passagemath-graphs 10.6.1rc1__cp310-cp310-musllinux_1_2_aarch64.whl

sage/graphs/convexity_properties.pyx

@@ -0,0 +1,870 @@
+# sage_setup: distribution = sagemath-graphs
+# cython: binding=True
+r"""
+Convexity properties of graphs
+
+This class gathers the algorithms related to convexity in a graph. It implements
+the following methods:
+
+.. csv-table::
+    :class: contentstable
+    :widths: 30, 70
+    :delim: |
+
+    :meth:`ConvexityProperties.hull` | Return the convex hull of a set of vertices
+    :meth:`ConvexityProperties.hull_number` | Compute the hull number of a graph and a corresponding generating set
+    :meth:`geodetic_closure`| Return the geodetic closure of a set of vertices
+    :meth:`is_geodetic` | Check whether the input (di)graph is geodetic
+
+Some of these methods can be used through the :class:`ConvexityProperties`
+object returned by :meth:`Graph.convexity_properties`.
+
+Methods
+-------
+"""
+
+# ****************************************************************************
+#       Copyright (C) 2011 Nathann Cohen <nathann.cohen@gmail.com>
+#                     2021 David Coudert <david.coudert@inria.fr>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
+
+from sage.data_structures.binary_matrix cimport *
+from sage.numerical.backends.generic_backend cimport GenericBackend
+from sage.numerical.backends.generic_backend import get_solver
+from sage.graphs.distances_all_pairs cimport c_distances_all_pairs
+from cysignals.memory cimport sig_free
+from memory_allocator cimport MemoryAllocator
+from libc.stdint cimport uint32_t
+from sage.graphs.base.static_sparse_backend cimport StaticSparseCGraph
+from sage.graphs.base.static_sparse_backend cimport StaticSparseBackend
+from sage.graphs.base.static_sparse_graph cimport (short_digraph,
+                                                   init_short_digraph,
+                                                   free_short_digraph,
+                                                   out_degree,
+                                                   simple_BFS)
+
+
+cdef class ConvexityProperties:
+    r"""
+    This class gathers the algorithms related to convexity in a graph.
+
+    **Definitions**
+
+    A set `S \subseteq V(G)` of vertices is said to be convex if for all `u,v\in
+    S` the set `S` contains all the vertices located on a shortest path between
+    `u` and `v`. Alternatively, a set `S` is said to be convex if the distances
+    satisfy `\forall u,v\in S, \forall w\in V\backslash S : d_{G}(u,w) +
+    d_{G}(w,v) > d_{G}(u,v)`.
+
+    The convex hull `h(S)` of a set `S` of vertices is defined as the smallest
+    convex set containing `S`.
+
+    It is a closure operator, as trivially `S\subseteq h(S)` and `h(h(S)) =
+    h(S)`.
+
+    **What this class contains**
+
+    As operations on convex sets generally involve the computation of distances
+    between vertices, this class' purpose is to cache that information so that
+    computing the convex hulls of several different sets of vertices does not
+    imply recomputing several times the distances between the vertices.
+
+    In order to compute the convex hull of a set `S` it is possible to write the
+    following algorithm:
+
+        For any pair `u,v` of elements in the set `S`, and for any vertex `w`
+        outside of it, add `w` to `S` if `d_{G}(u,w) + d_{G}(w,v) =
+        d_{G}(u,v)`. When no vertex can be added anymore, the set `S` is convex
+
+    The distances are not actually that relevant. The same algorithm can be
+    implemented by remembering for each pair `u, v` of vertices the list of
+    elements `w` satisfying the condition, and this is precisely what this class
+    remembers, encoded as bitsets to make storage and union operations more
+    efficient.
+
+    .. NOTE::
+
+        * This class is useful if you compute the convex hulls of many sets in
+          the same graph, or if you want to compute the hull number itself as it
+          involves many calls to :meth:`hull`
+
+        * Using this class on non-connected graphs is a waste of space and
+          efficiency ! If your graph is disconnected, the best for you is to
+          deal independently with each connected component, whatever you are
+          doing.
+
+    **Possible improvements**
+
+    When computing a convex set, all the pairs of elements belonging to the set
+    `S` are enumerated several times.
+
+    * There should be a smart way to avoid enumerating pairs of vertices which
+      have already been tested. The cost of each of them is not very high, so
+      keeping track of those which have been tested already may be too expensive
+      to gain any efficiency.
+
+    * The ordering in which they are visited is currently purely lexicographic,
+      while there is a Poset structure to exploit. In particular, when two
+      vertices `u, v` are far apart and generate a set `h(\{u,v\})` of vertices,
+      all the pairs of vertices `u', v'\in h(\{u,v\})` satisfy `h(\{u',v'\})
+      \subseteq h(\{u,v\})`, and so it is useless to test the pair `u', v'` when
+      both `u` and `v` where present.
+
+    * The information cached is for any pair `u,v` of vertices the list of
+      elements `z` with `d_{G}(u,w) + d_{G}(w,v) = d_{G}(u,v)`. This is not in
+      general equal to `h(\{u,v\})` !
+
+    Nothing says these recommendations will actually lead to any actual
+    improvements. There are just some ideas remembered while writing this
+    code. Trying to optimize may well lead to lost in efficiency on many
+    instances.
+
+    EXAMPLES::
+
+        sage: from sage.graphs.convexity_properties import ConvexityProperties
+        sage: g = graphs.PetersenGraph()
+        sage: CP = ConvexityProperties(g)
+        sage: CP.hull([1, 3])
+        [1, 2, 3]
+        sage: CP.hull_number()                                                          # needs sage.numerical.mip
+        3
+
+    TESTS::
+
+        sage: ConvexityProperties(digraphs.Circuit(5))
+        Traceback (most recent call last):
+        ...
+        NotImplementedError: this is currently implemented for Graphs only, but only minor updates are needed if you want to make it support DiGraphs too
+    """
+
+    def __init__(self, G):
+        r"""
+        Constructor.
+
+        EXAMPLES::
+
+            sage: from sage.graphs.convexity_properties import ConvexityProperties
+            sage: g = graphs.PetersenGraph()
+            sage: ConvexityProperties(g)
+            <sage.graphs.convexity_properties.ConvexityProperties object at ...>
+        """
+        from sage.graphs.digraph import DiGraph
+        if isinstance(G, DiGraph):
+            raise NotImplementedError("this is currently implemented for Graphs only, "
+                                      "but only minor updates are needed if you want "
+                                      "to make it support DiGraphs too")
+
+        # Cached number of vertices
+        cdef int n = G.order()
+        self._n = n
+
+        cdef int i = 0
+        cdef int j, k
+
+        # Build mappings integer <-> vertices.
+        # Must be consistent with the mappings used in c_distances_all_pairs
+        self._list_integers_to_vertices = list(G)
+        self._dict_vertices_to_integers = {v: i for i, v in enumerate(self._list_integers_to_vertices)}
+
+        # Computation of distances between all pairs. Costly.
+        cdef unsigned short* c_distances = c_distances_all_pairs(G, vertex_list=self._list_integers_to_vertices)
+        # Temporary variables
+        cdef unsigned short* d_i
+        cdef unsigned short* d_j
+        cdef int d_ij
+
+        # We use a binary matrix with one row per pair of vertices,
+        # so n * (n - 1) / 2 rows. Row u * n + v is a bitset whose 1 bits are
+        # the vertices located on a shortest path from vertex u to v
+        #
+        # Note that  u < v
+        binary_matrix_init(self._cache_hull_pairs, n * (n - 1) / 2, n)
+        binary_matrix_fill(self._cache_hull_pairs, 0)
+        cdef bitset_t * p_bitset = self._cache_hull_pairs.rows
+
+        # Filling the cache
+        #
+        # The p_bitset variable iterates over the successive elements of the cache
+        #
+        # For any pair i, j of vertices (i < j), we built the bitset of all the
+        # elements k which are on a shortest path from i to j
+
+        for i in range(n):
+            # Caching the distances from i to the other vertices
+            d_i = c_distances + n * i
+
+            for j in range(i + 1, n):
+                # Caching the distances from j to the other vertices
+                d_j = c_distances + n * j
+
+                # Caching the distance between i and j
+                d_ij = d_i[j]
+
+                # Filling it
+                for k in range(n):
+                    if d_i[k] + d_j[k] == d_ij:
+                        bitset_add(p_bitset[0], k)
+
+                # Next bitset !
+                p_bitset = p_bitset + 1
+
+        sig_free(c_distances)
+
+    def __dealloc__(self):
+        r"""
+        Destructor.
+
+        EXAMPLES::
+
+            sage: from sage.graphs.convexity_properties import ConvexityProperties
+            sage: g = graphs.PetersenGraph()
+            sage: ConvexityProperties(g)
+            <sage.graphs.convexity_properties.ConvexityProperties object at ...>
+        """
+        binary_matrix_free(self._cache_hull_pairs)
+
+    cdef list _vertices_to_integers(self, vertices):
+        r"""
+        Convert a list of vertices to a list of integers with the cached data.
+        """
+        return [self._dict_vertices_to_integers[v] for v in vertices]
+
+    cdef list _integers_to_vertices(self, list integers):
+        r"""
+        Convert a list of integers to a list of vertices with the cached data.
+        """
+        cdef int i
+        return [self._list_integers_to_vertices[i] for i in integers]
+
+    cdef _bitset_convex_hull(self, bitset_t hull):
+        r"""
+        Compute the convex hull of a list of vertices given as a bitset.
+
+        (this method returns nothing and modifies the input)
+        """
+        cdef int count
+        cdef int tmp_count
+        cdef int i, j
+
+        cdef bitset_t * p_bitset
+
+        # Current size of the set
+        count = bitset_len(hull)
+
+        while True:
+
+            # Iterating over all the elements in the cache
+            p_bitset = self._cache_hull_pairs.rows
+
+            # For any vertex i
+            for i in range(self._n - 1):
+
+                # If i is not in the current set, we skip it !
+                if not bitset_in(hull, i):
+                    p_bitset = p_bitset + (self._n - 1 - i)
+                    continue
+
+                # If it is, we iterate over all the elements j
+                for j in range(i + 1, self._n):
+
+                    # If both i and j are inside, we add all the (cached)
+                    # vertices on a shortest ij-path
+
+                    if bitset_in(hull, j):
+                        bitset_union(hull, hull, p_bitset[0])
+
+                    # Next bitset !
+                    p_bitset = p_bitset + 1
+
+            tmp_count = bitset_len(hull)
+
+            # If we added nothing new during the previous loop, our set is
+            # convex !
+            if tmp_count == count:
+                return
+
+            # Otherwise, update and back to the loop
+            count = tmp_count
+
+    cpdef hull(self, list vertices):
+        r"""
+        Return the convex hull of a set of vertices.
+
+        INPUT:
+
+        - ``vertices`` -- list of vertices
+
+        EXAMPLES::
+
+            sage: from sage.graphs.convexity_properties import ConvexityProperties
+            sage: g = graphs.PetersenGraph()
+            sage: CP = ConvexityProperties(g)
+            sage: CP.hull([1, 3])
+            [1, 2, 3]
+        """
+        cdef bitset_t bs
+        bitset_init(bs, self._n)
+        bitset_set_first_n(bs, 0)
+
+        for v in vertices:
+            bitset_add(bs, <mp_bitcnt_t> self._dict_vertices_to_integers[v])
+
+        self._bitset_convex_hull(bs)
+
+        cdef list answer = self._integers_to_vertices(bitset_list(bs))
+
+        bitset_free(bs)
+
+        return answer
+
+    cdef _greedy_increase(self, bitset_t bs):
+        r"""
+        Given a bitset whose hull is not the whole set, greedily add vertices
+        and stop before its hull is the whole set.
+
+        .. NOTE::
+
+            * Counting the bits at each turn is not the best way...
+        """
+        cdef bitset_t tmp
+        bitset_init(tmp, self._n)
+
+        for i in range(self._n):
+            if not bitset_in(bs, i):
+                bitset_copy(tmp, bs)
+                bitset_add(tmp, i)
+                self._bitset_convex_hull(tmp)
+                if bitset_len(tmp) < self._n:
+                    bitset_add(bs, i)
+
+        bitset_free(tmp)
+
+    cpdef hull_number(self, value_only=True, verbose=False):
+        r"""
+        Compute the hull number and a corresponding generating set.
+
+        The hull number `hn(G)` of a graph `G` is the cardinality of a smallest
+        set of vertices `S` such that `h(S)=V(G)`.
+
+        INPUT:
+
+        - ``value_only`` -- boolean (default: ``True``); whether to return only
+          the hull number (default) or a minimum set whose convex hull is the
+          whole graph
+
+        - ``verbose`` -- boolean (default: ``False``); whether to display
+          information on the LP
+
+        **COMPLEXITY:**
+
+        This problem is NP-Hard [HLT1993]_, but seems to be of the "nice" kind.
+        Update this comment if you fall on hard instances `:-)`
+
+        **ALGORITHM:**
+
+        This is solved by linear programming.
+
+        As the function `h(S)` associating to each set `S` its convex hull is a
+        closure operator, it is clear that any set `S_G` of vertices such that
+        `h(S_G)=V(G)` must satisfy `S_G \not \subseteq C` for any *proper*
+        convex set `C \subsetneq V(G)`. The following formulation is hence
+        correct
+
+        .. MATH::
+
+            \text{Minimize :}& \sum_{v\in G}b_v\\
+            \text{Such that :}&\\
+            &\forall C\subsetneq V(G)\text{ a proper convex set }\\
+            &\sum_{v\in V(G)\backslash C} b_v \geq 1
+
+        Of course, the number of convex sets -- and so the number of constraints
+        -- can be huge, and hard to enumerate, so at first an incomplete
+        formulation is solved (it is missing some constraints). If the answer
+        returned by the LP solver is a set `S` generating the whole graph, then
+        it is optimal and so is returned. Otherwise, the constraint
+        corresponding to the set `h(S)` can be added to the LP, which makes the
+        answer `S` infeasible, and another solution computed.
+
+        This being said, simply adding the constraint corresponding to `h(S)` is
+        a bit slow, as these sets can be large (and the corresponding constraint
+        a bit weak). To improve it a bit, before being added, the set `h(S)` is
+        "greedily enriched" to a set `S'` with vertices for as long as
+        `h(S')\neq V(G)`. This way, we obtain a set `S'` with `h(S)\subseteq
+        h(S')\subsetneq V(G)`, and the constraint corresponding to `h(S')` --
+        which is stronger than the one corresponding to `h(S)` -- is added.
+
+        This can actually be seen as a hitting set problem on the complement of
+        convex sets.
+
+        EXAMPLES:
+
+        The Hull number of Petersen's graph::
+
+            sage: from sage.graphs.convexity_properties import ConvexityProperties
+            sage: g = graphs.PetersenGraph()
+            sage: CP = ConvexityProperties(g)
+            sage: CP.hull_number()                                                      # needs sage.numerical.mip
+            3
+            sage: generating_set = CP.hull_number(value_only=False)                     # needs sage.numerical.mip
+            sage: CP.hull(generating_set)                                               # needs sage.numerical.mip
+            [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+        """
+        cdef int i
+        cdef list constraint  # temporary variable to add constraints to the LP
+
+        if self._n <= 2:
+            if value_only:
+                return self._n
+            else:
+                return self._list_integers_to_vertices
+
+        cdef GenericBackend p = <GenericBackend> get_solver(constraint_generation=True)
+
+        # Minimization
+        p.set_sense(False)
+
+        # We have exactly n binary variables, all of them with a coefficient of
+        # 1 in the objective function
+        p.add_variables(self._n, 0, None, True, False, False, 1, None)
+
+        # We know that at least 2 vertices are required to cover the whole graph
+        p.add_linear_constraint([(i, 1) for i in range(self._n)], 2, None)
+
+        # The set of vertices generated by the current LP solution
+        cdef bitset_t current_hull
+        bitset_init(current_hull, self._n)
+
+        # Which is at first empty
+        bitset_set_first_n(current_hull, 1)
+
+        while True:
+
+            # Greedily increase it to obtain a better constraint
+            self._greedy_increase(current_hull)
+
+            if verbose:
+                print("Adding a constraint corresponding to convex set ",
+                      end="")
+                print(bitset_list(current_hull))
+
+            # Building the corresponding constraint
+            constraint = []
+            for i in range(self._n):
+                if not bitset_in(current_hull, i):
+                    constraint.append((i, 1))
+
+            p.add_linear_constraint(constraint, 1, None)
+
+            p.solve()
+
+            # Computing the current solution's convex hull
+            bitset_set_first_n(current_hull, 0)
+
+            for i in range(self._n):
+                if p.get_variable_value(i) > .5:
+                    bitset_add(current_hull, i)
+
+            self._bitset_convex_hull(current_hull)
+
+            # Are we done ?
+            if bitset_len(current_hull) == self._n:
+                break
+
+        bitset_free(current_hull)
+
+        if value_only:
+            return <int> p.get_objective_value()
+
+        constraint = []
+        for i in range(self._n):
+            if p.get_variable_value(i) > .5:
+                constraint.append(i)
+
+        return self._integers_to_vertices(constraint)
+
+
+def geodetic_closure(G, S):
+    r"""
+    Return the geodetic closure of the set of vertices `S` in `G`.
+
+    The geodetic closure `g(S)` of a subset of vertices `S` of a graph `G` is in
+    [HLT1993]_ as the set of all vertices that lie on a shortest `u-v` path for
+    any pair of vertices `u,v \in S`. We assume that `g(\emptyset) = \emptyset`
+    and that `g(\{u\}) = \{u\}` for any `u` in `G`.
+
+    .. WARNING::
+
+        This operation is **not** a closure function. Indeed, a closure function
+        must satisfy the property that `f(f(X))` should be equal to `f(X)`,
+        which is not always the case here.  The term ``closure`` is used here to
+        follow the terminology of the domain. See for instance [HLT1993]_.
+
+    Here, we implement a simple algorithm to determine this set. Roughly, for
+    each vertex `u \in S`, the algorithm first performs a breadth first search
+    from `u` to get distances, and then identifies the vertices of `G` lying on
+    a shortest path from `u` to any `v\in S` using a reversal traversal from
+    vertices in `S`.  This algorithm has time complexity in `O(|S|(n + m))` for
+    ``SparseGraph``, `O(|S|(n + m) + n^2)` for ``DenseGraph`` and
+    space complexity in `O(n + m)`.
+
+    INPUT:
+
+    - ``G`` -- a Sage graph
+
+    - ``S`` -- a subset of vertices of `G`
+
+    EXAMPLES:
+
+    The vertices of the Petersen graph can be obtained by a geodetic closure of
+    four of its vertices::
+
+        sage: from sage.graphs.convexity_properties import geodetic_closure
+        sage: G = graphs.PetersenGraph()
+        sage: geodetic_closure(G, [0, 2, 8, 9])
+        [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+
+    The vertices of a 2D grid can be obtained by a geodetic closure of
+    two vertices::
+
+        sage: G = graphs.Grid2dGraph(4, 4)
+        sage: c = G.geodetic_closure([(0, 0), (3, 3)])
+        sage: len(c) == G.order()
+        True
+
+    If two vertices belong to different connected components of a graph, their
+    geodetic closure is trivial::
+
+        sage: G = Graph([(0, 1), (2, 3)])
+        sage: geodetic_closure(G, [0, 2])
+        [0, 2]
+
+    The geodetic closure does not satisfy the closure function property that
+    `f(f(X))` should be equal to `f(X)`::
+
+        sage: G = graphs.DiamondGraph()
+        sage: G.subdivide_edge((1, 2), 1)
+        sage: geodetic_closure(G, [0, 3])
+        [0, 1, 2, 3]
+        sage: geodetic_closure(G, geodetic_closure(G, [0, 3]))
+        [0, 1, 2, 3, 4]
+
+    TESTS::
+
+        sage: G = graphs.DiamondGraph()
+        sage: geodetic_closure(G, [])
+        []
+        sage: geodetic_closure(G, [1])
+        [1]
+        sage: S = geodetic_closure(G, list(G))
+        sage: all(u in G for u in S) and len(S) == G.order()
+        True
+        sage: S = geodetic_closure(G, G)
+        sage: all(u in G for u in S) and len(S) == G.order()
+        True
+        sage: geodetic_closure(G, [1, 'foo'])
+        Traceback (most recent call last):
+        ...
+        ValueError: S is not a subset of vertices of the graph
+        sage: geodetic_closure(digraphs.Path(3), [0, 1])
+        Traceback (most recent call last):
+        ...
+        NotImplementedError: the geodetic closure of digraphs has not been implemented yet
+
+    The method is valid for immutable graphs::
+
+        sage: G = graphs.RandomGNP(10, .7)
+        sage: G._backend
+        <sage.graphs.base.sparse_graph.SparseGraphBackend ...>
+        sage: H = Graph(G, immutable=True)
+        sage: H._backend
+        <sage.graphs.base.static_sparse_backend.StaticSparseBackend ...>
+        sage: geodetic_closure(G, [0, 3]) == geodetic_closure(H, [0, 3])
+        True
+    """
+    if G.is_directed():
+        raise NotImplementedError("the geodetic closure of digraphs has not been implemented yet")
+    S = list(S)
+    if not S:
+        return []
+    elif any(v not in G for v in S):
+        raise ValueError("S is not a subset of vertices of the graph")
+    elif len(S) == 1 or len(S) == G.order():
+        return S
+    elif not G.is_connected():
+        L = []
+        for g in G.connected_components_subgraphs():
+            Sg = [u for u in S if u in g]
+            L.extend(geodetic_closure(g, Sg))
+        return L
+
+    cdef int n = G.order()
+    cdef int nS = len(S)
+    cdef list int_to_vertex
+    cdef dict vertex_to_int
+
+    # Copy the graph as a short digraph
+    cdef StaticSparseCGraph cg
+    cdef short_digraph sd
+    if isinstance(G, StaticSparseBackend):
+        cg = <StaticSparseCGraph> G._cg
+        sd = <short_digraph> cg.g
+        int_to_vertex = cg._vertex_to_labels
+        vertex_to_int = cg._vertex_to_int
+    else:
+        int_to_vertex = list(G)
+        vertex_to_int = {u: i for i, u in enumerate(int_to_vertex)}
+        init_short_digraph(sd, G, edge_labelled=False, vertex_list=int_to_vertex)
+
+    cdef list S_int = [vertex_to_int[u] for u in S]
+
+    # Allocate some data structures
+    cdef MemoryAllocator mem = MemoryAllocator()
+    cdef uint32_t * distances = <uint32_t *> mem.malloc(n * sizeof(uint32_t))
+    cdef uint32_t * waiting_list = <uint32_t *> mem.malloc(n * sizeof(uint32_t))
+    if not distances or not waiting_list:
+        free_short_digraph(sd)
+        raise MemoryError()
+    cdef bitset_t seen
+    cdef bitset_t visited
+    cdef bitset_t closure
+    bitset_init(seen, n)
+    bitset_init(visited, n)
+    bitset_init(closure, n)
+
+    cdef int ui, vi, xi, yi, i_begin, i_end, i, j, k
+
+    # Vertices in S are in the closure
+    bitset_clear(closure)
+    for ui in S_int:
+        bitset_add(closure, ui)
+
+    # We now explore geodesics between vertices in S, and we avoid visiting
+    # twice the geodesics between u and v
+    for i in range(nS - 1):
+        ui = S_int[i]
+
+        # Compute distances from ui using BFS
+        _ = simple_BFS(sd, ui, distances, NULL, waiting_list, seen)
+
+        # Perform a reverse BFS from vertices in S, following only vertices
+        # along a shortest path from ui to identify vertices of the geodetic
+        # closure.
+        bitset_clear(visited)
+        i_begin = 0
+        i_end = 0
+        for j in range(i + 1, nS):
+            vi = S_int[j]
+            if not bitset_in(seen, vi) or bitset_in(visited, vi):
+                # vi is not reachable from ui using BFS or has already been
+                # considered for the geodetic closure from ui
+                continue
+
+            # We explore all vertices on a shortest path from ui to vi
+            waiting_list[i_end] = vi
+            i_end += 1
+            bitset_add(visited, vi)
+
+            while i_begin < i_end:
+                xi = waiting_list[i_begin]
+                i_begin += 1
+
+                for k in range(out_degree(sd, xi)):
+                    yi = sd.neighbors[xi][k]
+                    if distances[xi] == distances[yi] + 1:
+                        # yi in on a shortest path to ui
+                        if not bitset_in(visited, yi):
+                            waiting_list[i_end] = yi
+                            i_end += 1
+                            bitset_add(visited, yi)
+
+        # Now, visited contains all vertices on geodesics from ui to any other
+        # vertex in S
+        bitset_union(closure, closure, visited)
+
+    cdef list ret = [int_to_vertex[ui] for ui in range(n) if bitset_in(closure, ui)]
+
+    bitset_free(seen)
+    bitset_free(visited)
+    bitset_free(closure)
+    if not isinstance(G, StaticSparseBackend):
+        free_short_digraph(sd)
+
+    return ret
+
+
+def is_geodetic(G):
+    r"""
+    Check whether the input (di)graph is geodetic.
+
+    A graph `G` is *geodetic* if there exists only one shortest path between
+    every pair of its vertices. This can be checked in time `O(nm)` for
+    ``SparseGraph`` and `O(nm+n^2)` for ``DenseGraph`` in unweighted (di)graphs
+    with `n` nodes and `m` edges. Examples of geodetic graphs are trees, cliques
+    and odd cycles. See the :wikipedia:`Geodetic_graph` for more details.
+
+    (Di)graphs with multiple edges are not considered geodetic.
+
+    INPUT:
+
+    - ``G`` -- a graph or a digraph
+
+    EXAMPLES:
+
+    Trees, cliques and odd cycles are geodetic::
+
+        sage: T = graphs.RandomTree(20)
+        sage: T.is_geodetic()
+        True
+        sage: all(graphs.CompleteGraph(n).is_geodetic() for n in range(8))
+        True
+        sage: all(graphs.CycleGraph(n).is_geodetic() for n in range(3, 16, 2))
+        True
+
+    Even cycles of order at least 4 are not geodetic::
+
+        sage: all(graphs.CycleGraph(n).is_geodetic() for n in range(4, 17, 2))
+        False
+
+    The Petersen graph is geodetic::
+
+        sage: P = graphs.PetersenGraph()
+        sage: P.is_geodetic()
+        True
+
+    Grid graphs are not geodetic::
+
+        sage: G = graphs.Grid2dGraph(2, 3)
+        sage: G.is_geodetic()
+        False
+
+    This method is also valid for digraphs::
+
+        sage: G = DiGraph(graphs.PetersenGraph())
+        sage: G.is_geodetic()
+        True
+        sage: G = digraphs.Path(5)
+        sage: G.add_path([0, 'a', 'b', 'c', 4])
+        sage: G.is_geodetic()
+        False
+
+    TESTS::
+
+        sage: all(g.is_geodetic() for g in graphs(3))                                   # needs nauty
+        True
+        sage: all((2*g).is_geodetic() for g in graphs(3))                               # needs nauty
+        True
+        sage: G = graphs.CycleGraph(5)
+        sage: G.allow_loops(True)
+        sage: G.add_edges([(u, u) for u in G])
+        sage: G.is_geodetic()
+        True
+        sage: G.allow_multiple_edges(True)
+        sage: G.is_geodetic()
+        True
+        sage: G.add_edge(G.random_edge())
+        sage: G.is_geodetic()
+        False
+
+    The method is valid for immutable graphs::
+
+        sage: G = graphs.RandomGNP(10, .7)
+        sage: G._backend
+        <sage.graphs.base.sparse_graph.SparseGraphBackend ...>
+        sage: H = Graph(G, immutable=True)
+        sage: H._backend
+        <sage.graphs.base.static_sparse_backend.StaticSparseBackend ...>
+        sage: G.is_geodetic() == H.is_geodetic()
+        True
+    """
+    if G.has_multiple_edges():
+        return False
+
+    if G.order() < 4:
+        return True
+
+    # Copy the graph as a short digraph
+    cdef int n = G.order()
+    cdef StaticSparseCGraph cg
+    cdef short_digraph sd
+    if isinstance(G, StaticSparseBackend):
+        cg = <StaticSparseCGraph> G._cg
+        sd = <short_digraph> cg.g
+    else:
+        init_short_digraph(sd, G, edge_labelled=False, vertex_list=list(G))
+
+    # Allocate some data structures
+    cdef MemoryAllocator mem = MemoryAllocator()
+    cdef uint32_t * distances = <uint32_t *> mem.malloc(n * sizeof(uint32_t))
+    cdef uint32_t * waiting_list = <uint32_t *> mem.malloc(n * sizeof(uint32_t))
+    if not distances or not waiting_list:
+        if not isinstance(G, StaticSparseBackend):
+            free_short_digraph(sd)
+        raise MemoryError()
+    cdef bitset_t seen
+    bitset_init(seen, n)
+
+    # We now explore geodesics between vertices in S, and we avoid visiting
+    # twice the geodesics between u and v
+
+    cdef uint32_t source, u, v
+    cdef uint32_t waiting_beginning
+    cdef uint32_t waiting_end
+    cdef uint32_t * p_tmp
+    cdef uint32_t * end
+    cdef uint32_t ** p_vertices = sd.neighbors
+
+    for source in range(n):
+
+        # Compute distances from source using BFS
+        bitset_clear(seen)
+        bitset_add(seen, source)
+        distances[source] = 0
+        waiting_beginning = 0
+        waiting_end = 0
+        waiting_list[waiting_beginning] = source
+
+        # For as long as there are vertices left to explore
+        while waiting_beginning <= waiting_end:
+
+            # We pick the first one
+            v = waiting_list[waiting_beginning]
+            p_tmp = p_vertices[v]
+            end = p_vertices[v + 1]
+
+            # and we iterate over all the outneighbors u of v
+            while p_tmp < end:
+                u = p_tmp[0]
+
+                # If we notice one of these neighbors is not seen yet, we set
+                # its parameters and add it to the queue to be explored later.
+                # Otherwise, we check whether we have detected a second shortest
+                # path between source and v.
+                if not bitset_in(seen, u):
+                    distances[u] = distances[v] + 1
+                    bitset_add(seen, u)
+                    waiting_end += 1
+                    waiting_list[waiting_end] = u
+                elif distances[u] == distances[v] + 1:
+                    # G is not geodetic
+                    bitset_free(seen)
+                    if not isinstance(G, StaticSparseBackend):
+                        free_short_digraph(sd)
+                    return False
+
+                p_tmp += 1
+
+            # We go to the next vertex in the queue
+            waiting_beginning += 1
+
+    bitset_free(seen)
+    if not isinstance(G, StaticSparseBackend):
+        free_short_digraph(sd)
+
+    # The graph is geodetic
+    return True