+  typeST st;
+
+  st.insert_simplex_and_subfaces({2, 1, 0}, 2.0);
+  st.insert_simplex_and_subfaces({3, 0}, 2.0);
+  st.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
+  
+  /* Inserted simplex:     */
+  /*    1                  */
+  /*    o                  */
+  /*   /X\                 */
+  /*  o---o---o---o        */
+  /*  2   0   3\X/4        */
+  /*            o          */
+  /*            5          */
+
+  std::cout << "Check default insertion ensures the filtration values are non decreasing" << std::endl;
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+
+  // Because of non decreasing property of simplex tree, { 0 } , { 1 } and { 0, 1 } are going to be set from value 2.0
+  // to 1.0
+  st.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
+  
+  // Inserted simplex:
+  //    1   6
+  //    o---o
+  //   /X\7/
+  //  o---o---o---o
+  //  2   0   3\X/4
+  //            o
+  //            5
+  
+  std::cout << "Check default second insertion ensures the filtration values are non decreasing" << std::endl;
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+  
+  // Copy original simplex tree
+  typeST st_copy = st;
+
+  // Modify specific values for st to become like st_copy thanks to make_filtration_non_decreasing
+  st.assign_filtration(st.find({0,1,6,7}), 0.8);
+  st.assign_filtration(st.find({0,1,6}), 0.9);
+  st.assign_filtration(st.find({0,6}), 0.6);
+  st.assign_filtration(st.find({3,4,5}), 1.2);
+  st.assign_filtration(st.find({3,4}), 1.1);
+  st.assign_filtration(st.find({4,5}), 1.99);
+  
+  std::cout << "Check the simplex_tree is rolled back in case of decreasing filtration values" << std::endl;
+  BOOST_CHECK(st.make_filtration_non_decreasing());
+  BOOST_CHECK(st == st_copy);
+
+  // Other simplex tree
+  typeST st_other;
+  st_other.insert_simplex_and_subfaces({2, 1, 0}, 3.0);  // This one is different from st
+  st_other.insert_simplex_and_subfaces({3, 0}, 2.0);
+  st_other.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
+  st_other.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
+
+  // Modify specific values for st to become like st_other thanks to make_filtration_non_decreasing
+  st.assign_filtration(st.find({2}), 3.0);
+  // By modifying just the simplex {2}
+  // {0,1,2}, {1,2} and {0,2} will be modified
+  
+  std::cout << "Check the simplex_tree is repaired in case of decreasing filtration values" << std::endl;
+  BOOST_CHECK(st.make_filtration_non_decreasing());
+  BOOST_CHECK(st == st_other);
+
+  // Modify specific values for st still to be non-decreasing
+  st.assign_filtration(st.find({0,1,2}), 10.0);
+  st.assign_filtration(st.find({0,2}), 9.0);
+  st.assign_filtration(st.find({0,1,6,7}), 50.0);
+  st.assign_filtration(st.find({0,1,6}), 49.0);
+  st.assign_filtration(st.find({0,1,7}), 48.0);
+  // Other copy simplex tree
+  typeST st_other_copy = st;
+  
+  std::cout << "Check the simplex_tree is not modified in case of non-decreasing filtration values" << std::endl;
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+  BOOST_CHECK(st == st_other_copy);
+  
+}
+
+BOOST_AUTO_TEST_CASE_TEMPLATE(make_filtration_non_decreasing_on_nan_values, typeST, list_of_tested_variants) {
+  typeST st;
+
+  st.insert_simplex_and_subfaces({2, 1, 0}, std::numeric_limits<double>::quiet_NaN());
+  st.insert_simplex_and_subfaces({3, 0},    std::numeric_limits<double>::quiet_NaN());
+  st.insert_simplex_and_subfaces({3, 4, 5}, std::numeric_limits<double>::quiet_NaN());
+  
+  /* Inserted simplex:     */
+  /*    1                  */
+  /*    o                  */
+  /*   /X\                 */
+  /*  o---o---o---o        */
+  /*  2   0   3\X/4        */
+  /*            o          */
+  /*            5          */
+
+  std::cout << "SPECIFIC CASE:" << std::endl;
+  std::cout << "Insertion with NaN values does not ensure the filtration values are non decreasing" << std::endl;
+  st.make_filtration_non_decreasing();
+
+  std::cout << "Check all filtration values are NaN" << std::endl;
+  for (auto f_simplex : st.filtration_simplex_range()) {
+    BOOST_CHECK(std::isnan(st.filtration(f_simplex)));
+  }
+
+  st.assign_filtration(st.find({0}), 0.);
+  st.assign_filtration(st.find({1}), 0.);
+  st.assign_filtration(st.find({2}), 0.);
+  st.assign_filtration(st.find({3}), 0.);
+  st.assign_filtration(st.find({4}), 0.);
+  st.assign_filtration(st.find({5}), 0.);
+
+  std::cout << "Check make_filtration_non_decreasing is modifying the simplicial complex" << std::endl;
+  BOOST_CHECK(st.make_filtration_non_decreasing());
+  
+  std::cout << "Check all filtration values are now defined" << std::endl;
+  for (auto f_simplex : st.filtration_simplex_range()) {
+    BOOST_CHECK(!std::isnan(st.filtration(f_simplex)));
+  }
+}
\ No newline at end of file
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index 58bfa8db..e739ad0a 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -791,90 +791,6 @@ BOOST_AUTO_TEST_CASE(non_contiguous) {
   BOOST_CHECK(++i == std::end(b));
 }
 
-BOOST_AUTO_TEST_CASE(make_filtration_non_decreasing) {
-  std::cout << "********************************************************************" << std::endl;
-  std::cout << "MAKE FILTRATION NON DECREASING" << std::endl;
-  typedef Simplex_tree<> typeST;
-  typeST st;
-
-  st.insert_simplex_and_subfaces({2, 1, 0}, 2.0);
-  st.insert_simplex_and_subfaces({3, 0}, 2.0);
-  st.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
-  
-  /* Inserted simplex:     */
-  /*    1                  */
-  /*    o                  */
-  /*   /X\                 */
-  /*  o---o---o---o        */
-  /*  2   0   3\X/4        */
-  /*            o          */
-  /*            5          */
-
-  std::cout << "Check default insertion ensures the filtration values are non decreasing" << std::endl;
-  BOOST_CHECK(!st.make_filtration_non_decreasing());
-
-  // Because of non decreasing property of simplex tree, { 0 } , { 1 } and { 0, 1 } are going to be set from value 2.0
-  // to 1.0
-  st.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
-  
-  // Inserted simplex:
-  //    1   6
-  //    o---o
-  //   /X\7/
-  //  o---o---o---o
-  //  2   0   3\X/4
-  //            o
-  //            5
-  
-  std::cout << "Check default second insertion ensures the filtration values are non decreasing" << std::endl;
-  BOOST_CHECK(!st.make_filtration_non_decreasing());
-  
-  // Copy original simplex tree
-  typeST st_copy = st;
-
-  // Modify specific values for st to become like st_copy thanks to make_filtration_non_decreasing
-  st.assign_filtration(st.find({0,1,6,7}), 0.8);
-  st.assign_filtration(st.find({0,1,6}), 0.9);
-  st.assign_filtration(st.find({0,6}), 0.6);
-  st.assign_filtration(st.find({3,4,5}), 1.2);
-  st.assign_filtration(st.find({3,4}), 1.1);
-  st.assign_filtration(st.find({4,5}), 1.99);
-  
-  std::cout << "Check the simplex_tree is rolled back in case of decreasing filtration values" << std::endl;
-  BOOST_CHECK(st.make_filtration_non_decreasing());
-  BOOST_CHECK(st == st_copy);
-
-  // Other simplex tree
-  typeST st_other;
-  st_other.insert_simplex_and_subfaces({2, 1, 0}, 3.0);  // This one is different from st
-  st_other.insert_simplex_and_subfaces({3, 0}, 2.0);
-  st_other.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
-  st_other.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
-
-  // Modify specific values for st to become like st_other thanks to make_filtration_non_decreasing
-  st.assign_filtration(st.find({2}), 3.0);
-  // By modifying just the simplex {2}
-  // {0,1,2}, {1,2} and {0,2} will be modified
-  
-  std::cout << "Check the simplex_tree is repaired in case of decreasing filtration values" << std::endl;
-  BOOST_CHECK(st.make_filtration_non_decreasing());
-  BOOST_CHECK(st == st_other);
-
-  // Modify specific values for st still to be non-decreasing
-  st.assign_filtration(st.find({0,1,2}), 10.0);
-  st.assign_filtration(st.find({0,2}), 9.0);
-  st.assign_filtration(st.find({0,1,6,7}), 50.0);
-  st.assign_filtration(st.find({0,1,6}), 49.0);
-  st.assign_filtration(st.find({0,1,7}), 48.0);
-  // Other copy simplex tree
-  typeST st_other_copy = st;
-  
-  std::cout << "Check the simplex_tree is not modified in case of non-decreasing filtration values" << std::endl;
-  BOOST_CHECK(!st.make_filtration_non_decreasing());
-  BOOST_CHECK(st == st_other_copy);
-  
-}
-
 
 typedef boost::mpl::list<boost::adjacency_list<boost::setS, boost::vecS, boost::directedS,
                                                boost::property<vertex_filtration_t, double>,
-- 
cgit v1.2.3


From 19ea0c10f283188282a78ebebf4c1a51f2f40040 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Thu, 5 Mar 2020 14:14:27 +0100
Subject: CR: use complex_simplex_range instead of filtration_simplex_range

---
 .../test/simplex_tree_make_filtration_non_decreasing_unit_test.cpp    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Simplex_tree/test/simplex_tree_make_filtration_non_decreasing_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_make_filtration_non_decreasing_unit_test.cpp
index a8130e25..4697ec05 100644
--- a/src/Simplex_tree/test/simplex_tree_make_filtration_non_decreasing_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_make_filtration_non_decreasing_unit_test.cpp
@@ -127,7 +127,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(make_filtration_non_decreasing_on_nan_values, type
   st.make_filtration_non_decreasing();
 
   std::cout << "Check all filtration values are NaN" << std::endl;
-  for (auto f_simplex : st.filtration_simplex_range()) {
+  for (auto f_simplex : st.complex_simplex_range()) {
     BOOST_CHECK(std::isnan(st.filtration(f_simplex)));
   }
 
@@ -142,7 +142,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(make_filtration_non_decreasing_on_nan_values, type
   BOOST_CHECK(st.make_filtration_non_decreasing());
   
   std::cout << "Check all filtration values are now defined" << std::endl;
-  for (auto f_simplex : st.filtration_simplex_range()) {
+  for (auto f_simplex : st.complex_simplex_range()) {
     BOOST_CHECK(!std::isnan(st.filtration(f_simplex)));
   }
 }
\ No newline at end of file
-- 
cgit v1.2.3


From b0bd6dfc34a3c93073e9f326292047f8debb7fb3 Mon Sep 17 00:00:00 2001
From: Marc Glisse <marc.glisse@inria.fr>
Date: Thu, 12 Mar 2020 23:46:03 +0100
Subject: Update hera

---
 ext/hera                                            | 2 +-
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 2 +-
 src/cmake/modules/GUDHI_user_version_target.cmake   | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/ext/hera b/ext/hera
index cb1838e6..0019cae9 160000
--- a/ext/hera
+++ b/ext/hera
@@ -1 +1 @@
-Subproject commit cb1838e682ec07f80720241cf9098400caeb83c7
+Subproject commit 0019cae9dc1e9d11aa03bc59681435ba7f21eea8
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 6db2c76b..2d010483 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -68,7 +68,7 @@ if(CGAL_FOUND)
 endif()
 
 # For those who dislike bundled dependencies, this indicates where to find a preinstalled Hera.
-set(HERA_WASSERSTEIN_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/geom_matching/wasserstein/include CACHE PATH "Directory where one can find Hera's wasserstein.h")
+set(HERA_WASSERSTEIN_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/wasserstein/include CACHE PATH "Directory where one can find Hera's wasserstein.h")
 
 option(WITH_GUDHI_USE_TBB "Build with Intel TBB parallelization" ON)
 
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index 5047252f..257d1939 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -55,7 +55,7 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                    copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
 
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                   copy_directory ${CMAKE_SOURCE_DIR}/ext/hera/geom_matching/wasserstein/include ${GUDHI_USER_VERSION_DIR}/ext/hera/geom_matching/wasserstein/include)
+                   copy_directory ${CMAKE_SOURCE_DIR}/ext/hera/wasserstein/include ${GUDHI_USER_VERSION_DIR}/ext/hera/wasserstein/include)
 
 set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
 
-- 
cgit v1.2.3


From ba24c58487f9a62e024138127c1b8375449334f9 Mon Sep 17 00:00:00 2001
From: Marc Glisse <marc.glisse@inria.fr>
Date: Fri, 13 Mar 2020 09:17:25 +0100
Subject: Mention git submodule sync

---
 .github/how_to_use_github_to_contribute_to_gudhi.md | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/how_to_use_github_to_contribute_to_gudhi.md b/.github/how_to_use_github_to_contribute_to_gudhi.md
index 6ab05e36..747ca39b 100644
--- a/.github/how_to_use_github_to_contribute_to_gudhi.md
+++ b/.github/how_to_use_github_to_contribute_to_gudhi.md
@@ -25,10 +25,10 @@ This creates a directory gudhi-devel, which you are free to move around or renam
 cd gudhi-devel
 ```
 
-Everytime you clone the repository, you will have to download the *submodules*.
+When you clone the repository, you also need to download the *submodules*.
 
 ## Submodules
-An interface to Hera for Wasserstein distance is available on an external git repository. To download it:
+Hera, used for Wasserstein distance, is available on an external git repository. To download it:
 ```bash
 git submodule update --init
 ```
@@ -60,8 +60,9 @@ This is a command you can run quite regularly.
 It tells git to check all that happened on github.
 It is safe, it will not mess with your files.
 
-**Reminder:** Everytime you checkout master or merge from master, afterwards, if the version of one the submodule has changed, or if a submodule was added, you will have to:
+**Reminder:** If the version of a submodule has changed, or if a submodule was added, you may need to:
 ```bash
+git submodule sync
 git submodule update --init
 ```
 
-- 
cgit v1.2.3