snappy 3.1__cp310-cp310-macosx_11_0_arm64.whl → 3.2__cp310-cp310-macosx_11_0_arm64.whl

snappy/dev/extended_ptolemy/phc_wrapper.py

@@ -41,9 +41,9 @@ def restore_forbidden(var_str):
 def ideal_to_file(ideal, filename):
     outfile = open(filename, 'w')
     polys = ideal.gens()
-    outfile.write('%d\n' % len(polys))
+    outfile.write(r'%d\n' % len(polys))
     for p in polys:
-        outfile.write('   ' + remove_forbidden(repr(p)) + ';\n')
+        outfile.write('   ' + remove_forbidden(repr(p)) + r';\n')
     outfile.close()
 
 def parse_file(filename, prec=53):
@@ -55,14 +55,14 @@ def parse_file(filename, prec=53):
     data = data.split('THE SOLUTIONS')[-1]
     data = re.subn('[*]{3,}', '', data)[0]
     ans = []
-    solutions = re.findall('(solution \d+ : \s* start residual .*?) ==', data, re.DOTALL)
+    solutions = re.findall(r'(solution \d+ : \s* start residual .*?) ==', data, re.DOTALL)
     for sol in solutions:
         kind = sol.split('=')[-1].strip()
         if kind == 'no solution':
             continue
-        mult = int(re.search('^m : (\d+)', sol, re.MULTILINE).group(1))
-        err = float(re.search('== err :\s+(.*?)\s+= ', sol).group(1))
-        coors = re.findall('^ (.*) :\s+(\S*)\s+(\S*)', sol, re.MULTILINE)
+        mult = int(re.search(r'^m : (\d+)', sol, re.MULTILINE).group(1))
+        err = float(re.search(r'== err :\s+(.*?)\s+= ', sol).group(1))
+        coors = re.findall(r'^ (.*) :\s+(\S*)\s+(\S*)', sol, re.MULTILINE)
         if kind.startswith('real'):
             coors = {restore_forbidden(var):RR(real) for var, real, imag in coors}
             ans.append({'kind':'real', 'mult':mult, 'err':err, 'coors':coors})
@@ -70,8 +70,8 @@ def parse_file(filename, prec=53):
             coors = {restore_forbidden(var):CC(RR(real), RR(imag)) for var, real, imag in coors}
             ans.append({'kind':'complex', 'mult':mult, 'err':err, 'coors':coors})
 
-    num_real = int(re.search('Number of real solutions\s+:\s(.*).', data).group(1))
-    num_complex = int(re.search('Number of complex solutions\s+:\s(.*).', data).group(1))
+    num_real = int(re.search(r'Number of real solutions\s+:\s(.*).', data).group(1))
+    num_complex = int(re.search(r'Number of complex solutions\s+:\s(.*).', data).group(1))
     kinds = [sol['kind'] for sol in ans]
     assert kinds.count('real') == num_real
     assert kinds.count('complex') == num_complex
@@ -185,9 +185,9 @@ def direct_hack(backend, ideal, **kwargs):
     polys = [repr(eqn) for eqn in ideal.gens()]
 
     data = {'backend':backend, 'vars':vars, 'polys':polys, 'kwargs':kwargs}
-    problem_data = json.dumps(data).encode('base64').replace('\n', '')
+    problem_data = json.dumps(data).encode('base64').replace(r'\n', '')
     ans_data = os.popen('sage -python ' + __file__ + ' ' + problem_data).read()
-    ans_data = re.sub('PHCv.*? released .*? works!\n', '',  ans_data)
+    ans_data = re.sub(r'PHCv.*? released .*? works!\n', '',  ans_data)
     if len(ans_data):
         ans = json.loads(ans_data)
         for sol in ans:

snappy/dev/vericlosed/oneVertexTruncatedComplex.py

@@ -5,7 +5,7 @@ from truncatedComplex import *
 class OneVertexTruncatedComplex(TruncatedComplex):
 
     def __init__(self, hyperbolic_structure):
-        super(OneVertexTruncatedComplex, self).__init__(
+        super().__init__(
             hyperbolic_structure.mcomplex)
 
         self.hyperbolic_structure = hyperbolic_structure

snappy/doc/_sources/credits.rst.txt

@@ -20,7 +20,10 @@ Additional contributions:
 
 * Robert Lipschitz and Jennet Dickinson, improvements to Spherogram.
 
-* Malik Obeidin, improvements to Spherogram and the manifold databases.
+* Malik Obeidin, improvements to Spherogram and the manifold
+  databases.
+
+* Malik Obeidin and Cameron Rudd, exterior to link diagram code.
 
 * Jose Sanchez, 3D printing code.
 
@@ -36,6 +39,8 @@ Additional contributions:
 *  `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

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::
@@ -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::
 
@@ -74,17 +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
@@ -95,12 +91,13 @@ 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
@@ -112,14 +109,12 @@ need to do, one must install additional tools.
   `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.  
@@ -137,7 +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"
@@ -152,7 +147,7 @@ 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::
   
@@ -212,28 +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

@@ -27,7 +27,78 @@ it, and watch the :doc:`tutorial<tutorial>`.
 News
 ====
 
-* Version 3.1 (May 2023):
+* 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 Python 3.13 and SageMath 10.5.
+
+    
+* Versions 3.1 (May 2023) and 3.1.1 (June 2023):
 
   - A method :meth:`exterior_to_link <snappy.Manifold.exterior_to_link>`
     for going from a link exterior to a link diagram taken from
@@ -65,10 +136,6 @@ News
 
   - Modernized styling of the documentation.
 
-* Version 3.0.3 (December 2021):
-
-  - Runs natively on Macs with Apple Silicon processors (M1, M2, and variants).
-
 * :doc:`Complete version history <news>`.
 
 Documentation