passagemath-graphs 10.5.43__cp312-cp312-macosx_14_0_arm64.whl → 10.6.1rc2__cp312-cp312-macosx_14_0_arm64.whl

sage/knots/link.py

@@ -1778,7 +1778,7 @@ class Link(SageObject):
             G.add_edge(c[3], c[1])
         return G.connected_components_number()
 
-    def is_knot(self):
+    def is_knot(self) -> bool:
         r"""
         Return ``True`` if ``self`` is a knot.
 
@@ -2051,7 +2051,7 @@ class Link(SageObject):
             conway += coeff * t_poly**M
         return conway
 
-    def khovanov_polynomial(self, var1='q', var2='t', base_ring=ZZ):
+    def khovanov_polynomial(self, var1='q', var2='t', torsion='T', ring=ZZ, base_ring=None):
         r"""
         Return the Khovanov polynomial of ``self``.
 
@@ -2060,32 +2060,43 @@ class Link(SageObject):
         INPUT:
 
         - ``var1`` -- (default: ``'q'``) the first variable. Its exponents
-          give the (torsion free) rank of the height of Khovanov homology
+          correspond to the height of Khovanov homology
         - ``var2`` -- (default: ``'t'``) the second variable. Its exponents
-          give the (torsion free) rank of the degree of Khovanov homology
-        - ``base_ring`` -- (default: ``ZZ``) the ring of the polynomial's
-          coefficients
+          correspond to the degree of Khovanov homology
+        - ``torsion`` -- (default: ``'T'``) additional variable to indicate
+          the torsion of the integral homology group corresponding to the
+          monomial; monomials without it correspond to torsion free ``ring``
+          modules; if it appears its exponents stands for the modulus of
+          the torsion
+        - ``ring`` -- (default: ``ZZ``) the ring of the homology. This will
+          be transferred to :meth:`khovanov_homology`
+
+        Here we follow the conventions used in
+        `KnotInfo <https://knotinfo.math.indiana.edu/descriptions/khovanov_unreduced_integral_polynomial.html>`__
 
         OUTPUT:
 
-        A two variate Laurent Polynomial over the ``base_ring``, more precisely an
-        instance of :class:`~sage.rings.polynomial.laurent_polynomial.LaurentPolynomial`.
+        A two or three (for integral homology) variate Laurent polynomial over
+        ``ZZ``, more precisely an instance of
+        :class:`~sage.rings.polynomial.laurent_polynomial.LaurentPolynomial_mpair`.
 
         EXAMPLES::
 
             sage: K = Link([[[1, -2, 3, -1, 2, -3]],[-1, -1, -1]])
             sage: K.khovanov_polynomial()                                               # needs sage.modules
-            q^-1 + q^-3 + q^-5*t^-2 + q^-9*t^-3
-            sage: K.khovanov_polynomial(base_ring=GF(2))                                # needs sage.modules
-            q^-1 + q^-3 + q^-5*t^-2 + q^-7*t^-2 + q^-9*t^-3
+            q^-1 + q^-3 + q^-5*t^-2 + q^-7*t^-2*T^2 + q^-9*t^-3
+            sage: K.khovanov_polynomial(ring=GF(2))                                     # needs sage.modules
+            q^-1 + q^-3 + q^-5*t^-2 + q^-7*t^-2 + q^-7*t^-3 + q^-9*t^-3
 
         The figure eight knot::
 
             sage: L = Link([[1, 6, 2, 7], [5, 2, 6, 3], [3, 1, 4, 8], [7, 5, 8, 4]])
             sage: L.khovanov_polynomial(var1='p')                                       # needs sage.modules
-            p^5*t^2 + p*t + p + p^-1 + p^-1*t^-1 + p^-5*t^-2
-            sage: L.khovanov_polynomial(var1='p', var2='s', base_ring=GF(4))            # needs sage.modules sage.rings.finite_rings
-            p^5*s^2 + p^3*s^2 + p*s + p + p^-1 + p^-1*s^-1 + p^-3*s^-1 + p^-5*s^-2
+            p^5*t^2 + p^3*t^2*T^2 + p*t + p + p^-1 + p^-1*t^-1
+              + p^-3*t^-1*T^2 + p^-5*t^-2
+            sage: L.khovanov_polynomial(var1='p', var2='s', ring=GF(4))                 # needs sage.modules sage.rings.finite_rings
+            p^5*s^2 + p^3*s^2 + p^3*s + p*s + p + p^-1 + p^-1*s^-1
+              + p^-3*s^-1 + p^-3*s^-2 + p^-5*s^-2
 
         The Hopf link::
 
@@ -2097,18 +2108,39 @@ class Link(SageObject):
 
         .. SEEALSO:: :meth:`khovanov_homology`
         """
-        L = LaurentPolynomialRing(base_ring, [var1, var2])
-        ch = base_ring.characteristic()
+        if base_ring:
+            ring = base_ring
+            from sage.misc.superseded import deprecation
+            deprecation(40149, "base_ring is deprecated, use argument ring instead.")
+
+        ch = ring.characteristic()
+        integral = False
+        if ch == 0 and not ring.is_field():
+            integral = True
+            L = LaurentPolynomialRing(ZZ, [var1, var2, torsion])
+        else:
+            L = LaurentPolynomialRing(ZZ, [var1, var2])
         coeff = {}
-        kh = self.khovanov_homology()
+        kh = self.khovanov_homology(ring=ring)
         from sage.rings.infinity import infinity
         for h in kh:
             for d in kh[h]:
                 H = kh[h][d]
-                gens = [g for g in H.gens() if g.order() == infinity or ch.divides(g.order())]
-                l = len(gens)
-                if l:
-                    coeff[(h, d)] = l
+                gens = {g: g.order() for g in H.gens()}
+                if integral:
+                    tor_count = {}
+                    for g, tor in gens.items():
+                        if tor in tor_count:
+                            tor_count[tor] += 1
+                        else:
+                            tor_count[tor] = 1
+                    for tor, ell in tor_count.items():
+                        if tor is infinity:
+                            coeff[(h, d, 0)] = ell
+                        else:
+                            coeff[(h, d, tor)] = ell
+                else:
+                    coeff[(h, d)] = len(gens)
         return L(coeff)
 
     def determinant(self):
@@ -2148,7 +2180,7 @@ class Link(SageObject):
         m = V + V.transpose()
         return Integer(abs(m.det()))
 
-    def is_alternating(self):
+    def is_alternating(self) -> bool:
         r"""
         Return whether the given knot diagram is alternating.
 
@@ -2462,9 +2494,9 @@ class Link(SageObject):
         if not new_pd:
             # trivial knot
             return type(self)([])
-        new_edges = flatten(new_pd)
+        new_edges = {elt for cr in new_pd for elt in cr}
         for cr in loop_crossings:
-            rem = set([e for e in cr if e in new_edges])
+            rem = {e for e in cr if e in new_edges}
             if len(rem) == 2:
                 # put remaining edges together
                 a, b = sorted(rem)
@@ -2871,8 +2903,8 @@ class Link(SageObject):
 
         cross = pd_code[0]
         rest = [list(vertex) for vertex in pd_code[1:]]
-        [a, b, c, d] = cross
-        if a == d and c == b and len(rest) > 0:
+        a, b, c, d = cross
+        if a == d and c == b and rest:
             return (~t + t**(-5)) * Link(rest)._bracket()
         elif a == b and c == d and len(rest) > 0:
             return (t + t**5) * Link(rest)._bracket()
@@ -3046,7 +3078,7 @@ class Link(SageObject):
             sage: # needs sage.libs.homfly
             sage: L = Link([[[1, -1], [2, -2]], [1, 1]])
             sage: L2 = Link([[1, 4, 2, 3], [2, 4, 1, 3]])
-            sage: L2.homfly_polynomial()
+            sage: L2.homfly_polynomial()  # not tested (:issue:`39544`)
             -L*M^-1 - L^-1*M^-1
             sage: L.homfly_polynomial()
             -L*M^-1 - L^-1*M^-1
@@ -3159,7 +3191,7 @@ class Link(SageObject):
 
         INPUT:
 
-        - ``n`` -- the number of colors to consider (if ommitted the
+        - ``n`` -- the number of colors to consider (if omitted the
           value of the determinant of ``self`` will be taken)
 
         OUTPUT: a matrix over the residue class ring of integers modulo ``n``
@@ -3203,7 +3235,7 @@ class Link(SageObject):
                     M[i, j] -= 1
         return M
 
-    def is_colorable(self, n=None):
+    def is_colorable(self, n=None) -> bool:
         r"""
         Return whether the link is ``n``-colorable.
 
@@ -3214,7 +3246,7 @@ class Link(SageObject):
 
         INPUT:
 
-        - ``n`` -- the number of colors to consider (if ommitted the
+        - ``n`` -- the number of colors to consider (if omitted the
           value of the determinant of ``self`` will be taken)
 
         EXAMPLES:
@@ -3267,7 +3299,7 @@ class Link(SageObject):
 
         INPUT:
 
-        - ``n`` -- the number of colors to consider (if ommitted the value
+        - ``n`` -- the number of colors to consider (if omitted the value
           of the determinant of ``self`` will be taken). Note that there
           are no colorings if n is coprime to the determinant of ``self``
 
@@ -3327,13 +3359,14 @@ class Link(SageObject):
 
     def coloring_maps(self, n=None, finitely_presented=False):
         r"""
-        Return the `n`-coloring maps of ``self``. These are group
-        homomorphisms from the fundamental group of ``self`` to the
-        `n`-th dihedral group.
+        Return the `n`-coloring maps of ``self``.
+
+        These are group homomorphisms from the fundamental group of
+        ``self`` to the `n`-th dihedral group.
 
         INPUT:
 
-        - ``n`` -- the number of colors to consider (if ommitted the value
+        - ``n`` -- the number of colors to consider (if omitted the value
           of the determinant of ``self`` will be taken). Note that there
           are no coloring maps if n is coprime to the determinant of ``self``
 
@@ -3953,7 +3986,7 @@ class Link(SageObject):
             return sb.is_conjugated(ob)
 
         if sb_ind > ob_ind:
-            # if the braid of self has more strands we have to perfom
+            # if the braid of self has more strands we have to perform
             # Markov II moves
             B = sb.parent()
             g = B.gen(ob_ind-1)
@@ -4489,7 +4522,7 @@ class Link(SageObject):
                 if proves[k]:
                     l += match_lists[k]
         else:
-            # for multi-component links there could regularily be more than one
+            # for multi-component links there could regularly be more than one
             # matching entry
             for k in match_lists.keys():
                 l += match_lists[k]
@@ -4525,7 +4558,7 @@ class Link(SageObject):
 
         return answer_list(l)
 
-    def is_isotopic(self, other):
+    def is_isotopic(self, other) -> bool:
         r"""
         Check whether ``self`` is isotopic to ``other``.
 
@@ -4645,7 +4678,7 @@ class Link(SageObject):
                         verbose('identified by KnotInfo uniquely (%s, %s)' % (sl[0], k))
                         return True
                     elif not self.is_knot():
-                        if len(set([l.series(oriented=True) for l in sl])) == 1:
+                        if len({l.series(oriented=True) for l in sl}) == 1:
                             # all matches are orientation mutants of each other
                             verbose('identified by KnotInfoSeries (%s, %s)' % (sl, k))
                             return True

sage/topology/cubical_complex.py

@@ -68,8 +68,9 @@ reflected in the fact that they have isomorphic homology groups.
    see the :mod:`Generic Cell Complex <sage.homology.cell_complex>`
    page instead.
 """
-
 from copy import copy
+from functools import total_ordering
+
 from .cell_complex import GenericCellComplex
 from sage.structure.sage_object import SageObject
 from sage.rings.integer import Integer
@@ -78,8 +79,6 @@ from sage.rings.integer_ring import ZZ
 from sage.rings.rational_field import QQ
 from sage.misc.cachefunc import cached_method
 from sage.misc.lazy_import import lazy_import
-from sage.misc.superseded import deprecation
-from functools import total_ordering
 
 lazy_import('sage.matrix.constructor', 'matrix')
 
@@ -1272,11 +1271,11 @@ class CubicalComplex(GenericCellComplex):
                 # nonzero via a dictionary.
                 matrix_data = {}
                 col = 0
-                if len(old) and len(current):
+                if old and current:
                     for cube in current:
                         faces = cube.faces_as_pairs()
                         sign = 1
-                        for (upper, lower) in faces:
+                        for upper, lower in faces:
                             # trac 32203: use two "try/except" loops
                             # in case lower is in old but upper is not.
                             try:

sage/topology/delta_complex.py

@@ -1010,10 +1010,10 @@ class DeltaComplex(GenericCellComplex):
                             # Simplex, as well as the function
                             # 'lattice_paths', in
                             # simplicial_complex.py.)
-                            for path in lattice_paths(list(range(k + 1)),
-                                                      list(range(n + 1)),
-                                                      length=d+1):
-                                path = tuple(path)
+                            for _path in lattice_paths(list(range(k + 1)),
+                                                       list(range(n + 1)),
+                                                       length=d+1):
+                                path = tuple(_path)
                                 new[(k, k_idx, n, n_idx, path)] = len(simplices)
                                 bdry_list = []
                                 for i in range(d+1):

sage/topology/simplicial_complex.py

@@ -168,7 +168,6 @@ from sage.categories.fields import Fields
 from sage.misc.cachefunc import cached_method
 from sage.misc.latex import latex
 from sage.misc.lazy_import import lazy_import
-from sage.misc.superseded import deprecation
 from sage.rings.integer import Integer
 from sage.rings.integer_ring import ZZ
 from sage.rings.polynomial.polynomial_ring import polygens

sage/topology/simplicial_complex_catalog.py

@@ -29,10 +29,12 @@ All of these examples are accessible by typing
 - :meth:`~sage.topology.examples.DunceHat`
 - :meth:`~sage.topology.examples.FareyMap`
 - :meth:`~sage.topology.examples.GenusSix`
+- :meth:`~sage.topology.examples.HochschildSphere`
 - :meth:`~sage.topology.examples.K3Surface`
 - :meth:`~sage.topology.examples.KleinBottle`
 - :meth:`~sage.topology.examples.MatchingComplex`
 - :meth:`~sage.topology.examples.MooreSpace`
+- :meth:`~sage.topology.examples.NoncrossingBipartiteComplex`
 - :meth:`~sage.topology.examples.NotIConnectedGraphs`
 - :meth:`~sage.topology.examples.PoincareHomologyThreeSphere`
 - :meth:`~sage.topology.examples.QuaternionicProjectivePlane`
@@ -84,3 +86,7 @@ from sage.topology.simplicial_complex_examples import (Sphere, Simplex, Torus,
                                                        SumComplex,
                                                        RandomTwoSphere, ShiftedComplex,
                                                        RudinBall, ZieglerBall, DunceHat)
+
+from sage.combinat.posets.hochschild_lattice import hochschild_simplicial_complex as HochschildSphere
+
+from sage.combinat.posets.bubble_shuffle import noncrossing_bipartite_complex as NoncrossingBipartiteComplex

sage/topology/simplicial_complex_examples.py

@@ -64,15 +64,6 @@ EXAMPLES::
     {0: 0, 1: C4, 2: 0}
     sage: simplicial_complexes.MatchingComplex(6).homology()                            # needs sage.modules
     {0: 0, 1: Z^16, 2: 0}
-
-TESTS::
-
-    sage: from sage.topology.simplicial_complex_examples import PseudoQuaternionicProjectivePlane
-    sage: H = PseudoQuaternionicProjectivePlane()                                       # needs sage.groups
-    doctest:warning...:
-    DeprecationWarning: PseudoQuaternionicProjectivePlane is deprecated.
-    Please use sage.topology.simplicial_complex_examples.QuaternionicProjectivePlane instead.
-    See https://github.com/sagemath/sage/issues/34568 for details.
 """
 
 from .simplicial_complex import SimplicialComplex
@@ -620,9 +611,6 @@ def QuaternionicProjectivePlane():
                                     for g in PermutationGroup([P, S])])
 
 
-PseudoQuaternionicProjectivePlane = deprecated_function_alias(34568, QuaternionicProjectivePlane)
-
-
 def PoincareHomologyThreeSphere():
     """
     A triangulation of the Poincaré homology 3-sphere.
@@ -1439,7 +1427,7 @@ def RandomTwoSphere(n):
     graph = RandomTriangulation(n)
 
     graph = graph.relabel(inplace=False)
-    triangles = [(u, v, w) for u, L in graph._embedding.items()
+    triangles = [(u, v, w) for u, L in graph.get_embedding().items()
                  for v, w in zip(L, L[1:] + [L[0]]) if u < v and u < w]
 
     return SimplicialComplex(triangles, maximality_check=False)
@@ -1484,10 +1472,10 @@ def ShiftedComplex(generators):
     """
     from sage.combinat.partition import Partitions
     Facets = []
-    for G in generators:
-        G = sorted(G, reverse=True)
+    for _G in generators:
+        G = sorted(_G, reverse=True)
         L = len(G)
-        for k in range(L * (L+1) // 2, sum(G) + 1):
+        for k in range(L * (L + 1) // 2, sum(G) + 1):
             for P in Partitions(k, length=L, max_slope=-1, outer=G):
                 Facets.append(list(reversed(P)))
     return SimplicialComplex(Facets)