passagemath-flint 10.6.1rc10__cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl

sage/graphs/all__sagemath_flint.py

@@ -0,0 +1 @@
+# sage_setup: distribution = sagemath-flint

sage/graphs/chrompoly.pyx

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+# sage_setup: distribution = sagemath-flint
+# cython: binding=True
+# sage.doctest: needs sage.libs.flint sage.graphs
+"""
+Chromatic polynomial
+
+AUTHORS:
+
+- Gordon Royle - original C implementation
+- Robert Miller - transplant
+
+REFERENCE:
+
+    See [Rea1968]_ and the :wikipedia:`Chromatic_polynomial` for more details
+    on this notion in graphs.
+
+"""
+
+# ****************************************************************************
+#       Copyright (C) 2008 Robert Miller
+#       Copyright (C) 2008 Gordon Royle
+#
+# 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 cysignals.signals cimport sig_check
+from memory_allocator cimport MemoryAllocator
+
+from sage.libs.gmp.mpz cimport *
+from sage.rings.integer_ring import ZZ
+from sage.rings.integer cimport Integer
+from sage.rings.ring cimport CommutativeRing
+from sage.rings.polynomial.polynomial_integer_dense_flint cimport Polynomial_integer_dense_flint
+from sage.rings.polynomial.polynomial_ring_constructor import PolynomialRing
+
+
+def chromatic_polynomial(G, return_tree_basis=False, algorithm='C', cache=None):
+    """
+    Compute the chromatic polynomial of the graph G.
+
+    The algorithm used is a recursive one, based on the following observations
+    of Read [Rea1968]_:
+
+        - The chromatic polynomial of a tree on n vertices is x(x-1)^(n-1).
+
+        - If e is an edge of G, G' is the result of deleting the edge e, and G''
+          is the result of contracting e, then the chromatic polynomial of G is
+          equal to that of G' minus that of G''.
+
+    INPUT:
+
+    - ``G`` -- a Sage graph
+
+    - ``return_tree_basis`` -- boolean (default: ``False``); not used yet
+
+    - ``algorithm`` -- string (default: ``'C'``); the algorithm to use among
+
+      - ``'C'``, an implementation in C by Robert Miller and Gordon Royle.
+
+      - ``'Python'``, an implementation in Python using caching to avoid
+        recomputing the chromatic polynomial of a graph that has already been
+        seen. This seems faster on some dense graphs.
+
+    - ``cache`` -- dictionary (default: ``None``); this parameter is used only
+      for algorithm ``'Python'``. It is a dictionary keyed by canonical
+      labelings of graphs and used to cache the chromatic polynomials of the
+      graphs generated by the algorithm. In other words, it avoids computing
+      twice the chromatic polynomial of isometric graphs. One will be created
+      automatically if not provided.
+
+    EXAMPLES::
+
+        sage: graphs.CycleGraph(4).chromatic_polynomial()
+        x^4 - 4*x^3 + 6*x^2 - 3*x
+        sage: graphs.CycleGraph(3).chromatic_polynomial()
+        x^3 - 3*x^2 + 2*x
+        sage: graphs.CubeGraph(3).chromatic_polynomial()
+        x^8 - 12*x^7 + 66*x^6 - 214*x^5 + 441*x^4 - 572*x^3 + 423*x^2 - 133*x
+        sage: graphs.PetersenGraph().chromatic_polynomial()
+        x^10 - 15*x^9 + 105*x^8 - 455*x^7 + 1353*x^6 - 2861*x^5 + 4275*x^4 - 4305*x^3 + 2606*x^2 - 704*x
+        sage: graphs.CompleteBipartiteGraph(3,3).chromatic_polynomial()
+        x^6 - 9*x^5 + 36*x^4 - 75*x^3 + 78*x^2 - 31*x
+        sage: for i in range(2,7):
+        ....:     graphs.CompleteGraph(i).chromatic_polynomial().factor()
+        (x - 1) * x
+        (x - 2) * (x - 1) * x
+        (x - 3) * (x - 2) * (x - 1) * x
+        (x - 4) * (x - 3) * (x - 2) * (x - 1) * x
+        (x - 5) * (x - 4) * (x - 3) * (x - 2) * (x - 1) * x
+        sage: graphs.CycleGraph(5).chromatic_polynomial().factor()
+        (x - 2) * (x - 1) * x * (x^2 - 2*x + 2)
+        sage: graphs.OctahedralGraph().chromatic_polynomial().factor()
+        (x - 2) * (x - 1) * x * (x^3 - 9*x^2 + 29*x - 32)
+        sage: graphs.WheelGraph(5).chromatic_polynomial().factor()
+        (x - 2) * (x - 1) * x * (x^2 - 5*x + 7)
+        sage: graphs.WheelGraph(6).chromatic_polynomial().factor()
+        (x - 3) * (x - 2) * (x - 1) * x * (x^2 - 4*x + 5)
+        sage: C(x)=graphs.LCFGraph(24, [12,7,-7], 8).chromatic_polynomial()  # long time (6s on sage.math, 2011)
+        sage: C(2)  # long time
+        0
+
+    By definition, the chromatic number of a graph G is the least integer k such that
+    the chromatic polynomial of G is strictly positive at k::
+
+        sage: G = graphs.PetersenGraph()
+        sage: P = G.chromatic_polynomial()
+        sage: min(i for i in range(11) if P(i) > 0) == G.chromatic_number()             # needs cliquer
+        True
+
+        sage: G = graphs.RandomGNP(10,0.7)
+        sage: P = G.chromatic_polynomial()
+        sage: min(i for i in range(11) if P(i) > 0) == G.chromatic_number()             # needs cliquer
+        True
+
+    Check that algorithms ``'C'`` and ``'Python'`` return the same results::
+
+        sage: G = graphs.RandomGNP(8, randint(1, 9)*0.1)
+        sage: c = G.chromatic_polynomial(algorithm='C')
+        sage: p = G.chromatic_polynomial(algorithm='Python')
+        sage: c == p
+        True
+
+    TESTS:
+
+    Check that :issue:`21502` is solved::
+
+        sage: graphs.EmptyGraph().chromatic_polynomial()
+        1
+
+    Check that :issue:`27966` is solved::
+
+        sage: Graph([[1, 1]], multiedges=True, loops=True).chromatic_polynomial()
+        0
+
+    Giving a wrong algorithm::
+
+        sage: Graph().chromatic_polynomial(algorithm='foo')
+        Traceback (most recent call last):
+        ...
+        ValueError: algorithm must be "C" or "Python"
+    """
+    algorithm = algorithm.lower()
+    if algorithm not in ['c', 'python']:
+        raise ValueError('algorithm must be "C" or "Python"')
+    if algorithm == 'python':
+        return chromatic_polynomial_with_cache(G, cache=cache)
+
+    R = ZZ['x']
+    if not G:
+        return R.one()
+    if G.has_loops():
+        return R.zero()
+    if not G.is_connected():
+        return R.prod(chromatic_polynomial(g, algorithm='C') for g in G.connected_components_subgraphs())
+    x = R.gen()
+    if G.is_tree():
+        return x * (x - 1) ** (G.num_verts() - 1)
+
+    cdef int nverts, nedges, i, j, u, v, top, bot, num_chords, next_v
+    cdef int *queue
+    cdef int *chords1
+    cdef int *chords2
+    cdef int *bfs_reorder
+    cdef int *parent
+    cdef mpz_t m, coeff
+    cdef mpz_t *tot
+    cdef mpz_t *coeffs
+    G = G.relabel(inplace=False)
+    G.remove_multiple_edges()
+    G.remove_loops()
+    nverts = G.num_verts()
+    nedges = G.num_edges()
+
+    cdef MemoryAllocator mem = MemoryAllocator()
+    queue = <int *> mem.allocarray(nverts, sizeof(int))
+    chords1 = <int *> mem.allocarray((nedges - nverts + 1), sizeof(int))
+    chords2 = <int *> mem.allocarray((nedges - nverts + 1), sizeof(int))
+    parent = <int *> mem.allocarray(nverts, sizeof(int))
+    bfs_reorder = <int *> mem.allocarray(nverts, sizeof(int))
+    tot = <mpz_t *> mem.allocarray((nverts+1), sizeof(mpz_t))
+    coeffs = <mpz_t *> mem.allocarray((nverts+1), sizeof(mpz_t))
+    num_chords = 0
+
+    # Breadth first search from 0:
+    bfs_reorder[0] = 0
+    mpz_init(tot[0])  # sets to 0
+    for i in range(1, nverts):
+        bfs_reorder[i] = -1
+        mpz_init(tot[i])  # sets to 0
+    mpz_init(tot[nverts])  # sets to 0
+    queue[0] = 0
+    top = 1
+    bot = 0
+    next_v = 1
+    while top > bot:
+        v = queue[bot]
+        bot += 1
+        for u in G.neighbor_iterator(v):
+            if bfs_reorder[u] == -1:  # if u is not yet in tree
+                bfs_reorder[u] = next_v
+                next_v += 1
+                queue[top] = u
+                top += 1
+                parent[bfs_reorder[u]] = bfs_reorder[v]
+            else:
+                if bfs_reorder[u] > bfs_reorder[v]:
+                    chords1[num_chords] = bfs_reorder[u]
+                    chords2[num_chords] = bfs_reorder[v]
+                else:
+                    continue
+                i = num_chords
+                num_chords += 1
+                # bubble sort the chords
+                while i > 0:
+                    if chords1[i-1] > chords1[i]:
+                        break
+                    if chords1[i-1] == chords1[i] and chords2[i-1] > chords2[i]:
+                        break
+                    j = chords1[i-1]
+                    chords1[i-1] = chords1[i]
+                    chords1[i] = j
+                    j = chords2[i-1]
+                    chords2[i-1] = chords2[i]
+                    chords2[i] = j
+                    i -= 1
+    try:
+        contract_and_count(chords1, chords2, num_chords, nverts, tot, parent)
+    except BaseException:
+        for i in range(nverts):
+            mpz_clear(tot[i])
+        raise
+    for i in range(nverts + 1):
+        mpz_init(coeffs[i])  # also sets them to 0
+    mpz_init(coeff)
+    mpz_init_set_si(m, -1)
+    # start with the zero polynomial: f(x) = 0
+    for i in range(nverts, 0, -1):  # nverts >= i > 0
+        if not mpz_sgn(tot[i]):
+            continue
+        mpz_neg(m, m)
+
+        # do this:
+        # f += tot[i]*m*x*(x-1)**(i-1)
+        mpz_addmul(coeffs[i], m, tot[i])
+        mpz_set_si(coeff, 1)
+        for j in range(1, i):
+            # an iterative method for binomial coefficients...
+            mpz_mul_si(coeff, coeff, j-i)
+            mpz_divexact_ui(coeff, coeff, j)
+            # coeffs[i-j] += tot[i]*m*coeff
+            mpz_mul(coeff, coeff, m)
+            mpz_addmul(coeffs[i-j], coeff, tot[i])
+            mpz_mul(coeff, coeff, m)
+    coeffs_ZZ = []
+    cdef Integer c_ZZ
+    for i in range(nverts + 1):
+        c_ZZ = Integer(0)
+        mpz_set(c_ZZ.value, coeffs[i])
+        coeffs_ZZ.append(c_ZZ)
+    f = R(coeffs_ZZ)
+
+    for i in range(nverts + 1):
+        mpz_clear(tot[i])
+        mpz_clear(coeffs[i])
+
+    mpz_clear(coeff)
+    mpz_clear(m)
+
+    return f
+
+
+cdef int contract_and_count(int *chords1, int *chords2, int num_chords, int nverts,
+                            mpz_t *tot, int *parent) except -1:
+    if num_chords == 0:
+        mpz_add_ui(tot[nverts], tot[nverts], 1)
+        return 0
+    cdef MemoryAllocator mem = MemoryAllocator()
+    cdef int *new_chords1 = <int *> mem.allocarray(num_chords, sizeof(int))
+    cdef int *new_chords2 = <int *> mem.allocarray(num_chords, sizeof(int))
+    cdef int *ins_list1 = <int *> mem.allocarray(num_chords, sizeof(int))
+    cdef int *ins_list2 = <int *> mem.allocarray(num_chords, sizeof(int))
+    cdef int i, j, k, x1, xj, z, num, insnum, parent_checked
+    for i in range(num_chords):
+        sig_check()
+
+        # contract chord i, and recurse
+        z = chords1[i]
+        x1 = chords2[i]
+        j = i + 1
+        insnum = 0
+        parent_checked = 0
+        while j < num_chords and chords1[j] == z:
+            xj = chords2[j]
+            if parent[z] > xj:
+                parent_checked = 1
+                # now try adding {x1, parent[z]} to the list
+                if not parent[x1] == parent[z]:
+                    if x1 > parent[z]:
+                        ins_list1[insnum] = x1
+                        ins_list2[insnum] = parent[z]
+                    else:
+                        ins_list1[insnum] = parent[z]
+                        ins_list2[insnum] = x1
+                    insnum += 1
+            if not parent[x1] == xj:  # then {x1, xj} isn't already a tree edge
+                ins_list1[insnum] = x1
+                ins_list2[insnum] = xj
+                insnum += 1
+            j += 1
+        if not parent_checked:
+            if not parent[x1] == parent[z]:
+                if x1 > parent[z]:
+                    ins_list1[insnum] = x1
+                    ins_list2[insnum] = parent[z]
+                else:
+                    ins_list1[insnum] = parent[z]
+                    ins_list2[insnum] = x1
+                insnum += 1
+
+        # now merge new_chords and ins_list
+        num = 0
+        k = 0
+        while k < insnum and j < num_chords:
+            if (chords1[j] > ins_list1[k] or
+                    (chords1[j] == ins_list1[k] and chords2[j] > ins_list2[k])):
+                new_chords1[num] = chords1[j]
+                new_chords2[num] = chords2[j]
+                num += 1
+                j += 1
+            elif (chords1[j] < ins_list1[k] or
+                  (chords1[j] == ins_list1[k] and chords2[j] < ins_list2[k])):
+                new_chords1[num] = ins_list1[k]
+                new_chords2[num] = ins_list2[k]
+                num += 1
+                k += 1
+            else:
+                new_chords1[num] = chords1[j]
+                new_chords2[num] = chords2[j]
+                num += 1
+                j += 1
+                k += 1
+        if j == num_chords:
+            while k < insnum:
+                new_chords1[num] = ins_list1[k]
+                new_chords2[num] = ins_list2[k]
+                num += 1
+                k += 1
+        elif k == insnum:
+            while j < num_chords:
+                new_chords1[num] = chords1[j]
+                new_chords2[num] = chords2[j]
+                num += 1
+                j += 1
+        contract_and_count(new_chords1, new_chords2, num, nverts - 1, tot, parent)
+    mpz_add_ui(tot[nverts], tot[nverts], 1)
+
+
+#
+# Chromatic Polynomial with caching
+#
+
+def chromatic_polynomial_with_cache(G, cache=None):
+    r"""
+    Return the chromatic polynomial of the graph ``G``.
+
+    The algorithm used is here is the non recursive version of a recursive
+    algorithm based on the following observations of Read:
+
+        - The chromatic polynomial of a tree on `n` vertices is `x(x-1)^{n-1}`.
+
+        - If `e` is an edge of `G`, `G'` is the result of deleting the edge `e`,
+          and `G''` is the result of contracting `e`, then the chromatic
+          polynomial of `G` is equal to that of `G'` minus that of `G''`.
+
+        - If `G` is not connected, its the chromatic polynomial is the product
+          of the chromatic polynomials of its connected components.
+
+    Since this method makes extensive use of canonical labelings, it is
+    recommended to install optional package ``bliss``.
+
+    INPUT:
+
+    - ``G`` -- a Sage graph
+
+    - ``cache`` -- dictionary (default: ``None``); dictionary keyed by canonical
+      labelings of graphs and used to cache the chromatic polynomials of the
+      graphs generated by the algorithm. In other words, it avoids computing
+      twice the chromatic polynomial of isometric graphs. One will be created
+      automatically if not provided.
+
+    EXAMPLES::
+
+        sage: from sage.graphs.chrompoly import chromatic_polynomial_with_cache
+        sage: chromatic_polynomial_with_cache(graphs.CycleGraph(4))
+        x^4 - 4*x^3 + 6*x^2 - 3*x
+        sage: chromatic_polynomial_with_cache(graphs.CycleGraph(3))
+        x^3 - 3*x^2 + 2*x
+        sage: chromatic_polynomial_with_cache(graphs.CubeGraph(3))
+        x^8 - 12*x^7 + 66*x^6 - 214*x^5 + 441*x^4 - 572*x^3 + 423*x^2 - 133*x
+        sage: chromatic_polynomial_with_cache(graphs.PetersenGraph())
+        x^10 - 15*x^9 + 105*x^8 - 455*x^7 + 1353*x^6 - 2861*x^5 + 4275*x^4 - 4305*x^3 + 2606*x^2 - 704*x
+        sage: chromatic_polynomial_with_cache(graphs.CompleteBipartiteGraph(3,3))
+        x^6 - 9*x^5 + 36*x^4 - 75*x^3 + 78*x^2 - 31*x
+
+    If a cache is provided, it is fed::
+
+        sage: cache = {}
+        sage: G = graphs.CycleGraph(4)
+        sage: p = chromatic_polynomial_with_cache(graphs.CycleGraph(4), cache=cache)
+        sage: key = frozenset(G.canonical_label().edges(labels=False, sort=False))
+        sage: cache[key]
+        x^4 - 4*x^3 + 6*x^2 - 3*x
+
+    TESTS:
+
+    Corner cases::
+
+        sage: from sage.graphs.chrompoly import chromatic_polynomial_with_cache
+        sage: chromatic_polynomial_with_cache(graphs.EmptyGraph())
+        1
+        sage: chromatic_polynomial_with_cache(Graph(1))
+        x
+        sage: chromatic_polynomial_with_cache(Graph(2))
+        x^2
+        sage: chromatic_polynomial_with_cache(Graph(3))
+        x^3
+        sage: chromatic_polynomial_with_cache(Graph([[1, 1]], loops=True))
+        0
+
+    Parameter ``cache`` must be a dictionary::
+
+        sage: chromatic_polynomial_with_cache(Graph(2), cache=[])
+        Traceback (most recent call last):
+        ...
+        TypeError: parameter cache must be a dictionary or None
+    """
+    cdef CommutativeRing R = PolynomialRing(ZZ, "x", implementation="FLINT")
+    cdef Polynomial_integer_dense_flint one = R.one()
+    cdef Polynomial_integer_dense_flint zero = R.zero()
+    cdef Polynomial_integer_dense_flint x = R.gen()
+
+    if not G:
+        return one
+    if G.has_loops():
+        return zero
+
+    # Make a copy of the input graph and ensure that it's labeled [0..n-1]
+    G = G.relabel(inplace=False)
+    G.remove_multiple_edges()
+
+    # We use a cache to avoid computing twice the chromatic polynomial of
+    # isomorphic graphs
+    if cache is None:
+        cache = dict()
+    elif not isinstance(cache, dict):
+        raise TypeError("parameter cache must be a dictionary or None")
+
+    # We use a digraph to store intermediate values and store the current state
+    # of a vertex (either a graph, a key or a polynomial)
+    from sage.graphs.digraph import DiGraph
+    D = DiGraph(1)
+    D.set_vertex(0, G)
+
+    cdef int op_none = 0
+    cdef int op_mult = 1
+    cdef int op_diff = 2
+
+    # We use a stack to order operations in a depth first search fashion
+    from collections import deque
+    stack = deque()
+    stack.append((0, True, (op_none, )))
+    cdef bint firstseen
+    cdef int u, v, w, a, b
+    cdef tuple com
+
+    while stack:
+
+        v, firstseen, com = stack.pop()
+
+        if firstseen:
+            g = D.get_vertex(v)
+            key = frozenset(g.canonical_label().edges(labels=False, sort=False))
+            if key in cache:
+                D.set_vertex(v, cache[key])
+
+            elif g.has_loops():
+                D.set_vertex(v, zero)
+                cache[key] = D.get_vertex(v)
+
+            elif not g.is_connected():
+                # We have to compute the product of the chromatic polynomials of
+                # the connected components
+                D.set_vertex(v, key)
+                stack.append((v, False, (op_mult, )))
+                for h in g.connected_components_subgraphs():
+                    w = D.add_vertex()
+                    D.set_vertex(w, h)
+                    D.add_edge(v, w)
+                    stack.append((w, True, (op_none, )))
+
+            elif g.order() == g.size() + 1:
+                # g is a tree
+                D.set_vertex(v, x*(x - one)**(g.order() - 1))
+                cache[key] = D.get_vertex(v)
+
+            else:
+                # Otherwise, the chromatic polynomial of g is the chromatic
+                # polynomial of g without edge e minus the chromatic polynomial
+                # of g after the contraction of edge e
+                a = D.add_vertex()
+                b = D.add_vertex()
+                D.add_edge(v, a)
+                D.add_edge(v, b)
+                D.set_vertex(v, key)
+                stack.append((v, False, (op_diff, a, b)))
+                # We try to select an edge that could disconnect the graph
+                for u, w in g.bridges(labels=False):
+                    break
+                else:
+                    u, w = next(g.edge_iterator(labels=False))
+
+                g.delete_edge(u, w)
+                D.set_vertex(a, g.copy())
+                stack.append((a, True, (op_none, )))
+                g.add_edge(u, w)
+                g.merge_vertices([u, w])
+                g.remove_multiple_edges()
+                D.set_vertex(b, g)
+                stack.append((b, True, (op_none, )))
+
+        elif com[0] == op_mult:
+            # We compute the product of the connected components of the graph
+            # and delete the children from D
+            key = D.get_vertex(v)
+            cache[key] = R.prod(D.get_vertex(w) for w in D.neighbor_out_iterator(v))
+            D.set_vertex(v, cache[key])
+            D.delete_vertices(D.neighbor_out_iterator(v))
+
+        elif com[0] == op_diff:
+            # We compute the difference of the chromatic polynomials of the 2
+            # children and remove them from D
+            key = D.get_vertex(v)
+            cache[key] = D.get_vertex(com[1]) - D.get_vertex(com[2])
+            D.set_vertex(v, cache[key])
+            D.delete_vertices(D.neighbor_out_iterator(v))
+
+        else:
+            # We should never end here
+            raise ValueError("something goes wrong")
+
+    return D.get_vertex(0)