remove empty folder in combinatorial polyhedron

Author: Jonathan Kliem

src/module_list.py

@@ -302,20 +302,28 @@ def uname_specific(name, value, alternative):
               sources = ['sage/geometry/polyhedron/combinatorial_polyhedron/base.pyx']),
 
     Extension('sage.geometry.polyhedron.combinatorial_polyhedron.list_of_faces',
-              sources = ['sage/geometry/polyhedron/combinatorial_polyhedron/list_of_faces.pyx']),
-
-    Extension('sage.geometry.polyhedron.combinatorial_polyhedron.bit_vector_operations.cc',
-              sources = ['sage/geometry/polyhedron/combinatorial_polyhedron/bit_vector_operations.cc'],
+              sources = ['sage/geometry/polyhedron/combinatorial_polyhedron/list_of_faces.pyx'],
+              depends = ['sage/geometry/polyhedron/combinatorial_polyhedron/bit_vector_operations.cc'],
+              language="c++",
               extra_compile_args=['-std=c++11']),
 
     Extension('sage.geometry.polyhedron.combinatorial_polyhedron.face_iterator',
-              sources = ['sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.pyx']),
+              sources = ['sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.pyx'],
+              depends = ['sage/geometry/polyhedron/combinatorial_polyhedron/bit_vector_operations.cc'],
+              language="c++",
+              extra_compile_args=['-std=c++11']),
 
     Extension('sage.geometry.polyhedron.combinatorial_polyhedron.polyhedron_face_lattice',
-              sources = ['sage/geometry/polyhedron/combinatorial_polyhedron/polyhedron_face_lattice.pyx']),
+              sources = ['sage/geometry/polyhedron/combinatorial_polyhedron/polyhedron_face_lattice.pyx'],
+              depends = ['sage/geometry/polyhedron/combinatorial_polyhedron/bit_vector_operations.cc'],
+              language="c++",
+              extra_compile_args=['-std=c++11']),
 
     Extension('sage.geometry.polyhedron.combinatorial_polyhedron.combinatorial_face',
-              sources = ['sage/geometry/polyhedron/combinatorial_polyhedron/combinatorial_face.pyx']),
+              sources = ['sage/geometry/polyhedron/combinatorial_polyhedron/combinatorial_face.pyx'],
+              depends = ['sage/geometry/polyhedron/combinatorial_polyhedron/bit_vector_operations.cc'],
+              language="c++",
+              extra_compile_args=['-std=c++11']),
 
     Extension('sage.geometry.polyhedron.combinatorial_polyhedron.conversions',
               sources = ['sage/geometry/polyhedron/combinatorial_polyhedron/conversions.pyx']),

src/sage/geometry/polyhedron/combinatorial_polyhedron/combinatorial_face.pyx

@@ -70,10 +70,23 @@ import numbers
 from sage.rings.integer         cimport smallInteger
 from .conversions               cimport bit_rep_to_Vrep_list
 from .base                      cimport CombinatorialPolyhedron
-from .bit_vector_operations     cimport count_atoms, bit_rep_to_coatom_rep
 from .polyhedron_face_lattice   cimport PolyhedronFaceLattice
 from libc.string                cimport memcpy
 
+cdef extern from "bit_vector_operations.cc":
+    cdef size_t count_atoms(uint64_t *A, size_t face_length)
+#        Return the number of atoms/vertices in A.
+#        This is the number of set bits in A.
+#        ``face_length`` is the length of A in terms of uint64_t.
+
+    cdef size_t bit_rep_to_coatom_rep(
+            uint64_t *face, uint64_t **coatoms, size_t n_coatoms,
+            size_t face_length, size_t *output)
+#        Write the coatom-representation of face in output. Return length.
+#        ``face_length`` is the length of ``face`` and ``coatoms[i]``
+#        in terms of uint64_t.
+#        ``n_coatoms`` length of ``coatoms``.
+
 cdef extern from "Python.h":
     int unlikely(int) nogil  # Defined by Cython
 

src/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.pyx

@@ -161,7 +161,57 @@ from sage.rings.integer     cimport smallInteger
 from cysignals.signals      cimport sig_check, sig_on, sig_off
 from .conversions           cimport bit_rep_to_Vrep_list
 from .base                  cimport CombinatorialPolyhedron
-from .bit_vector_operations cimport get_next_level, count_atoms, bit_rep_to_coatom_rep
+
+cdef extern from "bit_vector_operations.cc":
+    cdef size_t get_next_level(
+        uint64_t **faces, const size_t n_faces, uint64_t **nextfaces,
+        uint64_t **nextfaces2, uint64_t **visited_all,
+        size_t n_visited_all, size_t face_length)
+#        Set ``newfaces`` to be the facets of ``faces[n_faces -1]``
+#        that are not contained in a face of ``visited_all``.
+
+#        INPUT:
+
+#        - ``maybe_newfaces`` -- quasi of type ``uint64_t[n_faces -1][face_length]``,
+#          needs to be ``chunksize``-Bit aligned
+#        - ``newfaces`` -- quasi of type ``*uint64_t[n_faces -1]
+#        - ``visited_all`` -- quasi of type ``*uint64_t[n_visited_all]
+#        - ``face_length`` -- length of the faces
+
+#        OUTPUT:
+
+#        - return number of ``newfaces``
+#        - set ``newfaces`` to point to the new faces
+
+#        ALGORITHM:
+
+#        To get all facets of ``faces[n_faces-1]``, we would have to:
+#        - Intersect the first ``n_faces-1`` faces of ``faces`` with the last face.
+#        - Add all the intersection of ``visited_all`` with the last face
+#        - Out of both the inclusion-maximal ones are of codimension 1, i.e. facets.
+
+#        As we have visited all faces of ``visited_all``, we alter the algorithm
+#        to not revisit:
+#        Step 1: Intersect the first ``n_faces-1`` faces of ``faces`` with the last face.
+#        Step 2: Out of thosse the inclusion-maximal ones are some of the facets.
+#                At least we obtain all of those, that we have not already visited.
+#                Maybe, we get some more.
+#        Step 3: Only keep those that we have not already visited.
+#                We obtain exactly the facets of ``faces[n_faces-1]`` that we have
+#                not visited yet.
+
+    cdef size_t count_atoms(uint64_t *A, size_t face_length)
+#        Return the number of atoms/vertices in A.
+#        This is the number of set bits in A.
+#        ``face_length`` is the length of A in terms of uint64_t.
+
+    cdef size_t bit_rep_to_coatom_rep(
+            uint64_t *face, uint64_t **coatoms, size_t n_coatoms,
+            size_t face_length, size_t *output)
+#        Write the coatom-representation of face in output. Return length.
+#        ``face_length`` is the length of ``face`` and ``coatoms[i]``
+#        in terms of uint64_t.
+#        ``n_coatoms`` length of ``coatoms``.
 
 cdef extern from "Python.h":
     int unlikely(int) nogil  # Defined by Cython

src/sage/geometry/polyhedron/combinatorial_polyhedron/list_of_faces.pyx

@@ -11,7 +11,7 @@ to bit-representations of vertices stored in :class:`ListOfFaces`.
 Moreover, :class:`ListOfFaces` calculates the dimension of a polyhedron, assuming the
 faces are the facets of this polyhedron.
 
-Each face is stored over-aligned according to :meth:`~sage.geometry.polyhedron.combinatorial_polyhedron.bit_vector_operations.chunktype`.
+Each face is stored over-aligned according to the ``chunktype``.
 
 .. SEEALSO::
 
@@ -83,9 +83,54 @@ AUTHOR:
 from sage.structure.element import is_Matrix
 
 from cysignals.signals      cimport sig_on, sig_off
-from .bit_vector_operations cimport chunksize, get_next_level, count_atoms
 from libc.string            cimport memcpy
 
+cdef extern from "bit_vector_operations.cc":
+    # Any Bit-representation is assumed to be `chunksize`-Bit aligned.
+    cdef const size_t chunksize
+
+    cdef size_t get_next_level(
+        uint64_t **faces, const size_t n_faces, uint64_t **nextfaces,
+        uint64_t **nextfaces2, uint64_t **visited_all,
+        size_t n_visited_all, size_t face_length)
+#        Set ``newfaces`` to be the facets of ``faces[n_faces -1]``
+#        that are not contained in a face of ``visited_all``.
+
+#        INPUT:
+
+#        - ``maybe_newfaces`` -- quasi of type ``uint64_t[n_faces -1][face_length]``,
+#          needs to be ``chunksize``-Bit aligned
+#        - ``newfaces`` -- quasi of type ``*uint64_t[n_faces -1]
+#        - ``visited_all`` -- quasi of type ``*uint64_t[n_visited_all]
+#        - ``face_length`` -- length of the faces
+
+#        OUTPUT:
+
+#        - return number of ``newfaces``
+#        - set ``newfaces`` to point to the new faces
+
+#        ALGORITHM:
+
+#        To get all facets of ``faces[n_faces-1]``, we would have to:
+#        - Intersect the first ``n_faces-1`` faces of ``faces`` with the last face.
+#        - Add all the intersection of ``visited_all`` with the last face
+#        - Out of both the inclusion-maximal ones are of codimension 1, i.e. facets.
+
+#        As we have visited all faces of ``visited_all``, we alter the algorithm
+#        to not revisit:
+#        Step 1: Intersect the first ``n_faces-1`` faces of ``faces`` with the last face.
+#        Step 2: Out of thosse the inclusion-maximal ones are some of the facets.
+#                At least we obtain all of those, that we have not already visited.
+#                Maybe, we get some more.
+#        Step 3: Only keep those that we have not already visited.
+#                We obtain exactly the facets of ``faces[n_faces-1]`` that we have
+#                not visited yet.
+
+    cdef size_t count_atoms(uint64_t *A, size_t face_length)
+#        Return the number of atoms/vertices in A.
+#        This is the number of set bits in A.
+#        ``face_length`` is the length of A in terms of uint64_t.
+
 cdef extern from "Python.h":
     int unlikely(int) nogil  # Defined by Cython
 

src/sage/geometry/polyhedron/combinatorial_polyhedron/polyhedron_face_lattice.pyx

@@ -68,7 +68,21 @@ from libc.string            cimport memcmp, memcpy, memset
 from .conversions           cimport Vrep_list_to_bit_rep, bit_rep_to_Vrep_list
 from .base                  cimport CombinatorialPolyhedron
 from .face_iterator         cimport FaceIterator
-from .bit_vector_operations cimport intersection, bit_rep_to_coatom_rep
+
+cdef extern from "bit_vector_operations.cc":
+    cdef void intersection(uint64_t *A, uint64_t *B, uint64_t *C,
+                           size_t face_length)
+#    Return ``A & ~B == 0``.
+#    A is not subset of B, iff there is a vertex in A, which is not in B.
+#    ``face_length`` is the length of A and B in terms of uint64_t.
+
+    cdef size_t bit_rep_to_coatom_rep(
+            uint64_t *face, uint64_t **coatoms, size_t n_coatoms,
+            size_t face_length, size_t *output)
+#        Write the coatom-representation of face in output. Return length.
+#        ``face_length`` is the length of ``face`` and ``coatoms[i]``
+#        in terms of uint64_t.
+#        ``n_coatoms`` length of ``coatoms``.
 
 cdef extern from "Python.h":
     int unlikely(int) nogil  # Defined by Cython