1. 17 Feb, 2019 1 commit
  2. 15 Feb, 2019 1 commit
  3. 14 Feb, 2019 6 commits
  4. 13 Feb, 2019 16 commits
    • Release Manager's avatar
      Trac #27269: Use time.process_time() on Python 3 · 119fa6f8
      Release Manager authored
      `time.process_time()` is suggested as replacement for the deprecated
      `time.clock()` on Python 3.
      
      URL: https://trac.sagemath.org/27269
      Reported by: jdemeyer
      Ticket author(s): Jeroen Demeyer
      Reviewer(s): Vincent Klein
      119fa6f8
    • Release Manager's avatar
      Trac #27260: zn_poly tries to run "python" and "2to3" · b32df2da
      Release Manager authored
      This breaks on systems where only `python3` is installed but not
      `python` or `2to3`.
      
      '''Upstream patch''':
      sagemath/zn_poly!2
      
      URL: https://trac.sagemath.org/27260
      Reported by: jdemeyer
      Ticket author(s): Jeroen Demeyer
      Reviewer(s): Travis Scrimshaw
      b32df2da
    • Release Manager's avatar
      Trac #27254: MP_LIBRARY, BLAS, PYTHON need inst_ in Makefile.in · 903bb20b
      Release Manager authored
      In particular to properly handle "dummy" targets like gmp/mpir,
      `sagelib` should depend upon `$(inst_$(MP_LIBRARY))`.
      
      Also, `sagelib` in `deps` should only depend on one Python:
      {{{#!diff
      -               $(inst_python2) \
      -               $(inst_python3) \
      +               $(inst_$(PYTHON)) \
      }}}
      
      URL: https://trac.sagemath.org/27254
      Reported by: dimpase
      Ticket author(s): Dima Pasechnik
      Reviewer(s): Erik Bray
      903bb20b
    • Release Manager's avatar
      Trac #27253: networkx fails to build with SAGE_CHECK="yes" · 8af4edb6
      Release Manager authored
      After #26326, {{{networkx}}} fails to build with {{{SAGE_CHECK="yes"}}}
      unless the optional package {{{nose}}} is installed.
      
      {{{
      [networkx-2.2] Running the test suite for networkx-2.2...
      [networkx-2.2] Testing networkx requires the package nose to be
      installed
      [networkx-2.2]
      [networkx-2.2] real     0m0.004s
      [networkx-2.2] user     0m0.004s
      [networkx-2.2] sys      0m0.001s
      [networkx-2.2]
      ************************************************************************
      [networkx-2.2] Error testing package networkx-2.2
      [networkx-2.2]
      ************************************************************************
      }}}
      
      URL: https://trac.sagemath.org/27253
      Reported by: Konrad127123
      Ticket author(s): Konrad K. Dabrowski
      Reviewer(s): Dima Pasechnik
      8af4edb6
    • Release Manager's avatar
      Trac #27251: fpylll: add patch for Cython 3.0 · db518300
      Release Manager authored
      Add [https://github.com/fplll/fpylll/commit/28e5fcaeabe26d46167e75815e0d
      9a4fdfa1a973 this patch] to fpylll to make it compatible with Cython
      master. The default value for `language_level` has changed, so the
      `language_level` is best specified explicitly.
      
      This makes absolutely no difference with Cython 0.29.x, so it doesn't
      affect distributions.
      
      The patch just makes it possible to compile Sage with Cython master
      (something that I regularly do when contributing to Cython).
      
      URL: https://trac.sagemath.org/27251
      Reported by: jdemeyer
      Ticket author(s): Jeroen Demeyer
      Reviewer(s): Martin Albrecht
      db518300
    • Release Manager's avatar
      Trac #27176: py3: fix doctest in generic_graph (part 1) · 6c3a7a7a
      Release Manager authored
      We fix doctests in
      - `incidence_matrix`: we change the example from `CubeGraph` to
      `PetersenGraph` as it is stable for `py2` and `py3`. It is possible to
      fix the order of the rows of the matrix with parameter `vertices`, but
      the order of the columns depends on `.edge_iterator()` which itself
      depends on `.vertex_iterator()` which is not always the same in py3 than
      in py2. An alternative would be to add parameter `edges` to the method
      to specify the ordering of the columns...
      
      - `eulerian_circuit`: we fix the issue by changing the way the graph. It
      changes the internal order of vertices and edges and this is sufficient
      for getting same result in py2 and py3. With original construction, the
      internal order of vertices was depending on the order of the keys of the
      input dict (might be different in py2 and py3)
      
      - `min_spanning_tree`: we sort the edges of the solution.
      
      URL: https://trac.sagemath.org/27176
      Reported by: dcoudert
      Ticket author(s): David Coudert
      Reviewer(s): Kevin Dilks
      6c3a7a7a
    • Release Manager's avatar
      Trac #27183: py3: fix doctest in generic_graph (part 5) · 6cc2e309
      Release Manager authored
      Fix doctests in
      - `lex_BFS`: mark some doctests as `py2` or `py3`
      - `_color_by_label`: mark some doctests as `py2` or `py3`
      - `layout_extend_randomly`: mark a doctest as `# random` and add another
      test
      
      URL: https://trac.sagemath.org/27183
      Reported by: dcoudert
      Ticket author(s): David Coudert
      Reviewer(s): Jean-Florent Raymond
      6cc2e309
    • Release Manager's avatar
      Trac #27165: py3: fix doctests in c_graph.pyx · 1ff08158
      Release Manager authored
      One doctest is fixed replacing a call to `.edges()` by a call to
      `.edges_incident(1)`
      
      For the doctest of `depth_first_search`, we distinguish py2 and py3. The
      ordering in py3 is unstable, so we use `...`.
      
      For the doctest of `breadth_first_search`, we change the graph to ensure
      that there is a unique solution for the last visited vertex. So the same
      doctest is valid for py2 and py3.
      
      URL: https://trac.sagemath.org/27165
      Reported by: dcoudert
      Ticket author(s): David Coudert
      Reviewer(s): Vincent Klein
      1ff08158
    • Release Manager's avatar
      Trac #27085: documentation: Improve sphinx_plot to create scalable graphics · f62ce0df
      Release Manager authored
      The function `sphinx_plot`, introduced in #17498 to support the `..
      PLOT::` directive provided by the matplotlib sphinx extension, creates
      all graphics by saving to a temporary PNG file first.
      
      This ticket improves this function so that 2d graphics (including
      `GraphicsArray`s) are shipped out directly via matplotlib. In this way,
      proper SVG graphics can be generated for the HTML documentation.
      
      URL: https://trac.sagemath.org/27085
      Reported by: mkoeppe
      Ticket author(s): Matthias Koeppe
      Reviewer(s): John Palmieri
      f62ce0df
    • Release Manager's avatar
      Trac #26679: clean generic_graph.py (part 13) - searches and constructors · 7eca460d
      Release Manager authored
      Here, we clean (PEP8 and avoid `.vertices` / `.edges`) methods:
      - searches: `breadth_first_search`, `depth_first_search` (`lex_BFS` is
      done in #26630)
      - constructors: `add_clique`, `add_cycle`, `add_path`, `complement`,
      `to_simple`, `disjoint_union`, `cartesian_product`, `tensor_product`,
      `lexicographic_product`, `strong_product`, `disjunctive_product`
      (methods `transitive_...` are done in #26634)
      
      URL: https://trac.sagemath.org/26679
      Reported by: dcoudert
      Ticket author(s): David Coudert
      Reviewer(s): Vincent Klein
      7eca460d
    • Release Manager's avatar
      Trac #27263: Upgrade to giac 1.5 fails to build with older libstdc++ · 6772ac9c
      Release Manager authored
      #26315 broke building giac on some systems that have a old-ish
      libstdc++.  It is completely mysterious to me ''why'' this broke when it
      worked before, and without a repository it's very difficult to determine
      what change between the versions is responsible, as there is little
      difference between the two versions in the relevant code.
      
      Nevertheless, it can be fixed by explicitly using `std::isnan` and
      `std::isinf` so that there is no risk of them conflicting with the libc
      math.h equivalents thereof.
      
      URL: https://trac.sagemath.org/27263
      Reported by: embray
      Ticket author(s): Erik Bray
      Reviewer(s): Dima Pasechnik
      6772ac9c
    • David Coudert's avatar
      78ba5cf1
    • jdemeyer's avatar
      Use time.process_time() on Python 3 · 628f8f07
      jdemeyer authored
      628f8f07
    • David Coudert's avatar
      trac #27183: Merged with 8.7.beta3 · d0dc10a5
      David Coudert authored
      d0dc10a5
    • David Coudert's avatar
      trac #26679: reviewer's comments · 5e97618a
      David Coudert authored
      5e97618a
    • David Coudert's avatar
      trac #26679: Merged with 8.7.beta3 · e2784a3d
      David Coudert authored
      e2784a3d
  5. 12 Feb, 2019 3 commits
  6. 11 Feb, 2019 13 commits
    • Release Manager's avatar
      Trac #27249: fix doctest in graph_latex · 714748d8
      Release Manager authored
      Reported on `https://groups.google.com/forum/#!topic/sage-
      release/0QvdNonpGEg`.
      Doctest failing in `dot2tex_picture` with 8.7.beta3 and optional package
      `dot2tex`.
      
      URL: https://trac.sagemath.org/27249
      Reported by: dcoudert
      Ticket author(s): David Coudert
      Reviewer(s): Sébastien Labbé
      714748d8
    • Release Manager's avatar
      Trac #27248: py3: some care for divisions · 4c716d96
      Release Manager authored
      in reflection groups and rubik cube
      
      URL: https://trac.sagemath.org/27248
      Reported by: chapoton
      Ticket author(s): Frédéric Chapoton
      Reviewer(s): David Coudert
      4c716d96
    • Release Manager's avatar
      Trac #27243: py3: fix doctests in generic_graph (part 7) -- relabel · 2b165816
      Release Manager authored
      URL: https://trac.sagemath.org/27243
      Reported by: dcoudert
      Ticket author(s): David Coudert
      Reviewer(s): Kevin Dilks
      2b165816
    • Release Manager's avatar
      Trac #27234: Implement method `gap` of class `PermutationGroupElement` properly. · 76ecbbf3
      Release Manager authored
      This is a follow up ticket of #26750. In that ticket the method has been
      implemented as synonym of {{{_gap_}}}, since at that time libgap
      produced an error for large permutations.
      
      {{{
      ┌────────────────────────────────────────────────────────────────────┐
      │ SageMath version 8.5, Release Date: 2018-12-22                     │
      │ Using Python 2.7.15. Type "help()" for help.                       │
      └────────────────────────────────────────────────────────────────────┘
      sage: P = PGU(8,2)
      sage: p1, p2 = P.gens()
      sage: libgap(p1)
      python2: libgap.c:184: libgap_get_input: Assertion
      `strlen(libGAP_stdin_buffer) < length' failed.
      Traceback (most recent call last):
      ...
      ValueError: libGAP: Aborted
      }}}
      
      This error has been fixed in 8.6.beta0. Therefore, we may have {{{gap}}}
      using {{{libgap}}}, right now!
      
      URL: https://trac.sagemath.org/27234
      Reported by: soehms
      Ticket author(s): Sebastian Oehms
      Reviewer(s): Travis Scrimshaw
      76ecbbf3
    • Release Manager's avatar
      Trac #27231: Interface nauty's directg command with sage · 3192e1f4
      Release Manager authored
      Allow to call nauty's directg command from sage.\\
      
      This is implemented as a {{{DiGraph}}} generator (file:
      {{{digraph_generators.py}}}).
      
      Note to reviewers: Any idea for useful examples in documentation is
      welcome.
      
      URL: https://trac.sagemath.org/27231
      Reported by: vklein
      Ticket author(s): Vincent Klein
      Reviewer(s): David Coudert
      3192e1f4
    • Release Manager's avatar
      Trac #27208: Make comparison of Matrix_gfpn_dense more efficient · 03d17097
      Release Manager authored
      Currently, when comparing two matrices of type `Matrix_gfpn_dense`, the
      data of both is translated into a python string and then the two python
      strings are compared. That's very inefficient (because of copying data).
      
      Original suggestion: Use the upstream matrix comparison function.
      
      However, it turned out that the upstream function isn't faster than
      comparison of Python bytes. So, what this ticket does is to fix a
      potential owerflow.
      
      URL: https://trac.sagemath.org/27208
      Reported by: SimonKing
      Ticket author(s): Simon King
      Reviewer(s): Travis Scrimshaw
      03d17097
    • Release Manager's avatar
      Trac #27196: make sagelib work and doctest even if SAGE_ROOT is None · 8eaad1f1
      Release Manager authored
      This is a push to be able to use and doctest sage without SAGE_ROOT
      being defined. This is mainly useful for distro or if you import sage
      from python directly without running sage-env first.
      
      * `sage/misc/persist.pyx` is dealt with in #27192
      * in `sage/misc/citation.pyx` `SAGE_ROOT` is replaced with `""` but for
      all cases I have seen `SAGE_LIB` would be correct. I have only gone for
      `SAGE_LOCAL` in case something in `SAGE_LOCAL/bin` needs to be picked
      up.
      * in `bin/sage-notebook` and `sage/misc/package.py`, `SAGE_ROOT` is
      imported but not used. So I removed it while I was at it.
      
      This ticket doesn't deal with `SAGE_ROOT` used in
      `src/sage/misc/copying.py`.
      
      URL: https://trac.sagemath.org/27196
      Reported by: fbissey
      Ticket author(s): François Bissey
      Reviewer(s): Jeroen Demeyer, François Bissey
      8eaad1f1
    • Release Manager's avatar
      Trac #27000: Upgrade NumPy to 1.16.1 · 63f8a3c6
      Release Manager authored
      !NumPy 1.16.0 was released on 2019-01-14, and !NumPy 1.16.1 on
      2019-02-01.
      
      - '''Tarball''': https://files.pythonhosted.org/packages/2b/26/07472b0de
      91851b6656cbc86e2f0d5d3a3128e7580f23295ef58b6862d6c/numpy-1.16.1.zip
      
      From the [https://mail.python.org/pipermail/numpy-
      discussion/2019-January/079130.html release announcement for NumPy
      1.16.0]:
      
      > This is the last !NumPy release to support Python 2.7 and will be
      > maintained as a long term release with bug fixes until 2020.  This
      release
      > has seen a lot of refactoring and features many bug fixes, improved
      code
      > organization, and better cross platform compatibility. Not all of
      these
      > improvements will be visible to users, but they should help make
      > maintenance easier going forward. Highlights are
      >
      >    - Experimental support for overriding numpy functions in downstream
      projects.
      >    - The matmul function is now a ufunc and can be overridden using
      >    `__array_ufunc__`.
      >    - Improved support for the ARM, POWER, and SPARC architectures.
      >    - Improved support for AIX and !PyPy.
      >    - Improved interoperation with ctypes.
      >    - Improved support for PEP 3118.
      
      From the [https://mail.python.org/pipermail/numpy-
      discussion/2019-January/079157.html Release announcement for NumPy
      1.16.1]:
      
      > This release fixes bugs reported against the 1.16.0 release, and
      > also backports several enhancements from master that seem appropriate
      for a
      > release series that is the last to support Python 2.7. [...]
      >
      > If you are installing using pip, you may encounter a problem with
      older
      > installed versions of !NumPy that pip did not delete becoming mixed
      with the
      > current version, resulting in an `ImportError`. That problem is
      > particularly common on Debian derived distributions due to a modified
      pip.
      > The fix is to make sure all previous !NumPy versions installed by pip
      have
      > been removed. See [https://github.com/numpy/numpy/issues/12736 NumPy
      issue 12736]
      > for discussion of the issue. Note that previously this problem
      resulted in
      > an `AttributeError`.
      
      Both release announcements indicate:
      
      > The wheels on PyPI are linked with OpenBLAS v0.3.4+, which should
      > fix the known threading issues found in previous OpenBLAS versions.
      > Downstream developers building this release should use Cython >=
      0.29.2
      > and, if linking OpenBLAS, OpenBLAS > v0.3.4.
      
      So this depends on the upgrade to OpenBLAS 0.3.5 (from 0.3.3) in #27020,
      and on the upgrade to Cython 0.29.2 in #27058.
      
      Debian developers warn us that !NumPy 1.16 in Debian leads to
      some deprecation warnings:
      
      {{{
      DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use
      a.item() instead
      }}}
      These are fixed by adding a patch to matplotlib in #26288.
      
      URL: https://trac.sagemath.org/27000
      Reported by: thansen
      Ticket author(s): Jeroen Demeyer
      Reviewer(s): Dima Pasechnik
      63f8a3c6
    • Release Manager's avatar
      Trac #26815: pep8 cleaning in distances and distance_all_pairs · 4af82fdf
      Release Manager authored
      URL: https://trac.sagemath.org/26815
      Reported by: dcoudert
      Ticket author(s): David Coudert
      Reviewer(s): Vincent Klein
      4af82fdf
    • Dima Pasechnik's avatar
      356621a3
    • Vincent Klein's avatar
      ccc2cd32
    • Vincent Klein's avatar
      Trac #27231: support single input of empty Graph · 18d1ea39
      Vincent Klein authored
      - add a link to Graph method orientations
      - small fixe
      18d1ea39
    • Vincent Klein's avatar
      Trac #27231: add nauty_directg method ... · 8e302c6a
      Vincent Klein authored
      ... in digraph_generators.py header documentation
      8e302c6a