snappy 3.0.3__cp38-cp38-macosx_11_0_arm64.whl → 3.2__cp38-cp38-macosx_11_0_arm64.whl

snappy/doc/_sources/development.rst.txt

@@ -17,11 +17,11 @@ macOS
 
 Here is how to get a clean development setup under macOS.
 
-- Install the latest Python 3.8 from Python.org using the `Mac
+- 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/3.8/bin/python3
+    /Library/Frameworks/Python.framework/Versions/3.13/bin/python3
 
 - Use `pip <https://pip.pypa.io/en/latest/index.html>`_ to install the
   following packages::
@@ -31,7 +31,7 @@ Here is how to get a clean development setup under macOS.
     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
+    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
@@ -47,8 +47,8 @@ Here is how to get a clean development setup under macOS.
     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".
+  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::
 
@@ -62,7 +62,6 @@ Here is how to get a clean development setup under macOS.
     cd ../snappy
     python3 setup.py pip_install
     python3 setup.py test   # Run the tests; pretty picture should appear.
-    python3 setup.py build_docs pip_install
     python3 -m snappy.app   #SnapPy starts!
 
   To build the clickable app, just do the following::
@@ -75,17 +74,13 @@ Here is how to get a clean development setup under macOS.
     
 Some major parts of the SnapPy codebase are:
 
-- "SnapPy.pyx", "SnapPycore.pxi", "SnapPy.pxi": The Cython interface
+- ``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
-
-In addition, Jeff's old prototype for a Tk-based UI can be found in
-"misc/JeffsOldUI/SnapPeaGUI.py"; just run Python on this file to try it
-out, after installing `PythonMegaWidgets <http://pmw.sf.net>`_.
+- ``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
@@ -96,31 +91,30 @@ 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 3.7 <https://www.python.org/downloads/windows/>`_,
-  specifically the 32 bit version (Windows x86 not Windows x86-64).
+- 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:\Python37`` which is not the default.
+  ``C:\Python313`` which is not the default.
 
-- With Python 3.7.4, you need the MSVC command line tools.  You can
+- 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",
-  "Testsing tools core features", "C++/CLI support for v142", and
+  "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 whichever version of `MSYS2 <http://msys2.github.io>`_ is
-  appropriate for your version Windows.  Most commonly, you will have
-  a 64-bit Windows and hence want the "x86_64" installer; for
-  concreteness the rest of these instructions assume this. (Technical
-  note: even if you want to build 32-bit binaries, if your Windows is
-  64-bit you want the x86_64 installer.) Follow the instructions on
-  the webpage to update everything to the very latest MSYS2
-  (``pacman -Sy pacman; pacman -Syu; pacman -Su`` etc.).
+- 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.  
@@ -138,7 +132,7 @@ need to do, one must install additional tools.
   as well as work around some stupid bug, by making the end of your
   "~/.bash_profile" file to read::
 
-    PATH=/c/Python37:/c/Python37/Scripts:$PATH
+    PATH=/c/Python313:/c/Python313/Scripts:$PATH
     PATH=$PATH:'/c/Program Files (x86)/Inno Setup 5'
     export PATH
     alias emacs="/mingw64/bin/emacs"
@@ -153,12 +147,12 @@ need to do, one must install additional tools.
 
     python --version
 
-  You should see something like ``Python 3.7.4``.
+  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
+    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::
@@ -213,28 +207,53 @@ need to do, one must install additional tools.
     mklink /D Downloads "C:\Users\Nathan Dunfield\Downloads"
 
 
-- To build CyPari, first install the 32-bit gcc compiler::
+Linux
+-----
 
-    pacman -S mingw-w64-i686-gcc
+Things you'll need:
 
-  Then open a *MinGW32 terminal window*, which is **different** than a
-  MSYS2 terminal, and can be started via `c:\msys64\mingw32.exe`.
-  This will put the 32-bit gcc in your path and set the correct
-  "uname".  Now do::
+- 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".
 
-    git clone https://github.com/3-manifolds/CyPari.git
-    cd CyPari
-    sh build_pari.sh
-    python setup.py build --compiler=mingw32
-    python setup.py install
-    python -m cypari.test   # About 30 tests will fail.
+- Test that Python is in order by installing PLink from source::
 
-  Warning: CyPari will not build if there are spaces in the path to
-  the CyPari directory.  
+      python3 -m pip install --user plink
+      python3 -m plink.app  # Should start the link editor!
 
+.. _openglmesa:
 
-Linux
------
+- 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::
 
-See the :ref:`installation instructions on generic Unix
-<installing:Generic Unix>` for how to build SnapPy from source.
+    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

snappy/doc/_sources/index.rst.txt

@@ -9,8 +9,9 @@ SnapPy
 What is SnapPy?
 ===============
 
-..  image:: images/SnapPy-196.png 
+..  image:: images/SnapPy-196.png
     :align: right
+    :alt: SnapPy logo
 
 
 SnapPy is a program for studying the topology and geometry of
@@ -26,80 +27,114 @@ it, and watch the :doc:`tutorial<tutorial>`.
 News
 ====
 
-* Version 3.0.3 (December 2021):
-
-  - Runs natively on Macs with Apple Silicon processors (M1, M1 Pro, M1 Max).
-
-* Version 3.0.2 (November 2021):
+* Version 3.2 (January 2025):
+
+  - An alternative implementation of the length spectrum. It supports verified
+    computations and is significantly faster in some cases. See
+    :meth:`length_spectrum_alt <snappy.Manifold.length_spectrum_alt>`
+    and
+    :meth:`length_spectrum_alt_gen <snappy.Manifold.length_spectrum_alt_gen>`.
+
+  - :meth:`isometry_signature <snappy.Manifold.isometry_signature>` now also
+    works for closed manifolds.
+
+  - A paper plane or eye ball in the
+    :meth:`inside_view <snappy.Manifold.inside_view>` showing the position
+    and bearing of the user in the hyperbolic manifold. By default, we now show
+    the paper plane instead of the edges of the triangulation so that the view
+    is intrinsic to the manifold. The geodesics window now also features a
+    button to put the camera onto a geodesic. Here are some examples:
+
+    .. list-table::
+       :width: 100%
+       :class: borderless
+
+       * - .. image:: images/o9_00000_systole_paper_plane.jpg
+              :width: 90%
+              :align: center
+              :alt: Paper plane near shortest geodesic of o9_00000
+         - .. image:: images/o9_00000_systole_paper_plane_closer.jpg
+              :width: 90%
+              :align: center
+              :alt: Paper plane very near shortest geodesic of o9_00000
+         - .. image:: images/m004_paper_plane_on_systole.jpg
+              :width: 90%
+              :align: center
+              :alt: Paper plane on shortest geodesic of m004
+         - .. image:: images/m125_paper_plane.jpg
+              :width: 90%
+              :align: center
+              :alt: Paper plane coming out of a cusp of m125
+
+  - A faster and more robust algorithm to the compute maximal cusp area matrix.
+    The new algorithm is now the default for
+    :meth:`~snappy.Manifold.cusp_area_matrix`,
+    :meth:`~snappy.Manifold.cusp_areas`,
+    :meth:`~snappy.Manifold.short_slopes` and
+    :meth:`~snappy.Manifold.cusp_translations`.
+
+  - New options ``ignore_curves`` and ``ignore_filling_orientations``
+    for :meth:`~snappy.Triangulation.triangulation_isosig`. Also
+    fixing a subtle bug where the filling coefficients returned by
+    :meth:`triangulation_isosig <snappy.Triangulation.triangulation_isosig>` were
+    not canonical when ``ignore_curve_orientations = True``.
+
+  - :meth:`~snappy.Manifold.canonical_retriangulation`
+    and
+    :meth:`~snappy.Manifold.isometry_signature` fail with
+    exceptions rather than silently returning ``None``. In particular, it now
+    safe to compare isometry signatures (without further checks) to determine
+    whether M and N are isometric hyperbolic manifolds::
+
+        >>> M.isometry_signature(verified=True) == N.isometry_signature(verified=True)
+
+  - Bug fix to :meth:`slice_obstruction_HKL
+    <snappy.Manifold.slice_obstruction_HKL>`: earlier versions
+    incorrectly allowed looking at mod 2 homology of the branched
+    cover, where the theory does not directly apply.
+
+  - New self-contained SnapPy application for Linux. 
   
-  - Support for SageMath 9.4 and 9.5, Python 3.10, and macOS Monterey.
-
-* Version 3.0 (April 2021): New features include:
-
-  - Incorporates Zoltán Szabó's `program
-    <https://web.math.princeton.edu/~szabo/HFKcalc.html>`_ for
-    computing Knot Floer homology, see :meth:`knot_floer_homology
-    <spherogram.Link.knot_floer_homology>`.  This can compute the
-    Seifert genus of a 25 crossing knot in mere seconds!
-
-  - Topological slice obstructions of Herald-Kirk-Livingston, see
-    :meth:`slice_obstruction_HKL <snappy.Manifold.slice_obstruction_HKL>`.
-
-  - Faster "local" algorithm for :meth:`jones_polynomial
-    <spherogram.Link.jones_polynomial>`.
-
-  - `Cohomology fractals <https://arxiv.org/abs/2010.05840>`_ added to
-    :meth:`inside_view <snappy.Manifold.inside_view>`.
-
-  - Convention changes: Sign of knot signature (now positive knots have
-    negative signatures), choice of braid generators (now positive
-    generators give positive crossings).
-
-  - Updates to methods :meth:`cusp_translations
-    <snappy.Manifold.cusp_translations>`, :meth:`cusp_areas
-    <snappy.Manifold.cusp_areas>`, :meth:`short_slopes
-    <snappy.Manifold.short_slopes>`. Also :meth:`Link <spherogram.Link>`
-    now accepts DT codes.
-
-  - Support for SageMath 9.3, Python 3.9, and macOS Big Sur.
-
-  - macOS app now code-signed and notarized.
-
-  - SnapPy now requires Python 3.6 or newer.
+  - Support for Python 3.13 and SageMath 10.5.
 
+    
+* Versions 3.1 (May 2023) and 3.1.1 (June 2023):
 
-* Version 2.8 (June 2020): New features include:
+  - A method :meth:`exterior_to_link <snappy.Manifold.exterior_to_link>`
+    for going from a link exterior to a link diagram taken from
+    `Dunfield-Obeidin-Rudd <https://arxiv.org/abs/2112.03251>`_.
 
-  - Raytraced interior views of a hyperbolic 3-manifold via the 
-    :meth:`inside_view <snappy.Manifold.inside_view>` method, see also
-    `images <https://im.icerm.brown.edu/portfolio/snappy-views/>`_ and
-    `demo video <https://youtu.be/CAERhmUCkRs>`_.
+  - Covers now computed by the stand-alone `low_index
+    <https://pypi.org/project/low-index/>`_ module, which uses
+    multiple processor cores and is typically much faster than the old
+    code.  In some cases, it is dramatically faster than even GAP or
+    Magma.
 
-  - :doc:`verify`: Several new features:
+  - Added geodesics to the :meth:`inside_view
+    <snappy.Manifold.inside_view>`.  Here are some intersecting tubes
+    about closed geodesics in the manifold ``v3539(5,1)``:
 
-    * Complex volume (and thus the Chern-Simons invariant) for both
-      cusped and closed manifolds, see
-      :meth:`complex_volume <snappy.Manifold.complex_volume>`.
-      
-    * Disjoint cusp neighborhoods by the method :meth:`cusp_areas
-      <snappy.Manifold.cusp_areas>` which uses
-      :meth:`cusp_area_matrix <snappy.Manifold.cusp_area_matrix>`.
+    .. image:: images/geodesics.jpg
+       :width: 50%
+       :align: center
+       :alt: Geodesic tubes for v3539(5,1)
 
-    * Cusp shapes (see :meth:`cusp_info <snappy.Manifold.cusp_info>`).
-      
-    * Finding all :meth:`short_slopes <snappy.Manifold.short_slopes>`
-      in disjoint embedded cusp neighborhoods.
+  - Added drilling any simple geodesic with :meth:`drill_word
+    <snappy.Manifold.drill_word>` and :meth:`drill_words
+    <snappy.Manifold.drill_words>`, not just those that are
+    :meth:`combinatorially simple <snappy.Manifold.dual_curves>`.
 
-  - The census :class:`HTLinkExteriors <snappy.HTLinkExteriors>` has
-    been extended to 15 crossing knots (contributed by Malik
-    Obeidin).
+  - Added `ignore_orientation` flag to :meth:`triangulation_isosig
+    <snappy.Triangulation.triangulation_isosig>`.
 
-  - The census :class:`CensusKnots <snappy.CensusKnots>` has been
-    extended to triangulations with 9 ideal tetrahedra.
+  - Added `include_words` flag to :meth:`length_spectrum
+    <snappy.Manifold.length_spectrum>` for getting the word
+    corresponding to a geodesic which can be given to
+    :meth:`drill_word <snappy.Manifold.drill_word>`.
 
-  - Support for SageMath 9.0 and macOS Catalina.
+  - Support for Python 3.11 and SageMath 10.0.
 
-  - Development moved to `GitHub <https://github.com/3-manifolds>`_.
+  - Modernized styling of the documentation.
 
 * :doc:`Complete version history <news>`.
 
@@ -109,8 +144,8 @@ Documentation
 .. toctree::
    :maxdepth: 1
 
-   installing 
-   screenshots   
+   installing
+   screenshots
    tutorial
    snappy
    plink