1. 27 Nov, 2018 1 commit
  2. 26 Nov, 2018 2 commits
  3. 25 Nov, 2018 1 commit
  4. 24 Nov, 2018 9 commits
  5. 23 Nov, 2018 20 commits
    • Release Manager's avatar
      Trac #26732: Docker image fails to start jupyter notebook · e7a1a04d
      Release Manager authored
      In the latest beta, 8.5.beta4, the docker images that we build
      automatically failed its self tests because it could not spawn the
      jupyter notebook anymore:
      {{{
      docker run --name sage-jupyter -d sagemath/sagemath:8.5.beta4 sage-
      jupyter
      […]
      [I 01:44:23.585 NotebookApp] Using MathJax:
      nbextensions/mathjax/MathJax.js
      [I 01:44:23.649 NotebookApp] Writing notebook server cookie secret to
      /home/sage/.local/share/jupyter/runtime/notebook_cookie_secret
      SageMath version 8.5.beta4, Release Date: 2018-11-18
      Please wait while the Sage Jupyter Notebook server starts...
      Traceback (most recent call last):
        File "/home/sage/sage/src/bin/sage-notebook", line 268, in <module>
          launcher(unknown)
        File "/home/sage/sage/src/bin/sage-notebook", line 100, in __init__
          main(argv)
        File "/home/sage/sage/local/lib/python2.7/site-
      packages/jupyter_core/application.py", line 266, in launch_instance
          return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
        File "/home/sage/sage/local/lib/python2.7/site-
      packages/traitlets/config/application.py", line 657, in launch_instance
          app.initialize(argv)
        File "<decorator-gen-7>", line 2, in initialize
        File "/home/sage/sage/local/lib/python2.7/site-
      packages/traitlets/config/application.py", line 87, in
      catch_config_error
          return method(app, *args, **kwargs)
        File "/home/sage/sage/local/lib/python2.7/site-
      packages/notebook/notebookapp.py", line 1629, in initialize
          self.init_webapp()
        File "/home/sage/sage/local/lib/python2.7/site-
      packages/notebook/notebookapp.py", line 1379, in init_webapp
          self.jinja_environment_options,
        File "/home/sage/sage/local/lib/python2.7/site-
      packages/notebook/notebookapp.py", line 158, in __init__
          default_url, settings_overrides, jinja_env_options)
        File "/home/sage/sage/local/lib/python2.7/site-
      packages/notebook/notebookapp.py", line 251, in init_settings
          allow_remote_access=jupyter_app.allow_remote_access,
        File "/home/sage/sage/local/lib/python2.7/site-
      packages/traitlets/traitlets.py", line 556, in __get__
          return self.get(obj, cls)
        File "/home/sage/sage/local/lib/python2.7/site-
      packages/traitlets/traitlets.py", line 535, in get
          value = self._validate(obj, dynamic_default())
        File "/home/sage/sage/local/lib/python2.7/site-
      packages/notebook/notebookapp.py", line 872, in _default_allow_remote
          for info in socket.getaddrinfo(self.ip, self.port, 0,
      socket.SOCK_STREAM):
      socket.gaierror: [Errno -2] Name or service not known
      }}}
      
      Apparently one of the parameters of jupyter has changed with one of the
      recent upgrades, see https://stackoverflow.com/questions/52706238
      /jupyter-throwing-error-socket-gaierror-errno-2-name-or-service-not-
      known.
      
      URL: https://trac.sagemath.org/26732
      Reported by: saraedum
      Ticket author(s): Julian Rüth
      Reviewer(s): Erik Bray
      e7a1a04d
    • David Coudert's avatar
      trac #26748: clean graph_generators_pyx · fd7e2f15
      David Coudert authored
      fd7e2f15
    • Salvatore Stella's avatar
      One more · 77940601
      Salvatore Stella authored
      77940601
    • Salvatore Stella's avatar
      Still not perfect yet · 2a971d9e
      Salvatore Stella authored
      2a971d9e
    • Salvatore Stella's avatar
      Fix random doctest · d01cdce2
      Salvatore Stella authored
      d01cdce2
    • Frédéric Chapoton's avatar
      py3 fixes for cluster algebra.py · 3a6f494a
      Frédéric Chapoton authored
      3a6f494a
    • Frédéric Chapoton's avatar
      trac 26739 reviewer suggestion · 395631d3
      Frédéric Chapoton authored
      395631d3
    • Frédéric Chapoton's avatar
      fixing pyflakes warning · b106f04d
      Frédéric Chapoton authored
      b106f04d
    • Release Manager's avatar
      Trac #26734: small cleanup for alternating sign matrices · 73b2d396
      Release Manager authored
      * partial pep
      * remove deprecated stuff
      * other details
      
      URL: https://trac.sagemath.org/26734
      Reported by: chapoton
      Ticket author(s): Frédéric Chapoton
      Reviewer(s): Travis Scrimshaw
      73b2d396
    • Release Manager's avatar
      Trac #25708: Rename SBox methods for difference_distribution_matrix and similar to _table · 9713da62
      Release Manager authored
      The `SBox` class defines three methods
      (`difference_distribution_matrix`, `linear_approximation_matrix` and
      `boomerang_connectivity_matrix`) that are typically called `..._table`
      in the literature.
      
      IMO we should adjust these names (and correctly deprecate the old names,
      of course).
      
      URL: https://trac.sagemath.org/25708
      Reported by: asante
      Ticket author(s): Friedrich Wiemer
      Reviewer(s): Rusydi H. Makarim
      9713da62
    • Release Manager's avatar
      Trac #26742: py3: fix threejs viewer interface · d45e4d9b
      Release Manager authored
      URL: https://trac.sagemath.org/26742
      Reported by: chapoton
      Ticket author(s): Frédéric Chapoton
      Reviewer(s): Eric Gourgoulhon
      d45e4d9b
    • Release Manager's avatar
      Trac #26737: py3: some work on finite state machines · 53b87f16
      Release Manager authored
      but only partial fixes
      
      URL: https://trac.sagemath.org/26737
      Reported by: chapoton
      Ticket author(s): Frédéric Chapoton
      Reviewer(s): Vincent Klein
      53b87f16
    • Release Manager's avatar
      Trac #26728: Remove ellipsis in one findstat doctest · 3ce45035
      Release Manager authored
      Following the [[https://groups.google.com/d/msg/sage-
      release/cfpqGTMwcBU/oZgSlOz4AwAJ|report by Sébastien Labbé on sage-
      release]] and the [[https://groups.google.com/d/msg/sage-
      release/cfpqGTMwcBU/iJEvwmYBBAAJ|analysis by Martin Rubey]].
      
      URL: https://trac.sagemath.org/26728
      Reported by: slelievre
      Ticket author(s): Martin Rubey
      Reviewer(s): Frédéric Chapoton
      3ce45035
    • Release Manager's avatar
      Trac #26726: Py3: Some python3 fixes in geometry module. · 7853331f
      Release Manager authored
      Fix polyhedron/palp_database, linear_expression and fan_isomorphism
      modules for python3.
      
      URL: https://trac.sagemath.org/26726
      Reported by: vklein
      Ticket author(s): Vincent Klein
      Reviewer(s): Frédéric Chapoton
      7853331f
    • Release Manager's avatar
      Trac #26704: Py3 : database.oeis implement __getitem__ to replace __getslice__ · 7d7d7eac
      Release Manager authored
      Fix database.oeis module for python3 :
      - Remove a useless test
      - Define {{{__getitem__}}} method with for {{{FancyTuple}}} object. It
      replace {{{__getslice__}}} method in python3.
      As {{{__getslice__}}} is still defined in tuple in python 2.7 we still
      need a {{{__getslice__}}} method in {{{FancyTuple}}} to override it.
      
      {{{__getslice__}}} is deprecated since python 2.6 and removed in python
      3.x
      
      URL: https://trac.sagemath.org/26704
      Reported by: vklein
      Ticket author(s): Vincent Klein
      Reviewer(s): Frédéric Chapoton
      7d7d7eac
    • Release Manager's avatar
      Trac #26596: Replace expect r interface with rpy2 · 2599afd5
      Release Manager authored
      Using rpy2 instead of manually interacting with the r repl gives us many
      benefits, the biggest of which is that we don't have to maintain the
      details of the interface ourselves. This should solve the dputs issue in
      #25674 and make sage compatible with r 3.4.x as well as 3.5.x (not
      actually tested yet).
      
      The interface currently still inherits from the Expect interface since
      untangling that seems non-trivial. It is a bit awkward to force rpy2's
      output into the output sage expects. That output also isn't documented
      (it seems like its basically "whatever dput gave us"). I've implemented
      conversions so that the doctests pass, but there are likely differences
      between the presentation of r objects that are not covered by the
      doctesting framework.
      
      URL: https://trac.sagemath.org/26596
      Reported by: gh-timokau
      Ticket author(s): Timo Kaufmann
      Reviewer(s): François Bissey
      2599afd5
    • Release Manager's avatar
      Trac #26168: Add parallelism for two tensor calculus functions · a38120a7
      Release Manager authored
      1. Computation of tensor components in a new frame
      
          In `FreeModuleTensor.components()` \\
          loop `for ind_new in new_comp.non_redundant_index_generator():` \\
          line 1101, file `src/sage/tensor/modules/free_module_tensor.py`
      
      2. Pullback of a tensor field
      
          In `DiffMap.pullback()` \\
          loop `for ind_new in ptcomp.non_redundant_index_generator():`\\
          line 980, file `src/sage/manifolds/differentiable/diff_map.py`
      
      URL: https://trac.sagemath.org/26168
      Reported by: mmancini
      Ticket author(s): Marco Mancini
      Reviewer(s): Frédéric Chapoton, Eric Gourgoulhon, Samuel Lelièvre
      a38120a7
    • Release Manager's avatar
      Trac #25473: 20 internet doctests failed in sage/finance/stock.py · b150b57d
      Release Manager authored
      As reported on [https://groups.google.com/d/msg/sage-
      release/l635YEuT7Hs/WkHCnmWhAQAJ sage-release 8.3.beta3],
      
      {{{
      sage -t --optional=sage,internet src/sage/finance/stock.py
      }}}
      
      gives
      
      {{{
      Running doctests with ID 2018-05-30-22-48-41-52141b2a.
      Using --optional=internet,sage
      Doctesting 1 file.
      sage -t --warn-long 82.6 src/sage/finance/stock.py
      **********************************************************************
      File "src/sage/finance/stock.py", line 156, in
      sage.finance.stock.Stock.__init__
      Failed example:
          S        # optional -- internet
      Expected:
          IBM (...)
      Got:
          <repr(<instance at 0x7f2fcce08680>) failed: URLError: <urlopen error
      [Errno -2] Name or service not known>>
      **********************************************************************
      ...
      **********************************************************************
      File "src/sage/finance/stock.py", line 626, in
      sage.finance.stock.Stock._get_data
      Failed example:
          finance.Stock('whatever').history() # optional -- internet
      Expected:
          Traceback (most recent call last):
          ...
          RuntimeError: Google reported a wrong request (did you specify a
      cid?)
      Got:
          <BLANKLINE>
          Traceback (most recent call last):
            File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-
      packages/sage/doctest/forker.py", line 562, in _run
              self.compile_and_execute(example, compiler, test.globs)
            File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-
      packages/sage/doctest/forker.py", line 972, in compile_and_execute
              exec(compiled, globs)
            File "<doctest sage.finance.stock.Stock._get_data[1]>", line 1, in
      <module>
              finance.Stock('whatever').history() # optional -- internet
            File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-
      packages/sage/finance/stock.py", line 385, in history
              R = self._get_data('NASDAQ:', startdate, enddate, histperiod)
            File "/home/slabbe/GitBox/sage/local/lib/python2.7/site-
      packages/sage/finance/stock.py", line 637, in _get_data
              data = urlopen(url).read()
            File "/home/slabbe/GitBox/sage/local/lib/python2.7/urllib2.py",
      line 154, in urlopen
              return opener.open(url, data, timeout)
            File "/home/slabbe/GitBox/sage/local/lib/python2.7/urllib2.py",
      line 435, in open
              response = meth(req, response)
            File "/home/slabbe/GitBox/sage/local/lib/python2.7/urllib2.py",
      line 548, in http_response
              'http', request, response, code, msg, hdrs)
            File "/home/slabbe/GitBox/sage/local/lib/python2.7/urllib2.py",
      line 473, in error
              return self._call_chain(*args)
            File "/home/slabbe/GitBox/sage/local/lib/python2.7/urllib2.py",
      line 407, in _call_chain
              result = func(*args)
            File "/home/slabbe/GitBox/sage/local/lib/python2.7/urllib2.py",
      line 556, in http_error_default
              raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
          HTTPError: HTTP Error 403: Forbidden
      **********************************************************************
      8 items had failures:
         1 of   3 in sage.finance.stock.Stock.__init__
         1 of   2 in sage.finance.stock.Stock.__repr__
         2 of   3 in sage.finance.stock.Stock._get_data
         4 of   6 in sage.finance.stock.Stock.close
         2 of   3 in sage.finance.stock.Stock.current_price_data
         5 of   6 in sage.finance.stock.Stock.history
         1 of   2 in sage.finance.stock.Stock.market_value
         4 of   6 in sage.finance.stock.Stock.open
          [43 tests, 20 failures, 10.21 s]
      ----------------------------------------------------------------------
      sage -t --warn-long 82.6 src/sage/finance/stock.py  # 20 doctests failed
      ----------------------------------------------------------------------
      Total time for all tests: 10.2 seconds
          cpu time: 0.4 seconds
          cumulative wall time: 10.2 seconds
      }}}
      
      Full log on [https://framabin.org/p/?cd13e7717c5eaa11#k2r/88vX7mrhCnDc+R
      TfXh115dLbqOJMzdgc0xo3ZfA= framabin] against 8.5.beta0.
      
      URL: https://trac.sagemath.org/25473
      Reported by: slabbe
      Ticket author(s): Sébastien Labbé
      Reviewer(s): Frédéric Chapoton
      b150b57d
    • Release Manager's avatar
      Trac #23547: isl + polylib + barvinok packages · d11cabb0
      Release Manager authored
      We package Sven Verdoolaege's [http://barvinok.gforge.inria.fr/
      barvinok] package (for lattice points in polytopes etc). It has
      dependency [http://isl.gforge.inria.fr/ isl] and
      [http://icps.u-strasbg.fr/polylib/ polylib.].
      
      Source codes at
      
      - source http://repo.or.cz/w/barvinok.git
      - source http://repo.or.cz/w/isl.git
      - source http://repo.or.cz/w/polylib.git
      
      Tarballs at
      
      - http://barvinok.gforge.inria.fr/barvinok-0.41.1.tar.bz2
      - http://isl.gforge.inria.fr/isl-0.20.tar.bz2
      - http://icps.u-strasbg.fr/polylib/polylib_src/polylib-5.22.5.tar.gz
      
      --------------------
      
      Remarks
      
      - [pet](http://repo.or.cz/w/pet.git) is an optional dependency of
      barvinok and might be treated later on.
      
      - [https://pypi.python.org/pypi/islpy islpy] provides Python bindings to
      `isl` and can be installed using pip. Though it will bring its own copy
      of `isl`... [https://documen.tician.de/islpy/index.html Documentation].
      The `islpy` package also claims  to provide bindings for `barvinok`
      (haven't tested). To enable:
      {{{
      ./sage -pip install --verbose --install-option
      --conf:'USE_BARVINOK=True' --install-option
      --conf:'USE_SHIPPED_ISL=False' --install-option
      --conf:'USE_SHIPPED_IMATH=False' islpy
      }}}
      - Related Python library: [https://github.com/tobig/islplot islplot]
      (last update 4 years ago...)
      - More resources at http://polycomp.gforge.inria.fr/
      
      URL: https://trac.sagemath.org/23547
      Reported by: mkoeppe
      Ticket author(s): Vincent Delecroix
      Reviewer(s): Vincent Klein, Sébastien Labbé
      d11cabb0
    • Release Manager's avatar
      Trac #23341: port lcalc to C++11 · 269bd3da
      Release Manager authored
      lcalc doesn't use standard C++:
      
      - `using namespace std;` needs an include with stuff from `std::` before
      it
      
      - `typeof` is a gcc extension - C++11 has `decltype` instead
      
      - plain C must not be compiled with C++ compiler - thus a makefile
      change
      
      URL: https://trac.sagemath.org/23341
      Reported by: dimpase
      Ticket author(s): Dima Pasechnik, François Bissey
      Reviewer(s): Dima Pasechnik, François Bissey, Jeroen Demeyer, Ralf
      Stephan
      269bd3da
  6. 22 Nov, 2018 7 commits