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refactor: Move list of pairs to dedicated class
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-222
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‎src/sage/data_structures/binary_list.pxd

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cimport cython
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cdef struct pair_s:
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size_t first
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size_t second
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@cython.final
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cdef class BinaryList:
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cdef pair_s** _lists
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cdef size_t length
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cdef inline int enlarge(self) except -1
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cdef inline int add(self, size_t first, size_t second) except -1
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cdef inline pair_s* get(self, size_t index) except NULL

‎src/sage/data_structures/binary_list.pyx

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r"""
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A data structure to store lists of integer pairs of large size.
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"""
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# ****************************************************************************
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# Copyright (C) 2022 Jonathan Kliem <[email protected]>
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 2 of the License, or
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# (at your option) any later version.
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# https://www.gnu.org/licenses/
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# ****************************************************************************
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from cysignals.memory cimport check_reallocarray, check_allocarray, sig_free
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from sage.rings.integer cimport smallInteger
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# Should be a power of two.
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# Should be neither exposed nor modified.
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cdef size_t length_per_list = 16348
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cdef class BinaryList:
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def __dealloc__(self):
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cdef size_t n_lists = self.length // length_per_list
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cdef size_t i
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for i in range(n_lists):
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sig_free(self._lists[i])
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sig_free(self._lists)
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cdef inline int enlarge(self) except -1:
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"""
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Increase size of list by one.
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"""
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if self.length % length_per_list:
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self.length += 1
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return 0
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cdef size_t n_lists = self.length // length_per_list
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self._lists = <pair_s**> check_reallocarray(self._lists, n_lists + 1, sizeof(pair_s*))
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self._lists[n_lists] = <pair_s*> check_allocarray(length_per_list, sizeof(pair_s))
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self.length += 1
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cdef inline pair_s* get(self, size_t index) except NULL:
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if not (0 <= index < self.length):
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raise IndexError
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cdef size_t list_index = index // length_per_list
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cdef size_t index_in_list = index - list_index * length_per_list
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return &self._lists[list_index][index_in_list]
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def __getitem__(self, size_t index):
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r"""
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Get item of specified index.
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EXAMPLES::
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sage: from sage.data_structures.binary_list import BinaryList
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sage: l = BinaryList()
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sage: l[0] = [1, 5]
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sage: l[0]
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(1, 5)
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sage: l[1]
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Traceback (most recent call last):
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...
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IndexError
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sage: l[-1]
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Traceback (most recent call last):
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...
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OverflowError: can't convert negative value to size_t
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"""
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cdef pair_s pair = self.get(index)[0]
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return (smallInteger(pair.first), smallInteger(pair.second))
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def __setitem__(self, size_t index, value):
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r"""
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Set item of specified index.
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Allows increasing the size of the list by at most 1.
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EXAMPLES::
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sage: from sage.data_structures.binary_list import BinaryList
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sage: l = BinaryList()
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sage: l[0] = (2, 1)
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sage: l[1] = (1, 2)
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sage: l[0]
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(2, 1)
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sage: l[1]
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(1, 2)
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sage: l[10] = (5, 3)
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Traceback (most recent call last):
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...
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IndexError
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sage: l[2] = 2
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Traceback (most recent call last):
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...
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TypeError: 'sage.rings.integer.Integer' object is not iterable
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"""
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cdef size_t first, second
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(first, second) = value
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if (index == self.length):
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self.add(first, second)
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return
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cdef pair_s* pair_pt = self.get(index)
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pair_pt[0].first = first
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pair_pt[0].second = second
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cdef inline int add(self, size_t first, size_t second) except -1:
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"""
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Add a pair to the list.
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"""
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self.enlarge()
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cdef pair_s* last = self.get(self.length - 1)
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last[0].first = first
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last[0].second = second

‎src/sage/geometry/polyhedron/combinatorial_polyhedron/base.pxd

Lines changed: 12 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,10 @@
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cimport cython
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from sage.structure.sage_object cimport SageObject
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from .face_iterator cimport FaceIterator, CombinatorialFace
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from .list_of_faces cimport ListOfFaces
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from .face_data_structure cimport face_t
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from .polyhedron_face_lattice cimport PolyhedronFaceLattice
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from sage.data_structures.binary_list cimport BinaryList
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from sage.structure.sage_object cimport SageObject
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from .face_iterator cimport FaceIterator, CombinatorialFace
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from .list_of_faces cimport ListOfFaces
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from .face_data_structure cimport face_t
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from .polyhedron_face_lattice cimport PolyhedronFaceLattice
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@cython.final
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cdef class CombinatorialPolyhedron(SageObject):
@@ -24,22 +25,10 @@ cdef class CombinatorialPolyhedron(SageObject):
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cdef tuple _far_face_tuple
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cdef tuple _f_vector
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# Edges, ridges and incidences are stored in a pointer of pointers.
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# The first edge has vertices ``edges[0][0]`` and ``edges[0][1]``,
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# the second edge has vertices ``edges[0][2]`` and ``edges[0][3]``, etc.
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# There are ``_length_edges_list`` edges in ``edges[i]``, so the edge
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# ``_length_edges_list + 1`` has vertices ``edges[1][0]`` and ``edges[1][1]``.
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# Likewise for ridges and incidences.
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cdef size_t _length_edges_list
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cdef size_t **_edges # stores edges labeled by vertex indices
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cdef size_t _n_edges
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cdef size_t **_ridges # stores ridges labeled by facet indices
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cdef size_t _n_ridges
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cdef size_t **_face_lattice_incidences # stores incidences in Hasse diagram labeled indices of the faces
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cdef size_t _n_face_lattice_incidences
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cdef PolyhedronFaceLattice _all_faces # class to generate Hasse diagram incidences
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cdef BinaryList _edges # stores edges labeled by vertex indices
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cdef BinaryList _ridges # stores ridges labeled by facet indices
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cdef BinaryList _face_lattice_incidences # stores incidences in Hasse diagram labeled indices of the faces
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cdef PolyhedronFaceLattice _all_faces # class to generate Hasse diagram incidences
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cdef tuple Vrep(self)
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cdef tuple facet_names(self)
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cdef int _compute_edges_or_ridges(self, int dual, bint do_edges) except -1
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cdef size_t _compute_edges_or_ridges_with_iterator(
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self, FaceIterator face_iter, const bint do_atom_rep, const bint do_f_vector,
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size_t ***edges_pt, size_t *counter_pt, size_t *current_length_pt,
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size_t* f_vector) except -1
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cdef int _compute_face_lattice_incidences(self) except -1
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BinaryList edges, size_t* f_vector) except -1
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cdef inline int _set_edge(self, size_t a, size_t b, size_t ***edges_pt, size_t *counter_pt, size_t *current_length_pt) except -1
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cdef inline void _free_edges(self, size_t ***edges_pt, size_t counter)
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cdef inline size_t _get_edge(self, size_t **edges, size_t edge_number, size_t vertex) except -1
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cdef int _compute_face_lattice_incidences(self) except -1

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