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

8 files changed, 93 insertions, 75 deletions

diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx
index e04dc652..d75e374a 100644
--- a/src/python/gudhi/alpha_complex.pyx
+++ b/src/python/gudhi/alpha_complex.pyx
@@ -27,11 +27,11 @@ __license__ = "GPL v3"
 
 cdef extern from "Alpha_complex_interface.h" namespace "Gudhi":
     cdef cppclass Alpha_complex_interface "Gudhi::alpha_complex::Alpha_complex_interface":
-        Alpha_complex_interface(vector[vector[double]] points) except +
+        Alpha_complex_interface(vector[vector[double]] points) nogil except +
         # bool from_file is a workaround for cython to find the correct signature
-        Alpha_complex_interface(string off_file, bool from_file) except +
-        vector[double] get_point(int vertex) except +
-        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except +
+        Alpha_complex_interface(string off_file, bool from_file) nogil except +
+        vector[double] get_point(int vertex) nogil except +
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) nogil except +
 
 # AlphaComplex python interface
 cdef class AlphaComplex:
@@ -70,6 +70,7 @@ cdef class AlphaComplex:
 
     # The real cython constructor
     def __cinit__(self, points = None, off_file = ''):
+        cdef vector[vector[double]] pts
         if off_file:
             if os.path.isfile(off_file):
                 self.thisptr = new Alpha_complex_interface(
@@ -80,7 +81,9 @@ cdef class AlphaComplex:
             if points is None:
                 # Empty Alpha construction
                 points=[]
-            self.thisptr = new Alpha_complex_interface(points)
+            pts = points
+            with nogil:
+                self.thisptr = new Alpha_complex_interface(pts)
                 
 
     def __dealloc__(self):
@@ -113,6 +116,8 @@ cdef class AlphaComplex:
         :rtype: SimplexTree
         """
         stree = SimplexTree()
+        cdef double mas = max_alpha_square
         cdef intptr_t stree_int_ptr=stree.thisptr
-        self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr, max_alpha_square)
+        with nogil:
+            self.thisptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr, mas)
         return stree
diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py
index 03fc9066..6a74a6ca 100644
--- a/src/python/gudhi/persistence_graphical_tools.py
+++ b/src/python/gudhi/persistence_graphical_tools.py
@@ -72,11 +72,11 @@ def plot_persistence_barcode(
     """This function plots the persistence bar code from persistence values list
     , a np.array of shape (N x 2) (representing a diagram 
     in a single homology dimension), 
-    or from a :doc:`persistence file <fileformats>`.
+    or from a `persistence diagram <fileformats.html#persistence-diagram>`_ file.
 
     :param persistence: Persistence intervals values list. Can be grouped by dimension or not.
     :type persistence: an array of (dimension, array of (birth, death)) or an array of (birth, death).
-    :param persistence_file: A :doc:`persistence file <fileformats>` style name
+    :param persistence_file: A `persistence diagram <fileformats.html#persistence-diagram>`_ file style name
         (reset persistence if both are set).
     :type persistence_file: string
     :param alpha: barcode transparency value (0.0 transparent through 1.0
@@ -213,11 +213,11 @@ def plot_persistence_diagram(
 ):
     """This function plots the persistence diagram from persistence values
     list, a np.array of shape (N x 2) representing a diagram in a single
-    homology dimension, or from a :doc:`persistence file <fileformats>`.
+    homology dimension, or from a `persistence diagram <fileformats.html#persistence-diagram>`_ file`.
 
     :param persistence: Persistence intervals values list. Can be grouped by dimension or not.
     :type persistence: an array of (dimension, array of (birth, death)) or an array of (birth, death).
-    :param persistence_file: A :doc:`persistence file <fileformats>` style name
+    :param persistence_file: A `persistence diagram <fileformats.html#persistence-diagram>`_ file style name
         (reset persistence if both are set).
     :type persistence_file: string
     :param alpha: plot transparency value (0.0 transparent through 1.0
@@ -368,17 +368,19 @@ def plot_persistence_density(
     """This function plots the persistence density from persistence
     values list, np.array of shape (N x 2) representing a diagram
     in a single homology dimension,
-    or from a :doc:`persistence file <fileformats>`. Be
-    aware that this function does not distinguish the dimension, it is
+    or from a `persistence diagram <fileformats.html#persistence-diagram>`_ file.
+    Be aware that this function does not distinguish the dimension, it is
     up to you to select the required one. This function also does not handle
     degenerate data set (scipy correlation matrix inversion can fail).
 
+    :Requires: `SciPy <installation.html#scipy>`_
+
     :param persistence: Persistence intervals values list. 
                         Can be grouped by dimension or not.
     :type persistence: an array of (dimension, array of (birth, death)) 
                         or an array of (birth, death).
-    :param persistence_file: A :doc:`persistence file <fileformats>`
-        style name (reset persistence if both are set).
+    :param persistence_file: A `persistence diagram <fileformats.html#persistence-diagram>`_
+        file style name (reset persistence if both are set).
     :type persistence_file: string
     :param nbins: Evaluate a gaussian kde on a regular grid of nbins x
         nbins over data extents (default is 300)
diff --git a/src/python/gudhi/point_cloud/knn.py b/src/python/gudhi/point_cloud/knn.py
index 65896847..4652fe80 100644
--- a/src/python/gudhi/point_cloud/knn.py
+++ b/src/python/gudhi/point_cloud/knn.py
@@ -19,6 +19,10 @@ __license__ = "MIT"
 class KNearestNeighbors:
     """
     Class wrapping several implementations for computing the k nearest neighbors in a point set.
+
+    :Requires: `PyKeOps <installation.html#pykeops>`_, `SciPy <installation.html#scipy>`_,
+        `Scikit-learn <installation.html#scikit-learn>`_, and/or `Hnswlib <installation.html#hnswlib>`_
+        in function of the selected `implementation`.
     """
 
     def __init__(self, k, return_index=True, return_distance=False, metric="euclidean", **kwargs):
diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
index f01df442..5292e752 100644
--- a/src/python/gudhi/point_cloud/timedelay.py
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -10,9 +10,8 @@ import numpy as np
 
 
 class TimeDelayEmbedding:
-    """Point cloud transformation class.
-    Embeds time-series data in the R^d according to [Takens' Embedding Theorem]
-    (https://en.wikipedia.org/wiki/Takens%27s_theorem) and obtains the 
+    """Point cloud transformation class. 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
diff --git a/src/python/gudhi/representations/metrics.py b/src/python/gudhi/representations/metrics.py
index ce416fb1..8a32f7e9 100644
--- a/src/python/gudhi/representations/metrics.py
+++ b/src/python/gudhi/representations/metrics.py
@@ -223,7 +223,9 @@ class SlicedWassersteinDistance(BaseEstimator, TransformerMixin):
 
 class BottleneckDistance(BaseEstimator, TransformerMixin):
     """
-    This is a class for computing the bottleneck distance matrix from a list of persistence diagrams. 
+    This is a class for computing the bottleneck distance matrix from a list of persistence diagrams.
+
+    :Requires: `CGAL <installation.html#cgal>`_ :math:`\geq` 4.11.0
     """
     def __init__(self, epsilon=None):
         """
diff --git a/src/python/gudhi/rips_complex.pyx b/src/python/gudhi/rips_complex.pyx
index deb8057a..72e82c79 100644
--- a/src/python/gudhi/rips_complex.pyx
+++ b/src/python/gudhi/rips_complex.pyx
@@ -23,12 +23,12 @@ __license__ = "MIT"
 
 cdef extern from "Rips_complex_interface.h" namespace "Gudhi":
     cdef cppclass Rips_complex_interface "Gudhi::rips_complex::Rips_complex_interface":
-        Rips_complex_interface()
-        void init_points(vector[vector[double]] values, double threshold)
-        void init_matrix(vector[vector[double]] values, double threshold)
-        void init_points_sparse(vector[vector[double]] values, double threshold, double sparse)
-        void init_matrix_sparse(vector[vector[double]] values, double threshold, double sparse)
-        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max) except +
+        Rips_complex_interface() nogil
+        void init_points(vector[vector[double]] values, double threshold) nogil
+        void init_matrix(vector[vector[double]] values, double threshold) nogil
+        void init_points_sparse(vector[vector[double]] values, double threshold, double sparse) nogil
+        void init_matrix_sparse(vector[vector[double]] values, double threshold, double sparse) nogil
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max) nogil except +
 
 # RipsComplex python interface
 cdef class RipsComplex:
@@ -97,6 +97,7 @@ cdef class RipsComplex:
         """
         stree = SimplexTree()
         cdef intptr_t stree_int_ptr=stree.thisptr
-        self.thisref.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr,
-            max_dimension)
+        cdef int maxdim = max_dimension
+        with nogil:
+            self.thisref.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr, maxdim)
         return stree
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 1d4ed926..e748ac40 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -25,57 +25,56 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         pass
 
     cdef cppclass Simplex_tree_simplices_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Complex_simplex_iterator":
-        Simplex_tree_simplices_iterator()
-        Simplex_tree_simplex_handle& operator*()
-        Simplex_tree_simplices_iterator operator++()
-        bint operator!=(Simplex_tree_simplices_iterator)
+        Simplex_tree_simplices_iterator() nogil
+        Simplex_tree_simplex_handle& operator*() nogil
+        Simplex_tree_simplices_iterator operator++() nogil
+        bint operator!=(Simplex_tree_simplices_iterator) nogil
 
     cdef cppclass Simplex_tree_skeleton_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Skeleton_simplex_iterator":
-        Simplex_tree_skeleton_iterator()
-        Simplex_tree_simplex_handle& operator*()
-        Simplex_tree_skeleton_iterator operator++()
-        bint operator!=(Simplex_tree_skeleton_iterator)
+        Simplex_tree_skeleton_iterator() nogil
+        Simplex_tree_simplex_handle& operator*() nogil
+        Simplex_tree_skeleton_iterator operator++() nogil
+        bint operator!=(Simplex_tree_skeleton_iterator) nogil
 
 
     cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>":
-        Simplex_tree()
-        double simplex_filtration(vector[int] simplex)
-        void assign_simplex_filtration(vector[int] simplex, double filtration)
-        void initialize_filtration()
-        int num_vertices()
-        int num_simplices()
-        void set_dimension(int dimension)
-        int dimension()
-        int upper_bound_dimension()
-        bool find_simplex(vector[int] simplex)
-        bool insert(vector[int] simplex, double filtration)
-        vector[pair[vector[int], double]] get_star(vector[int] simplex)
-        vector[pair[vector[int], double]] get_cofaces(vector[int] simplex,
-                                                          int dimension)
-        void expansion(int max_dim) except +
-        void remove_maximal_simplex(vector[int] simplex)
-        bool prune_above_filtration(double filtration)
-        bool make_filtration_non_decreasing()
-        void compute_extended_filtration()
-        vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(vector[pair[int, pair[double, double]]] dgm, double min_persistence)
+        Simplex_tree() nogil
+        double simplex_filtration(vector[int] simplex) nogil
+        void assign_simplex_filtration(vector[int] simplex, double filtration) nogil
+        void initialize_filtration() nogil
+        int num_vertices() nogil
+        int num_simplices() nogil
+        void set_dimension(int dimension) nogil
+        int dimension() nogil
+        int upper_bound_dimension() nogil
+        bool find_simplex(vector[int] simplex) nogil
+        bool insert(vector[int] simplex, double filtration) nogil
+        vector[pair[vector[int], double]] get_star(vector[int] simplex) nogil
+        vector[pair[vector[int], double]] get_cofaces(vector[int] simplex, int dimension) nogil
+        void expansion(int max_dim) nogil except +
+        void remove_maximal_simplex(vector[int] simplex) nogil
+        bool prune_above_filtration(double filtration) nogil
+        bool make_filtration_non_decreasing() nogil
+        void compute_extended_filtration() nogil
+        vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(vector[pair[int, pair[double, double]]] dgm, double min_persistence) nogil
         # Iterators over Simplex tree
-        pair[vector[int], double] get_simplex_and_filtration(Simplex_tree_simplex_handle f_simplex)
-        Simplex_tree_simplices_iterator get_simplices_iterator_begin()
-        Simplex_tree_simplices_iterator get_simplices_iterator_end()
-        vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_begin()
-        vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_end()
-        Simplex_tree_skeleton_iterator get_skeleton_iterator_begin(int dimension)
-        Simplex_tree_skeleton_iterator get_skeleton_iterator_end(int dimension)
+        pair[vector[int], double] get_simplex_and_filtration(Simplex_tree_simplex_handle f_simplex) nogil
+        Simplex_tree_simplices_iterator get_simplices_iterator_begin() nogil
+        Simplex_tree_simplices_iterator get_simplices_iterator_end() nogil
+        vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_begin() nogil
+        vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_end() nogil
+        Simplex_tree_skeleton_iterator get_skeleton_iterator_begin(int dimension) nogil
+        Simplex_tree_skeleton_iterator get_skeleton_iterator_end(int dimension) nogil
 
 cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
     cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>":
-        Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * st, bool persistence_dim_max)
-        void compute_persistence(int homology_coeff_field, double min_persistence)
-        vector[pair[int, pair[double, double]]] get_persistence()
-        vector[int] betti_numbers()
-        vector[int] persistent_betti_numbers(double from_value, double to_value)
-        vector[pair[double,double]] intervals_in_dimension(int dimension)
-        void write_output_diagram(string diagram_file_name) except +
-        vector[pair[vector[int], vector[int]]] persistence_pairs()
-        pair[vector[vector[int]], vector[vector[int]]] lower_star_generators()
-        pair[vector[vector[int]], vector[vector[int]]] flag_generators()
+        Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * st, bool persistence_dim_max) nogil
+        void compute_persistence(int homology_coeff_field, double min_persistence) nogil
+        vector[pair[int, pair[double, double]]] get_persistence() nogil
+        vector[int] betti_numbers() nogil
+        vector[int] persistent_betti_numbers(double from_value, double to_value) nogil
+        vector[pair[double,double]] intervals_in_dimension(int dimension) nogil
+        void write_output_diagram(string diagram_file_name) nogil except +
+        vector[pair[vector[int], vector[int]]] persistence_pairs() nogil
+        pair[vector[vector[int]], vector[vector[int]]] lower_star_generators() nogil
+        pair[vector[vector[int]], vector[vector[int]]] flag_generators() nogil
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index b23885b4..9cb24221 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -33,7 +33,7 @@ cdef class SimplexTree:
     cdef public intptr_t thisptr
 
     # Get the pointer casted as it should be
-    cdef Simplex_tree_interface_full_featured* get_ptr(self):
+    cdef Simplex_tree_interface_full_featured* get_ptr(self) nogil:
         return <Simplex_tree_interface_full_featured*>(self.thisptr)
 
     cdef Simplex_tree_persistence_interface * pcohptr
@@ -345,7 +345,9 @@ cdef class SimplexTree:
         :param max_dim: The maximal dimension.
         :type max_dim: int.
         """
-        self.get_ptr().expansion(max_dim)
+        cdef int maxdim = max_dim
+        with nogil:
+            self.get_ptr().expansion(maxdim)
 
     def make_filtration_non_decreasing(self):
         """This function ensures that each simplex has a higher filtration
@@ -451,8 +453,12 @@ cdef class SimplexTree:
         """
         if self.pcohptr != NULL:
             del self.pcohptr
-        self.pcohptr = new Simplex_tree_persistence_interface(self.get_ptr(), persistence_dim_max)
-        self.pcohptr.compute_persistence(homology_coeff_field, min_persistence)
+        cdef bool pdm = persistence_dim_max
+        cdef int coef = homology_coeff_field
+        cdef double minp = min_persistence
+        with nogil:
+            self.pcohptr = new Simplex_tree_persistence_interface(self.get_ptr(), pdm)
+            self.pcohptr.compute_persistence(coef, minp)
 
     def betti_numbers(self):
         """This function returns the Betti numbers of the simplicial complex.