snappy 3.1.1__cp310-cp310-win_amd64.whl → 3.2__cp310-cp310-win_amd64.whl

snappy/doc/_sources/verify.rst.txt

@@ -1,150 +1,210 @@
-Verified computations
-========================================
-
-Overview
---------
-
-When used inside `Sage <http://sagemath.org>`_, SnapPy can verify the
-following computations:
-
-* Complex intervals for the shapes that are guaranteed to contain a true
-  but not necessarily geometric solution to the rectangular gluing equations::
-
-      sage: M = Manifold("m015(3,1)")
-      sage: M.tetrahedra_shapes('rect', intervals=True)
-      [0.625222762246? + 3.177940133813?*I,
-       -0.0075523593782? + 0.5131157955971?*I,
-       0.6515818912107? - 0.1955023488930?*I]
-
-  (Specify :py:attr:`bits_prec` or :py:attr:`dec_prec` for higher precision intervals.)
-  
-* Verify the hyperbolicity
-  of an orientable 3-manifold giving complex intervals for the
-  shapes corresponding to a hyperbolic structure or holonomy representation with
-  :py:meth:`~snappy.Manifold.verify_hyperbolicity`::
-
-   sage: M = Manifold("m015")
-   sage: M.verify_hyperbolicity()
-   (True,
-    [0.6623589786224? + 0.5622795120623?*I,
-     0.6623589786224? + 0.5622795120623?*I,
-     0.6623589786224? + 0.5622795120623?*I])
-   sage: M.verify_hyperbolicity(holonomy=True)[1].SL2C('a')
-   [-0.324717957? - 1.124559024?*I -0.704807293? + 0.398888830?*I]
-   [ 1.409614585? - 0.797777659?*I       -1.000000000? + 0.?e-9*I]
-
-* Intervals for the volume and complex volume of a hyperbolic orientable 3-manifold::
-
-   sage: M = Manifold("m003(-3,1)")
-   sage: M.volume(verified=True, bits_prec = 100)
-   0.942707362776927720921299603?
-   sage: M = Manifold("m015")
-   sage: M.complex_volume(verified_modulo_2_torsion=True)
-   2.8281220883? + 1.9106738240?*I
-
-  (Note that when using verified computation, the Chern-Simons invariant is only computed
-  modulo pi^2/2 even though it is defined modulo pi^2.)
-
-* Give the :doc:`canonical retriangulation <verify_canon>` (a close
-  relative to the canonical cell decomposition) of a cusped hyperbolic
-  manifold using intervals or exact arithmetic if necessary with
-  :py:meth:`~snappy.Manifold.canonical_retriangulation`::
-
-   sage: M = Manifold("m412")
-   sage: K = M.canonical_retriangulation(verified = True)
-   sage: len(K.isomorphisms_to(K)) # Certified size of isometry group
-   8
- 
-  **Remark:** For the case of non-tetrahedral canonical cell, exact values
-  are used which are found
-  using the   `LLL-algorithm 
-  <http://en.wikipedia.org/wiki/Lenstra%E2%80%93Lenstra%E2%80%93Lov%C3%A1sz_lattice_basis_reduction_algorithm>`_
-  and then verified using exact computations. These computations can be slow. A massive speed-up was achieved by
-  recent improvements so that the computation of the isometry signature of any manifold in ``OrientableCuspedCensus``
-  takes at most a couple of seconds, typically, far less. Manifolds with more simplices might require setting
-  a higher value for 
-  :py:attr:`exact_bits_prec_and_degrees`.
-
-* The :doc:`isometry signature <verify_canon>` which is a complete invariant of the isometry type
-  of a cusped hyperbolic manifold (i.e., two manifolds are isometric if and only
-  if they have the same isometry signature)::
-
-   sage: M = Manifold("m412")
-   sage: M.isometry_signature(verified = True)
-   'mvvLALQQQhfghjjlilkjklaaaaaffffffff'
-
-  The isometry signature can be strengthened to include the peripheral curves
-  such that it is a complete invariant of a hyperbolic link::
-
-   sage: M = Manifold("L5a1")
-   sage: M.isometry_signature(of_link = True, verified = True)
-   'eLPkbdcddhgggb_baCbbaCb'
-
-  See :py:meth:`~snappy.Manifold.isometry_signature` for details.
-
-  **Remark:** The isometry signature is based on the canonical
-  retriangulation so the same warning applies.
-
-* The maximal cusp area matrix which characterizes the configuration
-  space of disjoint cusp neighborhoods with
-  :py:meth:`~snappy.Manifold.cusp_area_matrix`::
-
-   sage: M=Manifold("m203")
-   sage: M.cusp_area_matrix(method='maximal', verified=True)
-   [   27.000000? 9.0000000000?]
-   [9.0000000000?   27.0000000?]
-
-  In this example, the cusp neighborhood about cusp 0 or 1 is only
-  embedded if and only if its area is less than sqrt(27). The cusp
-  neighborhood about cusp 0 is only disjoint from the one about cusp 1
-  if and only if the product of their areas is less than 9.
-
-* Compute areas for disjoint cusp neighborhoods with
-  :py:meth:`~snappy.Manifold.cusp_areas`::
-
-   sage: M=Manifold("m203")
-   sage: M.cusp_areas(policy = 'unbiased', method='maximal', verified = True)
-   [3.00000000000?, 3.00000000000?]
-
-  With the above parameters, the result is intrinsic to the hyperbolic
-  manifold with labeled cusped.
-
-* Find all slopes of length less or equal to 6 when measured on the boundary
-  of disjoint cusp neighborhoods::
-
-   sage: M=Manifold("m203")
-   sage: M.short_slopes(policy = 'unbiased', method='maximal', verified = True)
-   [[(1, 0), ...,  (1, 2)], [(1, 0), ...,  (1, 2)]]
-
-  First block has all short slopes for first cusp, ..., see
-  :py:meth:`~snappy.Manifold.short_slopes` for details.
-
-  By `Agol's <http://arxiv.org/abs/math/9906183>`_ and `Lackenby's
-  <http://arxiv.org/abs/math/9808120>`_ 6-Theorem any Dehn-filling
-  resulting in a non-hyperbolic manifold must contain one of the above
-  slopes.  Thus, :py:meth:`~snappy.Manifold.short_slopes` can be used
-  to implement the techniques to find exceptional Dehn surgeries
-  (`arXiv:1109.0903 <https://arxiv.org/abs/1109.0903>`_ and
-  `arXiv:1310.3472 <https://arxiv.org/abs/1310.3472>`_).
-
-This is all based on a reimplementation of `HIKMOT
-<http://www.oishi.info.waseda.ac.jp/~takayasu/hikmot/>`_ which
-pioneered the use of interval methods for hyperbolic manifolds (also see
-`Zgliczynski's notes <http://ww2.ii.uj.edu.pl/~zgliczyn/cap07/krawczyk.pdf>`_). It
-can be used in a way very similar to HIKMOT, but uses Sage's complex
-interval types for certification. It furthermore makes use of code by 
-`Dunfield, Hoffman, Licata <http://arxiv.org/abs/1407.7827/>`_. The code to
-compute the isomorphism signature was ported over from
-`Regina <https://regina-normal.github.io/>`_.
-
-This verification code was contributed by Matthias Goerner.  
-
-
-Verified computation topics
----------------------------
-
-.. toctree::
-   :maxdepth: 1
-
-   verify_canon   
-   verify_internals
+Verified computations
+========================================
+
+.. _verify-primer:
+
+Introduction
+------------
+
+Several SnapPy methods use numerical computations with floating point
+approximations and can potentially result in incorrect results. This even
+applies to methods whose output is purely combinatorial such as
+:meth:`~snappy.Manifold.canonical_retriangulation`.
+
+Many of these SnapPy methods can be supplied with a :attr:`verified` flag to
+ensure that the result is provably correct. Note that verified computations are
+only available when using SnapPy inside `SageMath <http://sagemath.org>`_.
+If the flag :attr:`verified=True` is specified, an incorrect result is
+never returned. Instead the method clearly indicates a failure, usually through
+an exception::
+
+  sage: M=Manifold("m004")
+  sage: M.drill_word('abc', verified=True, bits_prec = 40)
+  ...
+  InsufficientPrecisionError: When re-tracing the geodesic, the intersection with the next tetrahedron face was too close to the previous to tell them apart. Increasing the precision will probably avoid this problem.
+
+Often, such a failure can be advoided by increasing the precision. In
+particular, this applies if the exception is a (subclass of)
+:class:`InsufficientPrecisionError`::
+         
+  sage: M.drill_word('abc', verified=True, bits_prec = 60)
+  m004_drilled(0,0)(0,0)
+
+Note that, :meth:`~snappy.Manifold.verify_hyperbolicity` is different though
+and does not throw an exception. Instead, it returns a bool indicating success
+as part of its output. This is for compatibility with
+`HIKMOT <http://www.oishi.info.waseda.ac.jp/~takayasu/hikmot/>`_'s
+``verify_hyperbolicty``::
+
+  sage: M.verify_hyperbolicity(bits_prec=10)
+  (False, [])
+  sage: M.verify_hyperbolicity()
+  (True,
+   [0.50000000000000? + 0.86602540378444?*I,
+    0.50000000000000? + 0.86602540378444?*I])
+
+As illustrated above, the result consists of intervals
+(of type SageMath's ``RealIntervalField`` or
+``ComplexIntervalField``) if the output of a computation is numerical
+and :attr:`verified=True` is specified. These intervals contain the true
+value.
+
+Overview
+--------
+
+Some examples of verified computations are:
+
+* Verify the hyperbolicity
+  of an orientable 3-manifold giving complex intervals for the
+  shapes corresponding to a hyperbolic structure or holonomy representation with
+  :meth:`~snappy.Manifold.verify_hyperbolicity`::
+
+   sage: M = Manifold("m015")
+   sage: M.verify_hyperbolicity()
+   (True,
+    [0.6623589786224? + 0.5622795120623?*I,
+     0.6623589786224? + 0.5622795120623?*I,
+     0.6623589786224? + 0.5622795120623?*I])
+   sage: M.verify_hyperbolicity(holonomy=True)[1].SL2C('a')
+   [-0.324717957? - 1.124559024?*I -0.704807293? + 0.398888830?*I]
+   [ 1.409614585? - 0.797777659?*I       -1.000000000? + 0.?e-9*I]
+
+* Intervals for the volume and complex volume of a hyperbolic orientable 3-manifold::
+
+   sage: M = Manifold("m003(-3,1)")
+   sage: M.volume(verified=True, bits_prec = 100)
+   0.942707362776927720921299603?
+   sage: M = Manifold("m015")
+   sage: M.complex_volume(verified_modulo_2_torsion=True)
+   2.8281220883? + 1.9106738240?*I
+
+  (Note that when using verified computation, the Chern-Simons invariant is only computed
+  modulo pi^2/2 even though it is defined modulo pi^2.)
+
+* Give the (a close relative to the canonical cell decomposition) of a cusped
+  hyperbolic manifold using intervals or exact arithmetic if necessary with
+  :meth:`~snappy.Manifold.canonical_retriangulation`::
+
+   sage: M = Manifold("m412")
+   sage: K = M.canonical_retriangulation(verified = True)
+   sage: len(K.isomorphisms_to(K)) # Certified size of isometry group
+   8
+ 
+  **Remark:** For the case of non-tetrahedral canonical cell, exact values
+  are used which are found
+  using the   `LLL-algorithm 
+  <http://en.wikipedia.org/wiki/Lenstra%E2%80%93Lenstra%E2%80%93Lov%C3%A1sz_lattice_basis_reduction_algorithm>`_
+  and then verified using exact computations. These computations can be slow. A massive speed-up was achieved by
+  recent improvements so that the computation of the isometry signature of any manifold in ``OrientableCuspedCensus``
+  takes at most a couple of seconds, typically, far less. Manifolds with more simplices might require setting
+  a higher value for 
+  :attr:`exact_bits_prec_and_degrees`.
+
+* The isometry signature which is a complete invariant of the isometry type
+  of a cusped hyperbolic manifold (i.e., two manifolds are isometric if and only
+  if they have the same isometry signature)::
+
+   sage: M = Manifold("m412")
+   sage: M.isometry_signature(verified = True)
+   'mvvLALQQQhfghjjlilkjklaaaaaffffffff'
+
+  The isometry signature can be strengthened to include the peripheral curves
+  such that it is a complete invariant of a hyperbolic link::
+
+   sage: M = Manifold("L5a1")
+   sage: M.isometry_signature(of_link = True, verified = True)
+   'eLPkbdcddhgggb_baCbbaCb'
+
+  See :meth:`~snappy.Manifold.isometry_signature` for details.
+
+  **Remark:** The isometry signature is based on the canonical
+  retriangulation so the same warning applies.
+
+* The maximal cusp area matrix which characterizes the configuration
+  space of disjoint cusp neighborhoods with
+  :meth:`~snappy.Manifold.cusp_area_matrix`::
+
+   sage: M=Manifold("m203")
+   sage: M.cusp_area_matrix(method='maximal', verified=True)
+   [   27.000000? 9.0000000000?]
+   [9.0000000000?   27.0000000?]
+
+  In this example, the cusp neighborhood about cusp 0 or 1 is only
+  embedded if and only if its area is less than sqrt(27). The cusp
+  neighborhood about cusp 0 is only disjoint from the one about cusp 1
+  if and only if the product of their areas is less than 9.
+
+* Compute areas for disjoint cusp neighborhoods with
+  :meth:`~snappy.Manifold.cusp_areas`::
+
+   sage: M=Manifold("m203")
+   sage: M.cusp_areas(policy = 'unbiased', method='maximal', verified = True)
+   [3.00000000000?, 3.00000000000?]
+
+  With the above parameters, the result is intrinsic to the hyperbolic
+  manifold with labeled cusped.
+
+* Find all slopes of length less or equal to 6 when measured on the boundary
+  of disjoint cusp neighborhoods::
+
+   sage: M=Manifold("m203")
+   sage: M.short_slopes(policy = 'unbiased', method='maximal', verified = True)
+   [[(1, 0), ...,  (1, 2)], [(1, 0), ...,  (1, 2)]]
+
+  First block has all short slopes for first cusp, ..., see
+  :meth:`~snappy.Manifold.short_slopes` for details.
+
+  By `Agol's <http://arxiv.org/abs/math/9906183>`_ and `Lackenby's
+  <http://arxiv.org/abs/math/9808120>`_ 6-Theorem any Dehn-filling
+  resulting in a non-hyperbolic manifold must contain one of the above
+  slopes.  Thus, :meth:`~snappy.Manifold.short_slopes` can be used
+  to implement the techniques to find exceptional Dehn surgeries
+  (`arXiv:1109.0903 <https://arxiv.org/abs/1109.0903>`_ and
+  `arXiv:1310.3472 <https://arxiv.org/abs/1310.3472>`_).
+
+* An example of finding all geodesics up to length 1::
+
+    sage: from sage.all import RIF
+    sage: L = RIF(1)
+    sage: M = Manifold("m003")
+    sage: spec = M.length_spectrum_alt_gen(verified=True)
+    sage: n = 0
+    sage: for g in spec:
+    ...       if g.length.real() > L:
+    ...           break # Done! All subsequent geodesics will be longer.
+    ...       if g.length.real() < L:
+    ...           n += 1
+    ...           continue
+    ...       raise Exception("Interval too large. Increase precision.")
+    sage: n
+    4
+
+Additionally, we can compute complex intervals for the shapes that are
+guaranteed to contain a true solution to the rectangular gluing equations
+that is not necessarily a geometric solution (specify :attr:`bits_prec`
+or :attr:`dec_prec` for higher precision intervals.)::
+
+      sage: M = Manifold("m015(3,1)")
+      sage: M.tetrahedra_shapes('rect', intervals=True)
+      [0.625222762246? + 3.177940133813?*I,
+       -0.0075523593782? + 0.5131157955971?*I,
+       0.6515818912107? - 0.1955023488930?*I]
+
+This is all based on a reimplementation of `HIKMOT
+<http://www.oishi.info.waseda.ac.jp/~takayasu/hikmot/>`_ which
+pioneered the use of interval methods for hyperbolic manifolds (also see
+`Zgliczynski's notes <http://ww2.ii.uj.edu.pl/~zgliczyn/cap07/krawczyk.pdf>`_). It
+can be used in a way very similar to HIKMOT, but uses Sage's complex
+interval types for certification. It furthermore makes use of code by 
+`Dunfield, Hoffman, Licata <http://arxiv.org/abs/1407.7827/>`_.
+
+This verification code was contributed by Matthias Goerner.  
+
+
+Verified computation topics
+---------------------------
+
+.. toctree::
+   :maxdepth: 1
+
+   verify_internals

snappy/doc/_sources/verify_internals.rst.txt

@@ -1,90 +1,79 @@
-Internals of verified computations
-==================================
-
-
-
-Naming
-------
-
-The names of methods containing ``check`` will raise an exception if
-the desired property cannot be certified. There are different types of
-Exceptions to indicate how the certification failed. This type can be
-used by other methods to perform some action such as changing the
-triangulation or increasing precision or to give up.
-
-The user-facing methods have names starting with ``verify`` or
-``verified`` and will fail more gracefully returning ``False`` or
-``None`` in such a case.
-
-
-
-Generating certified shape intervals
-------------------------------------
-
-The recommended way to obtain certified intervals for the shapes is via
-``manifold.tetrahedra_shapes(intervals=True)`` as :doc:`described
-earlier <verify>`. Here we document the ``KrawczykShapesEngine`` and
-``IntervalNewtonShapesEngine`` which is implemented internally to
-generate the intervals. It is of interest for those users who want to
-understand the underlying interval math and experiment with the Newton
-interval method or the Krawczyk test.  ``CertifiedShapesEngine`` is an
-alias of either ``KrawczykShapesEngine`` or
-``IntervalNewtonShapesEngine`` to determine the default method used by
-verify.
-
-..   automodule:: snappy.verify
-..   autoclass:: CertifiedShapesEngine
-     :members:
-     :inherited-members:
-
-..   autoclass:: IntervalNewtonShapesEngine
-     :members:
-     :inherited-members:
-
-..   autoclass:: KrawczykShapesEngine
-     :members:
-     :inherited-members:
-
-
-Verification of hyperbolicity
------------------------------
-
-Methods containing ``check`` will raise an exception if the desired property
-cannot be certified. Methods containing ``verify`` or ``verified`` will fail
-more gracefully returning ``False`` or ``None`` in such a case.
-
-..   autofunction:: snappy.verify.verifyHyperbolicity.check_logarithmic_gluing_equations_and_positively_oriented_tets
-
-Cusp cross sections
--------------------
-
-..   autoclass:: snappy.verify.RealCuspCrossSection
-     :members:
-     :inherited-members:
-
-..   autoclass:: snappy.verify.ComplexCuspCrossSection
-     :members:
-     :inherited-members:
-
-Verified canonical cell decompositions
---------------------------------------
-
-..   autofunction:: snappy.verify.verifyCanonical.interval_checked_canonical_triangulation
-..   autofunction:: snappy.verify.verifyCanonical.exactly_checked_canonical_retriangulation
-
-Exact computations for cusp cross sections
-------------------------------------------
-
-..   automodule:: snappy.verify.squareExtensions
-
-..   autofunction:: snappy.verify.squareExtensions.find_shapes_as_complex_sqrt_lin_combinations
-..   autoclass:: SqrtLinCombination
-     :members:
-..   autoclass:: ComplexSqrtLinCombination
-     :members:
-
-Exceptions
-----------
-
-..   automodule:: snappy.verify.exceptions
-     :members:
+Internals of verified computations
+==================================
+
+
+
+Naming
+------
+
+The names of methods containing ``check`` will raise an exception if
+the desired property cannot be certified. There are different types of
+Exceptions to indicate how the certification failed. This type can be
+used by other methods to perform some action such as changing the
+triangulation or increasing precision or to give up.
+
+The user-facing methods have names starting with ``verify`` or
+``verified`` and will fail more gracefully returning ``False`` or
+``None`` in such a case.
+
+
+
+Generating certified shape intervals
+------------------------------------
+
+The recommended way to obtain certified intervals for the shapes is via
+``manifold.tetrahedra_shapes(intervals=True)`` as :doc:`described
+earlier <verify>`. Here we document the ``KrawczykShapesEngine`` and
+``IntervalNewtonShapesEngine`` which is implemented internally to
+generate the intervals. It is of interest for those users who want to
+understand the underlying interval math and experiment with the Newton
+interval method or the Krawczyk test.  ``CertifiedShapesEngine`` is an
+alias of either ``KrawczykShapesEngine`` or
+``IntervalNewtonShapesEngine`` to determine the default method used by
+verify.
+
+..   automodule:: snappy.verify
+..   autoclass:: CertifiedShapesEngine
+     :members:
+     :inherited-members:
+
+..   autoclass:: IntervalNewtonShapesEngine
+     :members:
+     :inherited-members:
+
+..   autoclass:: KrawczykShapesEngine
+     :members:
+     :inherited-members:
+
+
+Verification of hyperbolicity
+-----------------------------
+
+Methods containing ``check`` will raise an exception if the desired property
+cannot be certified. Methods containing ``verify`` or ``verified`` will fail
+more gracefully returning ``False`` or ``None`` in such a case.
+
+..   autofunction:: snappy.verify.hyperbolicity.check_logarithmic_gluing_equations_and_positively_oriented_tets
+
+Verified canonical cell decompositions
+--------------------------------------
+
+..   autofunction:: snappy.verify.canonical.interval_checked_canonical_triangulation
+..   autofunction:: snappy.verify.canonical.exactly_checked_canonical_retriangulation
+
+Exact computations for cusp cross sections
+------------------------------------------
+
+..   automodule:: snappy.verify.square_extensions
+
+..   autofunction:: snappy.verify.square_extensions.find_shapes_as_complex_sqrt_lin_combinations
+..   autoclass:: SqrtLinCombination
+     :members:
+..   autoclass:: ComplexSqrtLinCombination
+     :members:
+
+Exceptions
+----------
+
+..   automodule:: snappy.verify.exceptions
+     :members: