Some experiments about structuring the code better

src/snappy/__init__.py

@@ -28,22 +28,40 @@
 
 from typing import Union, Tuple, List, Optional
 
+class BaseTriangulation:
+    from .exterior_to_link import exterior_to_link
+
+class BaseManifold(BaseTriangulation):
+    from .verify import verify_hyperbolicity
+    from .margulis import margulis
+    from .len_spec import (length_spectrum_alt_gen,
+                           length_spectrum_alt)
+    from .isometry_signature import isometry_signature
+    from .cusps import (cusp_areas,
+                        short_slopes,
+                        cusp_translations)
+    from .cusps.cusp_area_matrix import cusp_area_matrix
+    from .raytracing import inside_view
+
 # Subclass to be able to monkey-patch
-class Triangulation(extensions.SnapPy.Triangulation):
-    __doc__ = extensions.SnapPy.Triangulation.__doc__
+class Triangulation(
+        extensions.SnapPy.KernelTriangulation, BaseTriangulation):
+    __doc__ = extensions.SnapPy.KernelTriangulation.__doc__
 
 # Subclass to be able to monkey-patch
-class TriangulationHP(extensions.SnapPyHP.Triangulation):
-    __doc__ = extensions.SnapPyHP.Triangulation.__doc__
+class TriangulationHP(
+        extensions.SnapPyHP.KernelTriangulation, BaseTriangulation):
+    __doc__ = extensions.SnapPyHP.KernelTriangulation.__doc__
 
 # We want Manifold to be a subclass of Triangulation.
 # Unfortunately, that introduces a diamond pattern here.
 # Luckily, the python resolves methods and bases classes
 # in the presence of a diamond pattern seem to work just
 # fine. In particular, we do not double allocate the underlying
 # C structures.
-class Manifold(extensions.SnapPy.Manifold, Triangulation):
-    __doc__ = extensions.SnapPy.Manifold.__doc__
+class Manifold(
+        extensions.SnapPy.KernelManifold, Triangulation, BaseManifold):
+    __doc__ = extensions.SnapPy.KernelManifold.__doc__
 
     def identify(self, extends_to_link=False):
         """
@@ -98,8 +116,9 @@ def low_precision(self):
 
 # We want ManifoldHP to be a subclass of TriangulationHP.
 # See comment about Manifold and the diamond pattern.
-class ManifoldHP(extensions.SnapPyHP.Manifold, TriangulationHP):
-    __doc__ = extensions.SnapPyHP.Manifold.__doc__
+class ManifoldHP(
+        extensions.SnapPyHP.KernelManifold, TriangulationHP, BaseManifold):
+    __doc__ = extensions.SnapPyHP.KernelManifold.__doc__
 
     def low_precision(self):
         """
@@ -219,7 +238,7 @@ def is_isometric_to(self,
         resolved_other,
         return_isometries=return_isometries)
 
-is_isometric_to.__doc__ = extensions.SnapPy.Manifold._is_isometric_to.__doc__
+is_isometric_to.__doc__ = extensions.SnapPy.KernelManifold._is_isometric_to.__doc__
 Manifold.is_isometric_to = is_isometric_to
 ManifoldHP.is_isometric_to = is_isometric_to
 
@@ -233,57 +252,17 @@ def isomorphisms_to(self,
     return resolved_self._isomorphisms_to(
         resolved_other)
 
-isomorphisms_to.__doc__ = extensions.SnapPy.Triangulation._isomorphisms_to.__doc__
-Triangulation.isomorphisms_to = isomorphisms_to
-TriangulationHP.isomorphisms_to = isomorphisms_to
+isomorphisms_to.__doc__ = extensions.SnapPy.KernelTriangulation._isomorphisms_to.__doc__
+BaseTriangulation.isomorphisms_to = isomorphisms_to
 
 from . import snap
-snap.add_methods(Manifold)
-snap.add_methods(ManifoldHP)
-snap.add_methods(Triangulation, hyperbolic=False)
-snap.add_methods(TriangulationHP, hyperbolic=False)
-
-from . import exterior_to_link
-Triangulation.exterior_to_link = exterior_to_link.exterior_to_link
-TriangulationHP.exterior_to_link = exterior_to_link.exterior_to_link
-
-from . import verify
-Manifold.verify_hyperbolicity = verify.verify_hyperbolicity
-ManifoldHP.verify_hyperbolicity = verify.verify_hyperbolicity
-
-from . import margulis
-Manifold.margulis = margulis.margulis
-ManifoldHP.margulis = margulis.margulis
-
-from . import len_spec
-Manifold.length_spectrum_alt_gen = len_spec.length_spectrum_alt_gen
-ManifoldHP.length_spectrum_alt_gen = len_spec.length_spectrum_alt_gen
-Manifold.length_spectrum_alt = len_spec.length_spectrum_alt
-ManifoldHP.length_spectrum_alt = len_spec.length_spectrum_alt
+snap.add_methods(BaseManifold)
+snap.add_methods(BaseTriangulation, hyperbolic=False)
 
 from . import canonical
 Manifold.canonical_retriangulation = canonical.canonical_retriangulation
 ManifoldHP.canonical_retriangulation = canonical.canonical_retriangulation_hp
 
-from . import isometry_signature
-
-Manifold.isometry_signature = isometry_signature.isometry_signature
-ManifoldHP.isometry_signature = isometry_signature.isometry_signature
-
-from .cusps import cusp_area_matrix
-
-Manifold.cusp_area_matrix = cusp_area_matrix.cusp_area_matrix
-ManifoldHP.cusp_area_matrix = cusp_area_matrix.cusp_area_matrix
-
-from . import cusps
-
-Manifold.cusp_areas = cusps.cusp_areas
-ManifoldHP.cusp_areas = cusps.cusp_areas
-Manifold.short_slopes = cusps.short_slopes
-ManifoldHP.short_slopes = cusps.short_slopes
-Manifold.cusp_translations = cusps.cusp_translations
-ManifoldHP.cusp_translations = cusps.cusp_translations
-
 def complex_volume(manifold, verified_modulo_2_torsion=False,
                    bits_prec=None):
     """
@@ -349,12 +328,6 @@ def complex_volume(manifold, verified_modulo_2_torsion=False,
 drilling._add_methods(Manifold)
 drilling._add_methods(ManifoldHP, high_precision=True)
 
-from . import raytracing
-
-Manifold.inside_view = raytracing.inside_view
-ManifoldHP.inside_view = raytracing.inside_view
-
-
 def all_translations(self, verified=False, bits_prec=None):
     """
     Returns the (complex) Euclidean translations of the meridian

src/snappy/extensions/SnapPy/cython_src/core/basic.pyx

@@ -612,7 +612,7 @@ cdef IsometryListToIsometries(IsometryList *isometries):
 # PLink communication
 
 def _plink_callback(LE):
-    cdef Manifold manifold
+    cdef KernelManifold manifold
     cdef c_Triangulation* c_triangulation = NULL
     if LE.manifold is None:
         LE.manifold = _manifold_class('empty')
@@ -637,10 +637,10 @@ def _plink_callback(LE):
 
 # Conversion functions Manifold <-> Triangulation
 
-def Manifold_from_Triangulation(Triangulation T, recompute=True,
+def Manifold_from_Triangulation(KernelTriangulation T, recompute=True,
                                 manifold_class=None):
     cdef c_Triangulation *c_triangulation
-    cdef Manifold M
+    cdef KernelManifold M
 
     M = _manifold_class('empty') if manifold_class is None else manifold_class('empty')
     if T.c_triangulation is NULL:
@@ -663,9 +663,9 @@ def Manifold_from_Triangulation(Triangulation T, recompute=True,
     return M
 
 
-def Triangulation_from_Manifold(Manifold M):
+def Triangulation_from_Manifold(KernelManifold M):
     cdef c_Triangulation *c_triangulation
-    cdef Triangulation T
+    cdef KernelTriangulation T
 
     if M.c_triangulation is NULL:
         return _triangulation_class('empty')

src/snappy/extensions/SnapPy/cython_src/core/cusp_neighborhoods.pyx

@@ -10,7 +10,7 @@ cdef class CCuspNeighborhood():
     def _number_(n):
         return number.number_to_native_number(n)
 
-    def __cinit__(self, Manifold manifold):
+    def __cinit__(self, KernelManifold manifold):
         if manifold.c_triangulation is NULL:
             raise ValueError('The Triangulation is empty.')
         is_complete = manifold.cusp_info('is_complete')
@@ -41,7 +41,7 @@ cdef class CCuspNeighborhood():
         Return a Manifold built from the current canonical triangulation.
         """
         cdef c_Triangulation *c_triangulation
-        cdef Manifold M
+        cdef KernelManifold M
 
         copy_triangulation(self.c_cusp_neighborhood.its_triangulation,
                            &c_triangulation)

src/snappy/extensions/SnapPy/cython_src/core/dirichlet.pyx

@@ -104,7 +104,7 @@ cdef class CDirichletDomain():
         return number.number_to_native_number(n)
 
     def __cinit__(self,
-                  Manifold manifold=None,
+                  KernelManifold manifold=None,
                   vertex_epsilon=default_vertex_epsilon,
                   displacement=None,
                   centroid_at_origin=True,
@@ -538,7 +538,7 @@ cdef class CDirichletDomain():
 
     cdef triangulate(self, return_class):
         cdef c_Triangulation *c_triangulation
-        cdef Triangulation M
+        cdef KernelTriangulation M
         c_triangulation = Dirichlet_to_triangulation(self.c_dirichlet_domain)
         if c_triangulation is NULL:
             raise ValueError('The Dirichlet domain could not be '

src/snappy/extensions/SnapPy/cython_src/core/fundamental_group.pyx

@@ -105,7 +105,7 @@ cdef class CFundamentalGroup():
     cdef c_Triangulation *c_triangulation
     cdef readonly num_cusps
 
-    def __cinit__(self, Triangulation triangulation,
+    def __cinit__(self, KernelTriangulation triangulation,
                   simplify_presentation=True,
                   fillings_may_affect_generators=True,
                   minimize_number_of_generators=True,

src/snappy/extensions/SnapPy/cython_src/core/manifold.pyx

@@ -1,6 +1,6 @@
 # Manifolds
 
-cdef class Manifold(Triangulation):
+cdef class KernelManifold(KernelTriangulation):
     """
     A Manifold is a :class:`Triangulation` together with a geometric structure.
     That is, a Manifold is an ideal triangulation of the interior of a
@@ -205,7 +205,7 @@ cdef class Manifold(Triangulation):
         cdef c_Triangulation *c_retriangulated_triangulation
         cdef int n = get_num_tetrahedra(self.c_triangulation)
         cdef result
-        cdef Triangulation new_tri
+        cdef KernelTriangulation new_tri
 
         if self.c_triangulation is NULL:
             return ""
@@ -257,7 +257,7 @@ cdef class Manifold(Triangulation):
         False
         """
 
-        cdef Manifold M
+        cdef KernelManifold M
         M = self.copy()
         M.canonize()
         canonical_retriangulation(M.c_triangulation)
@@ -276,7 +276,7 @@ cdef class Manifold(Triangulation):
         >>> N.volume() # doctest: +NUMERIC6
         5.13794120
         """
-        Triangulation._from_string(self, string)
+        KernelTriangulation._from_string(self, string)
         if initialize_structure:
             self.init_hyperbolic_structure()
 
@@ -290,7 +290,7 @@ cdef class Manifold(Triangulation):
         >>> N.is_isometric_to(M)
         True
         """
-        Triangulation._from_bytes(self, bytestring)
+        KernelTriangulation._from_bytes(self, bytestring)
         if initialize_structure:
             self.init_hyperbolic_structure()
 
@@ -299,7 +299,7 @@ cdef class Manifold(Triangulation):
         Fill an empty manifold from an isosig generated by
         triangulation_isosig.
         """
-        Triangulation._from_isosig(self, isosig)
+        KernelTriangulation._from_isosig(self, isosig)
         if self.c_triangulation == NULL:
             return
         if initialize_structure:
@@ -488,7 +488,7 @@ cdef class Manifold(Triangulation):
         cdef c_SymmetryGroup* symmetries_of_manifold = NULL
         cdef c_SymmetryGroup* symmetries_of_link = NULL
         cdef c_Triangulation* c_symmetric_triangulation = NULL
-        cdef Manifold symmetric_triangulation
+        cdef KernelManifold symmetric_triangulation
         cdef Boolean is_full_group
         cdef c_FuncResult result
         cdef SymmetryGroup symmetry_group
@@ -611,7 +611,7 @@ cdef class Manifold(Triangulation):
           sage: N2 == N4                                     #doctest: +SKIP
           True
         """
-        cover = Triangulation.cover(self, permutation_rep)
+        cover = KernelTriangulation.cover(self, permutation_rep)
         return Manifold_from_Triangulation(cover, recompute=False,
                                            manifold_class=self.__class__)
 
@@ -656,7 +656,7 @@ cdef class Manifold(Triangulation):
         argument method = 'gap' If you have Magma installed, you can
         used it to do the heavy lifting by specifying method='magma'.
         """
-        covers = Triangulation.covers(self, degree, method,cover_type)
+        covers = KernelTriangulation.covers(self, degree, method,cover_type)
         return [Manifold_from_Triangulation(cover,
                                             recompute=False,
                                             manifold_class=self.__class__)
@@ -1282,7 +1282,7 @@ cdef class Manifold(Triangulation):
 
         Does not return a new Manifold.
         """
-        Triangulation.dehn_fill(self, filling_data, which_cusp)
+        KernelTriangulation.dehn_fill(self, filling_data, which_cusp)
         do_Dehn_filling(self.c_triangulation)
         self._cache.clear(message='Manifold.dehn_fill')
 
@@ -1397,7 +1397,7 @@ cdef class Manifold(Triangulation):
                 install_shortest_bases(self.c_triangulation)
 
         else:
-            return Triangulation.set_peripheral_curves(
+            return KernelTriangulation.set_peripheral_curves(
                 self, peripheral_data, which_cusp,return_matrices)
 
     def dual_curves(self, max_segments=6):
@@ -1518,7 +1518,7 @@ cdef class Manifold(Triangulation):
         cdef int num_curves
         cdef DualOneSkeletonCurve **curve_list
         cdef c_Triangulation *c_triangulation
-        cdef Triangulation result
+        cdef KernelTriangulation result
         cdef char* c_new_name
 
         if isinstance(which_curve, DualCurveInfo):
@@ -1550,7 +1550,7 @@ cdef class Manifold(Triangulation):
             return result
 
     def _is_isometric_to(self,
-                         Manifold other,
+                         KernelManifold other,
                          return_isometries : bool = False):
         """
         Returns ``True`` if M and N are isometric, ``False`` if they not.
@@ -1786,7 +1786,7 @@ cdef class Manifold(Triangulation):
         cdef c_FuncResult result
         cdef int num_surfaces
         cdef c_Triangulation *pieces[2]
-        cdef Manifold M0, M1
+        cdef KernelManifold M0, M1
 
         if self.c_triangulation is NULL:
             raise ValueError('The Triangulation is empty.')