snappy 3.2__cp311-cp311-macosx_10_12_x86_64.whl

snappy/dev/vericlosed/verifyHyperbolicStructureEngine.py

@@ -0,0 +1,177 @@
+from .gimbalLoopFinder import GimbalLoopFinder
+from .truncatedComplex import TruncatedComplex
+from .hyperbolicStructure import HyperbolicStructure
+from .verificationError import *
+
+from sage.all import matrix, prod, RealDoubleField, pi
+
+__all__ = [ 'VerifyHyperbolicStructureEngine']
+
+
+class VerifyHyperbolicStructureEngine:
+    def __init__(self, hyperbolic_structure):
+        self.hyperbolic_structure = hyperbolic_structure
+        self.mcomplex = self.hyperbolic_structure.mcomplex
+
+        if not hyperbolic_structure.exact_edges:
+            raise RuntimeError(
+                'Need to specify "exact edges", i.e., edges for which we '
+                'already know by, e.g., the Krawczyk test that their edge '
+                'equations are fullfilled')
+
+        num_edges = len(self.mcomplex.Edges)
+        exact_edges = set(hyperbolic_structure.exact_edges)
+
+        self.approx_edges = [i for i in range(num_edges)
+                             if i not in exact_edges]
+
+        self.truncated_complex = TruncatedComplex(self.mcomplex)
+
+        self.gimbal_loops = [
+            GimbalLoopFinder(self.truncated_complex,
+                             vertex,
+                             self.approx_edges).compute_grouped_loop()
+            for vertex in self.mcomplex.Vertices ]
+
+        self.rotations_and_derivatives_for_approx_edges = {
+            e : HyperbolicStructure.so3_matrix_and_derivative_for_z_rotation(
+                self.hyperbolic_structure.angle_sums[e])
+            for e in self.approx_edges
+        }
+        
+    def gimbal_derivative(self):
+
+        self.edge_index_to_column_index = {
+            e : i for i, e in enumerate(self.approx_edges)
+        }
+
+        RIF = self.hyperbolic_structure.vertex_gram_matrices[0].base_ring()
+        num_rows = 3 * len(self.mcomplex.Vertices)
+        num_cols = len(self.approx_edges)
+        result = matrix(RIF, num_rows, num_cols)
+
+        for i, gimbal_loop in enumerate(self.gimbal_loops):
+            path_matrices = [
+                self.hyperbolic_structure.so3_matrix_for_path(edgePath)
+                for edgeLoop, edgePath in gimbal_loop ]
+
+            for j, (edgeLoop, edgePath) in enumerate(gimbal_loop):
+                col = self.edge_index_to_column_index[edgeLoop.edge_index]
+                m = self._gimbal_derivative_matrix(
+                    gimbal_loop, path_matrices, j)
+                result[3 * i    , col] += m[0,1]
+                result[3 * i + 1, col] += m[0,2]
+                result[3 * i + 2, col] += m[1,2]
+
+        return result
+
+    def assert_avoiding_gimbal_lock(self):
+        d = self.gimbal_derivative()
+        if not VerifyHyperbolicStructureEngine.is_invertible(d):
+            raise GimbalDerivativeNotInvertibleError(d, d.determinant())
+
+    def assert_two_pi_in_ange_sum_intervals(self):
+        RIF = self.hyperbolic_structure.angle_sums[0].parent()
+        two_pi = RIF(2 * pi)
+
+        for angle in self.hyperbolic_structure.angle_sums:
+            if two_pi not in angle:
+                raise AngleSumIntervalNotContainingTwoPiError()
+
+    def assert_vertex_gram_matrices_valid(self):
+        for G_adj in self.hyperbolic_structure.vertex_gram_adjoints:
+            _assert_vertex_gram_adjoint_valid(G_adj)
+        for G     in self.hyperbolic_structure.vertex_gram_matrices:
+            _assert_vertex_gram_matrix_valid (G    )
+
+    def assert_verified_hyperbolic(self):
+        self.assert_vertex_gram_matrices_valid()
+        self.assert_avoiding_gimbal_lock()
+        self.assert_two_pi_in_ange_sum_intervals()
+
+    @staticmethod
+    def is_invertible(m):
+        r, c = m.dimensions()
+        if r != c:
+            raise AssertionError("Not a square matrix in invertible check "
+                                 "of VerifyHyperbolicStructureEngine.")
+
+        RIF = m.base_ring()
+        max_entry = RIF(1) / (r * c)
+
+        real_m = matrix(RealDoubleField(), m)
+        try:
+            real_approx_inv = real_m.inverse()
+        except ZeroDivisionError:
+            return False
+
+        approx_inv = real_approx_inv.change_ring(RIF)
+        idMatrix = matrix.identity(RIF, r)
+        t = approx_inv * m - idMatrix
+
+        for row in t:
+            for entry in row:
+                if not (entry < max_entry):
+                    return False
+        return True
+        
+    def _gimbal_derivative_matrix(self, gimbal_loop, path_matrices, j):
+
+        def term(i):
+            edgeLoop, path = gimbal_loop[i]
+            rotation_and_derivative = (
+                self.rotations_and_derivatives_for_approx_edges[
+                    edgeLoop.edge_index])
+            
+            if i == j:
+                return path_matrices[i] * rotation_and_derivative[1]
+            else:
+                return path_matrices[i] * rotation_and_derivative[0]
+
+        return prod([term(i) for i in range(len(gimbal_loop) - 1, -1, -1)])
+
+def _assert_vertex_gram_adjoint_valid(G_adj):
+    for i in range(4):
+        if not (G_adj[i, i] < 0):
+            raise BadVertexGramMatrixError(
+                "Failed to verify diagonal %d cofactor < 0" % i)
+        for j in range(4):
+            if i != j:
+                if not (G_adj[i, j] ** 2 < G_adj[i, i] * G_adj[j, j]):
+                    raise BadVertexGramMatrixError(
+                        "Failed to verify cofactor inequality for (%d,%d)" % (i,j))
+
+def _assert_vertex_gram_matrix_valid(G):
+    for i in range(4):
+        for j in range(4):
+            if not (G[i,j] <= -1):
+                raise BadVertexGramMatrixError(
+                    "Failed to verify entry (%d,%d) <= - 1" % (i, j))
+
+    p = G.characteristic_polynomial()
+
+    # Budan-Fourier theorem (see e.g.,
+    # Saugata Basu, Richard Pollack, Marie-Francoise Roy
+    # Algorithms in Real Algebraic Geometry)
+    # it is sufficient to verify that a_0 < 0, a_1 > 0, a_2 < 0.
+    # for the characteristic polynomial
+    # p_G(x) = det(xI-G) = x^4 + 4x^3 + a_2 x^2 + a_1x + a_0.
+    #
+    a0, a1, a2, a3, a4 = p.coefficients(sparse = False)
+
+    if not a3 == 4:
+        raise BadVertexGramMatrixError(
+            "Failed to verify a3 = 4 for characteristic polynomial")
+    if not a4 == 1:
+        raise BadVertexGramMatrixError(
+            "Failed to verify a4 = 1 for characteristic polynomial")
+
+    if not (a0 < 0):
+        raise BadVertexGramMatrixError(
+            "Failed to verify a0 < 0 for characteristic polynomial")
+    if not (a1 > 0):
+        raise BadVertexGramMatrixError(
+            "Failed to verify a1 > 0 for characteristic polynomial")
+    if not (a2 < 0):
+        raise BadVertexGramMatrixError(
+            "Failed to verify a2 < 0 for characteristic polynomial")

snappy/doc/_sources/additional_classes.rst.txt

@@ -0,0 +1,40 @@
+==================
+Additional Classes
+==================
+
+..   automodule:: snappy
+
+AbelianGroup
+============
+
+
+..   autoclass:: AbelianGroup
+     :members:
+     :inherited-members:
+     :exclude-members: coefficients
+
+FundamentalGroup
+================
+
+..   autoclass:: HolonomyGroup
+     :members:
+     :inherited-members:
+
+SymmetryGroup
+=============
+..   autoclass:: SymmetryGroup
+     :members:
+     :inherited-members:
+
+DirichletDomain
+===============
+..   autoclass:: DirichletDomain
+     :members:
+     :inherited-members:
+
+CuspNeighborhood
+================
+
+..   autoclass:: CuspNeighborhood
+     :members:
+     :inherited-members:

snappy/doc/_sources/bugs.rst.txt

@@ -0,0 +1,14 @@
+.. Reporting bugs and other problems
+
+Reporting bugs and other problems
+=================================
+
+We very much welcome reports of any difficulties you encounter
+installing or using SnapPy. While we do significant testing before
+each release, with so many supported platforms/configurations and only
+three core developers, we need your help to keep things running
+smoothly. To report a problem, you may either `open a formal issue
+ticket <https://github.com/3-manifolds/SnapPy/issues>`_ or `write to the
+developers <snappy-help@computop.org>`_. As always, it is most helpful
+if you include the details of your computer's configuration as well as
+verbatim copies of any error messages.

snappy/doc/_sources/censuses.rst.txt

@@ -0,0 +1,51 @@
+Census manifolds
+================
+
+Snappy comes with a large library of manifolds, which can be accessed
+individually through the Manifold and Triangulation constructors but
+can also be iterated through using the objects described on this
+page.
+
+SnapPy's iterators support several flexible methods for accessing
+manifolds.  They can be sliced (i.e. restricted to subranges) either
+by index or by volume.  Calling the iterator with keyword arguments
+such as num_tets=1, betti=2 or num_cusps=3 returns an iterator which
+is filtered by the specified conditions.  In addition these iterators
+can determine whether they contain a given manifold.  They support
+python's "A in B" syntax, and also provide an identify method which
+will return a copy of the census manifold which is isometric to the
+manifold passed as an argument.
+
+..   currentmodule:: snappy
+..   autodata:: OrientableCuspedCensus
+..   autodata:: OrientableClosedCensus
+..   autodata:: CensusKnots
+..   autodata:: LinkExteriors
+..   autodata:: HTLinkExteriors
+..   autodata:: NonorientableCuspedCensus
+..   autodata:: NonorientableClosedCensus
+
+There are also:
+
+.. toctree::
+   :maxdepth: 1
+
+   platonic_census
+
+As instances of subclasses of ManifoldTable, the objects above
+support the following methods.
+
+..   autoclass:: snappy.database.ManifoldTable
+     :members:
+     :inherited-members:
+
+Because of the large size of their datasets, the classes below
+can only iterate through slices by index, and do not provide
+the identification methods.
+
+..   autoclass:: AlternatingKnotExteriors
+     :members:
+     :inherited-members:
+..   autoclass:: NonalternatingKnotExteriors
+     :members: 
+     :inherited-members:

snappy/doc/_sources/credits.rst.txt

@@ -0,0 +1,75 @@
+Credits
+=======
+
+Primary development and maintenance:
+
+* `Marc Culler <http://www.math.uic.edu/~culler>`_ 
+* `Nathan Dunfield <http://dunfield.info>`_
+* `Matthias Goerner <http://www.unhyperbolic.org/>`_
+* `Jeff Weeks <http://www.geometrygames.org>`_
+
+Additional contributions:
+
+* Mark Bell, Tracy Hall, Saul Schleimer, `Twister <https://github.com/MarkCBell/twister>`_.
+
+* Jim Hoste and Morwen Thistlethwaite, manifold and link censuses.
+
+* Ben Burton, manifold censuses and isosig code.  
+
+* Abhijit Champanerkar and Ilya Kofman, knot censuses.  
+
+* Robert Lipschitz and Jennet Dickinson, improvements to Spherogram.
+
+* Malik Obeidin, improvements to Spherogram and the manifold
+  databases.
+
+* Malik Obeidin and Cameron Rudd, exterior to link diagram code.
+
+* Jose Sanchez, 3D printing code.
+
+* Jean-Philippe Burelle, SL(2, C) character variety code.
+
+* David Bachman, Henry Segerman and Saul Schleimer, initial code the
+  raytraced inside view is based on.
+
+* Zoltán Szabó, computing Knot Floer homology.
+
+* `PARI library <http://pari.math.u-bordeaux.fr/>`_.  
+
+*  `QD quad-double library
+   <http://crd-legacy.lbl.gov/~dhbailey/mpdist/>`_.
+
+* Frédéric Chapoton, code cleanup and linting.
+
+* Others, please let Marc or Nathan know if we've forgotten you. 
+
+Citing SnapPy
+-------------
+
+Please cite as: 
+
+M. Culler, N. M. Dunfield, M. Goerner, and J. R. Weeks, SnapPy, a computer program
+for studying the geometry and topology of 3-manifolds, http://snappy.computop.org  
+
+or in BibTeX format ::
+
+   @misc{SnapPy,
+        author={Culler, Marc and Dunfield, Nathan M. and Goerner,
+	Matthias and Weeks, Jeffrey R.},
+        title={Snap{P}y, a computer program for studying the geometry and topology of $3$-manifolds},
+        howpublished={Available at \url{http://snappy.computop.org} (DD/MM/YYYY)},
+   }
+
+or as an AMSRef::
+
+  \bib{SnapPy}{misc}{
+       author={Culler, Marc},
+       author={Dunfield, Nathan M.},
+       author={Goerner, Matthias},
+       author={Weeks, Jeffrey R.},
+       title={Snap{P}y, a computer program for studying the geometry and topology of $3$-manifolds},
+       note={Available at \url{http://snappy.computop.org} (DD/MM/YYYY)}
+  }
+
+where DD/MM/YYYY should be replaced by the date when you downloaded your
+copy of SnapPy.

snappy/doc/_sources/development.rst.txt

@@ -0,0 +1,259 @@
+Development Basics
+==================
+
+Submitting patches
+------------------
+
+The source code for SnapPy and its various parts are `hosted on GitHub
+<https://github.com/3-manifolds>`_ as `Git repositories
+<https://git-scm.com/>`_.  To contribute a patch, create a free
+GitHub account, fork the appropriate repository, and then send us a
+pull request, as described in `here
+<https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request>`_.
+
+
+macOS
+-----
+
+Here is how to get a clean development setup under macOS.
+
+- Install the latest Python 3.13 from Python.org using the `Mac
+  Installer Disk Image <http://www.python.org/download/>`_.  Set your
+  path so that "python3" is::
+      
+    /Library/Frameworks/Python.framework/Versions/3.13/bin/python3
+
+- Use `pip <https://pip.pypa.io/en/latest/index.html>`_ to install the
+  following packages::
+
+    python3 -m pip install --upgrade setuptools virtualenv wheel pip
+    python3 -m pip install cython        # Used for Python-C interfacing
+    python3 -m pip install sphinx        # For building the documentation
+    python3 -m pip install ipython       # Improved Python shell
+    python3 -m pip install py2app        # For making app bundles
+    python3 -m pip install pyx FXrays low_index
+
+- Get the source code from the repository, using Git. For
+  example you can install Git via its `package installer
+  <https://www.git-scm.org/>`_.  Now do::
+
+    git clone https://github.com/3-manifolds/plink.git
+    git clone https://github.com/3-manifolds/spherogram.git
+    git clone https://github.com/3-manifolds/snappy.git
+
+- Test the stand-alone link editor::
+
+    cd plink
+    python3 setup.py pip_install
+    python3 -m plink.app   # Link editor appears!
+
+  This last command runs the script ``plink/app.py``; the real code for
+  the link editor is in ``plink/__init__.py``.
+
+- Build and install Spherogram::
+
+    cd ../spherogram
+    python3 setup.py pip_install
+    python3 setup.py test
+
+- Now build SnapPy itself.  One builds it twice to generate the
+  documentation, much of which is extracted from the installed module::
+
+    cd ../snappy
+    python3 setup.py pip_install
+    python3 setup.py test   # Run the tests; pretty picture should appear.
+    python3 -m snappy.app   #SnapPy starts!
+
+  To build the clickable app, just do the following::
+
+    cd mac_osx_app
+    python3 release.py --manual
+
+  though for general development purposes ``python3 -m snappy.app`` is
+  usually the way to go.
+    
+Some major parts of the SnapPy codebase are:
+
+- ``SnapPy.pyx``, ``SnapPycore.pxi``, ``SnapPy.pxi``: The Cython interface
+  to the SnapPea kernel
+- ``opengl/CyOpenGL*.pyx``: The Cython interface to OpenGL*
+- ``snappy/app.py``: The core GUI code
+- ``snappy/polyviewer.py``: The GUI code for Dirichlet domains
+- ``snappy/horoviewer.py``: The GUI code for horoball pictures
+- ``snappy/database.py``: Interacts with the sqlite3 manifold database
+
+
+Windows
+-------
+
+These instructions have been tested on Windows 10, and describe
+setting up a development environment using the (free) MSVC
+compiler. To build the CyPari subcomponent, which few will want or
+need to do, one must install additional tools.
+
+- Install `Python 3.13.1
+  <https://www.python.org/downloads/windows/>`_, specifically the
+  default 64-bit version (the file name will end in ``amd64.exe``).
+  These instructions assume it has been installed in the directory
+  ``C:\Python313`` which is not the default.
+
+- With Python 3.13.1, you need the MSVC command line tools.  You can
+  get them by using Microsoft's free `Build Tools for Visual Studio 2019
+  <https://visualstudio.microsoft.com/thank-you-downloading-visual-studio/?sku=BuildTools&rel=16>`_
+  installer and selecting the "C++ command line tools" and installing
+  the following subpackages: "MSVC v142 - VS 2019 C++ build tools",
+  "Testing tools core features", "C++/CLI support for v142", and
+  "Windows 10 SDK (most recent version)".
+  
+  If you would like to make your own installer you will also need
+  `Inno Setup <http://www.jrsoftware.org/isdl.php>`_, specifically the
+  unicode version; tested with version 5.5.9.
+
+- Install `MSYS2 <http://msys2.github.io>`_ as appropriate for your
+  version Windows.  Follow the instructions on the webpage to update
+  everything to the very latest MSYS2 (``pacman -Sy pacman; pacman
+  -Syu; pacman -Su`` etc.).  You should also install the ucrt toolchain::
+
+    pacman -S mingw-w64-ucrt-x86_64-toolchain
+
+- Make a shortcut to ``c:\msys64\msys2.exe`` as you will be using it all
+  the time; alternatively, pin ``mys2.exe`` to your taskbar.  
+
+- Install some additional packages::
+
+    pacman -S git make nano openssh perl tar unzip wget winpty patch
+
+- Install your favorite text editor, for example you can install Emacs
+  via::
+
+    pacman -S  mingw-w64-x86_64-emacs
+
+- Make it so that MinGW, Python, and Inno Setup are all in your PATH,
+  as well as work around some stupid bug, by making the end of your
+  "~/.bash_profile" file to read::
+
+    PATH=/c/Python313:/c/Python313/Scripts:$PATH
+    PATH=$PATH:'/c/Program Files (x86)/Inno Setup 5'
+    export PATH
+    alias emacs="/mingw64/bin/emacs"
+    winpty bash; exit
+
+  For example, do::
+
+    nano ~/.bash_profile
+
+- Make sure you have the right version of Python in your path by
+  typing::
+
+    python --version
+
+  You should see something like ``Python 3.13.1``.
+
+- Use pip to install some basic tools::
+  
+    python -m pip install --upgrade pip setuptools wheel  # Upgrades pip to the current version.
+    python -m pip install pyreadline sphinx cython cypari pyx FXrays low_index
+
+- Fetch the latest development versions of the source straight from
+  the t3m repository::
+
+    git clone https://github.com/3-manifolds/plink.git
+    git clone https://github.com/3-manifolds/spherogram.git
+    git clone https://github.com/3-manifolds/snappy.git
+
+- Build the components, from easiest to hardest, and then test::
+
+    cd plink
+    python setup.py pip_install
+    cd ../Spherogram
+    python setup.py pip_install
+    cd ../SnapPy
+    python setup.py pip_install
+    cd ..
+    python -m SnapPy.test
+
+- To run the app, you can just do::
+
+    python -m snappy.app
+
+- To build the binary installer, you need PyInstaller::
+  
+    python -m pip install pyinstaller
+
+  To build the binary installer do::
+
+    cd windows_exe
+    python make.py
+
+  You will need to close the SnapPy window that pops up here to
+  complete the build process. 
+
+- Useful tips for those coming from Unix.  In MSYS2, your home
+  directory is really something like::
+
+    c:\msys2\home\Nathan Dunfield
+
+  whereas your Windows 10 home directory is::
+
+    c:\Users\Nathan Dunfield
+
+  It is handy to have symbolic links from your MSYS2 home directory to
+  the Downloads and Desktop folders on the Windows side.  `See this
+  discussion <http://www.howtogeek.com/howto/16226/>`_, but basically
+  you start a "Command Prompt" as Administrator and do::
+
+    cd "C:\msys64\home\Nathan Dunfield"
+    mklink /D Desktop "C:\Users\Nathan Dunfield\Desktop"
+    mklink /D Downloads "C:\Users\Nathan Dunfield\Downloads"
+
+
+Linux
+-----
+
+Things you'll need:
+
+- Python 3 with Tkinter: You'll need to have `Python
+  <http://python.org>`_ (version 3.9 or newer) and `Tk
+  <http://tcl.tk>`_ (at least version 8.5) with `Tkinter
+  <http://wiki.python.org/moin/TkInter>`_ to connect them, including
+  the header files.  For instance, on Debian or Ubuntu, install the
+  packages "python3-tk", "python3-pip", and "python3-dev". On Fedora,
+  you'll want e.g. "python3-tkinter", "python3-pip", and
+  "python3-devel", and "python3-wheel".
+
+- Test that Python is in order by installing PLink from source::
+
+      python3 -m pip install --user plink
+      python3 -m plink.app  # Should start the link editor!
+
+.. _openglmesa:
+
+- Support for OpenGL (3D graphics): This is built in on OS X and the
+  most installations of Fedora and Ubuntu.  But you'll need the `MESA
+  <http://www.mesa3d.org/>`_ header files "gl.h" and "glu.h" to compile
+  SnapPy.  On Debian and Ubuntu, install "libglu1-mesa-dev"; On Fedora install
+  "mesa-libGLU-devel".
+
+- `Cython <http://cython.org>`_, which you can install via::
+
+    python3 -m pip install --user cython
+
+- The gcc C++ compiler, g++.
+
+- Fetch the latest development versions of the source straight from
+  the repository::
+
+    git clone https://github.com/3-manifolds/PLink.git
+    git clone https://github.com/3-manifolds/Spherogram.git
+    git clone https://github.com/3-manifolds/Snappy.git
+
+- Build the components, from easiest to hardest, and then test::
+
+    cd PLink
+    python setup.py pip_install
+    cd ../Spherogram
+    python setup.py pip_install
+    cd ../SnapPy
+    python setup.py pip_install
+    cd ..
+    python -m SnapPy.test