[arch-commits] Commit in sagemath/repos (16 files)
Antonio Rojas
arojas at archlinux.org
Wed May 15 21:31:13 UTC 2019
Date: Wednesday, May 15, 2019 @ 21:31:13
Author: arojas
Revision: 467483
archrelease: copy trunk to community-staging-x86_64
Added:
sagemath/repos/community-staging-x86_64/
sagemath/repos/community-staging-x86_64/PKGBUILD
(from rev 467482, sagemath/trunk/PKGBUILD)
sagemath/repos/community-staging-x86_64/fes02.patch
(from rev 467482, sagemath/trunk/fes02.patch)
sagemath/repos/community-staging-x86_64/latte-count.patch
(from rev 467482, sagemath/trunk/latte-count.patch)
sagemath/repos/community-staging-x86_64/package.patch
(from rev 467482, sagemath/trunk/package.patch)
sagemath/repos/community-staging-x86_64/sagemath-cremona.patch
(from rev 467482, sagemath/trunk/sagemath-cremona.patch)
sagemath/repos/community-staging-x86_64/sagemath-ecl-sigfpe.patch
(from rev 467482, sagemath/trunk/sagemath-ecl-sigfpe.patch)
sagemath/repos/community-staging-x86_64/sagemath-env.patch
(from rev 467482, sagemath/trunk/sagemath-env.patch)
sagemath/repos/community-staging-x86_64/sagemath-gap-4.10.1.patch
(from rev 467482, sagemath/trunk/sagemath-gap-4.10.1.patch)
sagemath/repos/community-staging-x86_64/sagemath-linbox-1.6.patch
(from rev 467482, sagemath/trunk/sagemath-linbox-1.6.patch)
sagemath/repos/community-staging-x86_64/sagemath-python3-notebook.patch
(from rev 467482, sagemath/trunk/sagemath-python3-notebook.patch)
sagemath/repos/community-staging-x86_64/sagemath-singular-4.1.2.patch
(from rev 467482, sagemath/trunk/sagemath-singular-4.1.2.patch)
sagemath/repos/community-staging-x86_64/sagemath-sphinx-1.8.patch
(from rev 467482, sagemath/trunk/sagemath-sphinx-1.8.patch)
sagemath/repos/community-staging-x86_64/sagemath-threejs-100.patch
(from rev 467482, sagemath/trunk/sagemath-threejs-100.patch)
sagemath/repos/community-staging-x86_64/sagemath-threejs.patch
(from rev 467482, sagemath/trunk/sagemath-threejs.patch)
sagemath/repos/community-staging-x86_64/test-optional.patch
(from rev 467482, sagemath/trunk/test-optional.patch)
---------------------------------+
PKGBUILD | 167 ++++++++++++++++
fes02.patch | 57 +++++
latte-count.patch | 89 ++++++++
package.patch | 39 +++
sagemath-cremona.patch | 31 +++
sagemath-ecl-sigfpe.patch | 147 ++++++++++++++
sagemath-env.patch | 141 ++++++++++++++
sagemath-gap-4.10.1.patch | 381 ++++++++++++++++++++++++++++++++++++++
sagemath-linbox-1.6.patch | 191 +++++++++++++++++++
sagemath-python3-notebook.patch | 27 ++
sagemath-singular-4.1.2.patch | 102 ++++++++++
sagemath-sphinx-1.8.patch | 28 ++
sagemath-threejs-100.patch | 52 +++++
sagemath-threejs.patch | 11 +
test-optional.patch | 25 ++
15 files changed, 1488 insertions(+)
Copied: sagemath/repos/community-staging-x86_64/PKGBUILD (from rev 467482, sagemath/trunk/PKGBUILD)
===================================================================
--- community-staging-x86_64/PKGBUILD (rev 0)
+++ community-staging-x86_64/PKGBUILD 2019-05-15 21:31:13 UTC (rev 467483)
@@ -0,0 +1,167 @@
+# 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>
+
+pkgbase=sagemath
+pkgname=(sagemath sagemath-jupyter)
+pkgver=8.7
+pkgrel=3
+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 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-pplpy python2-future
+ gap flintqs lcalc lrcalc arb eclib zn_poly gd python2-cvxopt pynac linbox m4rie rubiks pari-galdata pari-seadata-small planarity rankwidth tachyon
+ sage-data-combinatorial_designs sage-data-elliptic_curves sage-data-graphs sage-data-polytopes_db sage-data-conway_polynomials
+ iml libgiac libhomfly libbraiding three.js)
+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'
+ 'coxeter: Coxeter groups implementation'
+ 'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes'
+ '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'
+ 'shared_meataxe: faster matrix arithmetic over finite fields' 'openblas: faster linear algebra'
+ 'sirocco: for computing the fundamental group of the complement of a plane curve' 'primecount: faster prime_pi implementation'
+ 'dot2tex: for displaying some diagrams' 'cryptominisat5: SAT solver' 'python2-pycosat: picosat SAT solver'
+ 'python2-pip: to install optional packages with sage -pip')
+makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc sirocco
+ mcqd coxeter bliss tdlib python2-pkgconfig shared_meataxe libfes primecount)
+source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
+ sagemath-env.patch
+ package.patch
+ latte-count.patch
+ sagemath-python3-notebook.patch
+ test-optional.patch
+ fes02.patch
+ sagemath-threejs.patch
+ sagemath-cremona.patch
+ sagemath-sphinx-1.8.patch
+ sagemath-singular-4.1.2.patch
+ sagemath-ecl-sigfpe.patch
+ sagemath-gap-4.10.1.patch
+ sagemath-threejs-100.patch
+ sagemath-linbox-1.6.patch)
+sha256sums=('263c3b3fc956b8bebc532f3b51e68c1b0d559d3b7e7c9fadffdfc0f4dbae18ab'
+ 'e0e36f2a39b634a76e1c3ad9a31f9ab60e734dd53b43203557b76613277d53b9'
+ 'b1068a8d5750051c2b5cfcb89d3d5870cf4233ab445e71c398543fb8b1e6281a'
+ 'b66d5bb692159910cec83c80262c43a687d3a678010c7ae4c7070f7cf3a0d5cb'
+ '12cd410035ae644c2495b0dcd3a5138133a471ecc07912d37114c46ee837eb0e'
+ 'f12bd2a53ad51549015093aacc89978f4d796d9ab5bcd3d737aa0d57a5815b54'
+ '7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94'
+ 'd3c50256cfcf84a90336647f8a1164386b6b8034f47c45361d57be487e92d2c1'
+ '4c6df9e4e5a7b29ecf6189eda3e5a79f69b6e1b4d29c1b9559663149b8c0af96'
+ '22f5e44a42c8276025b8512f45cac1c36d576c29c7fd9d36fde8b19ff87867d8'
+ '961bfb5694b67d425d21240d71490cb71714b5207c23448c89be0966512ff8f9'
+ 'a42f3b152b1aedb8abf16bc70971419919d1fe30328574e7fef8305f9d07d938'
+ '9ec56a3788e32c54f35abeaeedf7cadf6670fa10d39007050b23b93d3c35278e'
+ '3ee624bb47f757516a860799d817168fe9cf74e603416e18e70c93c692259242'
+ '7e126c73d12c39be9012a66f979897fa630d540d30906dadff6c1384af4ec166')
+
+prepare(){
+ cd sage-$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
+# 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 three.js plotting backend
+ patch -p1 -i ../sagemath-threejs.patch
+# fix introspection with sphinx 1.8
+ patch -p1 -i ../sagemath-sphinx-1.8.patch
+# port to GAP 4.10.1 API changes
+ patch -p1 -i ../sagemath-gap-4.10.1.patch
+# fix build with linbox 1.6
+ patch -p1 -i ../sagemath-linbox-1.6.patch
+
+# Upstream patches
+# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
+ patch -p1 -i ../fes02.patch
+# use Features to detect Cremona databases https://trac.sagemath.org/ticket/25825
+ patch -p1 -i ../sagemath-cremona.patch
+# Fixes for singular 4.1.2 https://trac.sagemath.org/ticket/25993
+ patch -p1 -i ../sagemath-singular-4.1.2.patch
+# Fix SIGFPE crashes with ecl 16.1.3 https://trac.sagemath.org/ticket/22191
+ patch -p1 -i ../sagemath-ecl-sigfpe.patch
+# Fix rendering with three.js r100 https://trac.sagemath.org/ticket/26718
+ patch -p1 -i ../sagemath-threejs-100.patch
+
+# use python2
+ sed -e 's|sage-python23|python2|' -e 's|#!/usr/bin/env python\b|#!/usr/bin/env 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\b|exec ipython2|' -e 's|cygdb|cygdb2|g' -i src/bin/sage
+ sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython
+ sed -e 's|"python"|"python2"|' -i src/sage/env.py
+}
+
+
+build() {
+ cd sage-$pkgver/src
+
+ export CC=gcc
+ export SAGE_ROOT="$PWD"
+ export SAGE_SRC="$PWD"
+ export SAGE_NUM_THREADS=10
+ python2 setup.py build
+}
+
+package_sagemath() {
+ optdepends+=('sagemath-jupyter: Jupyter kernel')
+
+ cd sage-$pkgver/src
+
+ export SAGE_ROOT="$PWD"
+ export SAGE_LOCAL="/usr"
+ export SAGE_EXTCODE="$PWD"/ext
+ python2 setup.py install --root="$pkgdir" --optimize=1
+
+ mkdir -p "$pkgdir"/usr/bin
+ cp bin/{sage,math-readline} "$pkgdir"/usr/bin
+ for _i in cachegrind callgrind cleaner coverage coverageall cython env eval grep grepdoc inline-fortran ipynb2rst \
+ ipython massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2sws rst2txt run \
+ run-cython runtests startuptime.py sws2rst valgrind version.sh
+ do
+ cp bin/sage-$_i "$pkgdir"/usr/bin
+ done
+
+ mkdir -p "$pkgdir"/usr/share/sage
+ cp -r ext "$pkgdir"/usr/share/sage
+
+# Remove sage_setup
+ rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
+
+# Split jupyter kernel
+ rm -r "$pkgdir"/usr/share/jupyter
+}
+
+package_sagemath-jupyter() {
+ pkgdesc='Jupyter kernel for SageMath'
+ depends=(sagemath python2-jupyter_client python2-ipywidgets jsmol)
+ optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter')
+
+ cd sage-$pkgver/src
+
+ export SAGE_ROOT="$PWD"
+ export SAGE_LOCAL="/usr"
+
+ python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update(prefix='$pkgdir/usr')"
+# fix symlinks to assets
+ for _i in $(ls ext/notebook-ipython); do
+ rm "$pkgdir"/usr/share/jupyter/kernels/sagemath/$_i
+ ln -s /usr/share/sage/ext/notebook-ipython/$_i "$pkgdir"/usr/share/jupyter/kernels/sagemath/
+ done
+}
Copied: sagemath/repos/community-staging-x86_64/fes02.patch (from rev 467482, sagemath/trunk/fes02.patch)
===================================================================
--- community-staging-x86_64/fes02.patch (rev 0)
+++ community-staging-x86_64/fes02.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -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-staging-x86_64/latte-count.patch (from rev 467482, sagemath/trunk/latte-count.patch)
===================================================================
--- community-staging-x86_64/latte-count.patch (rev 0)
+++ community-staging-x86_64/latte-count.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -0,0 +1,89 @@
+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
+@@ -94,7 +94,7 @@ 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: ...
+@@ -113,7 +113,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False,
+ # Check that LattE is present
+ Latte().require()
+
+- args = ['count']
++ args = ['latte-count']
+ if ehrhart_polynomial and multivariate_generating_function:
+ raise ValueError
+ if ehrhart_polynomial:
+diff --git a/src/sage/features/latte.py b/src/sage/features/latte.py
+index 63d227fd35..040a5cf1f9 100644
+--- a/src/sage/features/latte.py
++++ b/src/sage/features/latte.py
+@@ -10,10 +10,10 @@ from . import Executable, Feature, FeatureTestResult
+
+ class Latte_count(Executable):
+ r"""
+- Feature for the executable ``count`` from the LattE suite.
++ Feature for the executable ``latte-count`` from the LattE suite.
+ """
+ def __init__(self):
+- Executable.__init__(self, "count", executable="count", spkg="latte_int", url="https://www.math.ucdavis.edu/~latte/software.php")
++ Executable.__init__(self, "latte-count", executable="latte-count", spkg="latte_int", url="https://www.math.ucdavis.edu/~latte/software.php")
+
+ class Latte_integrate(Executable):
+ r"""
+
Copied: sagemath/repos/community-staging-x86_64/package.patch (from rev 467482, sagemath/trunk/package.patch)
===================================================================
--- community-staging-x86_64/package.patch (rev 0)
+++ community-staging-x86_64/package.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -0,0 +1,39 @@
+--- 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
+@@ -335,7 +335,7 @@
+ Use the framework provided by :mod:`sage.features` to check
+ whether a library is installed and functional.
+ """
+- return any(p.split('-')[0] == package for p in installed_packages(exclude_pip))
++ return True
+
+
+ def package_versions(package_type, local=False):
+--- 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 list_packages
+
+-all_packages = list_packages(local=True)
+-
+
+ class CythonizeExtension(Extension):
+ """
+@@ -76,15 +74,7 @@
+ condition = kwds.pop("condition")
+ except KeyError:
+ pkg = kwds.pop("package")
+- from sage.misc.package import is_package_installed
+- 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-staging-x86_64/sagemath-cremona.patch (from rev 467482, sagemath/trunk/sagemath-cremona.patch)
===================================================================
--- community-staging-x86_64/sagemath-cremona.patch (rev 0)
+++ community-staging-x86_64/sagemath-cremona.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -0,0 +1,31 @@
+diff --git a/src/sage/databases/cremona.py b/src/sage/databases/cremona.py
+index 3f8dd62..ed5726a 100644
+--- a/src/sage/databases/cremona.py
++++ b/src/sage/databases/cremona.py
+@@ -53,7 +53,7 @@ from sage.misc.prandom import randint
+
+ import sage.schemes.elliptic_curves.constructor as elliptic
+ from .sql_db import SQLDatabase, verify_column
+-from sage.misc.package import is_package_installed
++from sage.features.databases import DatabaseCremona
+ from sage.env import CREMONA_MINI_DATA_DIR, CREMONA_LARGE_DATA_DIR
+ from sage.misc.all import walltime
+
+@@ -835,7 +835,7 @@ class MiniCremonaDatabase(SQLDatabase):
+ if N < self.largest_conductor():
+ message = "There is no elliptic curve with label " + label \
+ + " in the database"
+- elif is_package_installed('database_cremona_ellcurve'):
++ elif DatabaseCremona().is_present():
+ message = "There is no elliptic curve with label " + label \
+ + " in the currently available databases"
+ else:
+@@ -1683,7 +1683,7 @@ def CremonaDatabase(name=None,mini=None,set_global=None):
+ if name is None and not set_global:
+ return _db
+ if set_global and name is None:
+- if is_package_installed('database_cremona_ellcurve'):
++ if DatabaseCremona().is_present():
+ name = 'cremona'
+ else:
+ name = 'cremona mini'
Copied: sagemath/repos/community-staging-x86_64/sagemath-ecl-sigfpe.patch (from rev 467482, sagemath/trunk/sagemath-ecl-sigfpe.patch)
===================================================================
--- community-staging-x86_64/sagemath-ecl-sigfpe.patch (rev 0)
+++ community-staging-x86_64/sagemath-ecl-sigfpe.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -0,0 +1,147 @@
+diff --git a/src/sage/libs/ecl.pyx b/src/sage/libs/ecl.pyx
+index e408866..fa24ac0 100644
+--- a/src/sage/libs/ecl.pyx
++++ b/src/sage/libs/ecl.pyx
+@@ -16,7 +16,7 @@ from __future__ import print_function, absolute_import
+ #adapted to work with pure Python types.
+
+ from libc.stdlib cimport abort
+-from libc.signal cimport SIGINT, SIGBUS, SIGSEGV, SIGCHLD
++from libc.signal cimport SIGINT, SIGBUS, SIGSEGV, SIGCHLD, SIGFPE
+ from libc.signal cimport raise_ as signal_raise
+ from posix.signal cimport sigaction, sigaction_t
+ cimport cysignals.signals
+@@ -48,9 +48,14 @@ cdef extern from "eclsig.h":
+ void ecl_sig_off()
+ cdef sigaction_t ecl_sigint_handler
+ cdef sigaction_t ecl_sigbus_handler
++ cdef sigaction_t ecl_sigfpe_handler
+ cdef sigaction_t ecl_sigsegv_handler
+ cdef mpz_t ecl_mpz_from_bignum(cl_object obj)
+ cdef cl_object ecl_bignum_from_mpz(mpz_t num)
++ cdef int fegetexcept()
++ cdef int feenableexcept(int)
++ cdef int fedisableexcept(int)
++ cdef int ecl_feflags
+
+ cdef cl_object string_to_object(char * s):
+ return ecl_read_from_cstring(s)
+@@ -239,6 +244,7 @@ def init_ecl():
+ global ecl_has_booted
+ cdef char *argv[1]
+ cdef sigaction_t sage_action[32]
++ cdef int sage_fpes
+ cdef int i
+
+ if ecl_has_booted:
+@@ -258,6 +264,8 @@ def init_ecl():
+ for i in range(1,32):
+ sigaction(i, NULL, &sage_action[i])
+
++ sage_fpes = fegetexcept()
++
+ #initialize ECL
+ ecl_set_option(ECL_OPT_SIGNAL_HANDLING_THREAD, 0)
+ cl_boot(1, argv)
+@@ -265,8 +273,12 @@ def init_ecl():
+ #save signal handler from ECL
+ sigaction(SIGINT, NULL, &ecl_sigint_handler)
+ sigaction(SIGBUS, NULL, &ecl_sigbus_handler)
++ sigaction(SIGFPE, NULL, &ecl_sigfpe_handler)
+ sigaction(SIGSEGV, NULL, &ecl_sigsegv_handler)
+
++ #save ECL's floating point exception flags
++ ecl_feflags = fegetexcept()
++
+ #verify that no SIGCHLD handler was installed
+ cdef sigaction_t sig_test
+ sigaction(SIGCHLD, NULL, &sig_test)
+@@ -277,6 +289,9 @@ def init_ecl():
+ for i in range(1,32):
+ sigaction(i, &sage_action[i], NULL)
+
++ fedisableexcept(ecl_feflags)
++ feenableexcept(sage_fpes)
++
+ #initialise list of objects and bind to global variable
+ # *SAGE-LIST-OF-OBJECTS* to make it rooted in the reachable tree for the GC
+ list_of_objects=cl_cons(Cnil,cl_cons(Cnil,Cnil))
+@@ -320,7 +335,6 @@ def init_ecl():
+ (values nil (princ-to-string cnd)))))
+ """))
+ safe_funcall_clobj=cl_eval(string_to_object(b"(symbol-function 'sage-safe-funcall)"))
+-
+ ecl_has_booted = 1
+
+ cdef cl_object ecl_safe_eval(cl_object form) except NULL:
+diff --git a/src/sage/libs/eclsig.h b/src/sage/libs/eclsig.h
+index f9f2690..a7e1f40 100644
+--- a/src/sage/libs/eclsig.h
++++ b/src/sage/libs/eclsig.h
+@@ -9,24 +9,66 @@
+
+
+ #include <signal.h>
++
++/* Rummage around to determine how ECL was configured */
++#define ECL_AVOID_FPE_H /* Prevent some local includes */
++#include <ecl/config-internal.h>
++
++#ifdef HAVE_FENV_H
++#include <fenv.h>
++#ifndef FE_ALL_EXCEPT
++#define FE_ALL_EXCEPT FE_DIVBYZERO | FE_OVERFLOW | FE_UNDERFLOW | FE_INVALID
++#endif
++#else
++#ifndef FE_ALL_EXCEPT
++#define FE_ALL_EXCEPT 0
++#endif
++#define feclearexcept(flags) do {} while (0)
++#endif
++
++#ifndef HAVE_FEENABLEEXCEPT
++/* These are GNU extensions */
++#define fegetexcept() 0
++#define feenablexcept(flags) do {} while (0)
++#define fdisableexcept(flags) do {} while (0)
++#endif
++
+ static struct sigaction ecl_sigint_handler;
+ static struct sigaction ecl_sigbus_handler;
++static struct sigaction ecl_sigfpe_handler;
+ static struct sigaction ecl_sigsegv_handler;
+ static struct sigaction sage_sigint_handler;
+ static struct sigaction sage_sigbus_handler;
++static struct sigaction sage_sigfpe_handler;
+ static struct sigaction sage_sigsegv_handler;
++static int ecl_feflags;
++static int sage_feflags;
+
+ static inline void set_ecl_signal_handler(void)
+ {
+ sigaction(SIGINT, &ecl_sigint_handler, &sage_sigint_handler);
+ sigaction(SIGBUS, &ecl_sigbus_handler, &sage_sigbus_handler);
++ sigaction(SIGFPE, &ecl_sigfpe_handler, &sage_sigfpe_handler);
+ sigaction(SIGSEGV, &ecl_sigsegv_handler, &sage_sigsegv_handler);
++
++ /* first clear pending floating point exceptions, if any */
++ feclearexcept(FE_ALL_EXCEPT);
++
++ /* sage_feflags should be 0; we don't set them otherwise */
++ sage_feflags = fedisableexcept(FE_ALL_EXCEPT);
++ feenableexcept(ecl_feflags);
+ }
+
+ static inline void unset_ecl_signal_handler(void)
+ {
++ /* clear pending exceptions and restore previous exception mask */
++ feclearexcept(FE_ALL_EXCEPT);
++ ecl_feflags = fedisableexcept(FE_ALL_EXCEPT);
++ feenableexcept(sage_feflags);
++
+ sigaction(SIGINT, &sage_sigint_handler, NULL);
+ sigaction(SIGBUS, &sage_sigbus_handler, NULL);
++ sigaction(SIGFPE, &sage_sigfpe_handler, NULL);
+ sigaction(SIGSEGV, &sage_sigsegv_handler, NULL);
+ }
+
Copied: sagemath/repos/community-staging-x86_64/sagemath-env.patch (from rev 467482, sagemath/trunk/sagemath-env.patch)
===================================================================
--- community-staging-x86_64/sagemath-env.patch (rev 0)
+++ community-staging-x86_64/sagemath-env.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -0,0 +1,141 @@
+--- 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 +111,6 @@
+ }
+
+
+-# 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
+
+
+ # Don't execute the commands more than once for the same version of
+@@ -174,33 +174,9 @@
+ export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION
+
+ export SAGE_ROOT="$NEW_SAGE_ROOT"
++export SAGE_LOCAL='/usr'
++export SAGE_SCRIPTS_DIR='/usr/bin'
+
+-
+-# sage-env must know where the Sage's script files are.
+-# Note that SAGE_SCRIPTS_DIR is only used here, so it does not need to
+-# be exported.
+-if [ -z "$SAGE_SCRIPTS_DIR" ]; then
+- if [ -n "$SAGE_LOCAL" ] && [ -f "$SAGE_LOCAL/bin/sage-env-config" ]; then
+- SAGE_SCRIPTS_DIR="$SAGE_LOCAL/bin"
+- elif [ -f "$SAGE_ROOT/src/bin/sage-env-config" ]; then
+- SAGE_SCRIPTS_DIR="$SAGE_ROOT/src/bin"
+- else
+- echo >&2 "Error: You must set either the SAGE_LOCAL or SAGE_SCRIPTS_DIR environment variable to run this"
+- return 1
+- fi
+-elif [ ! -f "$SAGE_SCRIPTS_DIR/sage-env-config" ]; then
+- echo >&2 "Error: SAGE_SCRIPTS_DIR is set to a bad value:"
+- echo >&2 "SAGE_SCRIPTS_DIR=$SAGE_SCRIPTS_DIR"
+- echo >&2 "You must correct it or erase it and rerun this script"
+- return 1
+-fi
+-
+-# Set environment variables (like SAGE_LOCAL) depending on ./configure
+-. "$SAGE_SCRIPTS_DIR/sage-env-config"
+-if [ $? -ne 0 ]; then
+- echo >&2 "Error: failed to source $SAGE_SCRIPTS_DIR/sage-env-config"
+- return 1
+-fi
+
+ # The compilers are set in order of priority by
+ # 1) environment variables
+@@ -296,8 +296,8 @@
+ export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
+ export SAGE_SPKG_SCRIPTS="$SAGE_LOCAL/var/lib/sage/scripts"
+ export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
+-export SAGE_SRC="$SAGE_ROOT/src"
+-export SAGE_DOC_SRC="$SAGE_SRC/doc"
++export SAGE_SRC="$SAGE_LOCAL/lib/python2.7/site-packages"
++export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
+ export SAGE_DOC="$SAGE_SHARE/doc/sage"
+
+ if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
+@@ -409,28 +409,8 @@
+ 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="$DOT_SAGE/.python-eggs"
+- export PYTHON_EGG_CACHE
+-fi
+-
+-# Set PYTHONUSERBASE to avoid picking up non-Sage versions of
+-# Matplotlib, numpy, etc. See http://trac.sagemath.org/ticket/19612.
+-#
+-# For more history (it used to be PYTHONNOUSERSITE=yes which killed
+-# the ability to do "sage -pip install PACKAGE --user"), see
+-# http://trac.sagemath.org/ticket/14243 and
+-# http://trac.sagemath.org/ticket/18955.
+-
+-if [ "$PYTHONUSERBASE" = "" ]; then
+- PYTHONUSERBASE="$DOT_SAGE/local"
+- export PYTHONUSERBASE
+-fi
+-
+-if [ -n "$PYTHONHOME" ]; then
+- >&2 echo "Warning: PYTHONHOME must not be set when running Sage, clearing env..."
+- unset PYTHONHOME
+-fi
+
+ LDFLAGS="-L$SAGE_LOCAL/lib -Wl,-rpath,$SAGE_LOCAL/lib $LDFLAGS"
+ export LDFLAGS
+@@ -495,8 +495,6 @@
+ fi
+ fi
+
+-export MAXIMA_PREFIX="$SAGE_LOCAL"
+-export MAXIMA_USERDIR="$DOT_SAGE/maxima"
+
+ PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
+
+@@ -607,9 +607,6 @@
+ LD_LIBRARY_PATH="$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
Copied: sagemath/repos/community-staging-x86_64/sagemath-gap-4.10.1.patch (from rev 467482, sagemath/trunk/sagemath-gap-4.10.1.patch)
===================================================================
--- community-staging-x86_64/sagemath-gap-4.10.1.patch (rev 0)
+++ community-staging-x86_64/sagemath-gap-4.10.1.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -0,0 +1,381 @@
+diff --git a/src/sage/interfaces/tests.py b/src/sage/interfaces/tests.py
+index 6bcbfef..fc77f12 100644
+--- a/src/sage/interfaces/tests.py
++++ b/src/sage/interfaces/tests.py
+@@ -33,8 +33,8 @@ Test that write errors to stderr are handled gracefully by GAP
+ sage: kwds = dict(shell=True, stdout=f, stderr=f)
+ sage: subprocess.call("echo syntax error | ecl", **kwds)
+ 0
+- sage: subprocess.call("echo syntax error | gap", **kwds)
+- 0
++ sage: subprocess.call("echo syntax error | gap", **kwds) in (0, 1)
++ True
+ sage: subprocess.call("echo syntax error | gp", **kwds)
+ 0
+ sage: subprocess.call("echo syntax error | ipython", **kwds) in (0, 1, 120)
+diff --git a/src/sage/libs/gap/gap_includes.pxd b/src/sage/libs/gap/gap_includes.pxd
+index 864a13b..f624ccd 100644
+--- a/src/sage/libs/gap/gap_includes.pxd
++++ b/src/sage/libs/gap/gap_includes.pxd
+@@ -10,14 +10,14 @@
+ ###############################################################################
+
+
+-cdef extern from "<gap/system.h>":
++cdef extern from "gap/system.h" nogil:
+ ctypedef char Char
+ ctypedef int Int
+ ctypedef unsigned int UInt
+ ctypedef void* Obj
+
+
+-cdef extern from "<gap/ariths.h>":
++cdef extern from "gap/ariths.h" nogil:
+ Obj SUM(Obj, Obj)
+ Obj DIFF(Obj, Obj)
+ Obj PROD(Obj, Obj)
+@@ -28,12 +28,12 @@ cdef extern from "<gap/ariths.h>":
+ bint LT(Obj opL, Obj opR)
+
+
+-cdef extern from "<gap/bool.h>":
++cdef extern from "gap/bool.h" nogil:
+ cdef Obj GAP_True "True"
+ cdef Obj GAP_False "False"
+
+
+-cdef extern from "<gap/calls.h>":
++cdef extern from "gap/calls.h" nogil:
+ bint IS_FUNC(Obj)
+ Obj CALL_0ARGS(Obj f) # 0 arguments
+ Obj CALL_1ARGS(Obj f, Obj a1) # 1 argument
+@@ -45,49 +45,47 @@ cdef extern from "<gap/calls.h>":
+ Obj CALL_XARGS(Obj f, Obj args) # more than 6 arguments
+
+
+-cdef extern from "<gap/gasman.h>":
++cdef extern from "gap/gasman.h" nogil:
+ Obj NewBag "NewBag"(UInt type, UInt size)
+ void MarkBag(Obj bag)
+ UInt CollectBags(UInt size, UInt full)
+
+
+-cdef extern from "<gap/gasman_intern.h>":
++cdef extern from "gap/gasman_intern.h" nogil:
+ void CallbackForAllBags(void (*func)(Obj))
+
+
+-cdef extern from "<gap/gvars.h>":
++cdef extern from "gap/gvars.h" nogil:
+ UInt GVarName "GVarName"(char* name)
+ void AssGVar "AssGVar"(UInt gvar, Obj val)
+
+
+-cdef extern from "<gap/integer.h>":
++cdef extern from "gap/integer.h" nogil:
+ Int IS_INT(Obj)
+
+
+-cdef extern from "<gap/intobj.h>":
++cdef extern from "gap/intobj.h" nogil:
+ bint IS_INTOBJ(Obj obj)
+ Obj INTOBJ_INT(Int)
+ Int INT_INTOBJ(Obj)
+
+
+-cdef extern from "<gap/io.h>":
++cdef extern from "gap/io.h" nogil:
+ UInt OpenOutputStream(Obj stream)
+ UInt CloseOutput()
+
+
+-cdef extern from "<gap/libgap-api.h>":
+- ctypedef void (*CallbackFunc)()
+- void GAP_Initialize(int argc, char ** argv, char ** env,
+- CallbackFunc, CallbackFunc)
+- Obj GAP_EvalString(const char *) except *
+- Obj GAP_EvalStringNoExcept "GAP_EvalString"(const char *)
+- Obj GAP_ValueGlobalVariable(const char *)
+-
+-
+-cdef extern from "<gap/libgap-api.h>" nogil:
++cdef extern from "gap/libgap-api.h" nogil:
+ """
+ #define sig_GAP_Enter() {int t = GAP_Enter(); if (!t) sig_error();}
+ """
++ ctypedef void (*GAP_CallbackFunc)()
++ void GAP_Initialize(int argc, char ** argv,
++ GAP_CallbackFunc markBagsCallback, GAP_CallbackFunc errorCallback,
++ int handleSignals)
++ Obj GAP_EvalString(const char *) except *
++ Obj GAP_EvalStringNoExcept "GAP_EvalString"(const char *)
++ Obj GAP_ValueGlobalVariable(const char *)
+ cdef void GAP_EnterStack()
+ cdef void GAP_LeaveStack()
+ cdef int GAP_Enter() except 0
+@@ -96,7 +94,7 @@ cdef extern from "<gap/libgap-api.h>" nogil:
+ cdef int GAP_Error_Setjmp() except 0
+
+
+-cdef extern from "<gap/lists.h>":
++cdef extern from "gap/lists.h" nogil:
+ bint IS_LIST(Obj lst)
+ int LEN_LIST(Obj lst)
+ Obj ELM_LIST(Obj lst, int pos)
+@@ -104,15 +102,15 @@ cdef extern from "<gap/lists.h>":
+ void ASS_LIST(Obj lst, int pos, Obj elt)
+
+
+-cdef extern from "<gap/listfunc.h>":
++cdef extern from "gap/listfunc.h" nogil:
+ void AddList(Obj list, Obj obj)
+
+
+-cdef extern from "<gap/macfloat.h>":
++cdef extern from "gap/macfloat.h" nogil:
+ double VAL_MACFLOAT(Obj obj)
+
+
+-cdef extern from "<gap/objects.h>":
++cdef extern from "gap/objects.h" nogil:
+ bint IS_MUTABLE_OBJ(Obj obj)
+ Obj SHALLOW_COPY_OBJ(Obj obj)
+ Obj CopyObj(Obj obj, int mut)
+@@ -121,28 +119,34 @@ cdef extern from "<gap/objects.h>":
+ UInt TNUM_OBJ(Obj obj)
+ char* TNAM_OBJ(Obj obj)
+
+- cdef int T_INTPOS
+- cdef int T_INTNEG
+- cdef int T_RAT
+- cdef int T_CYC
+- cdef int T_FFE
+- cdef int T_PERM2
+- cdef int T_PERM4
+- cdef int T_BOOL
+- cdef int T_CHAR
+- cdef int T_FUNCTION
+- cdef int T_MACFLOAT
+- cdef int T_PLIST
+- cdef int T_PLIST_CYC
+- cdef int T_BLIST
+- cdef int T_STRING
+- cdef int T_COMOBJ
+- cdef int T_POSOBJ
+- cdef int T_DATOBJ
+- cdef int T_WPOBJ
+-
+-
+-cdef extern from "<gap/precord.h>":
++ cdef enum TNUM:
++ T_INT
++ T_INTPOS
++ T_INTNEG
++ T_RAT
++ T_CYC
++ T_FFE
++ T_MACFLOAT
++ T_PERM2
++ T_PERM4
++ T_TRANS2
++ T_TRANS4
++ T_PPERM2
++ T_PPERM4
++ T_BOOL
++ T_CHAR
++ T_FUNCTION
++ T_PLIST
++ T_PLIST_CYC
++ T_BLIST
++ T_STRING
++ T_COMOBJ
++ T_POSOBJ
++ T_DATOBJ
++ T_WPOBJ
++
++
++cdef extern from "gap/precord.h" nogil:
+ Obj NEW_PREC(int len)
+ int LEN_PREC(Obj rec)
+ int GET_RNAM_PREC(Obj rec, int i)
+@@ -150,14 +154,14 @@ cdef extern from "<gap/precord.h>":
+ void AssPRec(Obj rec, UInt rnam, Obj val)
+
+
+-cdef extern from "<gap/records.h>":
++cdef extern from "gap/records.h" nogil:
+ char* NAME_RNAM(UInt rnam)
+ bint IS_REC(Obj obj)
+ Obj ELM_REC(Obj rec, UInt rnam)
+ UInt RNamName(Char* name)
+
+
+-cdef extern from "<gap/stringobj.h>":
++cdef extern from "gap/stringobj.h" nogil:
+ char* CSTR_STRING(Obj list)
+ bint IS_STRING(Obj obj)
+ bint IsStringConv(Obj obj)
+diff --git a/src/sage/libs/gap/libgap.pyx b/src/sage/libs/gap/libgap.pyx
+index e78b88a..e66be59 100644
+--- a/src/sage/libs/gap/libgap.pyx
++++ b/src/sage/libs/gap/libgap.pyx
+@@ -232,15 +232,6 @@ from sage.misc.superseded import deprecated_function_alias, deprecation
+ ### Debugging ##############################################################
+ ############################################################################
+
+-
+-cdef void report(Obj bag):
+- print(TNAM_OBJ(bag), <int>SIZE_OBJ(bag))
+-
+-
+-cdef void print_gasman_objects():
+- CallbackForAllBags(report)
+-
+-
+ from sage.misc.lazy_import import is_during_startup
+ if is_during_startup():
+ import sys, traceback
+diff --git a/src/sage/libs/gap/util.pyx b/src/sage/libs/gap/util.pyx
+index 7f6a924..27609f8 100644
+--- a/src/sage/libs/gap/util.pyx
++++ b/src/sage/libs/gap/util.pyx
+@@ -14,19 +14,16 @@ Utility functions for GAP
+
+ from __future__ import print_function, absolute_import
+
+-import os
+-import signal
+-import warnings
++from libc.signal cimport signal, SIGCHLD, SIG_DFL
+ from posix.dlfcn cimport dlopen, dlclose, RTLD_NOW, RTLD_GLOBAL
+-from libc.string cimport strcpy, strlen
+
+ from cpython.exc cimport PyErr_Fetch, PyErr_Restore
+ from cpython.object cimport Py_LT, Py_LE, Py_EQ, Py_NE, Py_GT, Py_GE
+ from cpython.ref cimport PyObject, Py_XINCREF, Py_XDECREF
+-from cysignals.memory cimport sig_malloc
+-from cysignals.pysignals import containsignals
+-from cysignals.signals cimport sig_on, sig_off, sig_error
++from cysignals.signals cimport sig_on, sig_off
+
++import os
++import warnings
+ import sage.env
+
+ from .gap_includes cimport *
+@@ -105,7 +102,7 @@ cdef class ObjWrapper(object):
+ sage: hash(x)
+ 0
+ """
+- return <int>(self.value)
++ return <Py_hash_t>(self.value)
+
+
+ cdef ObjWrapper wrap_obj(Obj obj):
+@@ -197,7 +194,6 @@ def gap_root():
+
+ # To ensure that we call initialize_libgap only once.
+ cdef bint _gap_is_initialized = False
+-cdef extern char **environ
+
+
+ cdef char* _reset_error_output_cmd = """\
+@@ -216,33 +212,6 @@ MakeImmutable(libgap_errout);
+ """
+
+
+-cdef char** copy_environ(char** env):
+- """
+- Make a copy of the environment block given by ``env``.
+-
+- Returns a pointer to the copy, which is the caller's responsibility to
+- free.
+- """
+-
+- cdef char** env_copy
+- cdef int envc = 0;
+- cdef int idx
+- cdef size_t size
+-
+- while env[envc]:
+- envc += 1
+-
+- env_copy = <char**>sig_malloc((envc + 1) * sizeof(char*))
+-
+- for idx in range(envc):
+- size = strlen(env[idx]) + 1
+- env_copy[idx] = <char*>sig_malloc(size)
+- strcpy(env_copy[idx], env[idx])
+-
+- env_copy[envc] = NULL
+- return env_copy
+-
+-
+ cdef initialize():
+ """
+ Initialize the GAP library, if it hasn't already been
+@@ -253,7 +222,7 @@ cdef initialize():
+ sage: libgap(123) # indirect doctest
+ 123
+ """
+- global _gap_is_initialized, environ
++ global _gap_is_initialized
+ if _gap_is_initialized: return
+ # Hack to ensure that all symbols provided by libgap are loaded into the
+ # global symbol table
+@@ -268,10 +237,9 @@ cdef initialize():
+ "be loaded!")
+ dlclose(handle)
+
+- # Define argv and environ variables, which we will pass in to
++ # Define argv variable, which we will pass in to
+ # initialize GAP. Note that we must pass define the memory pool
+ # size!
+- cdef char** env
+ cdef char* argv[18]
+ argv[0] = "sage"
+ argv[1] = "-l"
+@@ -318,21 +286,15 @@ cdef initialize():
+
+ argv[argc] = NULL
+
+- env = copy_environ(environ)
+-
+- # Need to save/restore current SIGINT handling since GAP_Initialize
+- # currently clobbers it; it doesn't matter what we set SIGINT to
+- # temporarily.
+- with containsignals():
+- sig_on()
+- try:
+- # Initialize GAP and capture any error messages. The
+- # initialization just prints any errors and does not
+- # use the error handler.
+- GAP_Initialize(argc, argv, env, &gasman_callback,
+- &error_handler)
+- finally:
+- sig_off()
++ sig_on()
++ # Initialize GAP but disable their SIGINT handler
++ GAP_Initialize(argc, argv, gasman_callback, error_handler,
++ handleSignals=False)
++ sig_off()
++
++ # Disable GAP's SIGCHLD handler ChildStatusChanged(), which calls
++ # waitpid() on random child processes.
++ signal(SIGCHLD, SIG_DFL)
+
+ # Set the ERROR_OUTPUT global in GAP to an output stream in which to
+ # receive error output
+diff --git a/src/sage/tests/books/judson-abstract-algebra/sylow-sage.py b/src/sage/tests/books/judson-abstract-algebra/sylow-sage.py
+index b3312b8..6d81f0a 100644
+--- a/src/sage/tests/books/judson-abstract-algebra/sylow-sage.py
++++ b/src/sage/tests/books/judson-abstract-algebra/sylow-sage.py
+@@ -225,7 +225,7 @@ r"""
+
+ ~~~~~~~~~~~~~~~~~~~~~~ ::
+
+- sage: gap.version()
++ sage: gap.version() # random
+ '4.10.0'
+
+ ~~~~~~~~~~~~~~~~~~~~~~ ::
Copied: sagemath/repos/community-staging-x86_64/sagemath-linbox-1.6.patch (from rev 467482, sagemath/trunk/sagemath-linbox-1.6.patch)
===================================================================
--- community-staging-x86_64/sagemath-linbox-1.6.patch (rev 0)
+++ community-staging-x86_64/sagemath-linbox-1.6.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -0,0 +1,191 @@
+diff --git a/src/sage/libs/linbox/fflas.pxd b/src/sage/libs/linbox/fflas.pxd
+index f3a7ce37ea..7d8d64d3b5 100644
+--- a/src/sage/libs/linbox/fflas.pxd
++++ b/src/sage/libs/linbox/fflas.pxd
+@@ -64,8 +64,8 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h" namespace "FFPACK":
+ Modular_double.Element* A, size_t A_stride, int nullity)
+
+ Modular_double.Element Det (Modular_double F,
+- size_t nrows, size_t ncols,
+- Modular_double.Element* A, size_t A_stride)
++ Modular_double.Element det, size_t ncols,
++ Modular_double.Element* A, size_t A_stride, size_t* P, size_t* Q)
+
+ int Rank (Modular_double,
+ size_t nrows, size_t ncols,
+@@ -98,8 +98,8 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h" namespace "FFPACK":
+ Modular_float.Element* A, size_t A_stride, int nullity)
+
+ Modular_float.Element Det (Modular_float F,
+- size_t nrows, size_t ncols,
+- Modular_float.Element* A, size_t A_stride)
++ Modular_float.Element det, size_t ncols,
++ Modular_float.Element* A, size_t A_stride, size_t* P, size_t* Q)
+
+ int Rank (Modular_float,
+ size_t nrows, size_t ncols,
+diff --git a/src/sage/libs/linbox/linbox.pxd b/src/sage/libs/linbox/linbox.pxd
+index 35a3fa0125..a4bda24c0e 100644
+--- a/src/sage/libs/linbox/linbox.pxd
++++ b/src/sage/libs/linbox/linbox.pxd
+@@ -125,7 +125,7 @@ cdef extern from "linbox/solutions/methods.h" namespace "LinBox":
+ pass
+ cdef struct WiedemannTraits:
+ pass
+- cdef struct BlasEliminationTraits:
++ cdef struct DenseEliminationTraits:
+ pass
+ cdef struct SparseEliminationTraits:
+ pass
+@@ -135,7 +135,7 @@ cdef extern from "linbox/solutions/methods.h" namespace "LinBox":
+ ctypedef BlackboxSpecifier Blackbox
+ ctypedef EliminationSpecifier Elimination
+ ctypedef WiedemannTraits Wiedemann
+- ctypedef BlasEliminationTraits BlasElimination
++ ctypedef DenseEliminationTraits DenseElimination
+ ctypedef SparseEliminationTraits SparseElimination
+
+ cdef extern from "linbox/solutions/charpoly.h" namespace "LinBox":
+@@ -157,19 +157,20 @@ cdef extern from "linbox/algorithms/gauss.h":
+ unsigned long Ni,
+ unsigned long Nj)
+
+-cdef extern from "linbox/algorithms/echelon-form.h":
++cdef extern from "linbox/solutions/echelon.h":
+ ## template<class Field>
+ ## class EchelonFormDomain
+ cdef cppclass EchelonForm_Modular_double "LinBox::EchelonFormDomain<Givaro::Modular<double>>":
+ ctypedef double Element
+ EchelonForm_Modular_double(Modular_double)
+- int rowReducedEchelon(DenseMatrix_Modular_double&, const DenseMatrix_Modular_double&)
+
+ cdef cppclass EchelonForm_Modular_float "LinBox::EchelonFormDomain<Givaro::Modular<float>>":
+ ctypedef float Element
+ EchelonForm_Modular_float(Modular_float)
+- int rowReducedEchelon(DenseMatrix_Modular_float, const DenseMatrix_Modular_float)
+
++ int reducedRowEchelon(DenseMatrix_Modular_double, const DenseMatrix_Modular_double)
++ int reducedRowEchelon(DenseMatrix_Modular_float, const DenseMatrix_Modular_float)
++
+ cdef extern from "linbox/solutions/rank.h" namespace "LinBox":
+ unsigned long & rank (unsigned long&, DenseMatrix_integer)
+ unsigned long & rank (unsigned long&, SparseMatrix_integer)
+@@ -185,7 +186,7 @@ cdef extern from "linbox/solutions/solve.h" namespace "LinBox":
+ Integer &,
+ SparseMatrix_integer &,
+ DenseVector_integer &,
+- Method.BlasElimination) except +
++ Method.DenseElimination) except +
+
+ DenseVector_integer& solve (DenseVector_integer &,
+ Integer &,
+diff --git a/src/sage/matrix/matrix_integer_sparse.pyx b/src/sage/matrix/matrix_integer_sparse.pyx
+index 7fa386eab7..5937720a03 100644
+--- a/src/sage/matrix/matrix_integer_sparse.pyx
++++ b/src/sage/matrix/matrix_integer_sparse.pyx
+@@ -1081,7 +1081,7 @@ cdef class Matrix_integer_sparse(Matrix_sparse):
+ elif method == METHOD_WIEDEMANN:
+ linbox.solve(res[0], D, A[0], b[0], linbox.Method.Wiedemann())
+ elif method == METHOD_BLAS_ELIMINATION:
+- linbox.solve(res[0], D, A[0], b[0], linbox.Method.BlasElimination())
++ linbox.solve(res[0], D, A[0], b[0], linbox.Method.DenseElimination())
+ elif method == METHOD_SPARSE_ELIMINATION:
+ linbox.solve(res[0], D, A[0], b[0], linbox.Method.SparseElimination())
+ elif method == METHOD_BLACKBOX:
+@@ -1192,7 +1192,7 @@ cdef class Matrix_integer_sparse(Matrix_sparse):
+ if algo == METHOD_DEFAULT:
+ linbox.solve(res[0], D, A[0], b[0])
+ elif algo == METHOD_BLAS_ELIMINATION:
+- linbox.solve(res[0], D, A[0], b[0], linbox.Method.BlasElimination())
++ linbox.solve(res[0], D, A[0], b[0], linbox.Method.DenseElimination())
+ elif algo == METHOD_SPARSE_ELIMINATION:
+ linbox.solve(res[0], D, A[0], b[0], linbox.Method.SparseElimination())
+ elif algo == METHOD_BLACKBOX:
+diff --git a/src/sage/matrix/matrix_modn_dense_double.pyx b/src/sage/matrix/matrix_modn_dense_double.pyx
+index c4b1a46444..4f140ad239 100644
+--- a/src/sage/matrix/matrix_modn_dense_double.pyx
++++ b/src/sage/matrix/matrix_modn_dense_double.pyx
+@@ -25,7 +25,7 @@ from sage.libs.linbox.givaro cimport \
+
+ from sage.libs.linbox.linbox cimport \
+ DenseMatrix_Modular_double as BlasMatrix, \
+- EchelonForm_Modular_double as EchelonFormDomain
++ reducedRowEchelon
+
+ from sage.libs.linbox.fflas cimport \
+ fgemm, fgemv, Det, Rank, ReducedRowEchelonForm, applyP, \
+diff --git a/src/sage/matrix/matrix_modn_dense_float.pyx b/src/sage/matrix/matrix_modn_dense_float.pyx
+index 89d1a94ab2..198896259b 100644
+--- a/src/sage/matrix/matrix_modn_dense_float.pyx
++++ b/src/sage/matrix/matrix_modn_dense_float.pyx
+@@ -24,7 +24,7 @@ from sage.libs.linbox.givaro cimport \
+
+ from sage.libs.linbox.linbox cimport \
+ DenseMatrix_Modular_float as BlasMatrix, \
+- EchelonForm_Modular_float as EchelonFormDomain
++ reducedRowEchelon
+
+ from sage.libs.linbox.fflas cimport \
+ fgemm, fgemv, Det, Rank, ReducedRowEchelonForm, applyP, \
+diff --git a/src/sage/matrix/matrix_modn_dense_template.pxi b/src/sage/matrix/matrix_modn_dense_template.pxi
+index 6a5e164ede..7eb70dae86 100644
+--- a/src/sage/matrix/matrix_modn_dense_template.pxi
++++ b/src/sage/matrix/matrix_modn_dense_template.pxi
+@@ -207,7 +207,6 @@ cdef inline linbox_echelonize_efd(celement modulus, celement* entries, Py_ssize_
+ return 0,[]
+
+ cdef ModField *F = new ModField(<long>modulus)
+- cdef EchelonFormDomain *EF = new EchelonFormDomain(F[0])
+ cdef BlasMatrix *A = new BlasMatrix(F[0], <uint64_t>nrows, <uint64_t>ncols)
+ cdef BlasMatrix *E = new BlasMatrix(F[0], <uint64_t>nrows, <uint64_t>ncols)
+
+@@ -218,7 +217,7 @@ cdef inline linbox_echelonize_efd(celement modulus, celement* entries, Py_ssize_
+ for j in range(ncols):
+ A.setEntry(i, j, <ModField.Element>entries[i*ncols+j])
+
+- cdef int r = EF.rowReducedEchelon(E[0], A[0])
++ cdef int r = reducedRowEchelon(E[0], A[0])
+ for i in range(nrows):
+ for j in range(ncols):
+ entries[i*ncols+j] = <celement>E.getEntry(i,j)
+@@ -232,7 +231,7 @@ cdef inline linbox_echelonize_efd(celement modulus, celement* entries, Py_ssize_
+ ii = j+1
+ break
+
+- del F, A, E, EF
++ del F, A, E
+ return r, pivots
+
+ cdef inline celement *linbox_copy(celement modulus, celement *entries, Py_ssize_t nrows, Py_ssize_t ncols) except? NULL:
+@@ -265,7 +264,8 @@ cdef inline celement linbox_det(celement modulus, celement* entries, Py_ssize_t
+ cdef ModField *F = new ModField(<long>modulus)
+ cdef celement *cpy = linbox_copy(modulus, entries, nrows, ncols)
+ if nrows*ncols > 1000: sig_on()
+- d = <celement>Det(F[0], nrows, ncols, <ModField.Element*>cpy, ncols)
++ cdef ModField.Element det
++ d = <celement>Det(F[0], det, ncols, <ModField.Element*>cpy, ncols, <size_t*>NULL, <size_t*>NULL)
+ if nrows*ncols > 1000: sig_off()
+ sig_free(cpy)
+ del F
+diff --git a/src/sage/matrix/matrix_modn_sparse.pyx b/src/sage/matrix/matrix_modn_sparse.pyx
+index 241167ace4..8e65cbb532 100644
+--- a/src/sage/matrix/matrix_modn_sparse.pyx
++++ b/src/sage/matrix/matrix_modn_sparse.pyx
+@@ -1026,7 +1026,7 @@ cdef class Matrix_modn_sparse(matrix_sparse.Matrix_sparse):
+ elif method == METHOD_WIEDEMANN:
+ linbox.solve(res[0], D, A[0], b[0], linbox.Method.Wiedemann())
+ elif method == METHOD_BLAS_ELIMINATION:
+- linbox.solve(res[0], D, A[0], b[0], linbox.Method.BlasElimination())
++ linbox.solve(res[0], D, A[0], b[0], linbox.Method.DenseElimination())
+ elif method == METHOD_SPARSE_ELIMINATION:
+ linbox.solve(res[0], D, A[0], b[0], linbox.Method.SparseElimination())
+ elif method == METHOD_BLACKBOX:
+@@ -1137,7 +1137,7 @@ cdef class Matrix_modn_sparse(matrix_sparse.Matrix_sparse):
+ if algo == METHOD_DEFAULT:
+ linbox.solve(res[0], D, A[0], b[0])
+ elif algo == METHOD_BLAS_ELIMINATION:
+- linbox.solve(res[0], D, A[0], b[0], linbox.Method.BlasElimination())
++ linbox.solve(res[0], D, A[0], b[0], linbox.Method.DenseElimination())
+ elif algo == METHOD_SPARSE_ELIMINATION:
+ linbox.solve(res[0], D, A[0], b[0], linbox.Method.SparseElimination())
+ elif algo == METHOD_BLACKBOX:
Copied: sagemath/repos/community-staging-x86_64/sagemath-python3-notebook.patch (from rev 467482, sagemath/trunk/sagemath-python3-notebook.patch)
===================================================================
--- community-staging-x86_64/sagemath-python3-notebook.patch (rev 0)
+++ community-staging-x86_64/sagemath-python3-notebook.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -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
+@@ -95,8 +95,7 @@ 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
+@@ -303,7 +303,6 @@ def have_prerequisites(debug=True):
+ True
+ """
+ try:
+- from notebook.notebookapp import NotebookApp
+ return True
+ except ImportError:
+ if debug:
+
Copied: sagemath/repos/community-staging-x86_64/sagemath-singular-4.1.2.patch (from rev 467482, sagemath/trunk/sagemath-singular-4.1.2.patch)
===================================================================
--- community-staging-x86_64/sagemath-singular-4.1.2.patch (rev 0)
+++ community-staging-x86_64/sagemath-singular-4.1.2.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -0,0 +1,102 @@
+diff --git a/src/sage/libs/singular/function.pyx b/src/sage/libs/singular/function.pyx
+index 87342e8..9a0d37d 100644
+--- a/src/sage/libs/singular/function.pyx
++++ b/src/sage/libs/singular/function.pyx
+@@ -1258,7 +1258,7 @@ cdef class SingularFunction(SageObject):
+ Traceback (most recent call last):
+ ...
+ RuntimeError: error in Singular function call 'size':
+- Wrong number of arguments (got 2 arguments, arity code is 300)
++ Wrong number of arguments (got 2 arguments, arity code is 302)
+ sage: size('foobar', ring=P)
+ 6
+
+@@ -1667,17 +1667,17 @@ def singular_function(name):
+ Traceback (most recent call last):
+ ...
+ RuntimeError: error in Singular function call 'factorize':
+- Wrong number of arguments (got 0 arguments, arity code is 303)
++ Wrong number of arguments (got 0 arguments, arity code is 305)
+ sage: factorize(f, 1, 2)
+ Traceback (most recent call last):
+ ...
+ RuntimeError: error in Singular function call 'factorize':
+- Wrong number of arguments (got 3 arguments, arity code is 303)
++ Wrong number of arguments (got 3 arguments, arity code is 305)
+ sage: factorize(f, 1, 2, 3)
+ Traceback (most recent call last):
+ ...
+ RuntimeError: error in Singular function call 'factorize':
+- Wrong number of arguments (got 4 arguments, arity code is 303)
++ Wrong number of arguments (got 4 arguments, arity code is 305)
+
+ The Singular function ``list`` can be called with any number of
+ arguments::
+diff --git a/src/sage/algebras/letterplace/free_algebra_element_letterplace.pyx b/src/sage/algebras/letterplace/free_algebra_element_letterplace.pyx
+index 8f6576b477..deaf0f5769 100644
+--- a/src/sage/algebras/letterplace/free_algebra_element_letterplace.pyx
++++ b/src/sage/algebras/letterplace/free_algebra_element_letterplace.pyx
+@@ -447,7 +447,7 @@ cdef class FreeAlgebraElement_letterplace(AlgebraElement):
+ return True
+ for i from 0 <= i < p_d-s_d:
+ s_poly = singular_system("stest",s_poly,1,
+- A._degbound,A.__ngens,ring=P)
++ ring=P)
+ if P.monomial_divides(s_poly,p_poly):
+ return True
+ return False
+@@ -601,7 +601,7 @@ cdef class FreeAlgebraElement_letterplace(AlgebraElement):
+ # we must put the polynomials into the same ring
+ left._poly = A._current_ring(left._poly)
+ right._poly = A._current_ring(right._poly)
+- rshift = singular_system("stest",right._poly,left._poly.degree(),A._degbound,A.__ngens, ring=A._current_ring)
++ rshift = singular_system("stest",right._poly,left._poly.degree(), ring=A._current_ring)
+ return FreeAlgebraElement_letterplace(A,left._poly*rshift, check=False)
+
+ def __pow__(FreeAlgebraElement_letterplace self, int n, k):
+@@ -629,7 +629,7 @@ cdef class FreeAlgebraElement_letterplace(AlgebraElement):
+ q = p = self._poly
+ cdef int i
+ for i from 0<i<n:
+- q = singular_system("stest",q,d,A._degbound,A.__ngens,
++ q = singular_system("stest",q,d,
+ ring=A._current_ring)
+ p *= q
+ return FreeAlgebraElement_letterplace(A, p, check=False)
+diff --git a/src/sage/algebras/letterplace/free_algebra_letterplace.pyx b/src/sage/algebras/letterplace/free_algebra_letterplace.pyx
+index 7a8400052e..b3474fa07c 100644
+--- a/src/sage/algebras/letterplace/free_algebra_letterplace.pyx
++++ b/src/sage/algebras/letterplace/free_algebra_letterplace.pyx
+@@ -683,7 +683,7 @@ cdef class FreeAlgebra_letterplace(Algebra):
+ degbound = self._degbound
+ cdef list G = [C(x._poly) for x in g]
+ for y in G:
+- out.extend([y]+[singular_system("stest",y,n+1,degbound,ngens,ring=C) for n in xrange(d-y.degree())])
++ out.extend([y]+[singular_system("stest",y,n+1,ring=C) for n in xrange(d-y.degree())])
+ return C.ideal(out)
+
+ ###########################
+diff --git a/src/sage/algebras/letterplace/letterplace_ideal.pyx b/src/sage/algebras/letterplace/letterplace_ideal.pyx
+index 5776c58cf7..e4ad267bd4 100644
+--- a/src/sage/algebras/letterplace/letterplace_ideal.pyx
++++ b/src/sage/algebras/letterplace/letterplace_ideal.pyx
+@@ -48,7 +48,7 @@ from sage.rings.infinity import Infinity
+ #####################
+ # Define some singular functions
+ lib("freegb.lib")
+-singular_system=singular_function("system")
++singular_std=singular_function("std")
+ poly_reduce=singular_function("NF")
+
+ class LetterplaceIdeal(Ideal_nc):
+@@ -276,8 +276,7 @@ class LetterplaceIdeal(Ideal_nc):
+ A.set_degbound(degbound)
+ P = A._current_ring
+ out = [FreeAlgebraElement_letterplace(A,X,check=False) for X in
+- singular_system("freegb",P.ideal([x._poly for x in self.__GB.gens()]),
+- degbound,A.__ngens, ring = P)]
++ singular_std(P.ideal([x._poly for x in self.__GB.gens()]), ring = P)]
+ libsingular_options['redTail'] = bck[0]
+ libsingular_options['redSB'] = bck[1]
+ self.__GB = A.ideal(out,side='twosided',coerce=False)
+
Copied: sagemath/repos/community-staging-x86_64/sagemath-sphinx-1.8.patch (from rev 467482, sagemath/trunk/sagemath-sphinx-1.8.patch)
===================================================================
--- community-staging-x86_64/sagemath-sphinx-1.8.patch (rev 0)
+++ community-staging-x86_64/sagemath-sphinx-1.8.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -0,0 +1,28 @@
+--- a/src/sage/misc/sphinxify.py 2018-09-14 20:13:32.788831484 +0200
++++ b/src/sage/misc/sphinxify.py 2018-09-14 20:14:07.142478667 +0200
+@@ -68,6 +68,7 @@
+ sage: assert n == len(sys.path)
+ """
+ srcdir = mkdtemp()
++ outdir = mkdtemp()
+ base_name = os.path.join(srcdir, 'docstring')
+ rst_name = base_name + '.rst'
+
+@@ -75,7 +76,7 @@
+ suffix = '.html'
+ else:
+ suffix = '.txt'
+- output_name = base_name + suffix
++ output_name = os.path.join(outdir, 'docstring') + suffix
+
+ with open(rst_name, 'w') as filed:
+ filed.write(docstring)
+@@ -93,7 +94,7 @@
+
+ import sys
+ old_sys_path = list(sys.path) # Sphinx modifies sys.path
+- sphinx_app = Sphinx(srcdir, confdir, srcdir, doctreedir, format,
++ sphinx_app = Sphinx(srcdir, confdir, outdir, doctreedir, format,
+ confoverrides, None, None, True)
+ sphinx_app.build(None, [rst_name])
+ sys.path = old_sys_path
Copied: sagemath/repos/community-staging-x86_64/sagemath-threejs-100.patch (from rev 467482, sagemath/trunk/sagemath-threejs-100.patch)
===================================================================
--- community-staging-x86_64/sagemath-threejs-100.patch (rev 0)
+++ community-staging-x86_64/sagemath-threejs-100.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -0,0 +1,52 @@
+diff --git a/src/ext/threejs/threejs_template.html b/src/ext/threejs/threejs_template.html
+index 0243bc1..48e8268 100644
+--- a/src/ext/threejs/threejs_template.html
++++ b/src/ext/threejs/threejs_template.html
+@@ -114,7 +114,7 @@ SAGE_SCRIPTS
+ scene.add( sprite );
+ }
+
+- if ( options.axes ) scene.add( new THREE.AxisHelper( Math.min( a[0]*b[1].x, a[1]*b[1].y, a[2]*b[1].z ) ) );
++ if ( options.axes ) scene.add( new THREE.AxesHelper( Math.min( a[0]*b[1].x, a[1]*b[1].y, a[2]*b[1].z ) ) );
+
+ var camera = new THREE.PerspectiveCamera( 45, window.innerWidth / window.innerHeight, 0.1, 1000 );
+ camera.up.set( 0, 0, 1 );
+@@ -177,7 +177,11 @@ SAGE_SCRIPTS
+ transparent: transparent, opacity: json.opacity,
+ alphaTest: .1 } );
+
+- var c = geometry.center().multiplyScalar( -1 );
++ var c = new THREE.Vector3();
++ geometry.computeBoundingBox();
++ geometry.boundingBox.getCenter( c );
++ geometry.translate( -c.x, -c.y, -c.z );
++
+ var mesh = new THREE.Points( geometry, material );
+ mesh.position.set( c.x, c.y, c.z );
+ scene.add( mesh );
+@@ -199,7 +203,11 @@ SAGE_SCRIPTS
+ var material = new THREE.LineBasicMaterial( { color: json.color, linewidth: json.linewidth,
+ transparent: transparent, opacity: json.opacity } );
+
+- var c = geometry.center().multiplyScalar( -1 );
++ var c = new THREE.Vector3();
++ geometry.computeBoundingBox();
++ geometry.boundingBox.getCenter( c );
++ geometry.translate( -c.x, -c.y, -c.z );
++
+ var mesh = new THREE.LineSegments( geometry, material );
+ mesh.position.set( c.x, c.y, c.z );
+ scene.add( mesh );
+@@ -235,7 +243,11 @@ SAGE_SCRIPTS
+ transparent: transparent, opacity: json.opacity,
+ shininess: 20 } );
+
+- var c = geometry.center().multiplyScalar( -1 );
++ var c = new THREE.Vector3();
++ geometry.computeBoundingBox();
++ geometry.boundingBox.getCenter( c );
++ geometry.translate( -c.x, -c.y, -c.z );
++
+ var mesh = new THREE.Mesh( geometry, material );
+ mesh.position.set( c.x, c.y, c.z );
+ scene.add( mesh );
Copied: sagemath/repos/community-staging-x86_64/sagemath-threejs.patch (from rev 467482, sagemath/trunk/sagemath-threejs.patch)
===================================================================
--- community-staging-x86_64/sagemath-threejs.patch (rev 0)
+++ community-staging-x86_64/sagemath-threejs.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -0,0 +1,11 @@
+--- a/src/sage/repl/rich_output/display_manager.py
++++ b/src/sage/repl/rich_output/display_manager.py
+@@ -746,7 +746,7 @@ class DisplayManager(SageObject):
+ """
+ if online:
+ from sage.misc.package import installed_packages
+- version = installed_packages()['threejs'].split('.')[0]
++ version = 'r100'
+ 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-staging-x86_64/test-optional.patch (from rev 467482, sagemath/trunk/test-optional.patch)
===================================================================
--- community-staging-x86_64/test-optional.patch (rev 0)
+++ community-staging-x86_64/test-optional.patch 2019-05-15 21:31:13 UTC (rev 467483)
@@ -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
+@@ -347,22 +347,6 @@
+ # 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))
+-
+ options.optional |= auto_optional_tags
+
+ self.options = options
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