[arch-commits] Commit in sagemath/repos (16 files)

Antonio Rojas arojas at archlinux.org
Sun Dec 10 19:13:17 UTC 2017


    Date: Sunday, December 10, 2017 @ 19:13:16
  Author: arojas
Revision: 273619

archrelease: copy trunk to community-testing-x86_64

Added:
  sagemath/repos/community-testing-x86_64/
  sagemath/repos/community-testing-x86_64/PKGBUILD
    (from rev 273618, sagemath/trunk/PKGBUILD)
  sagemath/repos/community-testing-x86_64/fes02.patch
    (from rev 273618, sagemath/trunk/fes02.patch)
  sagemath/repos/community-testing-x86_64/jupyter-path.patch
    (from rev 273618, sagemath/trunk/jupyter-path.patch)
  sagemath/repos/community-testing-x86_64/latte-count.patch
    (from rev 273618, sagemath/trunk/latte-count.patch)
  sagemath/repos/community-testing-x86_64/package.patch
    (from rev 273618, sagemath/trunk/package.patch)
  sagemath/repos/community-testing-x86_64/r-no-readline.patch
    (from rev 273618, sagemath/trunk/r-no-readline.patch)
  sagemath/repos/community-testing-x86_64/sagemath-detect-igraph.patch
    (from rev 273618, sagemath/trunk/sagemath-detect-igraph.patch)
  sagemath/repos/community-testing-x86_64/sagemath-ecl-no-sigfpe.patch
    (from rev 273618, sagemath/trunk/sagemath-ecl-no-sigfpe.patch)
  sagemath/repos/community-testing-x86_64/sagemath-env.patch
    (from rev 273618, sagemath/trunk/sagemath-env.patch)
  sagemath/repos/community-testing-x86_64/sagemath-linbox-1.5.patch
    (from rev 273618, sagemath/trunk/sagemath-linbox-1.5.patch)
  sagemath/repos/community-testing-x86_64/sagemath-networkx2.patch
    (from rev 273618, sagemath/trunk/sagemath-networkx2.patch)
  sagemath/repos/community-testing-x86_64/sagemath-pynac-0.7.14.patch
    (from rev 273618, sagemath/trunk/sagemath-pynac-0.7.14.patch)
  sagemath/repos/community-testing-x86_64/sagemath-python3-notebook.patch
    (from rev 273618, sagemath/trunk/sagemath-python3-notebook.patch)
  sagemath/repos/community-testing-x86_64/sagemath-threejs.patch
    (from rev 273618, sagemath/trunk/sagemath-threejs.patch)
  sagemath/repos/community-testing-x86_64/test-optional.patch
    (from rev 273618, sagemath/trunk/test-optional.patch)

---------------------------------+
 PKGBUILD                        |  164 ++++++++++++++++++++++
 fes02.patch                     |   57 +++++++
 jupyter-path.patch              |   22 +++
 latte-count.patch               |   71 +++++++++
 package.patch                   |   38 +++++
 r-no-readline.patch             |   11 +
 sagemath-detect-igraph.patch    |   21 ++
 sagemath-ecl-no-sigfpe.patch    |   12 +
 sagemath-env.patch              |  105 ++++++++++++++
 sagemath-linbox-1.5.patch       |  272 ++++++++++++++++++++++++++++++++++++++
 sagemath-networkx2.patch        |   26 +++
 sagemath-pynac-0.7.14.patch     |  167 +++++++++++++++++++++++
 sagemath-python3-notebook.patch |   27 +++
 sagemath-threejs.patch          |   11 +
 test-optional.patch             |   25 +++
 15 files changed, 1029 insertions(+)

Copied: sagemath/repos/community-testing-x86_64/PKGBUILD (from rev 273618, sagemath/trunk/PKGBUILD)
===================================================================
--- community-testing-x86_64/PKGBUILD	                        (rev 0)
+++ community-testing-x86_64/PKGBUILD	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,164 @@
+# Maintainer: Antonio Rojas <arojas at archlinux.org>
+# Contributor: Evgeniy Alekseev <arcanis.arch at gmail dot com>
+# Contributor: Daniel Wallace <danielwallace at gtmanfred dot com>
+# Contributor: Thomas Dziedzic <gostrc at gmail dot com>
+# Contributor: Osman Ugus <ugus11 at yahoo dot com>
+# Contributor: Stefan Husmann <stefan-husmann at t-online dot de>
+# Special thanks to Nareto for moving the compile from the .install to the PKGBUILD
+
+pkgbase=sagemath
+pkgname=(sagemath sagemath-jupyter)
+pkgver=8.1
+pkgrel=1
+pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"
+arch=(x86_64)
+url="http://www.sagemath.org"
+license=(GPL)
+depends=(ipython2 ppl palp brial cliquer maxima-ecl gfan sympow nauty python2-rpy2 python2-fpylll python2-psutil python2-cypari2
+  python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow python2-future libgap flintqs lcalc lrcalc arb
+  eclib gmp-ecm zn_poly gd python2-cvxopt pynac linbox rubiks pari-galdata pari-seadata-small planarity rankwidth
+  sage-data-combinatorial_designs sage-data-elliptic_curves sage-data-graphs sage-data-polytopes_db sage-data-conway_polynomials)
+optdepends=('cython2: to compile cython code' 'python2-pkgconfig: to compile cython code'
+  'jmol: 3D plots' 'sage-notebook: Flask notebook interface (deprecated)'
+  'sagemath-doc: Documentation and inline help' 'python2-igraph: igraph backend for graph theory'
+  'coin-or-cbc: COIN backend for numerical computations' 'coin-or-csdp: for computing Lovász theta-function of graphs'
+  'buckygen: for generating fullerene graphs' 'plantri: for generating some classes of graphs' 'benzene: for generating fusenes and benzenoids'
+  'ffmpeg: to export animations to video' 'imagemagick: to show animations'
+  'coxeter3: Coxeter groups implementation' 'cryptominisat5: SAT solver' 'gap-data: for computing Galois groups'
+  'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes'
+  'libhomfly: for computing the homfly polynomial of links' 'libbraiding: for computing in braid groups'
+  'libfes: exhaustive search of solutions for boolean equations' 'python2-pynormaliz: Normaliz backend for polyhedral computations'
+  'latte-integrale: integral point count in polyhedra' 'polymake: polymake backend for polyhedral computations'
+  'meataxe: faster matrix arithmetic over finite fields'
+  'sirocco: for computing the fundamental group of the complement of a plane curve'
+  'three.js: alternative 3D plots engine' 'tachyon: alternative 3D plots engine')
+makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding sirocco
+  mcqd coxeter3 bliss-graphs tdlib python2-pkgconfig meataxe libfes)
+source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
+        sagemath-env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch
+        r-no-readline.patch fes02.patch sagemath-ecl-no-sigfpe.patch sagemath-threejs.patch
+        sagemath-detect-igraph.patch sagemath-networkx2.patch sagemath-linbox-1.5.patch sagemath-pynac-0.7.14.patch)
+sha256sums=('a42b55c2c8ac244535dc9b87171b7d4dd7e1d498099518ab253354fbe2eaaa7b'
+            '6dc9b101310f80381c61c0312a3e5c648771bfe0de2e94ac46fafe7282a3e0ee'
+            'c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107'
+            '0b680e674c11c47afa86162d8b49645620b8912722e08133d23357c29ca9310a'
+            '2cad308f8adbb6c54e6603fa22b2f0eb60f6f09248d5d015000c3932ac14f646'
+            '962ce805c87147212b21fc2ab0ac9af9bd0033942c7a6905b9906645b48e8a4f'
+            'ef94908d4ab28d13af622e6e58ec191aa78817d17e4466c7bb6f64ee72a813b9'
+            'afd0952b9bb8f52fd428eae36cf719a58ff85a894baae88cbb2124e043768cc7'
+            '7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94'
+            'c31809f887bf9acc45c5bd9dd30bb93e73601d3efbf3016594c3c1d241731c8a'
+            '514135b920a43f999571a15e97b41e14f5bed59f65b19643864dc23555a7b830'
+            '28d7789b8d777922ab8871ca43b6afab751428cae875c0343d3962e6a2030b88'
+            '37c5c1e694a2aca06c0f1c7d99622ff81fd2bc6a51e8745762294889fa4673f6'
+            'a52d03e04c9d64bb957a1f8dcdae3280ebb9450a7fd76aaf5ae5de5c6f74774f'
+            '538f7b279d72f4b67edb445d386d267f3f7022c1079031ca7ea06f6ce392c906')
+
+prepare(){
+  cd sage-$pkgver
+
+# Arch-specific patches
+# assume all optional packages are installed
+  patch -p0 -i ../package.patch
+# set env variables
+  patch -p0 -i ../sagemath-env.patch
+# don't list optional packages when running tests
+  patch -p0 -i ../test-optional.patch
+# set jupyter path
+  patch -p0 -i ../jupyter-path.patch
+# fix freezes in R interface with readline 7 (Debian)
+  patch -p1 -i ../r-no-readline.patch
+# use correct latte-count binary name
+  patch -p1 -i ../latte-count.patch
+# make 'sage -notebook=jupyter' work with our python3 jupyter-notebook package
+  patch -p1 -i ../sagemath-python3-notebook.patch
+# fix Cremona database detection
+  sed -e "s|is_package_installed('database_cremona_ellcurve')|os.path.exists('/usr/share/cremona/cremona.db')|" \
+   -i src/sage/databases/cremona.py
+# fix python-igraph detection
+  patch -p1 -i ../sagemath-detect-igraph.patch
+# adapt to networkx 2 changes
+  patch -p1 -i ../sagemath-networkx2.patch
+# fix three.js plotting backend
+  patch -p1 -i ../sagemath-threejs.patch
+
+# Upstream patches  
+# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
+  patch -p1 -i ../fes02.patch
+# disable SIGFPE for ecl https://trac.sagemath.org/ticket/22191
+# patch -p1 -i ../sagemath-ecl-no-sigfpe.patch
+# fix build with linbox 1.5 https://trac.sagemath.org/ticket/24214
+  patch -p1 -i ../sagemath-linbox-1.5.patch
+# fix build with pynac 0.7.14 https://trac.sagemath.org/ticket/24329
+  patch -p1 -i ../sagemath-pynac-0.7.14.patch
+
+# use python2
+  sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/*
+  sed -e 's|cython {OPT}|cython2 {OPT}|' -e 's|python setup.py|python2 setup.py|' -i src/sage/misc/cython.py
+  sed -e 's|exec ipython|exec ipython2|' -e 's|cygdb|cygdb2|g' -i src/bin/sage
+  sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython
+  sed -e 's|bin/python|bin/python2|g' -i src/bin/sage-env
+}
+
+
+build() {
+  cd sage-$pkgver
+  autoreconf -vi
+  ./configure --prefix=/usr || true
+
+  cd src
+  export SAGE_LOCAL="/usr"
+  export SAGE_ROOT="$PWD"
+  export SAGE_SRC="$PWD"
+
+  python2 setup.py build
+}
+
+package_sagemath() {
+  optdepends+=('sagemath-jupyter: Jupyter kernel')
+
+  cd sage-$pkgver/src
+
+  export SAGE_ROOT="$PWD"
+  export SAGE_LOCAL="/usr"
+  export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
+
+  python2 setup.py install --root="$pkgdir" --optimize=1
+
+  mkdir -p "$pkgdir"/usr/bin
+  cp bin/sage "$pkgdir"/usr/bin
+  for _i in arch-env banner cachegrind callgrind cleaner coverage coverageall cython env env-config eval grep grepdoc inline-fortran \
+    ipython massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2sws rst2txt run \
+    run-cython runtests startuptime.py sws2rst valgrind version.sh
+  do
+    cp bin/sage-$_i "$pkgdir"/usr/bin
+  done
+  cp bin/math-readline "$pkgdir"/usr/bin
+  
+  mkdir -p "$pkgdir"/usr/share/sage
+  cp -r ext "$pkgdir"/usr/share/sage
+  
+# Create SAGE_SRC, needed for the notebook and help
+  mkdir "$pkgdir"/usr/share/sage/source
+  ln -s /usr/share/doc/sage "$pkgdir"/usr/share/sage/source/doc
+
+# Remove sage_setup
+  rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
+
+# Split jupyter kernel
+  rm -r "$pkgdir"/usr/share/jupyter
+}
+
+package_sagemath-jupyter() {
+  pkgdesc='Jupyter kernel for SageMath'
+  depends=(sagemath python2-jupyter_client python2-ipywidgets mathjax)
+  optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter')
+
+  cd sage-$pkgver/src
+
+  export SAGE_ROOT="$PWD"
+  export SAGE_LOCAL="/usr"
+  export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
+
+  python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update()"
+}

Copied: sagemath/repos/community-testing-x86_64/fes02.patch (from rev 273618, sagemath/trunk/fes02.patch)
===================================================================
--- community-testing-x86_64/fes02.patch	                        (rev 0)
+++ community-testing-x86_64/fes02.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,57 @@
+From b1f5e3ecc789db674fe17552812f2d0e2ab84be0 Mon Sep 17 00:00:00 2001
+From: Charles Bouillaguet <charles.bouillaguet at lifl.fr>
+Date: Thu, 19 Sep 2013 10:31:11 +0200
+Subject: updating the libFES binding to match a change in the interface
+
+---
+ src/sage/libs/fes.pyx | 12 +++++++-----
+ 1 file changed, 7 insertions(+), 5 deletions(-)
+
+diff --git a/src/sage/libs/fes.pyx b/src/sage/libs/fes.pyx
+index 40b9c23..d188cf0 100644
+--- a/src/sage/libs/fes.pyx
++++ b/src/sage/libs/fes.pyx
+@@ -1,17 +1,19 @@
+ """
+-Binding for the FES library.
++Binding for the libFES library.
+ 
+ Finding solutions of systems of boolean equations by exhaustive
+ search, via the fes library. This is usually (much) faster than
+ computing a Groebner basis, except in special cases where the latter
+ is particularly easy.
+ 
+-The FES library is presently only able to deal with polynomials in 64
++More information is available at [http://www.lifl.fr/~bouillag/fes].
++
++The libFES library is presently only able to deal with polynomials in 64
+ variables. Performing a full exhaustive search over 64 variables will
+ take a **long** time. The number of variables can be artificially
+ reduced to 64 by specializing some of them.
+ 
+-Note that the FES library **requires** at least of the equations to be
++Note that the libFES library **requires** at least of the equations to be
+ non-linear.
+ 
+ AUTHORS:
+@@ -71,7 +73,7 @@ from libc.stdint cimport uint64_t
+ cdef extern from "fes_interface.h":
+     ctypedef int (*solution_callback_t)(void *, uint64_t)
+ 
+-    void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose)
++    void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose, int T)
+ 
+ 
+ from sage.rings.integer import Integer
+@@ -217,7 +217,7 @@ def exhaustive_search(eqs,  max_sols=Infinity, verbose=False):
+ 
+     # ------- runs the library
+     sig_on()
+-    exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose)
++    exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose, 0)
+     sig_off()
+ 
+     # ------- frees memory occupied by the dense representation of the equations
+-- 
+cgit v1.0-1-gd88e
+

Copied: sagemath/repos/community-testing-x86_64/jupyter-path.patch (from rev 273618, sagemath/trunk/jupyter-path.patch)
===================================================================
--- community-testing-x86_64/jupyter-path.patch	                        (rev 0)
+++ community-testing-x86_64/jupyter-path.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,22 @@
+--- src/sage/repl/ipython_kernel/install.py.orig	2015-10-23 19:23:39.728456590 +0000
++++ src/sage/repl/ipython_kernel/install.py	2015-10-23 19:24:00.965018978 +0000
+@@ -13,8 +13,7 @@
+     SAGE_DOC, SAGE_LOCAL, SAGE_EXTCODE,
+     SAGE_VERSION
+ )
+-from jupyter_core.paths import ENV_JUPYTER_PATH
+-JUPYTER_PATH = ENV_JUPYTER_PATH[0]
++JUPYTER_PATH = os.environ.get('JUPYTER_PATH') 
+ 
+ 
+ class SageKernelSpec(object):
+@@ -225,7 +225,7 @@
+             sage: spec._symlink_resources()    # not tested
+         """
+         path = os.path.join(SAGE_EXTCODE, 'notebook-ipython')
+-        for filename in os.listdir(path):
++        for filename in os.listdir('ext/notebook-ipython'):
+             self.symlink(
+                 os.path.join(path, filename),
+                 os.path.join(self.kernel_dir, filename)
+

Copied: sagemath/repos/community-testing-x86_64/latte-count.patch (from rev 273618, sagemath/trunk/latte-count.patch)
===================================================================
--- community-testing-x86_64/latte-count.patch	                        (rev 0)
+++ community-testing-x86_64/latte-count.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,71 @@
+diff --git a/src/sage/geometry/polyhedron/base_ZZ.py b/src/sage/geometry/polyhedron/base_ZZ.py
+index 268af9db0d..70d41dfa30 100644
+--- a/src/sage/geometry/polyhedron/base_ZZ.py
++++ b/src/sage/geometry/polyhedron/base_ZZ.py
+@@ -171,7 +171,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             sage: p = P.ehrhart_polynomial(maxdet=5, verbose=True)  # optional - latte_int
+             This is LattE integrale ...
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin
+             ...
+             sage: p    # optional - latte_int
+             1/2*t^2 + 3/2*t + 1
+@@ -179,7 +179,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             sage: p = P.ehrhart_polynomial(dual=True, verbose=True)  # optional - latte_int
+             This is LattE integrale ...
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin
+             ...
+             sage: p   # optional - latte_int
+             1/2*t^2 + 3/2*t + 1
+@@ -187,7 +187,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             sage: p = P.ehrhart_polynomial(irrational_primal=True, verbose=True)   # optional - latte_int
+             This is LattE integrale ...
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin
+             ...
+             sage: p   # optional - latte_int
+             1/2*t^2 + 3/2*t + 1
+@@ -195,7 +195,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             sage: p = P.ehrhart_polynomial(irrational_all_primal=True, verbose=True)  # optional - latte_int
+             This is LattE integrale ...
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin
+             ...
+             sage: p   # optional - latte_int
+             1/2*t^2 + 3/2*t + 1
+@@ -207,7 +207,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             ...
+             RuntimeError: LattE integrale program failed (exit code 1):
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin
+             Unknown command/option --bim-bam-boum=19
+         """
+         if self.is_empty():
+diff --git a/src/sage/interfaces/latte.py b/src/sage/interfaces/latte.py
+index 066cedd401..302b39910d 100644
+--- a/src/sage/interfaces/latte.py
++++ b/src/sage/interfaces/latte.py
+@@ -88,7 +88,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False,
+         sage: n = count(cddin, cdd=True, verbose=True, raw_output=True)  # optional - latte_int
+         This is LattE integrale ...
+         ...
+-        Invocation: count '--redundancy-check=none' --cdd /dev/stdin
++        Invocation: latte-count '--redundancy-check=none' --cdd /dev/stdin
+         ...
+         Total Unimodular Cones: ...
+         Maximum number of simplicial cones in memory at once: ...
+@@ -108,7 +108,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False,
+     from sage.misc.misc import SAGE_TMP
+     from sage.rings.integer import Integer
+ 
+-    args = ['count']
++    args = ['latte-count']
+     if ehrhart_polynomial and multivariate_generating_function:
+         raise ValueError
+     if ehrhart_polynomial:

Copied: sagemath/repos/community-testing-x86_64/package.patch (from rev 273618, sagemath/trunk/package.patch)
===================================================================
--- community-testing-x86_64/package.patch	                        (rev 0)
+++ community-testing-x86_64/package.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,38 @@
+--- src/sage/misc/package.py.orig	2014-11-23 15:58:13.000000000 +0100
++++ src/sage/misc/package.py	2015-01-22 20:32:25.651383902 +0100
+@@ -320,7 +320,7 @@
+         sage: for pkg in list_packages('pip', local=True):
+         ....:     assert not is_package_installed(pkg)
+     """
+-    return any(p.split('-')[0] == package for p in installed_packages(exclude_pip))
++    return True
+ 
+ def package_versions(package_type, local=False):
+     r"""
+--- src/sage_setup/optional_extension.py.orig  2016-10-19 18:35:10.092577510 +0000
++++ src/sage_setup/optional_extension.py       2016-10-19 18:38:13.514765366 +0000
+@@ -21,8 +21,6 @@
+ from distutils.extension import Extension
+ from sage.misc.package import is_package_installed, list_packages
+ 
+-all_packages = list_packages(local=True)
+-
+ 
+ class CythonizeExtension(Extension):
+     """
+@@ -76,14 +74,7 @@
+         condition = kwds.pop("condition")
+     except KeyError:
+         pkg = kwds.pop("package")
+-        try:
+-            pkginfo = all_packages[pkg]
+-        except KeyError:
+-            # Might be an installed old-style package
+-            condition = is_package_installed(pkg)
+-        else:
+-            condition = (pkginfo["installed_version"] == pkginfo["remote_version"])
+-
++        condition = True
+     if condition:
+         return Extension(*args, **kwds)
+     else:

Copied: sagemath/repos/community-testing-x86_64/r-no-readline.patch (from rev 273618, sagemath/trunk/r-no-readline.patch)
===================================================================
--- community-testing-x86_64/r-no-readline.patch	                        (rev 0)
+++ community-testing-x86_64/r-no-readline.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,11 @@
+--- a/src/sage/interfaces/r.py
++++ b/src/sage/interfaces/r.py
+@@ -332,7 +332,7 @@
+                   prompt = '> ', #default, later comes the change
+ 
+                   # This is the command that starts up your program
+-                  command = "R --vanilla --quiet",
++                  command = "R --no-readline --vanilla --quiet",
+ 
+                   server=server,
+                   server_tmpdir=server_tmpdir,

Copied: sagemath/repos/community-testing-x86_64/sagemath-detect-igraph.patch (from rev 273618, sagemath/trunk/sagemath-detect-igraph.patch)
===================================================================
--- community-testing-x86_64/sagemath-detect-igraph.patch	                        (rev 0)
+++ community-testing-x86_64/sagemath-detect-igraph.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,21 @@
+diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
+index 252984f..ce19682 100644
+--- a/src/sage/graphs/generic_graph.py
++++ b/src/sage/graphs/generic_graph.py
+@@ -8188,10 +8188,12 @@ class GenericGraph(GenericGraph_pyx):
+         if algorithm is None:
+             if vertex_bound:
+                 algorithm = "LP"
+-            elif is_package_installed("python_igraph"):
+-                algorithm = "igraph"
+             else:
+-                algorithm = "FF"
++                algorithm = "igraph"
++                try:
++                    import igraph
++                except ImportError:
++                    algorithm = "FF"
+ 
+         if (algorithm == "FF"):
+             return self._ford_fulkerson(x,y, value_only=value_only, integer=integer, use_edge_labels=use_edge_labels)
+

Copied: sagemath/repos/community-testing-x86_64/sagemath-ecl-no-sigfpe.patch (from rev 273618, sagemath/trunk/sagemath-ecl-no-sigfpe.patch)
===================================================================
--- community-testing-x86_64/sagemath-ecl-no-sigfpe.patch	                        (rev 0)
+++ community-testing-x86_64/sagemath-ecl-no-sigfpe.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,12 @@
+diff --git a/src/sage/libs/ecl.pyx b/src/sage/libs/ecl.pyx
+index 1fafb6c..4f730ad 100644
+--- a/src/sage/libs/ecl.pyx
++++ b/src/sage/libs/ecl.pyx
+@@ -314,6 +314,7 @@ def init_ecl():
+         """))
+     safe_funcall_clobj=cl_eval(string_to_object("(symbol-function 'sage-safe-funcall)"))
+ 
++    cl_eval(string_to_object("(si::trap-fpe T NIL)"))
+     ecl_has_booted = 1
+ 
+ cdef cl_object ecl_safe_eval(cl_object form) except NULL:

Copied: sagemath/repos/community-testing-x86_64/sagemath-env.patch (from rev 273618, sagemath/trunk/sagemath-env.patch)
===================================================================
--- community-testing-x86_64/sagemath-env.patch	                        (rev 0)
+++ community-testing-x86_64/sagemath-env.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,105 @@
+--- src/bin/sage-env.orig	2015-01-06 10:46:04.469687605 +0100
++++ src/bin/sage-env	2015-01-06 10:49:59.547762019 +0100
+@@ -111,41 +111,7 @@
+ }
+ 
+ 
+-# New value for SAGE_ROOT: either SAGE_ROOT (if given)
+-# or a guessed value based on pwd.
+-if [ -n "$SAGE_ROOT" ]; then
+-    NEW_SAGE_ROOT="$SAGE_ROOT"
+-elif [ -f sage -a -d build ]; then
+-    NEW_SAGE_ROOT="."
+-elif [ -f ../../sage -a -d ../../build ]; then
+-    NEW_SAGE_ROOT="../.."
+-else
+-    # No idea what SAGE_ROOT should be...
+-    echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this"
+-    echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory."
+-    return 1
+-fi
+-
+-# Make NEW_SAGE_ROOT absolute
+-NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P`
+-
+-# Sanity check NEW_SAGE_ROOT
+-if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then
+-    :
+-else
+-    echo >&2 "Error: SAGE_ROOT is set to a bad value:"
+-    echo >&2 "SAGE_ROOT=$SAGE_ROOT"
+-    echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT"
+-    echo >&2 "or SAGE_ROOT/local/bin/ directory."
+-    return 1
+-fi
+-
+-# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT
+-if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then
+-    echo >&2 "Warning: overwriting SAGE_ROOT environment variable:"
+-    echo >&2 "Old SAGE_ROOT=$SAGE_ROOT"
+-    echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT"
+-fi
++NEW_SAGE_ROOT="/usr"
+ 
+ # Display the Sage startup banner, used in src/bin/sage
+ sage_banner() {
+@@ -185,6 +185,7 @@
+ export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION
+ 
+ export SAGE_ROOT="$NEW_SAGE_ROOT"
++export SAGE_LOCAL='/usr'
+ 
+ 
+ # sage-env must know where the Sage's script files are.
+@@ -307,8 +307,9 @@
+ export SAGE_EXTCODE="$SAGE_SHARE/sage/ext"
+ export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
+ export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
+-export SAGE_SRC="$SAGE_ROOT/src"
+-export SAGE_DOC_SRC="$SAGE_SRC/doc"
++export GAP_ROOT_DIR="/usr/lib/gap"
++export SAGE_SRC="$SAGE_SHARE/sage/source"
++export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
+ export SAGE_DOC="$SAGE_SHARE/doc/sage"
+ 
+ if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
+@@ -414,6 +414,9 @@
+     export SAGE_STARTUP_FILE
+ fi
+ 
++export LIBMTX="$DOT_SAGE/meataxe"
++[[ -d $LIBMTX ]] || mkdir -p $LIBMTX # Create meataxe data dir
++
+ if [ "$PYTHON_EGG_CACHE" = "" ]; then
+     PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs"
+     export PYTHON_EGG_CACHE
+@@ -499,7 +499,6 @@
+         fi
+     fi
+ fi
+-export MAXIMA_PREFIX="$SAGE_LOCAL"
+ 
+ PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
+ 
+@@ -619,9 +619,6 @@
+     LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH
+ fi
+ 
+-# See trac 7186 -- this is needed if ecl is moved
+-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR
+-
+ # Handle parallel building/testing/...
+ # See Trac Ticket #12016
+ # First, figure out the right values for SAGE_NUM_THREADS (default
+--- src/sage/env.py.orig       2017-12-07 19:51:25.554281539 +0000
++++ src/sage/env.py    2017-12-07 19:51:42.787654650 +0000
+@@ -118,7 +118,7 @@
+ 
+ # bunch of sage directories and files
+ _add_variable_or_fallback('SAGE_ROOT',       None)
+-_add_variable_or_fallback('SAGE_LOCAL',      None)
++_add_variable_or_fallback('SAGE_LOCAL',      '/usr')
+ _add_variable_or_fallback('SAGE_ETC',        opj('$SAGE_LOCAL', 'etc'))
+ _add_variable_or_fallback('SAGE_INC',        opj('$SAGE_LOCAL', 'include'))
+ _add_variable_or_fallback('SAGE_SHARE',      opj('$SAGE_LOCAL', 'share'))
+

Copied: sagemath/repos/community-testing-x86_64/sagemath-linbox-1.5.patch (from rev 273618, sagemath/trunk/sagemath-linbox-1.5.patch)
===================================================================
--- community-testing-x86_64/sagemath-linbox-1.5.patch	                        (rev 0)
+++ community-testing-x86_64/sagemath-linbox-1.5.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,272 @@
+diff --git a/src/sage/libs/linbox/fflas.pxd b/src/sage/libs/linbox/fflas.pxd
+index ca23d71..03bbee9 100644
+--- a/src/sage/libs/linbox/fflas.pxd
++++ b/src/sage/libs/linbox/fflas.pxd
+@@ -20,19 +20,29 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h" namespace "std":
+         iterator end()
+         size_t size()
+ 
+-    cdef cppclass list[T]:
+-        cppclass iterator:
+-            T operator*()
+-            iterator operator++()
+-            bint operator==(iterator)
+-            bint operator!=(iterator)
+-        void push_back(T&)
+-        void pop_front()
+-        T& front()
+-        iterator begin()
+-        iterator end()
++cdef extern from "givaro/givpoly1.h":
++    ## template < typename T, typename A=std::allocator<T> >
++    ## class givvector : public __GIV_STANDARD_VECTOR<T,A>
++    cdef cppclass givvector "Givaro::givvector" [T,ALLOCATOR=*]:
++        T& operator[](size_t i)
+         size_t size()
+-        void clear()
++
++ctypedef givvector[ModDoubleFieldElement] ModDoubleDensePolynomial
++ctypedef givvector[ModFloatFieldElement] ModFloatDensePolynomial
++
++cdef extern from "givaro/givpoly1.h":
++    ## template <class Domain, class StorageTag= Givaro::Dense>
++    ## class GivPolynomialRing : public Givaro::Poly1FactorDom< Domain,StorageTag>
++    cdef cppclass ModDoublePolynomialRing "Givaro::Poly1Dom<Givaro::Modular<double>, Givaro::Dense>":
++        ctypedef givvector[ModDoubleField] Element
++        ctypedef givvector[ModDoubleField] Polynomial
++        ModDoublePolynomialRing(ModDoubleField& F)
++    ## template <class Domain, class StorageTag= Givaro::Dense>
++    ## class GivPolynomialRing : public Givaro::Poly1FactorDom< Domain,StorageTag>
++    cdef cppclass ModFloatPolynomialRing "Givaro::Poly1Dom<Givaro::Modular<float>, Givaro::Dense>":
++        ctypedef givvector[ModFloatField] Element
++        ctypedef givvector[ModFloatField] Polynomial
++        ModFloatPolynomialRing(ModFloatField& F)
+ 
+ cdef extern from "fflas-ffpack/fflas-ffpack.h":
+     ctypedef enum fflas_trans_enum "FFLAS::FFLAS_TRANSPOSE":
+@@ -105,13 +115,12 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h":
+                                             size_t nr, size_t foo, size_t r,
+                                             ModDoubleFieldElement* matrix, size_t nc, size_t* Q)
+ 
+-    void ModDouble_MinPoly "FFPACK::MinPoly" ( ModDoubleField F,
++    void ModDouble_MinPoly "FFPACK::MinPoly" ( ModDoubleField& F,
+                                                vector[ModDoubleFieldElement] minP, size_t N,
+-                                               ModDoubleFieldElement* A, size_t lda,
+-                                               ModDoubleFieldElement* X, size_t ldx, size_t* P)
++                                               ModDoubleFieldElement*A, size_t lda)
+ 
+-    void ModDouble_CharPoly "FFPACK::CharPoly" ( ModDoubleField F,
+-                                                 list[vector[ModDoubleFieldElement]] charp, size_t N,
++    void ModDouble_CharPoly "FFPACK::CharPoly" ( ModDoublePolynomialRing& R,
++                                                 ModDoubleDensePolynomial& charp, size_t N,
+                                                  ModDoubleFieldElement* A, size_t lda)
+ 
+     # float
+@@ -142,9 +151,8 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h":
+ 
+     void ModFloat_MinPoly "FFPACK::MinPoly" ( ModFloatField F,
+                                               vector[ModFloatFieldElement] minP, size_t N,
+-                                              ModFloatFieldElement* A, size_t lda,
+-                                              ModFloatFieldElement* X, size_t ldx, size_t* P)
++                                              ModFloatFieldElement* A, size_t lda)
+ 
+-    void ModFloat_CharPoly "FFPACK::CharPoly" ( ModFloatField F,
+-                                                list[vector[ModFloatFieldElement]] charp, size_t N,
++    void ModFloat_CharPoly "FFPACK::CharPoly" ( ModFloatPolynomialRing& F,
++                                                ModFloatDensePolynomial& charp, size_t N,
+                                                 ModFloatFieldElement* A, size_t lda )
+diff --git a/src/sage/libs/linbox/linbox_flint_interface.pyx b/src/sage/libs/linbox/linbox_flint_interface.pyx
+index 02a6151..a00d303 100644
+--- a/src/sage/libs/linbox/linbox_flint_interface.pyx
++++ b/src/sage/libs/linbox/linbox_flint_interface.pyx
+@@ -76,19 +76,23 @@ cdef extern from "givaro/zring.h":
+         ctypedef GivaroInteger Element
+ 
+ 
+-cdef extern from "givaro/givpoly1.h":
+-    ## template < typename T, typename A=std::allocator<T> >
+-    ## class givvector : public __GIV_STANDARD_VECTOR<T,A>
+-    cdef cppclass givvector "Givaro::givvector" [T,ALLOCATOR=*]:
+-        T& operator[](size_t i)
++cdef extern from "linbox/polynomial/dense-polynomial.h":
++    ## template<class Field>
++    ## class DensePolynomial : public Givaro::Poly1FactorDom<Field, Givaro::Dense>::Element
++    cdef cppclass LinBoxIntegerDensePolynomial "LinBox::DensePolynomial<Givaro::ZRing<Givaro::Integer> >":
++        ctypedef GivaroIntegerRing BaseRing
++        ctypedef GivaroInteger BaseRingElement
++        LinBoxIntegerDensePolynomial(BaseRing &F)
++        LinBoxIntegerDensePolynomial(BaseRing &F, size_t s)
++        BaseRingElement& operator[](size_t i)
+         size_t size()
+ 
+-cdef extern from "linbox/ring/givaro-polynomial.h":
+-    ## template <class Domain, class StorageTag= Givaro::Dense>
+-    ## class GivPolynomialRing : public Givaro::Poly1FactorDom< Domain,StorageTag>
+-    cdef cppclass LinBoxIntegerPolynomialRing "LinBox::GivPolynomialRing<Givaro::ZRing<Givaro::Integer>, Givaro::Dense>":
+-        ctypedef givvector[GivaroInteger] Element
+-        ctypedef givvector[GivaroInteger] Polynomial
++cdef extern from "linbox/ring/polynomial-ring.h":
++    ## template <class BaseRing, class StorageTag= Givaro::Dense>
++    ##	class PolynomialRing : public Givaro::Poly1FactorDom<BaseRing,StorageTag>
++    cdef cppclass LinBoxIntegerPolynomialRing "LinBox::PolynomialRing<Givaro::ZRing<Givaro::Integer>, Givaro::Dense>":
++        ctypedef LinBoxIntegerDensePolynomial Element
++        ctypedef LinBoxIntegerDensePolynomial Polynomial
+ 
+ cdef extern from "linbox/matrix/matrix-domain.h":
+     ## template <class Field_ >
+@@ -190,40 +194,32 @@ cdef void linbox_fmpz_mat_mul(fmpz_mat_t C, fmpz_mat_t A, fmpz_mat_t B):
+ cdef void linbox_fmpz_mat_charpoly(fmpz_poly_t cp, fmpz_mat_t A):
+     cdef GivaroIntegerRing ZZ
+     cdef LinBoxIntegerDenseMatrix * LBA
+-    cdef LinBoxIntegerPolynomialRing.Element m_A
+-
+-    # FIXME: bug in LinBox
+-    # see https://github.com/linbox-team/linbox/issues/51
+-    if fmpz_mat_nrows(A) == 0:
+-        fmpz_poly_one(cp)
+-        return
++    cdef LinBoxIntegerDensePolynomial * m_A
+ 
+     LBA = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(A), fmpz_mat_ncols(A))
+     fmpz_mat_get_linbox(LBA[0], A)
+-    LinBoxIntegerDense_charpoly(m_A, LBA[0])
+-    fmpz_poly_set_linbox(cp, m_A)
++    m_A = new LinBoxIntegerDensePolynomial(ZZ, fmpz_mat_nrows(A))
++    LinBoxIntegerDense_charpoly(m_A[0], LBA[0])
++    fmpz_poly_set_linbox(cp, m_A[0])
+ 
+     del LBA
++    del m_A
+ 
+ 
+ # set mp to the minimal polynomial of A
+ cdef void linbox_fmpz_mat_minpoly(fmpz_poly_t mp, fmpz_mat_t A):
+     cdef GivaroIntegerRing ZZ
+     cdef LinBoxIntegerDenseMatrix * LBA
+-    cdef LinBoxIntegerPolynomialRing.Element m_A
+-
+-    # FIXME: bug in LinBox
+-    # see https://github.com/linbox-team/linbox/issues/51
+-    if fmpz_mat_nrows(A) == 0:
+-        fmpz_poly_one(mp)
+-        return
++    cdef LinBoxIntegerDensePolynomial * m_A
+ 
+     LBA = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(A), fmpz_mat_ncols(A))
++    m_A = new LinBoxIntegerDensePolynomial(ZZ)
+     fmpz_mat_get_linbox(LBA[0], A)
+-    LinBoxIntegerDense_minpoly(m_A, LBA[0])
+-    fmpz_poly_set_linbox(mp, m_A)
++    LinBoxIntegerDense_minpoly(m_A[0], LBA[0])
++    fmpz_poly_set_linbox(mp, m_A[0])
+ 
+     del LBA
++    del m_A
+ 
+ 
+ # return the rank of A
+diff --git a/src/sage/matrix/matrix_modn_dense_double.pyx b/src/sage/matrix/matrix_modn_dense_double.pyx
+index 15c35cb..b1f6154 100644
+--- a/src/sage/matrix/matrix_modn_dense_double.pyx
++++ b/src/sage/matrix/matrix_modn_dense_double.pyx
+@@ -27,7 +27,9 @@ from sage.libs.linbox.fflas cimport ModDouble_fgemm as Mod_fgemm, ModDouble_fgem
+     ModDoubleRank as ModRank, ModDouble_echelon as Mod_echelon, \
+     ModDouble_applyp as Mod_applyp, \
+     ModDouble_MinPoly as Mod_MinPoly, \
+-    ModDouble_CharPoly as Mod_CharPoly
++    ModDouble_CharPoly as Mod_CharPoly, \
++    ModDoublePolynomialRing as ModDensePolyRing,\
++    ModDoubleDensePolynomial as ModDensePoly
+ 
+ # Limit for LinBox Modular<double>
+ MAX_MODULUS = 2**23
+diff --git a/src/sage/matrix/matrix_modn_dense_float.pyx b/src/sage/matrix/matrix_modn_dense_float.pyx
+index 61457ce..eda8f0b 100644
+--- a/src/sage/matrix/matrix_modn_dense_float.pyx
++++ b/src/sage/matrix/matrix_modn_dense_float.pyx
+@@ -25,7 +25,10 @@ from sage.libs.linbox.fflas cimport ModFloat_fgemm as Mod_fgemm, ModFloat_fgemv
+         ModFloatRank as ModRank, ModFloat_echelon as Mod_echelon, \
+         ModFloat_applyp as Mod_applyp, \
+         ModFloat_MinPoly as Mod_MinPoly, \
+-        ModFloat_CharPoly as Mod_CharPoly
++        ModFloat_CharPoly as Mod_CharPoly, \
++        ModFloatPolynomialRing as ModDensePolyRing,\
++        ModFloatDensePolynomial as ModDensePoly
++
+ 
+ # LinBox supports up to 2^11 using float but that's double dog slow,
+ # so we pick a smaller value for crossover
+diff --git a/src/sage/matrix/matrix_modn_dense_template.pxi b/src/sage/matrix/matrix_modn_dense_template.pxi
+index 3da3e31..819ef2d 100644
+--- a/src/sage/matrix/matrix_modn_dense_template.pxi
++++ b/src/sage/matrix/matrix_modn_dense_template.pxi
+@@ -306,23 +306,15 @@ cdef inline linbox_minpoly(celement modulus, Py_ssize_t nrows, celement* entries
+     cdef Py_ssize_t i
+     cdef ModField *F = new ModField(<long>modulus)
+     cdef vector[ModFieldElement] *minP = new vector[ModFieldElement]()
+-    cdef ModFieldElement *X = <ModFieldElement*>check_allocarray(nrows * (nrows+1), sizeof(ModFieldElement))
+-    cdef size_t *P = <size_t*>check_allocarray(nrows, sizeof(size_t))
+-
+-    cdef celement *cpy = linbox_copy(modulus, entries, nrows, nrows)
+ 
+     if nrows*nrows > 1000: sig_on()
+-    Mod_MinPoly(F[0], minP[0], nrows, <ModFieldElement*>cpy, nrows, X, nrows, P)
++    Mod_MinPoly(F[0], minP[0], nrows, <ModFieldElement*>entries, nrows)
+     if nrows*nrows > 1000: sig_off()
+ 
+-    sig_free(cpy)
+-
+     l = []
+     for i in range(minP.size()):
+         l.append( <celement>minP.at(i) )
+ 
+-    sig_free(P)
+-    sig_free(X)
+     del F
+     return l
+ 
+@@ -332,27 +324,23 @@ cdef inline linbox_charpoly(celement modulus, Py_ssize_t nrows, celement* entrie
+     """
+     cdef Py_ssize_t i
+     cdef ModField *F = new ModField(<long>modulus)
+-    cdef std_list[vector[ModFieldElement]] P_list
+-    P_list.clear()
++    cdef ModDensePolyRing * R = new ModDensePolyRing(F[0])
++    cdef ModDensePoly  P
+ 
+     cdef celement *cpy = linbox_copy(modulus, entries, nrows, nrows)
+ 
+     if nrows*nrows > 1000: sig_on()
+-    Mod_CharPoly(F[0], P_list, nrows, <ModFieldElement*>cpy, nrows)
++    Mod_CharPoly(R[0], P, nrows, <ModFieldElement*>cpy, nrows)
+     if nrows*nrows > 1000: sig_off()
+ 
+     sig_free(cpy)
+ 
+-    cdef vector[ModFieldElement] tmp
+     l = []
+-    while P_list.size():
+-        l.append([])
+-        tmp = P_list.front()
+-        for i in range(tmp.size()):
+-            l[-1].append(<celement>tmp.at(i))
+-        P_list.pop_front()
++    for i in range(P.size()):
++        l.append(<celement>P[i])
+ 
+     del F
++    del R
+     return l
+ 
+ 
+@@ -1731,9 +1719,7 @@ cdef class Matrix_modn_dense_template(Matrix_dense):
+         R = self._base_ring[var]
+         # call linbox for charpoly
+         v = linbox_charpoly(self.p, self._nrows, self._entries)
+-        r = R(1)
+-        for e in v:
+-            r *= R(e)
++        r = R(v)
+         return r
+ 
+     def echelonize(self, algorithm="linbox", **kwds):

Copied: sagemath/repos/community-testing-x86_64/sagemath-networkx2.patch (from rev 273618, sagemath/trunk/sagemath-networkx2.patch)
===================================================================
--- community-testing-x86_64/sagemath-networkx2.patch	                        (rev 0)
+++ community-testing-x86_64/sagemath-networkx2.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,26 @@
+diff --git a/src/sage/graphs/digraph.py b/src/sage/graphs/digraph.py
+index 8c29602da6..e7a185d586 100644
+--- a/src/sage/graphs/digraph.py
++++ b/src/sage/graphs/digraph.py
+@@ -755,7 +755,7 @@ class DiGraph(GenericGraph):
+             self.allow_multiple_edges(multiedges,check=False)
+             self.allow_loops(loops,check=False)
+             self.add_vertices(data.nodes())
+-            self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True))
++            self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True))
+         elif format == 'igraph':
+             if not data.is_directed():
+                 raise ValueError("A *directed* igraph graph was expected. To "+
+diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py
+index b63135d8e6..5775042976 100644
+--- a/src/sage/graphs/graph.py
++++ b/src/sage/graphs/graph.py
+@@ -1199,7 +1199,7 @@ class Graph(GenericGraph):
+             self.allow_loops(loops, check=False)
+             self.allow_multiple_edges(multiedges, check=False)
+             self.add_vertices(data.nodes())
+-            self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True))
++            self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True))
+         elif format == 'igraph':
+             if data.is_directed():
+                 raise ValueError("An *undirected* igraph graph was expected. "+

Copied: sagemath/repos/community-testing-x86_64/sagemath-pynac-0.7.14.patch (from rev 273618, sagemath/trunk/sagemath-pynac-0.7.14.patch)
===================================================================
--- community-testing-x86_64/sagemath-pynac-0.7.14.patch	                        (rev 0)
+++ community-testing-x86_64/sagemath-pynac-0.7.14.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,167 @@
+diff --git a/src/sage/libs/pynac/pynac.pxd b/src/sage/libs/pynac/pynac.pxd
+index d4afc4e..6d1fcac 100644
+--- a/src/sage/libs/pynac/pynac.pxd
++++ b/src/sage/libs/pynac/pynac.pxd
+@@ -481,22 +481,17 @@ cdef extern from "pynac_wrap.h":
+     ctypedef GParamSet const_paramset_ref "const GiNaC::paramset&"
+ 
+     ctypedef struct py_funcs_struct:
+-        py_binomial(a, b)
+-        py_binomial_int(int n, unsigned int k)
+         py_gcd(a, b)
+         py_lcm(a, b)
+         py_real(a)
+         py_imag(a)
+         py_numer(a)
+         py_denom(a)
+-        py_conjugate(a)
+         bint py_is_rational(a)
+-        bint py_is_crational(a)
+         bint py_is_real(a)
+         bint py_is_integer(a)
+         bint py_is_equal(a, b)
+         bint py_is_even(a)
+-        bint py_is_cinteger(a)
+         bint py_is_prime(n)
+         bint py_is_exact(x)
+ 
+@@ -534,23 +529,14 @@ cdef extern from "pynac_wrap.h":
+         py_asinh(x)
+         py_acosh(x)
+         py_atanh(x)
+-        py_tgamma(x)
+-        py_lgamma(x)
+         py_isqrt(x)
+         py_sqrt(x)
+-        py_abs(x)
+         py_mod(x, y)
+         py_smod(x, y)
+         py_irem(x, y)
+-        py_iquo(x, y)
+-        py_iquo2(x, y)
+-        py_li(x, n, parent)
+-        py_li2(x)
+         py_psi(x)
+         py_psi2(n, x)
+ 
+-        int py_int_length(x) except -1
+-
+         py_eval_constant(unsigned serial, parent)
+         py_eval_unsigned_infinity()
+         py_eval_infinity()
+@@ -583,8 +569,6 @@ cdef extern from "pynac_wrap.h":
+         stdstring* py_latex_fderivative(unsigned id, params, args)
+         paramset_to_PyTuple(const_paramset_ref s)
+ 
+-        py_rational_power_parts(basis, exp)
+-
+     py_funcs_struct py_funcs "GiNaC::py_funcs"
+ 
+ cdef extern from "pynac/order.h":
+diff --git a/src/sage/libs/pynac/pynac.pyx b/src/sage/libs/pynac/pynac.pyx
+index f303184..419cc47 100644
+--- a/src/sage/libs/pynac/pynac.pyx
++++ b/src/sage/libs/pynac/pynac.pyx
+@@ -2432,23 +2432,18 @@ def init_function_table():
+     called before Pynac is used; otherwise, there will be segfaults.
+     """
+ 
+-    py_funcs.py_binomial_int = &py_binomial_int
+-    py_funcs.py_binomial = &py_binomial
+     py_funcs.py_gcd = &py_gcd
+     py_funcs.py_lcm = &py_lcm
+     py_funcs.py_real = &py_real
+     py_funcs.py_imag = &py_imag
+     py_funcs.py_numer = &py_numer
+     py_funcs.py_denom = &py_denom
+-    py_funcs.py_conjugate = &py_conjugate
+ 
+     py_funcs.py_is_rational = &py_is_rational
+-    py_funcs.py_is_crational = &py_is_crational
+     py_funcs.py_is_real = &py_is_real
+     py_funcs.py_is_integer = &py_is_integer
+     py_funcs.py_is_equal = &py_is_equal
+     py_funcs.py_is_even = &py_is_even
+-    py_funcs.py_is_cinteger = &py_is_cinteger
+     py_funcs.py_is_prime = &py_is_prime
+     py_funcs.py_is_exact = &py_is_exact
+ 
+@@ -2462,7 +2457,6 @@ def init_function_table():
+     py_funcs.py_mpq_from_rational = &py_mpq_from_rational
+ 
+     py_funcs.py_float = &py_float
+-    py_funcs.py_RDF_from_double = &py_RDF_from_double
+ 
+     py_funcs.py_factorial = &py_factorial
+     py_funcs.py_doublefactorial = &py_doublefactorial
+@@ -2486,23 +2480,14 @@ def init_function_table():
+     py_funcs.py_asinh = &py_asinh
+     py_funcs.py_acosh = &py_acosh
+     py_funcs.py_atanh = &py_atanh
+-    py_funcs.py_tgamma = &py_tgamma
+-    py_funcs.py_lgamma = &py_lgamma
+     py_funcs.py_isqrt = &py_isqrt
+     py_funcs.py_sqrt = &py_sqrt
+-    py_funcs.py_abs = &py_abs
+     py_funcs.py_mod = &py_mod
+     py_funcs.py_smod = &py_smod
+     py_funcs.py_irem = &py_irem
+-    py_funcs.py_iquo = &py_iquo
+-    py_funcs.py_iquo2 = &py_iquo2
+-    py_funcs.py_li = &py_li
+-    py_funcs.py_li2 = &py_li2
+     py_funcs.py_psi = &py_psi
+     py_funcs.py_psi2 = &py_psi2
+ 
+-    py_funcs.py_int_length = &py_int_length
+-
+     py_funcs.py_eval_constant = &py_eval_constant
+     py_funcs.py_eval_unsigned_infinity = &py_eval_unsigned_infinity
+     py_funcs.py_eval_infinity = &py_eval_infinity
+@@ -2531,7 +2516,6 @@ def init_function_table():
+     py_funcs.py_print_fderivative =  &py_print_fderivative
+     py_funcs.py_latex_fderivative =  &py_latex_fderivative
+     py_funcs.paramset_to_PyTuple = &paramset_to_PyTuple
+-    py_funcs.py_rational_power_parts = &py_rational_power_parts
+ 
+ init_function_table()
+ init_pynac_I()
+
+diff --git a/src/sage/functions/other.py b/src/sage/functions/other.py
+index 81cd485..931cecc 100644
+--- a/src/sage/functions/other.py
++++ b/src/sage/functions/other.py
+@@ -688,7 +688,6 @@ class Function_gamma(GinacFunction):
+             :meth:`sage.functions.other.gamma`
+         """
+         GinacFunction.__init__(self, 'gamma', latex_name=r"\Gamma",
+-                               ginac_name='tgamma',
+                                conversions={'mathematica':'Gamma',
+                                             'maple':'GAMMA',
+                                             'sympy':'gamma',
+diff --git a/src/sage/libs/pynac/pynac.pxd b/src/sage/libs/pynac/pynac.pxd
+index 1739067..d4afc4e 100644
+--- a/src/sage/libs/pynac/pynac.pxd
++++ b/src/sage/libs/pynac/pynac.pxd
+@@ -362,7 +362,7 @@ cdef extern from "pynac_wrap.h":
+     GEx g_zeta2 "GiNaC::zeta" (GEx m, GEx s)            except + # alternating Euler sum
+     GEx g_stieltjes "GiNaC::stieltjes" (GEx m)          except + # Stieltjes constants
+     GEx g_zetaderiv "GiNaC::zetaderiv" (GEx n, GEx x)   except + # derivatives of Riemann's zeta function
+-    GEx g_tgamma "GiNaC::tgamma" (GEx x)                except + # gamma function
++    GEx g_gamma "GiNaC::gamma" (GEx x)                  except + # gamma function
+     GEx g_lgamma "GiNaC::lgamma" (GEx x)                except + # logarithm of gamma function
+     GEx g_beta "GiNaC::beta" (GEx x, GEx y)             except + # beta function (tgamma(x)*tgamma(y)/tgamma(x+y))
+     GEx g_psi "GiNaC::psi" (GEx x)                      except + # psi (digamma) function
+diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
+index dfb8751..52303d1 100644
+--- a/src/sage/symbolic/expression.pyx
++++ b/src/sage/symbolic/expression.pyx
+@@ -8917,7 +8917,7 @@ cdef class Expression(CommutativeRingElement):
+         cdef GEx x
+         sig_on()
+         try:
+-            x = g_hold_wrapper(g_tgamma, self._gobj, hold)
++            x = g_hold_wrapper(g_gamma, self._gobj, hold)
+         finally:
+             sig_off()
+         return new_Expression_from_GEx(self._parent, x)

Copied: sagemath/repos/community-testing-x86_64/sagemath-python3-notebook.patch (from rev 273618, sagemath/trunk/sagemath-python3-notebook.patch)
===================================================================
--- community-testing-x86_64/sagemath-python3-notebook.patch	                        (rev 0)
+++ community-testing-x86_64/sagemath-python3-notebook.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,27 @@
+diff --git a/src/bin/sage-notebook b/src/bin/sage-notebook
+index 74192da240..0ede281aad 100755
+--- a/src/bin/sage-notebook
++++ b/src/bin/sage-notebook
+@@ -96,8 +96,7 @@ class NotebookJupyter(object):
+         if not have_prerequisites():
+             print(self.PREREQUISITE_ERROR)
+             raise SystemExit(1)
+-        from notebook.notebookapp import main
+-        main(argv)
++        os.execvp('jupyter-notebook', ['jupyter-notebook'] + argv)
+ 
+ 
+ class NotebookJupyterlab(object):
+diff --git a/src/sage/repl/ipython_kernel/install.py b/src/sage/repl/ipython_kernel/install.py
+index 3912b8cdf5..bd40cdadda 100644
+--- a/src/sage/repl/ipython_kernel/install.py
++++ b/src/sage/repl/ipython_kernel/install.py
+@@ -280,7 +280,6 @@ def have_prerequisites(debug=True):
+         True
+     """
+     try:
+-        from notebook.notebookapp import NotebookApp
+         return True
+     except ImportError:
+         if debug:
+

Copied: sagemath/repos/community-testing-x86_64/sagemath-threejs.patch (from rev 273618, sagemath/trunk/sagemath-threejs.patch)
===================================================================
--- community-testing-x86_64/sagemath-threejs.patch	                        (rev 0)
+++ community-testing-x86_64/sagemath-threejs.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,11 @@
+--- a/src/sage/repl/rich_output/display_manager.py
++++ b/src/sage/repl/rich_output/display_manager.py
+@@ -744,7 +744,7 @@ class DisplayManager(SageObject):
+         """
+         if online:
+             from sage.misc.package import installed_packages
+-            version = installed_packages()['threejs']
++            version = 'r80'
+             return """
+ <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/build/three.min.js"></script>
+ <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/examples/js/controls/OrbitControls.js"></script>

Copied: sagemath/repos/community-testing-x86_64/test-optional.patch (from rev 273618, sagemath/trunk/test-optional.patch)
===================================================================
--- community-testing-x86_64/test-optional.patch	                        (rev 0)
+++ community-testing-x86_64/test-optional.patch	2017-12-10 19:13:16 UTC (rev 273619)
@@ -0,0 +1,25 @@
+--- src/sage/doctest/control.py.orig       2016-10-20 19:39:53.714618246 +0200
++++ src/sage/doctest/control.py    2016-10-20 19:40:15.158049920 +0200
+@@ -320,22 +320,6 @@
+             if "all" in options.optional:
+                 # Special case to run all optional tests
+                 options.optional = True
+-            else:
+-                # We replace the 'optional' tag by all optional
+-                # packages for which the installed version matches the
+-                # latest available version (this implies in particular
+-                # that the package is actually installed).
+-                if 'optional' in options.optional:
+-                    options.optional.discard('optional')
+-                    from sage.misc.package import list_packages
+-                    for pkg in list_packages('optional', local=True).values():
+-                        if pkg['installed_version'] == pkg['remote_version']:
+-                            options.optional.add(pkg['name'])
+-
+-                # Check that all tags are valid
+-                for o in options.optional:
+-                    if not optionaltag_regex.search(o):
+-                        raise ValueError('invalid optional tag {!r}'.format(o))
+ 
+         self.options = options
+         self.files = args



More information about the arch-commits mailing list