Date: Friday, August 17, 2018 @ 22:28:57 Author: arojas Revision: 372568
Update to 8.3 Added: sagemath/trunk/sagemath-cremona.patch Modified: sagemath/trunk/PKGBUILD sagemath/trunk/latte-count.patch sagemath/trunk/package.patch sagemath/trunk/sagemath-env.patch sagemath/trunk/sagemath-gap-4.8.patch sagemath/trunk/sagemath-python3-notebook.patch sagemath/trunk/sagemath-singular-4.1.1.patch sagemath/trunk/sagemath-threejs.patch Deleted: sagemath/trunk/jupyter-path.patch sagemath/trunk/sagemath-cddlib-094j.patch sagemath/trunk/sagemath-detect-igraph.patch sagemath/trunk/sagemath-ignore-warnings.patch sagemath/trunk/sagemath-lrs.patch sagemath/trunk/sagemath-networkx2.patch ---------------------------------+ PKGBUILD | 86 +-- jupyter-path.patch | 22 latte-count.patch | 26 - package.patch | 11 sagemath-cddlib-094j.patch | 980 -------------------------------------- sagemath-cremona.patch | 31 + sagemath-detect-igraph.patch | 21 sagemath-env.patch | 43 + sagemath-gap-4.8.patch | 2 sagemath-ignore-warnings.patch | 25 sagemath-lrs.patch | 22 sagemath-networkx2.patch | 175 ------ sagemath-python3-notebook.patch | 2 sagemath-singular-4.1.1.patch | 814 +++++++++++++++++++++++++++++++ sagemath-threejs.patch | 6 15 files changed, 943 insertions(+), 1323 deletions(-) Modified: PKGBUILD =================================================================== --- PKGBUILD 2018-08-17 21:06:27 UTC (rev 372567) +++ PKGBUILD 2018-08-17 22:28:57 UTC (rev 372568) @@ -4,12 +4,11 @@ # 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=8.2 -pkgrel=14 +pkgver=8.3 +pkgrel=1 pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab" arch=(x86_64) url="http://www.sagemath.org" @@ -30,38 +29,44 @@ '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' + 'sirocco: for computing the fundamental group of the complement of a plane curve' 'primecount: faster prime_pi implementation' 'three.js: alternative 3D plots engine' 'dot2tex: for displaying some diagrams' 'python2-pip: to install optional packages with sage -pip') makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding sirocco - mcqd coxeter bliss-graphs tdlib python2-pkgconfig shared_meataxe libfes) + mcqd coxeter bliss-graphs 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 jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch - r-no-readline.patch fes02.patch sagemath-threejs.patch sagemath-ignore-warnings.patch - sagemath-detect-igraph.patch sagemath-networkx2.patch sagemath-scipy-1.0.patch sagemath-lrs.patch - sagemath-singular-4.1.1.patch sagemath-lcalc-c++11.patch sagemath-gap-4.8.patch + sagemath-env.patch + package.patch + latte-count.patch + sagemath-python3-notebook.patch + test-optional.patch + r-no-readline.patch + fes02.patch + sagemath-threejs.patch + sagemath-cremona.patch + sagemath-scipy-1.0.patch + sagemath-singular-4.1.1.patch + sagemath-lcalc-c++11.patch + sagemath-gap-4.8.patch sagemath-cypari2.patch::"https://git.sagemath.org/sage.git/patch?id=da380b32" - sagemath-cddlib-094j.patch sagemath-eclib-20180710.patch) -sha256sums=('41ba2c2dde7a02e1bb6880ae875d37ab058567cc26e760efe87eeb12188cd65b' - 'b3c5f5c159d72ba7bc2b186b7b0e50a02b1ca60caef49b3857dbaad3da36b6fc' - 'c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107' - '0b680e674c11c47afa86162d8b49645620b8912722e08133d23357c29ca9310a' - '2cad308f8adbb6c54e6603fa22b2f0eb60f6f09248d5d015000c3932ac14f646' - '962ce805c87147212b21fc2ab0ac9af9bd0033942c7a6905b9906645b48e8a4f' + sagemath-cddlib-0.94j.patch::"https://git.sagemath.org/sage.git/patch?id=af0e6066" + sagemath-eclib-20180710.patch) +sha256sums=('41fd0b4eb820f7a1274e12294b6fbdbbf60d0027bff98c22fdc84da140964929' + 'f483a448c045aeff186bec4b402da8109fa12547ff36219a9aa427c2561ec8e5' + '960afe4fcbffe2762b66119b8f14355386ced0d8ee52b535d0dac1dba90d365b' + 'ef265f88ceb6caf4aac2d86ea74850861d99a63d11c94fc52b2ce88053c26d1e' + 'fc393ee5fbf507dfb76d6ad0e9193d74a954acb13f35a371bf91e11bbcb08244' '18edeafb01cc1ed7270c2dfb41a58717918680c98e8eada1858736acd65d92ba' 'afd0952b9bb8f52fd428eae36cf719a58ff85a894baae88cbb2124e043768cc7' '7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94' - '2d13b15ad2d1511bb3d752a261497060a8901882b1c2fa9813219781b7a71d83' - 'a4a6c87b46ff23b89608aca66d00427334502e8bfb5dfe68b94497d19be1c7ae' - 'bfe49f0168fe0824f0eaf4ea793b08d5b3e43c4e3634eb5f664c70644a793a59' - '8253730940687992dd29d90d95bea7e2685bb4854db004090c8196ce92859b64' + '4722f9257f7b58a5dc8be2e9163ebba6d7b3ee011ff1ab9c0dbfb1330d367261' + 'f801be68d043f317cc2a85a5ca059010b68eaeafa3bbf5c9148f2c154e2a707d' '17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a' - 'c0f65534a845ba802de6196229159fe67fcc3f72f0cb1ce57d4ae5c9fe10282c' - '507bf761df222d1961d53ebeaf8e6a5a3dc2d7b9cb78748d71ed8cb1ee1c4ac6' + '600701ee849d296cef63fad2dbf57db4d6d6259e2e5e1415a7ceaa385d98d5b9' '5114c912f821900e5bfae1e2cfeb7984de946d0b23e1182b0bf15be1d803dfd0' - '6917cb74e50ae965ea8d7c39577e5f0a5068e4b6a67b53fc6f219149a7d06584' + 'b2c9b9695c358f868c3868790382cf7d112092184ce08f5733524d406ec20cac' '94847fc033fd36bc59217c8484d4cf48d0640ff35bb5ca5ffba88a8158c6dd44' - '092a928b77c8bb1e23399f22be39f67797a0065954128b690ead6a09f9ce1e44' + '9a690bda83c280c0801f6d04353e8a909da80ccfee92e06d200ae6eb9be9a5a8' '182b0765d58494978bf27628bada8b42c95ef7eb2671b91ddf9c67608560c662') prepare(){ @@ -74,8 +79,6 @@ 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 @@ -82,19 +85,8 @@ 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 -# fix lrs detection - patch -p1 -i ../sagemath-lrs.patch -# adapt to networkx 2 changes - patch -p1 -i ../sagemath-networkx2.patch # fix three.js plotting backend patch -p1 -i ../sagemath-threejs.patch -# don't show PARI stack size increase or GLPK warnings during doctesting (Debian) - patch -p1 -i ../sagemath-ignore-warnings.patch # remove deprecated scipy parameters patch -p1 -i ../sagemath-scipy-1.0.patch # fix build with Singular 4.1.1 @@ -109,14 +101,15 @@ # 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 # update to cypari2 https://trac.sagemath.org/ticket/25813 patch -p1 -i ../sagemath-cypari2.patch # port to cddlib 0.94j https://trac.sagemath.org/ticket/25344 - patch -p1 -i ../sagemath-cddlib-094j.patch + patch -p1 -i ../sagemath-cddlib-0.94j.patch # use python2 - sed -e 's|#!/usr/bin/env sage-python23|#!/usr/bin/env python2|' -e 's|#!/usr/bin/env python\b|#!/usr/bin/env python2|' \ - -e 's|exec python\b|exec python2|' -i src/bin/* + sed -e 's|#!/usr/bin/env sage-python23|#!/usr/bin/env 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|exec pip\b|exec pip2|' -e 's|cygdb|cygdb2|g' -i src/bin/sage sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython @@ -126,6 +119,7 @@ build() { cd sage-$pkgver/src + export CC=gcc export SAGE_ROOT="$PWD" export SAGE_SRC="$PWD" python2 setup.py build @@ -138,12 +132,12 @@ export SAGE_ROOT="$PWD" export SAGE_LOCAL="/usr" - export JUPYTER_PATH="$pkgdir"/usr/share/jupyter + export SAGE_EXTCODE="$PWD"/ext python2 setup.py install --root="$pkgdir" --optimize=1 mkdir -p "$pkgdir"/usr/bin cp bin/sage "$pkgdir"/usr/bin - for _i in arch-env cachegrind callgrind cleaner coverage coverageall cython env eval grep grepdoc inline-fortran \ + 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 @@ -170,7 +164,11 @@ 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()" + 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 } Deleted: jupyter-path.patch =================================================================== --- jupyter-path.patch 2018-08-17 21:06:27 UTC (rev 372567) +++ jupyter-path.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -1,22 +0,0 @@ ---- 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) - Modified: latte-count.patch =================================================================== --- latte-count.patch 2018-08-17 21:06:27 UTC (rev 372567) +++ latte-count.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -51,7 +51,7 @@ 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, +@@ -93,7 +93,7 @@ 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 ... ... @@ -60,9 +60,9 @@ ... 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 +@@ -112,7 +112,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False, + # Check that LattE is present + Latte().require() - args = ['count'] + args = ['latte-count'] @@ -69,3 +69,21 @@ 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""" + Modified: package.patch =================================================================== --- package.patch 2018-08-17 21:06:27 UTC (rev 372567) +++ package.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -1,8 +1,8 @@ --- 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) +@@ -328,7 +328,7 @@ + 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 @@ -13,7 +13,7 @@ +++ 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 + from sage.misc.package import list_packages -all_packages = list_packages(local=True) - @@ -20,10 +20,11 @@ class CythonizeExtension(Extension): """ -@@ -76,14 +74,7 @@ +@@ -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: Deleted: sagemath-cddlib-094j.patch =================================================================== --- sagemath-cddlib-094j.patch 2018-08-17 21:06:27 UTC (rev 372567) +++ sagemath-cddlib-094j.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -1,980 +0,0 @@ -diff --git a/src/sage/geometry/polyhedron/backend_cdd.py b/src/sage/geometry/polyhedron/backend_cdd.py -index 9e0ca53ba7b..8497741b0c4 100644 ---- a/src/sage/geometry/polyhedron/backend_cdd.py -+++ b/src/sage/geometry/polyhedron/backend_cdd.py -@@ -154,7 +154,9 @@ def _init_from_cdd_input(self, cdd_input_string, cmdline_arg='--all', verbose=Fa - ....: [0.62, -1.38, 0.38],[0.144, -1.04, 0.04], - ....: [0.1309090909, -1.0290909091, 0.04]] - sage: Polyhedron(point_list) -- A 3-dimensional polyhedron in RDF^3 defined as the convex hull of 14 vertices -+ Traceback (most recent call last): -+ ... -+ ValueError: *Error: Numerical inconsistency is found. Use the GMP exact arithmetic. - sage: Polyhedron(point_list, base_ring=QQ) - A 3-dimensional polyhedron in QQ^3 defined as the convex hull of 14 vertices - """ -@@ -286,7 +288,9 @@ def cdd_adjacencies(): - else: - n_cdd=n; - self._V_adjacency_matrix = matrix(ZZ, n, n, 0) -- expect_in_cddout('begin') -+ if not find_in_cddout('begin'): -+ raise ValueError('Error while parsing cdd output: could not ' -+ 'find "begin" after "Vertex graph"') - l = cddout.pop(0).split() - assert int(l[0]) == n_cdd, "Not enough V-adjacencies in cdd output?" - for i in range(n_cdd): -@@ -309,7 +313,9 @@ def cdd_adjacencies(): - if find_in_cddout('Facet graph'): - n = len(self._Hrepresentation); - self._H_adjacency_matrix = matrix(ZZ, n, n, 0) -- expect_in_cddout('begin') -+ if not find_in_cddout('begin'): -+ raise ValueError('Error while parsing cdd output: could not ' -+ 'find "begin" after "Facet graph"') - l = cddout.pop(0).split() - assert int(l[0]) == n, "Not enough H-adjacencies in cdd output?" - for i in range(n): ---- -diff --git a/src/sage/geometry/hasse_diagram.py b/src/sage/geometry/hasse_diagram.py -index 9d336ce..c5bff21 100644 ---- a/src/sage/geometry/hasse_diagram.py -+++ b/src/sage/geometry/hasse_diagram.py -@@ -44,7 +44,7 @@ def Hasse_diagram_from_incidences(atom_to_coatoms, coatom_to_atoms, - implementation will just return these two tuples as a tuple; - - - ``required_atoms`` -- list of atoms (default:None). Each -- non-empty "face" requires at least on of the specified atoms -+ non-empty "face" requires at least one of the specified atoms - present. Used to ensure that each face has a vertex. - - - ``key`` -- any hashable value (default: None). It is passed down -diff --git a/src/sage/geometry/polyhedron/backend_cdd.py b/src/sage/geometry/polyhedron/backend_cdd.py -index 8497741..85f6632 100644 ---- a/src/sage/geometry/polyhedron/backend_cdd.py -+++ b/src/sage/geometry/polyhedron/backend_cdd.py -@@ -1,6 +1,19 @@ --""" -+# -*- coding: utf-8 -*- -+r""" - The cdd backend for polyhedral computations - """ -+# **************************************************************************** -+# Copyright (C) 2011-2014 Volker Braun <vbraun.n...@gmail.com> -+# 2018 Timo Kaufmann <timo...@zoho.com> -+# 2018 Julian RĂ¼th <julian.ru...@fsfe.org> -+# -+# This program is free software: you can redistribute it and/or modify -+# it under the terms of the GNU General Public License as published by -+# the Free Software Foundation, either version 2 of the License, or -+# (at your option) any later version. -+# https://www.gnu.org/licenses/ -+# **************************************************************************** -+ - from __future__ import print_function - from __future__ import absolute_import - -@@ -13,12 +26,10 @@ from .base import Polyhedron_base - from .base_QQ import Polyhedron_QQ - from .base_RDF import Polyhedron_RDF - --######################################################################### - class Polyhedron_cdd(Polyhedron_base): -- """ -+ r""" - Base class for the cdd backend. - """ -- - def _init_from_Vrepresentation(self, vertices, rays, lines, verbose=False): - """ - Construct polyhedron from V-representation data. -@@ -49,8 +60,30 @@ class Polyhedron_cdd(Polyhedron_base): - """ - from .cdd_file_format import cdd_Vrepresentation - s = cdd_Vrepresentation(self._cdd_type, vertices, rays, lines) -- self._init_from_cdd_input(s, '--reps', verbose) -- -+ s = self._run_cdd(s, '--redcheck', verbose=verbose) -+ s = self._run_cdd(s, '--repall', verbose=verbose) -+ self._init_from_cdd_output(s) -+ if not self.base_ring().is_exact(): -+ # cdd's parser can not handle the full output of --repall, so we -+ # need to extract the first block before we feed it back into cdd -+ s = s.splitlines() -+ s = s[:s.index('end')+1] -+ s = '\n'.join(s) -+ t = self._run_cdd(s, '--rep', verbose=verbose) -+ -+ def parse(intro, data): -+ count = int(data[0][0]) -+ if count != len(self._cdd_V_to_sage_V): -+ # Upstream claims that nothing can be done about these -+ # cases/that they are features not bugs. Imho, cddlib is -+ # not really suitable for automatic parsing of its output, -+ # the implementation backed by doubles has not really been -+ # optimized for numerical stability, and makes some -+ # somewhat random numerical choices. (But I am not an -+ # expert in that field by any means.) See also -+ # https://github.com/cddlib/cddlib/pull/7. -+ raise ValueError("polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data") -+ Polyhedron_cdd._parse_block(t.splitlines(), 'V-representation', parse) - - def _init_from_Hrepresentation(self, ieqs, eqns, verbose=False): - """ -@@ -78,88 +111,32 @@ class Polyhedron_cdd(Polyhedron_base): - """ - from .cdd_file_format import cdd_Hrepresentation - s = cdd_Hrepresentation(self._cdd_type, ieqs, eqns) -- self._init_from_cdd_input(s, '--reps', verbose) -- -- -- def _init_facet_adjacency_matrix(self, verbose=False): -- """ -- Compute the facet adjacency matrix in case it has not been -- computed during initialization. -- -- INPUT: -- -- - ``verbose`` -- boolean (default: ``False``). Whether to print -- verbose output for debugging purposes. -- -- EXAMPLES:: -- -- sage: p = Polyhedron(vertices=[(0,0),(1,0),(0,1)], backend='cdd', base_ring=QQ) -- sage: '_H_adjacency_matrix' in p.__dict__ -- False -- sage: p._init_facet_adjacency_matrix() -- sage: p._H_adjacency_matrix -- [0 1 1] -- [1 0 1] -- [1 1 0] -- """ -- self._init_from_cdd_input(self.cdd_Hrepresentation(), -- '--adjacency', verbose) -- -- -- def _init_vertex_adjacency_matrix(self, verbose=False): -- """ -- Compute the vertex adjacency matrix in case it has not been -- computed during initialization. -- -- INPUT: -- -- - ``verbose`` -- boolean (default: ``False``). Whether to print -- verbose output for debugging purposes. -- -- EXAMPLES:: -- -- sage: p = Polyhedron(vertices=[(0,0),(1,0),(0,1)], backend='cdd', base_ring=QQ) -- sage: '_V_adjacency_matrix' in p.__dict__ -- False -- sage: p._init_vertex_adjacency_matrix() -- sage: p._V_adjacency_matrix -- [0 1 1] -- [1 0 1] -- [1 1 0] -- """ -- self._init_from_cdd_input(self.cdd_Vrepresentation(), -- '--adjacency', verbose) -- -- -- def _init_from_cdd_input(self, cdd_input_string, cmdline_arg='--all', verbose=False): -- """ -- Internal method: run cdd on a cdd H- or V-representation -- and initialize ourselves with the output. -- -- TESTS:: -- -- sage: p = Polyhedron(vertices=[[0,0,0],[1,0,0],[0,1,0],[0,0,1]], -- ....: backend='cdd', base_ring=QQ) -- sage: from sage.geometry.polyhedron.cdd_file_format import cdd_Vrepresentation -- sage: s = cdd_Vrepresentation('rational', [[0,0,1],[0,1,0],[1,0,0]], [], []) -- sage: p._init_from_cdd_input(s) -- sage: p.dim() -- 2 -- -- sage: point_list = [[0.132, -1.028, 0.028],[0.5, 0.5, -1.5], -- ....: [-0.5, 1.5, -0.5],[0.5, 0.5, 0.5],[1.5, -0.5, -0.5], -- ....: [-0.332, -0.332, -0.668],[-1.332, 0.668, 0.332], -- ....: [-0.932, 0.068, 0.932],[-0.38, -0.38, 1.38], -- ....: [-0.744, -0.12, 1.12],[-0.7781818182, -0.12, 0.9490909091], -- ....: [0.62, -1.38, 0.38],[0.144, -1.04, 0.04], -- ....: [0.1309090909, -1.0290909091, 0.04]] -- sage: Polyhedron(point_list) -- Traceback (most recent call last): -- ... -- ValueError: *Error: Numerical inconsistency is found. Use the GMP exact arithmetic. -- sage: Polyhedron(point_list, base_ring=QQ) -- A 3-dimensional polyhedron in QQ^3 defined as the convex hull of 14 vertices -- """ -+ s = self._run_cdd(s, '--redcheck', verbose=verbose) -+ s = self._run_cdd(s, '--repall', verbose=verbose) -+ self._init_from_cdd_output(s) -+ if not self.base_ring().is_exact(): -+ # cdd's parser can not handle the full output of --repall, so we -+ # need to extract the first block before we feed it back into cdd -+ s = s.splitlines() -+ s = s[:s.index('end')+1] -+ s = '\n'.join(s) -+ t = self._run_cdd(s, '--rep', verbose=verbose) -+ -+ def parse(intro, data): -+ count = int(data[0][0]) -+ infinite_count = len([d for d in data[1:] if d[0] == '1' and all(c == '0' for c in d[1:])]) -+ if count - infinite_count != len(self._Hrepresentation): -+ # Upstream claims that nothing can be done about these -+ # cases/that they are features not bugs. Imho, cddlib is -+ # not really suitable for automatic parsing of its output, -+ # the implementation backed by doubles has not really been -+ # optimized for numerical stability, and makes some -+ # somewhat random numerical choices. (But I am not an -+ # expert in that field by any means.) -+ raise ValueError("polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data") -+ Polyhedron_cdd._parse_block(t.splitlines(), 'H-representation', parse) -+ -+ def _run_cdd(self, cdd_input_string, cmdline_arg, verbose=False): - if verbose: - print('---- CDD input -----') - print(cdd_input_string) -@@ -175,157 +152,189 @@ class Polyhedron_cdd(Polyhedron_base): - if 'Error:' in ans + err: - # cdd reports errors on stdout and misc information on stderr - raise ValueError(ans.strip()) -- self._init_from_cdd_output(ans) -+ return ans -+ -+ @classmethod -+ def _parse_block(cls, cddout, header, parser): -+ r""" -+ Parse a block of cdd data identified by ``header`` by invoking -+ ``parser`` on it. -+ -+ EXAMPLES:: - -+ sage: cddout = r''' -+ ....: unrelated -+ ....: HEADER -+ ....: intro 0 1 2 -+ ....: begin -+ ....: data 0 1 2 -+ ....: data 3 4 5 -+ ....: end -+ ....: unrelated -+ ....: '''.splitlines() -+ sage: from sage.geometry.polyhedron.backend_cdd import Polyhedron_cdd -+ sage: def parser(intro, data): -+ ....: print("INTRO:", intro) -+ ....: print("DATA:", data) -+ sage: Polyhedron_cdd._parse_block(cddout, 'HEADER', parser) -+ INTRO: [['intro', '0', '1', '2']] -+ DATA: [['data', '0', '1', '2'], ['data', '3', '4', '5']] - -- def _init_from_cdd_output(self, cdd_output_string): -+ """ -+ try: -+ block = cddout[cddout.index(header)+1:] -+ except ValueError: -+ # section is missing in the cdd output -+ return -+ -+ intro = block[:block.index('begin')] -+ intro = [i.strip().split() for i in intro] -+ data = block[block.index('begin')+1:block.index('end')] -+ data = [d.strip().split() for d in data] -+ parser(intro, data) -+ -+ def _init_from_cdd_output(self, cddout): - """ - Initialize ourselves with the output from cdd. - - TESTS:: - -- sage: from sage.geometry.polyhedron.cdd_file_format import cdd_Vrepresentation -- sage: s = cdd_Vrepresentation('rational',[[0,0],[1,0],[0,1],[1,1]], [], []) -- sage: from subprocess import Popen, PIPE -- sage: cdd_proc = Popen(['cdd_both_reps_gmp', '--all'], stdin=PIPE, stdout=PIPE, stderr=PIPE) -- sage: ans, err = cdd_proc.communicate(input=s) -- sage: p = Polyhedron(vertices = [[0,0],[1,0],[0,1],[1,1]], backend='cdd', base_ring=QQ) -- sage: p._init_from_cdd_output(ans) -+ sage: p = Polyhedron(vertices = [[0,0],[1,0],[0,1],[1,1]], backend='cdd', base_ring=QQ) # indirect doctest - sage: p.vertices() - (A vertex at (0, 0), A vertex at (1, 0), A vertex at (0, 1), A vertex at (1, 1)) - """ -- cddout=cdd_output_string.splitlines() -- suppressed_vertex = False # whether cdd suppressed the vertex in output -- parent = self.parent() -- -- # nested function -- def expect_in_cddout(expected_string): -- l = cddout.pop(0).strip() -- if l!=expected_string: -- raise ValueError('Error while parsing cdd output: expected "' -- +expected_string+'" but got "'+l+'".\n') -- # nested function -- def cdd_linearities(): -- l = cddout[0].split() -- if l[0] != "linearity": -- return [] -- cddout.pop(0) -- assert len(l) == int(l[1])+2, "Not enough linearities given" -- return [int(i)-1 for i in l[2:]] # make indices pythonic -- -- # nested function -- def cdd_convert(string, base_ring=self.base_ring()): -- """ -- Converts the cdd output string to a numerical value. -- """ -- return [base_ring(x) for x in string.split()] -- -- # nested function -- def find_in_cddout(expected_string): -- """ -- Find the expected string in a list of strings, and -- truncates ``cddout`` to start at that point. Returns -- ``False`` if search fails. -- """ -- for pos in range(0,len(cddout)): -- l = cddout[pos].strip(); -- if l==expected_string: -- # must not assign to cddout in nested function -- for i in range(0,pos+1): -- cddout.pop(0) -- return True -- return False -- -- if find_in_cddout('V-representation'): -+ cddout = cddout.splitlines() -+ -+ def parse_indices(count, cdd_indices, cdd_indices_to_sage_indices=None): -+ cdd_indices = map(int, cdd_indices) -+ if cdd_indices_to_sage_indices is None: -+ cdd_indices_to_sage_indices = {i:i-1 for i in cdd_indices} -+ if count < 0: -+ assert cdd_indices_to_sage_indices is not None, "Did not expect negative counts here" -+ count = -count -+ cdd_indices = list(set(cdd_indices_to_sage_indices.keys()) - set(cdd_indices)) -+ assert count in [len(cdd_indices), len(cdd_indices) -1] -+ assert count == len(cdd_indices) -+ return [cdd_indices_to_sage_indices[i] for i in cdd_indices if cdd_indices_to_sage_indices[i] is not None] -+ -+ def parse_linearities(intro): -+ for entries in intro: -+ if entries and entries.pop(0) == 'linearity': -+ return parse_indices(int(entries.pop(0)), entries) -+ return [] -+ -+ def parse_H_representation(intro, data): -+ if '_Hrepresentation' in self.__dict__: -+ raise NotImplementedError("can not replace internal representation as this breaks caching") -+ self._Hrepresentation = [] -+ # we drop some entries in cdd's output and this changes the numbering; this dict keeps track of that -+ self._cdd_H_to_sage_H = {} -+ equations = parse_linearities(intro) -+ data[0].pop(2) # ignore data type, we know the base ring already -+ count, dimension = map(int, data.pop(0)) -+ assert self.ambient_dim() == dimension - 1, "Unexpected ambient dimension" -+ assert len(data) == count, "Unexpected number of lines" -+ for i, line in enumerate(data): -+ coefficients = map(self.base_ring(), line) -+ if coefficients[0] != 0 and all([e == 0 for e in coefficients[1:]]): -+ # cddlib sometimes includes an implicit plane at infinity: 1 0 0 ... 0 -+ # We do not care about this entry. -+ self._cdd_H_to_sage_H[i+1] = None -+ continue -+ -+ self._cdd_H_to_sage_H[i+1] = len(self._Hrepresentation) -+ if i in equations: -+ self.parent()._make_Equation(self, coefficients) -+ else: -+ self.parent()._make_Inequality(self, coefficients) -+ -+ self._Hrepresentation = tuple(self._Hrepresentation) -+ -+ def parse_V_representation(intro, data): -+ if '_Vrepresentation' in self.__dict__: -+ raise NotImplementedError("can not replace internal representation as this breaks caching") - self._Vrepresentation = [] -- lines = cdd_linearities() -- expect_in_cddout('begin') -- l = cddout.pop(0).split() -- assert self.ambient_dim() == int(l[1])-1, "Different ambient dimension?" -- suppressed_vertex = True -- for i in range(int(l[0])): -- l = cddout.pop(0).strip() -- l_type = l[0] -- l = l[1:] -+ # we drop some entries in cdd's output and this changes the numbering; this dict keeps track of that -+ self._cdd_V_to_sage_V = {} -+ lines = parse_linearities(intro) -+ data[0].pop(2) # ignore data type, we know the base ring already -+ count, dimension = map(int, data.pop(0)) -+ assert self.ambient_dim() == dimension - 1, "Unexpected ambient dimension" -+ assert len(data) == count, "Unexpected number of lines" -+ has_vertex = False -+ for i, line in enumerate(data): -+ kind = line.pop(0) -+ coefficients = map(self.base_ring(), line) -+ self._cdd_V_to_sage_V[i+1] = len(self._Vrepresentation) - if i in lines: -- parent._make_Line(self, cdd_convert(l)); -- elif l_type == '0': -- parent._make_Ray(self, cdd_convert(l)); -+ self.parent()._make_Line(self, coefficients); -+ elif kind == '0': -+ self.parent()._make_Ray(self, coefficients); - else: -- parent._make_Vertex(self, cdd_convert(l)); -- suppressed_vertex = False -- if suppressed_vertex and self.n_Vrepresentation()>0: -- # cdd does not output the vertex if it is only the origin -- parent._make_Vertex(self, [0] * self.ambient_dim()) -+ self.parent()._make_Vertex(self, coefficients) -+ has_vertex = True -+ if len(self._Vrepresentation) and not has_vertex: -+ # when the Polyhedron consists only of lines/rays from the -+ # origin, cddlib does not output the single vertex at the -+ # origin so we have to add it here as the Polyhedron class -+ # expects it to be there. -+ self.parent()._make_Vertex(self, [self.base_ring().zero()] * self.ambient_dim()) - self._Vrepresentation = tuple(self._Vrepresentation) -- expect_in_cddout('end') - -- if find_in_cddout('H-representation'): -- self._Hrepresentation = [] -- equations = cdd_linearities() -- expect_in_cddout('begin') -- l = cddout.pop(0).split() -- assert self.ambient_dim() == int(l[1])-1, "Different ambient dimension?" -- for i in range(int(l[0])): -- l = cddout.pop(0) -- if i in equations: -- parent._make_Equation(self, cdd_convert(l)); -- else: -- parent._make_Inequality(self, cdd_convert(l)); -- self._Hrepresentation = tuple(self._Hrepresentation) -- expect_in_cddout('end') -- -- # nested function -- def cdd_adjacencies(): -- l = cddout.pop(0).split() -- assert l[2] == ':', "Not a line of the adjacency data?" -- return [int(i)-1 for i in l[3:]] -- -- if find_in_cddout('Vertex graph'): -- n = len(self._Vrepresentation); -- if suppressed_vertex: -- n_cdd=n-1; -- else: -- n_cdd=n; -- self._V_adjacency_matrix = matrix(ZZ, n, n, 0) -- if not find_in_cddout('begin'): -- raise ValueError('Error while parsing cdd output: could not ' -- 'find "begin" after "Vertex graph"') -- l = cddout.pop(0).split() -- assert int(l[0]) == n_cdd, "Not enough V-adjacencies in cdd output?" -- for i in range(n_cdd): -- for a in cdd_adjacencies(): -- self._V_adjacency_matrix[i,a] = 1 -+ def parse_adjacency(intro, data, N, cdd_indices_to_sage_indices): -+ ret = matrix(ZZ, N, N, 0) -+ cdd_vertex_count = int(data.pop(0)[0]) -+ data.reverse() -+ for adjacencies in data: -+ assert adjacencies[2] == ':', "Not a line of adjacency data" -+ cdd_vertex = int(adjacencies[0]) -+ count = int(adjacencies[1]) -+ -+ # cdd sometimes prints implicit adjacencies for the plane at -+ # infinity at the end of the output (even though it's not part -+ # of the V/H representation) so we ignore indices that we do -+ # not know about. -+ if cdd_vertex not in cdd_indices_to_sage_indices: -+ cdd_indices_to_sage_indices[cdd_vertex] = None -+ v = cdd_indices_to_sage_indices[cdd_vertex] -+ if v is None: -+ continue -+ for w in parse_indices(count, adjacencies[3:], cdd_indices_to_sage_indices): -+ if w is None: -+ continue -+ ret[v, w] = 1 -+ return ret -+ -+ def parse_vertex_adjacency(intro, data): -+ if '_V_adjacency_matrix' in self.__dict__: -+ raise NotImplementedError("can not replace internal representation as this breaks caching") -+ N = len(self._Vrepresentation) -+ self._V_adjacency_matrix = parse_adjacency(intro, data, N, self._cdd_V_to_sage_V) -+ for i, v in enumerate(self._Vrepresentation): - # cdd reports that lines are never adjacent to anything. -- # I disagree, they are adjacent to everything! -- if self._Vrepresentation[i].is_line(): -- for j in range(n): -+ # we disagree, they are adjacent to everything. -+ if v.is_line(): -+ for j in range(len(self._Vrepresentation)): - self._V_adjacency_matrix[i,j] = 1 - self._V_adjacency_matrix[j,i] = 1 -- self._V_adjacency_matrix[i,i] = 0 -- if suppressed_vertex: # cdd implied that there is only one vertex -- for i in range(n-1): -- self._V_adjacency_matrix[i,n-1] = 1 -- self._V_adjacency_matrix[n-1,i] = 1 -+ self._V_adjacency_matrix[i,i] = 0 - self._V_adjacency_matrix.set_immutable() -- expect_in_cddout('end') -- -- if find_in_cddout('Facet graph'): -- n = len(self._Hrepresentation); -- self._H_adjacency_matrix = matrix(ZZ, n, n, 0) -- if not find_in_cddout('begin'): -- raise ValueError('Error while parsing cdd output: could not ' -- 'find "begin" after "Facet graph"') -- l = cddout.pop(0).split() -- assert int(l[0]) == n, "Not enough H-adjacencies in cdd output?" -- for i in range(n): -- for a in cdd_adjacencies(): -- self._H_adjacency_matrix[i,a] = 1 -+ self.vertex_adjacency_matrix.set_cache(self._V_adjacency_matrix) -+ -+ def parse_facet_adjacency(intro, data): -+ if '_H_adjacency_matrix' in self.__dict__: -+ raise NotImplementedError("can not replace internal representation as this breaks caching") -+ N = len(self._Hrepresentation) -+ self._H_adjacency_matrix = parse_adjacency(intro, data, N, self._cdd_H_to_sage_H) - self._H_adjacency_matrix.set_immutable() -- expect_in_cddout('end') -+ self.facet_adjacency_matrix.set_cache(self._H_adjacency_matrix) -+ -+ Polyhedron_cdd._parse_block(cddout, 'H-representation', parse_H_representation) -+ Polyhedron_cdd._parse_block(cddout, 'V-representation', parse_V_representation) -+ Polyhedron_cdd._parse_block(cddout, 'Facet adjacency', parse_facet_adjacency) -+ Polyhedron_cdd._parse_block(cddout, 'Vertex adjacency', parse_vertex_adjacency) - - --######################################################################### - class Polyhedron_QQ_cdd(Polyhedron_cdd, Polyhedron_QQ): - """ - Polyhedra over QQ with cdd -@@ -350,7 +359,7 @@ class Polyhedron_QQ_cdd(Polyhedron_cdd, Polyhedron_QQ): - - _cdd_type = 'rational' - -- _cdd_executable = 'cdd_both_reps_gmp' -+ _cdd_executable = 'cddexec_gmp' - - def __init__(self, parent, Vrep, Hrep, **kwds): - """ -@@ -369,7 +378,6 @@ class Polyhedron_QQ_cdd(Polyhedron_cdd, Polyhedron_QQ): - Polyhedron_cdd.__init__(self, parent, Vrep, Hrep, **kwds) - - --######################################################################### - class Polyhedron_RDF_cdd(Polyhedron_cdd, Polyhedron_RDF): - """ - Polyhedra over RDF with cdd -@@ -392,7 +400,7 @@ class Polyhedron_RDF_cdd(Polyhedron_cdd, Polyhedron_RDF): - """ - _cdd_type = 'real' - -- _cdd_executable = 'cdd_both_reps' -+ _cdd_executable = 'cddexec' - - def __init__(self, parent, Vrep, Hrep, **kwds): - """ -diff --git a/src/sage/geometry/polyhedron/base.py b/src/sage/geometry/polyhedron/base.py -index 34f0a3f..a8ca502 100644 ---- a/src/sage/geometry/polyhedron/base.py -+++ b/src/sage/geometry/polyhedron/base.py -@@ -47,10 +47,9 @@ from sage.categories.sets_cat import EmptySetError - # * derive from Polyhedron_base - # - # * you must implement _init_from_Vrepresentation and --# _init_from_Vrepresentationa -+# _init_from_Hrepresentation - # --# * You might want to override _init_empty_polyhedron, --# _init_facet_adjacency_matrix, _init_vertex_adjacency_matrix, and -+# * You might want to override _init_empty_polyhedron and - # _make_polyhedron_face. - # - # * You can of course also override any other method for which you -diff --git a/src/sage/geometry/polyhedron/library.py b/src/sage/geometry/polyhedron/library.py -index bbadbb3..2cdc728 100644 ---- a/src/sage/geometry/polyhedron/library.py -+++ b/src/sage/geometry/polyhedron/library.py -@@ -1100,18 +1100,23 @@ class Polytopes(): - - EXAMPLES:: - -- sage: td = polytopes.truncated_dodecahedron() # long time - 6secs -- sage: td.f_vector() # long time -+ sage: td = polytopes.truncated_dodecahedron() -+ sage: td.f_vector() - (1, 60, 90, 32, 1) -- sage: td.base_ring() # long time -+ sage: td.base_ring() - Number Field in sqrt5 with defining polynomial x^2 - 5 - -- A much faster implementation using floating point approximations:: -+ The faster implementation using floating point approximations does not -+ work unfortunately, see https://github.com/cddlib/cddlib/pull/7 for a -+ detailed discussion of this case:: - - sage: td = polytopes.truncated_dodecahedron(exact=False) -- sage: td.f_vector() -+ Traceback (most recent call last): -+ ... -+ ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data -+ sage: td.f_vector() # not tested - (1, 60, 90, 32, 1) -- sage: td.base_ring() -+ sage: td.base_ring() # not tested - Real Double Field - - Its faces are 20 triangles and 12 regular decagons:: -@@ -1323,21 +1328,25 @@ class Polytopes(): - sage: ti.base_ring() # long time - Number Field in sqrt5 with defining polynomial x^2 - 5 - -- A much faster implementation using floating point approximations:: -+ The faster implementation using floating point approximations does not -+ work unfortunately:: - - sage: ti = polytopes.truncated_icosidodecahedron(exact=False) -- sage: ti.f_vector() -+ Traceback (most recent call last): -+ ... -+ ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data -+ sage: ti.f_vector() # not tested - (1, 120, 180, 62, 1) -- sage: ti.base_ring() -+ sage: ti.base_ring() # not tested - Real Double Field - - Its faces are 30 squares, 20 hexagons and 12 decagons:: - -- sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 4) -+ sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 4) # long time - 30 -- sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 6) -+ sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 6) # long time - 20 -- sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 10) -+ sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 10) # long time - 12 - """ - if base_ring is None and exact: -@@ -1382,26 +1391,32 @@ class Polytopes(): - - - ``backend`` -- the backend to use to create the polytope. - -- EXAMPLES:: -+ EXAMPLES: -+ -+ Unfortunately, no polyhedra backend supports the construction of the -+ snub dodecahedron at the moment:: - - sage: sd = polytopes.snub_dodecahedron() -- sage: sd.f_vector() -+ Traceback (most recent call last): -+ ... -+ ValueError: *Error: Numerical inconsistency is found. Use the GMP exact arithmetic. -+ sage: sd.f_vector() # not tested - (1, 60, 150, 92, 1) -- sage: sd.base_ring() -+ sage: sd.base_ring() # not tested - Real Double Field - - Its faces are 80 triangles and 12 pentagons:: - -- sage: sum(1 for f in sd.faces(2) if len(f.vertices()) == 3) -+ sage: sum(1 for f in sd.faces(2) if len(f.vertices()) == 3) # not tested - 80 -- sage: sum(1 for f in sd.faces(2) if len(f.vertices()) == 5) -+ sage: sum(1 for f in sd.faces(2) if len(f.vertices()) == 5) # not tested - 12 - """ - if base_ring is None: - base_ring = RDF - phi = (1 + base_ring(5).sqrt()) / 2 -- xi = ((phi/2 + (phi - 5/27).sqrt()/2).nth_root(3) + -- (phi/2 - (phi - 5/27).sqrt()/2).nth_root(3)) -+ xi = ((phi/2 + (phi - 5/27).sqrt()/2)**(~ZZ(3)) + -+ (phi/2 - (phi - 5/27).sqrt()/2)**(~ZZ(3))) - - alpha = xi - 1 / xi - beta = xi * phi + phi**2 + phi / xi -@@ -1549,14 +1564,18 @@ class Polytopes(): - sage: gap # not tested - very long time - A 4-dimensional polyhedron in (Number Field in sqrt5 with defining polynomial x^2 - 5)^4 defined as the convex hull of 100 vertices - -- Computation with approximated coordinates is much faster:: -+ Computation with approximated coordinates would be much faster but is -+ not supported currently:: - - sage: gap = polytopes.grand_antiprism(exact=False) -- sage: gap -+ Traceback (most recent call last): -+ ... -+ ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data -+ sage: gap # not tested - A 4-dimensional polyhedron in RDF^4 defined as the convex hull of 100 vertices -- sage: gap.f_vector() -+ sage: gap.f_vector() # not tested - (1, 100, 500, 720, 320, 1) -- sage: len(list(gap.bounded_edges())) -+ sage: len(list(gap.bounded_edges())) # not tested - 500 - """ - from itertools import product -diff --git a/src/sage/libs/ppl.pyx b/src/sage/libs/ppl.pyx -index 5366c74..e318e86 100644 ---- a/src/sage/libs/ppl.pyx -+++ b/src/sage/libs/ppl.pyx -@@ -110,14 +110,11 @@ basis vectors:: - sage: C_Polyhedron(gs) - A 4-dimensional polyhedron in QQ^5 defined as the convex hull of 120 points - --The above computation (using PPL) finishes without noticeable delay (timeit --measures it to be 90 microseconds on sage.math). Below we do the same --computation with cddlib, which needs more than 3 seconds on the same --hardware:: -+The same computation with cddlib which is slightly slower:: - - sage: basis = list(range(5)) - sage: gs = [ tuple(coeff) for coeff in Permutations(basis) ] -- sage: Polyhedron(vertices=gs, backend='cdd') # long time (3s on sage.math, 2011) -+ sage: Polyhedron(vertices=gs, backend='cdd') - A 4-dimensional polyhedron in QQ^5 defined as the convex hull of 120 vertices - - DIFFERENCES VS. C++ -diff --git a/src/sage/categories/finite_coxeter_groups.py b/src/sage/categories/finite_coxeter_groups.py -index e0b2846..8395895 100644 ---- a/src/sage/categories/finite_coxeter_groups.py -+++ b/src/sage/categories/finite_coxeter_groups.py -@@ -712,11 +712,15 @@ class FiniteCoxeterGroups(CategoryWithAxiom): - If function is too slow, switching the base ring to - :class:`RDF` will almost certainly speed things up. - -- EXAMPLES:: -+ EXAMPLES: -+ -+ Unfortunately, an inexact base ring can not always be used:: - - sage: W = CoxeterGroup(['H',3], base_ring=RDF) - sage: W.permutahedron() -- A 3-dimensional polyhedron in RDF^3 defined as the convex hull of 120 vertices -+ Traceback (most recent call last): -+ ... -+ ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data - - sage: W = CoxeterGroup(['I',7]) - sage: W.permutahedron() -diff --git a/src/sage/geometry/polyhedron/backend_cdd.py b/src/sage/geometry/polyhedron/backend_cdd.py -index 85f6632..aaae546 100644 ---- a/src/sage/geometry/polyhedron/backend_cdd.py -+++ b/src/sage/geometry/polyhedron/backend_cdd.py -@@ -115,6 +115,10 @@ class Polyhedron_cdd(Polyhedron_base): - s = self._run_cdd(s, '--repall', verbose=verbose) - self._init_from_cdd_output(s) - if not self.base_ring().is_exact(): -+ if len(self._Vrepresentation) == 0: -+ # cdd (reasonably) refuses to handle empty polyhedra, so we -+ # skip this check -+ return - # cdd's parser can not handle the full output of --repall, so we - # need to extract the first block before we feed it back into cdd - s = s.splitlines() -diff --git a/src/sage/graphs/generators/smallgraphs.py b/src/sage/graphs/generators/smallgraphs.py -index bae02d7..084ed43 100644 ---- a/src/sage/graphs/generators/smallgraphs.py -+++ b/src/sage/graphs/generators/smallgraphs.py -@@ -4454,14 +4454,19 @@ def TruncatedIcosidodecahedralGraph(): - and 180 edges. For more information, see the - :wikipedia:`Truncated_icosidodecahedron`. - -- EXAMPLES:: -+ EXAMPLES: -+ -+ Unfortunately, this graph can not be constructed currently, due to numerical issues:: - - sage: g = graphs.TruncatedIcosidodecahedralGraph(); g -- Truncated Icosidodecahedron: Graph on 120 vertices -- sage: g.order(), g.size() -+ Traceback (most recent call last): -+ ... -+ ValueError: *Error: Numerical inconsistency is found. Use the GMP exact arithmetic. -+ sage: g.order(), g.size() # not tested - (120, 180) - """ - from sage.geometry.polyhedron.library import polytopes -+ # note that dropping exact=False here makes the construction take forever - G = polytopes.icosidodecahedron(exact=False).truncation().graph() - G.name("Truncated Icosidodecahedron") - return G --- -cgit v1.0-1-gd88e - - -From c4048677393f7088d1aa9a2c1392ed95d809d31c Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?Julian=20R=C3=BCth?= <julian.ru...@fsfe.org> -Date: Thu, 14 Jun 2018 12:00:27 +0200 -Subject: Relax cddlib sanity checks - -sometimes cddlib's output is useful even if it fails to transform back and forth ---- - src/sage/categories/finite_coxeter_groups.py | 9 ++--- - src/sage/geometry/polyhedron/backend_cdd.py | 6 ++- - src/sage/geometry/polyhedron/library.py | 56 +++++++++++++--------------- - 3 files changed, 33 insertions(+), 38 deletions(-) - -diff --git a/src/sage/categories/finite_coxeter_groups.py b/src/sage/categories/finite_coxeter_groups.py -index 8395895..78a89fd 100644 ---- a/src/sage/categories/finite_coxeter_groups.py -+++ b/src/sage/categories/finite_coxeter_groups.py -@@ -712,15 +712,14 @@ class FiniteCoxeterGroups(CategoryWithAxiom): - If function is too slow, switching the base ring to - :class:`RDF` will almost certainly speed things up. - -- EXAMPLES: -- -- Unfortunately, an inexact base ring can not always be used:: -+ EXAMPLES:: - - sage: W = CoxeterGroup(['H',3], base_ring=RDF) - sage: W.permutahedron() -- Traceback (most recent call last): -+ doctest:warning - ... -- ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data -+ UserWarning: This polyhedron data is numerically complicated; cdd could not convert between the inexact V and H representation without loss of data. The resulting object might show inconsistencies. -+ A 3-dimensional polyhedron in RDF^3 defined as the convex hull of 120 vertices - - sage: W = CoxeterGroup(['I',7]) - sage: W.permutahedron() -diff --git a/src/sage/geometry/polyhedron/backend_cdd.py b/src/sage/geometry/polyhedron/backend_cdd.py -index aaae546..64f3002 100644 ---- a/src/sage/geometry/polyhedron/backend_cdd.py -+++ b/src/sage/geometry/polyhedron/backend_cdd.py -@@ -82,7 +82,8 @@ class Polyhedron_cdd(Polyhedron_base): - # somewhat random numerical choices. (But I am not an - # expert in that field by any means.) See also - # https://github.com/cddlib/cddlib/pull/7. -- raise ValueError("polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data") -+ from warnings import warn -+ warn("This polyhedron data is numerically complicated; cdd could not convert between the inexact V and H representation without loss of data. The resulting object might show inconsistencies.") - Polyhedron_cdd._parse_block(t.splitlines(), 'V-representation', parse) - - def _init_from_Hrepresentation(self, ieqs, eqns, verbose=False): -@@ -137,7 +138,8 @@ class Polyhedron_cdd(Polyhedron_base): - # optimized for numerical stability, and makes some - # somewhat random numerical choices. (But I am not an - # expert in that field by any means.) -- raise ValueError("polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data") -+ from warnings import warn -+ warn("This polyhedron data is numerically complicated; cdd could not convert between the inexact V and H representation without loss of data. The resulting object might show inconsistencies.") - Polyhedron_cdd._parse_block(t.splitlines(), 'H-representation', parse) - - def _run_cdd(self, cdd_input_string, cmdline_arg, verbose=False): -diff --git a/src/sage/geometry/polyhedron/library.py b/src/sage/geometry/polyhedron/library.py -index 2cdc728..1115978 100644 ---- a/src/sage/geometry/polyhedron/library.py -+++ b/src/sage/geometry/polyhedron/library.py -@@ -1106,25 +1106,27 @@ class Polytopes(): - sage: td.base_ring() - Number Field in sqrt5 with defining polynomial x^2 - 5 - -- The faster implementation using floating point approximations does not -- work unfortunately, see https://github.com/cddlib/cddlib/pull/7 for a -- detailed discussion of this case:: -- -- sage: td = polytopes.truncated_dodecahedron(exact=False) -- Traceback (most recent call last): -- ... -- ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data -- sage: td.f_vector() # not tested -- (1, 60, 90, 32, 1) -- sage: td.base_ring() # not tested -- Real Double Field -- - Its faces are 20 triangles and 12 regular decagons:: - - sage: sum(1 for f in td.faces(2) if len(f.vertices()) == 3) - 20 - sage: sum(1 for f in td.faces(2) if len(f.vertices()) == 10) - 12 -+ -+ The faster implementation using floating point approximations does not -+ fully work unfortunately, see https://github.com/cddlib/cddlib/pull/7 -+ for a detailed discussion of this case:: -+ -+ sage: td = polytopes.truncated_dodecahedron(exact=False) -+ doctest:warning -+ ... -+ UserWarning: This polyhedron data is numerically complicated; cdd could not convert between the inexact V and H representation without loss of data. The resulting object might show inconsistencies. -+ sage: td.f_vector() -+ Traceback (most recent call last): -+ ... -+ KeyError: ... -+ sage: td.base_ring() -+ Real Double Field - """ - if base_ring is None and exact: - from sage.rings.number_field.number_field import QuadraticField -@@ -1328,25 +1330,21 @@ class Polytopes(): - sage: ti.base_ring() # long time - Number Field in sqrt5 with defining polynomial x^2 - 5 - -- The faster implementation using floating point approximations does not -- work unfortunately:: -+ The implementation using floating point approximations is much faster:: - - sage: ti = polytopes.truncated_icosidodecahedron(exact=False) -- Traceback (most recent call last): -- ... -- ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data -- sage: ti.f_vector() # not tested -+ sage: ti.f_vector() - (1, 120, 180, 62, 1) -- sage: ti.base_ring() # not tested -+ sage: ti.base_ring() - Real Double Field - - Its faces are 30 squares, 20 hexagons and 12 decagons:: - -- sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 4) # long time -+ sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 4) - 30 -- sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 6) # long time -+ sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 6) - 20 -- sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 10) # long time -+ sage: sum(1 for f in ti.faces(2) if len(f.vertices()) == 10) - 12 - """ - if base_ring is None and exact: -@@ -1564,18 +1562,14 @@ class Polytopes(): - sage: gap # not tested - very long time - A 4-dimensional polyhedron in (Number Field in sqrt5 with defining polynomial x^2 - 5)^4 defined as the convex hull of 100 vertices - -- Computation with approximated coordinates would be much faster but is -- not supported currently:: -+ Computation with approximated coordinates is much faster:: - - sage: gap = polytopes.grand_antiprism(exact=False) -- Traceback (most recent call last): -- ... -- ValueError: polyhedron data is numerically complicated; cdd could not convert between inexact V and H representation without loss of data -- sage: gap # not tested -+ sage: gap - A 4-dimensional polyhedron in RDF^4 defined as the convex hull of 100 vertices -- sage: gap.f_vector() # not tested -+ sage: gap.f_vector() - (1, 100, 500, 720, 320, 1) -- sage: len(list(gap.bounded_edges())) # not tested -+ sage: len(list(gap.bounded_edges())) - 500 - """ - from itertools import product --- -cgit v1.0-1-gd88e Added: sagemath-cremona.patch =================================================================== --- sagemath-cremona.patch (rev 0) +++ sagemath-cremona.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -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 SAGE_SHARE + from sage.misc.all import walltime + +@@ -825,7 +825,7 @@ 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: +@@ -1673,7 +1673,7 @@ 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' Deleted: sagemath-detect-igraph.patch =================================================================== --- sagemath-detect-igraph.patch 2018-08-17 21:06:27 UTC (rev 372567) +++ sagemath-detect-igraph.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -1,21 +0,0 @@ -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 -@@ -8480,10 +8480,12 @@ 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) - Modified: sagemath-env.patch =================================================================== --- sagemath-env.patch 2018-08-17 21:06:27 UTC (rev 372567) +++ sagemath-env.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -80,8 +80,8 @@ # The compilers are set in order of priority by # 1) environment variables @@ -296,8 +296,9 @@ - export SAGE_EXTCODE="$SAGE_SHARE/sage/ext" 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="$SAGE_SRC/doc" @@ -91,25 +91,48 @@ export SAGE_DOC="$SAGE_SHARE/doc/sage" if [ -z "${SAGE_ORIG_PATH_SET}" ]; then -@@ -403,6 +403,9 @@ +@@ -403,29 +403,8 @@ export SAGE_STARTUP_FILE fi +export LIBMTX="$DOT_SAGE/meataxe" +[[ -d $LIBMTX ]] || mkdir -p $LIBMTX # Create meataxe data dir -+ - if [ "$PYTHON_EGG_CACHE" = "" ]; then - PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs" - export PYTHON_EGG_CACHE -@@ -488,7 +488,6 @@ - fi +-if [ "$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 $LDFLAGS" + export LDFLAGS + +@@ -489,8 +489,6 @@ fi fi + -export MAXIMA_PREFIX="$SAGE_LOCAL" +-export MAXIMA_USERDIR="$DOT_SAGE/maxima" PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB -@@ -608,9 +608,6 @@ +@@ -601,9 +601,6 @@ LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH fi @@ -138,7 +161,7 @@ try: sitepackages_dirs = site.getsitepackages() -@@ -163,7 +163,7 @@ +@@ -164,7 +164,7 @@ _add_variable_or_fallback('GRAPHS_DATA_DIR', opj('$SAGE_SHARE','graphs')) _add_variable_or_fallback('ELLCURVE_DATA_DIR',opj('$SAGE_SHARE','ellcurves')) _add_variable_or_fallback('POLYTOPE_DATA_DIR',opj('$SAGE_SHARE','reflexive_polytopes')) Modified: sagemath-gap-4.8.patch =================================================================== --- sagemath-gap-4.8.patch 2018-08-17 21:06:27 UTC (rev 372567) +++ sagemath-gap-4.8.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -20,7 +20,7 @@ index 7bffcfc00d..51dad178d5 100644 --- a/src/sage/libs/gap/util.pyx +++ b/src/sage/libs/gap/util.pyx -@@ -166,7 +166,7 @@ def gap_root(): +@@ -170,7 +170,7 @@ def gap_root(): if os.path.exists(GAP_ROOT_DIR): return GAP_ROOT_DIR print('The gap-4.5.5.spkg (or later) seems to be not installed!') Deleted: sagemath-ignore-warnings.patch =================================================================== --- sagemath-ignore-warnings.patch 2018-08-17 21:06:27 UTC (rev 372567) +++ sagemath-ignore-warnings.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -1,25 +0,0 @@ -Description: Ignore warnings of PARI increasing the stack size when parsing doctests - Since we can't patch PARI to not produce the warnings and we don't want to - patch tons of doctests to expect the warnings, we patch the doctest parser - to ignore them. -Author: Tobias Hansen <than...@debian.org> ---- sage/src/sage/doctest/parsing.py -+++ sage/src/sage/doctest/parsing.py -@@ -40,6 +40,8 @@ - - float_regex = re.compile('\s*([+-]?\s*((\d*\.?\d+)|(\d+\.?))([eE][+-]?\d+)?)') - optional_regex = re.compile(r'(py2|py3|long time|not implemented|not tested|known bug)|([^ a-z]\s*optional\s*[:-]*((\s|\w)*))') -+pari_stack_warning_regex = re.compile(r'\s*\*\*\*.*(Warning: increasing stack size to )\d+\.') -+glpk_simplex_warning_regex = re.compile(r'(Long-step dual simplex will be used)') - find_sage_prompt = re.compile(r"^(\s*)sage: ", re.M) - find_sage_continuation = re.compile(r"^(\s*)\.\.\.\.:", re.M) - random_marker = re.compile('.*random', re.I) -@@ -935,6 +936,8 @@ - <type 'float'> - """ - got = self.human_readable_escape_sequences(got) -+ got = pari_stack_warning_regex.sub('', got) -+ got = glpk_simplex_warning_regex.sub('', got) - if isinstance(want, MarkedOutput): - if want.random: - return True Deleted: sagemath-lrs.patch =================================================================== --- sagemath-lrs.patch 2018-08-17 21:06:27 UTC (rev 372567) +++ sagemath-lrs.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -1,22 +0,0 @@ -diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/normal_form_game.py -index 2115de6800..da94aa5d45 100644 ---- a/src/sage/game_theory/normal_form_game.py -+++ b/src/sage/game_theory/normal_form_game.py -@@ -621,6 +621,7 @@ from sage.matrix.constructor import vector - from sage.misc.package import is_package_installed, PackageNotFoundError - from sage.misc.temporary_file import tmp_filename - from sage.numerical.mip import MixedIntegerLinearProgram -+import os - - try: - from gambit import Game -@@ -1636,7 +1637,7 @@ class NormalFormGame(SageObject, MutableMapping): - if not algorithm: - if self.is_constant_sum(): - algorithm = "lp" -- elif is_package_installed('lrslib'): -+ elif os.path.exists('/usr/bin/lrsnash'): - algorithm = "lrs" - else: - algorithm = "enumeration" - Deleted: sagemath-networkx2.patch =================================================================== --- sagemath-networkx2.patch 2018-08-17 21:06:27 UTC (rev 372567) +++ sagemath-networkx2.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -1,175 +0,0 @@ -diff --git a/src/sage/graphs/base/graph_backends.pyx b/src/sage/graphs/base/graph_backends.pyx -index ff1d02900a..bad4a18539 100644 ---- a/src/sage/graphs/base/graph_backends.pyx -+++ b/src/sage/graphs/base/graph_backends.pyx -@@ -800,9 +800,9 @@ class NetworkXGraphDeprecated(SageObject): - sage: X.multiedges = True - sage: G = X.mutate() - sage: G.edges() -- [(1, 2), (2, 3)] -+ MultiEdgeDataView([(1, 2), (2, 3)]) - sage: G.edges(data=True) -- [(1, 2, {'weight': 7}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})] -+ MultiEdgeDataView([(1, 2, {'weight': 7}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})]) - - """ - import networkx -@@ -868,11 +868,9 @@ class NetworkXDiGraphDeprecated(SageObject): - sage: X.multiedges = True - sage: G = X.mutate() - sage: G.edges() -- [(1, 2), (2, 1), (2, 3)] -+ OutMultiEdgeDataView([(1, 2), (2, 1), (2, 3)]) - sage: G.edges(data=True) -- [(1, 2, {'weight': 7}), -- (2, 1, {7: {}, 8: {}}), -- (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})] -+ OutMultiEdgeDataView([(1, 2, {'weight': 7}), (2, 1, {8: {}, 7: {}}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})]) - - """ - import networkx -@@ -1154,7 +1152,7 @@ class NetworkXGraphBackend(GenericGraphBackend): - import networkx - try: - if self._nxg.is_multigraph(): -- for k,d in self._nxg.edge[u][v].iteritems(): -+ for u0,v0,k,d in self._nxg.edges([u,v],True,keys=True): - if d.get('weight',None) == l: - self._nxg.remove_edge(u,v,k) - break -@@ -1223,7 +1221,7 @@ class NetworkXGraphBackend(GenericGraphBackend): - """ - cdef dict E - try: -- E = self._nxg.edge[u][v] -+ E = self._nxg.edges[u,v,0] - except KeyError: - from networkx import NetworkXError - raise NetworkXError("Edge (%s,%s) requested via get_edge_label does not exist."%(u,v)) -@@ -1412,7 +1410,7 @@ class NetworkXGraphBackend(GenericGraphBackend): - sage: G.iterator_nbrs(0) - <dictionary-keyiterator object at ...> - """ -- return self._nxg.neighbors_iter(v) -+ return self._nxg.neighbors(v) - - def iterator_in_nbrs(self, v): - """ -diff --git a/src/sage/graphs/digraph.py b/src/sage/graphs/digraph.py -index 003a8d6bcb..986137a9b0 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 "+ -@@ -2846,7 +2846,7 @@ class DiGraph(GenericGraph): - Using the NetworkX implementation :: - - sage: D.topological_sort(implementation = "NetworkX") -- [4, 5, 6, 9, 0, 1, 2, 3, 7, 8, 10] -+ [4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10] - - Using the NetworkX recursive implementation :: - -@@ -2872,9 +2872,7 @@ class DiGraph(GenericGraph): - sage: D = DiGraph({ 0:[1,2,3], 4:[2,5], 1:[8], 2:[7], 3:[7], - ....: 5:[6,7], 7:[8], 6:[9], 8:[10], 9:[10] }) - sage: N = D.networkx_graph() -- sage: networkx.topological_sort(N) -- [4, 5, 6, 9, 0, 1, 2, 3, 7, 8, 10] -- sage: networkx.topological_sort_recursive(N) -+ sage: list(networkx.topological_sort(N)) - [4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10] - - TESTS: -@@ -2897,10 +2895,7 @@ class DiGraph(GenericGraph): - - elif implementation == "NetworkX" or implementation == "recursive": - import networkx -- if implementation == "NetworkX": -- S = networkx.topological_sort(self.networkx_graph(copy=False)) -- else: -- S = networkx.topological_sort_recursive(self.networkx_graph(copy=False)) -+ S = list(networkx.topological_sort(self.networkx_graph(copy=False))) - if S is None: - raise TypeError('Digraph is not acyclic; there is no topological sort.') - else: -diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py -index 8f81333685..1540ec0dcc 100644 ---- a/src/sage/graphs/generators/families.py -+++ b/src/sage/graphs/generators/families.py -@@ -197,7 +197,7 @@ def BalancedTree(r, h): - gracefully:: - - sage: graphs.BalancedTree(1, 10) -- Balanced tree: Graph on 2 vertices -+ Balanced tree: Graph on 11 vertices - - sage: graphs.BalancedTree(-1, 10) - Balanced tree: Graph on 1 vertex -@@ -208,9 +208,6 @@ def BalancedTree(r, h): - sage: graphs.BalancedTree(3, 0) - Balanced tree: Graph on 1 vertex - -- sage: graphs.BalancedTree(5, -2) -- Balanced tree: Graph on 0 vertices -- - sage: graphs.BalancedTree(-2,-2) - Balanced tree: Graph on 0 vertices - """ -diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py -index 3550f990ef..490813e619 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. "+ -@@ -4621,7 +4621,7 @@ class Graph(GenericGraph): - - sage: g = Graph([(0,1,0), (1,2,999), (2,3,-5)]) - sage: g.matching(use_edge_labels=True) -- [(1, 2, 999)] -+ [(0, 1, 0), (2, 3, -5)] - sage: g.matching(algorithm="LP", use_edge_labels=True) - [(1, 2, 999)] - -@@ -4671,7 +4671,7 @@ class Graph(GenericGraph): - else: - for u, v in L: - g.add_edge(u, v) -- d = networkx.max_weight_matching(g) -+ d = dict(networkx.max_weight_matching(g).union(t[::-1] for t in networkx.max_weight_matching(g))) - if value_only: - if use_edge_labels: - return sum(W[u, v] for u, v in six.iteritems(d) if u < v) -@@ -6305,7 +6305,7 @@ class Graph(GenericGraph): - return networkx.number_of_cliques(self.networkx_graph(copy=False), vertices, cliques) - - @doc_index("Clique-related methods") -- def cliques_get_max_clique_graph(self, name=''): -+ def cliques_get_max_clique_graph(self): - """ - Return the clique graph. - -@@ -6336,7 +6336,7 @@ class Graph(GenericGraph): - sage: (G.cliques_get_max_clique_graph()).show(figsize=[2,2]) - """ - import networkx -- return Graph(networkx.make_max_clique_graph(self.networkx_graph(copy=False), name=name, create_using=networkx.MultiGraph())) -+ return Graph(networkx.make_max_clique_graph(self.networkx_graph(copy=False), create_using=networkx.MultiGraph())) - - @doc_index("Clique-related methods") - def cliques_get_clique_bipartite(self, **kwds): - Modified: sagemath-python3-notebook.patch =================================================================== --- sagemath-python3-notebook.patch 2018-08-17 21:06:27 UTC (rev 372567) +++ sagemath-python3-notebook.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -16,7 +16,7 @@ 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): +@@ -289,7 +289,6 @@ def have_prerequisites(debug=True): True """ try: Modified: sagemath-singular-4.1.1.patch =================================================================== --- sagemath-singular-4.1.1.patch 2018-08-17 21:06:27 UTC (rev 372567) +++ sagemath-singular-4.1.1.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -1,5 +1,16 @@ +From 426644f6d085e053fa0fcf3457702eac685b7cba Mon Sep 17 00:00:00 2001 +From: Antonio Rojas <aro...@archlinux.org> +Date: Sat, 7 Jul 2018 00:37:37 +0200 +Subject: Adapt to singular 4.1.1 API changes + +--- + src/sage/libs/singular/decl.pxd | 4 ++-- + .../rings/polynomial/multi_polynomial_libsingular.pyx | 16 ++++++++-------- + src/sage/rings/polynomial/plural.pyx | 4 ++-- + 3 files changed, 12 insertions(+), 12 deletions(-) + diff --git a/src/sage/libs/singular/decl.pxd b/src/sage/libs/singular/decl.pxd -index 676544ab1e..5c8639d362 100644 +index 4b658c4..84476a9 100644 --- a/src/sage/libs/singular/decl.pxd +++ b/src/sage/libs/singular/decl.pxd @@ -170,7 +170,7 @@ cdef extern from "singular/Singular/libsingular.h": @@ -21,7 +32,7 @@ # return the i-th power of p; p destroyed, requires global ring diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx -index 089524d6b4..ce6d58fc6f 100644 +index 2a8d9ae..f2a11a8 100644 --- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx @@ -190,8 +190,8 @@ from sage.libs.singular.decl cimport ( @@ -35,7 +46,7 @@ p_IsUnit, p_Series, p_Head, idInit, fast_map_common_subexp, id_Delete, p_IsHomogeneous, p_Homogen, p_Totaldegree,pLDeg1_Totaldegree, singclap_pdivide, singclap_factorize, idLift, IDELEMS, On, Off, SW_USE_CHINREM_GCD, SW_USE_EZGCD, -@@ -1692,8 +1697,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic): +@@ -1693,8 +1693,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_base): if not g._poly: raise ZeroDivisionError @@ -46,7 +57,7 @@ if coeff: if r.cf.type == n_unknown or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf): n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf) -@@ -1852,8 +1857,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic): +@@ -1853,8 +1853,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_base): and (<MPolynomial_libsingular>g) \ and g.parent() is self \ and p_LmDivisibleBy((<MPolynomial_libsingular>g)._poly, m, r): @@ -57,7 +68,7 @@ #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<MPolynomial_libsingular>g)._poly, r), r), r) p_SetCoeff(flt, n_Init(1, r), r) return new_MP(self,flt), g -@@ -4049,10 +4054,10 @@ cdef class MPolynomial_libsingular(MPolynomial): +@@ -4055,10 +4055,10 @@ cdef class MPolynomial_libsingular(MPolynomial): if _right.is_monomial(): p = _self._poly quo = p_ISet(0,r) @@ -71,10 +82,10 @@ quo = p_Add_q(quo, temp, r) p = pNext(p) diff --git a/src/sage/rings/polynomial/plural.pyx b/src/sage/rings/polynomial/plural.pyx -index 3b45a38419..c0227fd364 100644 +index d5439f7f..ad20ebc 100644 --- a/src/sage/rings/polynomial/plural.pyx +++ b/src/sage/rings/polynomial/plural.pyx -@@ -999,7 +999,7 @@ cdef class NCPolynomialRing_plural(Ring): +@@ -998,7 +998,7 @@ cdef class NCPolynomialRing_plural(Ring): if not g._poly: raise ZeroDivisionError @@ -83,7 +94,7 @@ if coeff: if (r.cf.type == n_unknown) or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf): n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf) -@@ -1194,7 +1194,7 @@ cdef class NCPolynomialRing_plural(Ring): +@@ -1193,7 +1193,7 @@ cdef class NCPolynomialRing_plural(Ring): if isinstance(g, NCPolynomial_plural) \ and (<NCPolynomial_plural>g) \ and p_LmDivisibleBy((<NCPolynomial_plural>g)._poly, m, r): @@ -92,11 +103,25 @@ #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<NCPolynomial_plural>g)._poly, r), r), r) p_SetCoeff(flt, n_Init(1, r), r) return new_NCP(self,flt), g +-- +cgit v1.0-1-gd88e + + +From d5fc2a4bc640856507d743c2f67ad454874700e7 Mon Sep 17 00:00:00 2001 +From: Antonio Rojas <aro...@archlinux.org> +Date: Sat, 7 Jul 2018 00:38:56 +0200 +Subject: Don't call singclap_pdivide for integer coefficients, it's no longer + supported + +--- + src/sage/rings/polynomial/multi_polynomial_libsingular.pyx | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx -index 809ca72c76..9610ce125d 100644 +index f2a11a8..774fecd 100644 --- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx -@@ -4881,7 +4881,7 @@ cdef class MPolynomial_libsingular(MPolynomial): +@@ -4888,7 +4888,7 @@ cdef class MPolynomial_libsingular(MPolynomial): if right.is_zero(): raise ZeroDivisionError @@ -105,4 +130,773 @@ py_quo = self//right py_rem = self - right*py_quo return py_quo, py_rem +-- +cgit v1.0-1-gd88e + +From 4763da19a9ea0be849ee3640fc39747d725cb5a1 Mon Sep 17 00:00:00 2001 +From: Antonio Rojas <aro...@archlinux.org> +Date: Sat, 21 Jul 2018 11:31:02 +0200 +Subject: Fix lcm of polynomials with integer coefficients and add test + +--- + src/sage/rings/polynomial/multi_polynomial_libsingular.pyx | 8 ++++++++ + 1 file changed, 8 insertions(+) + +diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +index 774fecd..bb5aca6 100644 +--- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx ++++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +@@ -4794,6 +4794,8 @@ cdef class MPolynomial_libsingular(MPolynomial): + sage: p = -x*y + x*z + 54*x - 2 + sage: (5*p^2).lcm(3*p) == 15*p^2 + True ++ sage: lcm(2*x,2*x*y) ++ 2*x*y + """ + cdef ring *_ring = self._parent_ring + cdef poly *ret +@@ -4805,6 +4807,12 @@ cdef class MPolynomial_libsingular(MPolynomial): + if _ring.cf.type != n_unknown: + if _ring.cf.type == n_Znm or _ring.cf.type == n_Zn or _ring.cf.type == n_Z2m : + raise TypeError("LCM over non-integral domains not available.") ++ if _ring.cf.type == n_Z: ++ f_content = self.content() ++ g_content = g.content() ++ f_primitivepart = self / f_content ++ g_primitivepart = g / g_content ++ return f_primitivepart.change_ring(RationalField()).lcm(g_primitivepart.change_ring(RationalField())) * f_content.lcm(g_content) + + if self._parent is not g._parent: + _g = self._parent._coerce_c(g) +-- +cgit v1.0-1-gd88e + + +From 544f67d45ce00142d99cbca7ca1ef39df95d3551 Mon Sep 17 00:00:00 2001 +From: Timo Kaufmann <timo...@zoho.com> +Date: Fri, 20 Jul 2018 16:58:48 +0200 +Subject: =?UTF-8?q?Revert=20"Trac=20#25313:=20Speed=20up=20exact=20divisio?= + =?UTF-8?q?n=20in=20=E2=84=A4[x,y,...]"?= +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + +This reverts commit 5ef19ad3901910976878348ef2ec76637420010b, reversing +changes made to 1c41c1d6cadf5bb863d5c0d125300a153f232fa5. +--- + .../rings/polynomial/multi_polynomial_libsingular.pyx | 15 +++++---------- + 1 file changed, 5 insertions(+), 10 deletions(-) + +diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +index bb5aca6..92d6ed5 100644 +--- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx ++++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +@@ -4023,16 +4023,6 @@ cdef class MPolynomial_libsingular(MPolynomial): + Traceback (most recent call last): + ... + NotImplementedError: Division of multivariate polynomials over non fields by non-monomials not implemented. +- +- TESTS:: +- +- sage: P.<x,y> = ZZ[] +- sage: p = 3*(-x^8*y^2 - x*y^9 + 6*x^8*y + 17*x^2*y^6 - x^3*y^2) +- sage: q = 7*(x^2 + x*y + y^2 + 1) +- sage: p*q//q == p +- True +- sage: p*q//p == q +- True + """ + cdef MPolynomialRing_libsingular parent = self._parent + cdef ring *r = self._parent_ring +@@ -4052,6 +4042,11 @@ cdef class MPolynomial_libsingular(MPolynomial): + _right = <MPolynomial_libsingular>right + + if r.cf.type != n_unknown: ++ if r.cf.type == n_Z: ++ P = parent.change_ring(RationalField()) ++ f = P(self)//P(right) ++ CM = list(f) ++ return parent(sum([c.floor()*m for c,m in CM])) + if _right.is_monomial(): + p = _self._poly + quo = p_ISet(0,r) +-- +cgit v1.0-1-gd88e + + +From 2cd8487ff5a7f74c6c75659b44be5f48d27639e6 Mon Sep 17 00:00:00 2001 +From: Timo Kaufmann <timo...@zoho.com> +Date: Fri, 20 Jul 2018 18:32:20 +0200 +Subject: singular: update doctests + +--- + src/sage/rings/polynomial/multi_polynomial_ideal.py | 1 + + src/sage/rings/polynomial/multi_polynomial_libsingular.pyx | 2 +- + src/sage/rings/polynomial/polynomial_singular_interface.py | 8 ++++---- + 3 files changed, 6 insertions(+), 5 deletions(-) + +diff --git a/src/sage/rings/polynomial/multi_polynomial_ideal.py b/src/sage/rings/polynomial/multi_polynomial_ideal.py +index 37dc45c..8bd5306 100644 +--- a/src/sage/rings/polynomial/multi_polynomial_ideal.py ++++ b/src/sage/rings/polynomial/multi_polynomial_ideal.py +@@ -2199,6 +2199,7 @@ class MPolynomialIdeal_singular_repr( + sage: I.variety() + verbose 0 (...: multi_polynomial_ideal.py, variety) Warning: computations in the complex field are inexact; variety may be computed partially or incorrectly. + verbose 0 (...: multi_polynomial_ideal.py, variety) Warning: falling back to very slow toy implementation. ++ ... + [{y: -0.86602540378443... - 0.500000000000000*I}, + {y: -0.86602540378443... + 0.500000000000000*I}, + {y: 0.86602540378443... - 0.500000000000000*I}, +diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +index 92d6ed5..619e7f0 100644 +--- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx ++++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +@@ -4869,7 +4869,7 @@ cdef class MPolynomial_libsingular(MPolynomial): + sage: f.quo_rem(y) + (2*x^2, x + 1) + sage: f.quo_rem(3*x) +- (2*x*y + 1, -4*x^2*y - 2*x + 1) ++ (0, 2*x^2*y + x + 1) + + TESTS:: + +diff --git a/src/sage/rings/polynomial/polynomial_singular_interface.py b/src/sage/rings/polynomial/polynomial_singular_interface.py +index 9331169..f753610 100644 +--- a/src/sage/rings/polynomial/polynomial_singular_interface.py ++++ b/src/sage/rings/polynomial/polynomial_singular_interface.py +@@ -81,8 +81,8 @@ class PolynomialRing_singular_repr: + sage: R.<x,y> = PolynomialRing(CC) + sage: singular(R) + polynomial ring, over a field, global ordering +- // coefficients: float[I](complex:15 digits, additional 0 digits)/(I^2+1) +- // number of vars : 2 ++ // coefficients: real[I](complex:15 digits, additional 0 digits)/(I^2+1) ++ // number of vars : 2 + // block 1 : ordering dp + // : names x y + // block 2 : ordering C +@@ -90,8 +90,8 @@ class PolynomialRing_singular_repr: + sage: R.<x,y> = PolynomialRing(RealField(100)) + sage: singular(R) + polynomial ring, over a field, global ordering +- // coefficients: float +- // number of vars : 2 ++ // coefficients: Float() ++ // number of vars : 2 + // block 1 : ordering dp + // : names x y + // block 2 : ordering C +-- +cgit v1.0-1-gd88e + + +From d9dc104b4ff3d3cc34fa8ec9483f83fce033f627 Mon Sep 17 00:00:00 2001 +From: Antonio Rojas <aro...@archlinux.org> +Date: Sun, 22 Jul 2018 00:54:38 +0200 +Subject: Make Singular error parser more granular + +--- + src/sage/interfaces/singular.py | 2 +- + src/sage/rings/polynomial/multi_polynomial_ideal.py | 1 - + 2 files changed, 1 insertion(+), 2 deletions(-) + +diff --git a/src/sage/interfaces/singular.py b/src/sage/interfaces/singular.py +index 9d65c9f..031172e 100644 +--- a/src/sage/interfaces/singular.py ++++ b/src/sage/interfaces/singular.py +@@ -654,7 +654,7 @@ class Singular(ExtraTabCompletion, Expect): + + s = Expect.eval(self, x, **kwds) + +- if s.find("error") != -1 or s.find("Segment fault") != -1: ++ if s.find("error occurred") != -1 or s.find("Segment fault") != -1: + raise SingularError('Singular error:\n%s'%s) + + if get_verbose() > 0: +diff --git a/src/sage/rings/polynomial/multi_polynomial_ideal.py b/src/sage/rings/polynomial/multi_polynomial_ideal.py +index 8bd5306..37dc45c 100644 +--- a/src/sage/rings/polynomial/multi_polynomial_ideal.py ++++ b/src/sage/rings/polynomial/multi_polynomial_ideal.py +@@ -2199,7 +2199,6 @@ class MPolynomialIdeal_singular_repr( + sage: I.variety() + verbose 0 (...: multi_polynomial_ideal.py, variety) Warning: computations in the complex field are inexact; variety may be computed partially or incorrectly. + verbose 0 (...: multi_polynomial_ideal.py, variety) Warning: falling back to very slow toy implementation. +- ... + [{y: -0.86602540378443... - 0.500000000000000*I}, + {y: -0.86602540378443... + 0.500000000000000*I}, + {y: 0.86602540378443... - 0.500000000000000*I}, +-- +cgit v1.0-1-gd88e + + +From ab851b1a2485c98b9f281e5bb5ea294e84f39040 Mon Sep 17 00:00:00 2001 +From: Antonio Rojas <aro...@archlinux.org> +Date: Sun, 22 Jul 2018 01:02:23 +0200 +Subject: Update some tests output + +--- + src/sage/interfaces/singular.py | 12 ++++++------ + 1 file changed, 6 insertions(+), 6 deletions(-) + +diff --git a/src/sage/interfaces/singular.py b/src/sage/interfaces/singular.py +index 031172e..f7972f5 100644 +--- a/src/sage/interfaces/singular.py ++++ b/src/sage/interfaces/singular.py +@@ -1079,7 +1079,7 @@ class Singular(ExtraTabCompletion, Expect): + sage: S = singular.ring('real', '(a,b)', 'lp') + sage: singular.current_ring() + polynomial ring, over a field, global ordering +- // coefficients: float ++ // coefficients: Float() + // number of vars : 2 + // block 1 : ordering lp + // : names a b +@@ -1157,7 +1157,7 @@ class Singular(ExtraTabCompletion, Expect): + sage: singular._tab_completion() + ['exteriorPower', + ... +- 'flintZ'] ++ 'crossprod'] + """ + p = re.compile("// *([a-z0-9A-Z_]*).*") #compiles regular expression + proclist = self.eval("listvar(proc)").splitlines() +@@ -1183,7 +1183,7 @@ class Singular(ExtraTabCompletion, Expect): + EXAMPLES:: + + sage: singular.version() +- "Singular ... version 4.1.0 ... ++ "Singular ... version 4.1.1 ... + """ + return singular_version() + +@@ -1992,7 +1992,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement): + sage: S = singular.ring('real', '(a,b)', 'lp') + sage: singular.current_ring() + polynomial ring, over a field, global ordering +- // coefficients: float ++ // coefficients: Float() + // number of vars : 2 + // block 1 : ordering lp + // : names a b +@@ -2072,7 +2072,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement): + sage: R._tab_completion() + ['exteriorPower', + ... +- 'flintZ'] ++ 'crossprod'] + """ + return self.parent()._tab_completion() + +@@ -2358,7 +2358,7 @@ def singular_version(): + EXAMPLES:: + + sage: singular.version() +- "Singular ... version 4.1.0 ... ++ "Singular ... version 4.1.1 ... + """ + return singular.eval('system("--version");') + +-- +cgit v1.0-1-gd88e + + +From 921cc310908e1880884af556dc9452c2b4ba8bc8 Mon Sep 17 00:00:00 2001 +From: Antonio Rojas <aro...@archlinux.org> +Date: Tue, 24 Jul 2018 18:45:26 +0200 +Subject: Fix real base ring detection + +Singular prints it as 'Float()' instead of 'real' now +--- + src/sage/interfaces/singular.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/sage/interfaces/singular.py b/src/sage/interfaces/singular.py +index f7972f5..3815951 100644 +--- a/src/sage/interfaces/singular.py ++++ b/src/sage/interfaces/singular.py +@@ -1562,7 +1562,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement): + elif charstr[0] in ['0', 'QQ']: + from sage.all import QQ + br = QQ +- elif charstr[0]=='real': ++ elif charstr[0].startswith('Float'): + from sage.all import RealField, ceil, log + prec = singular.eval('ringlist(basering)[1][2][1]') + br = RealField(ceil((ZZ(prec)+1)/log(2,10))) +-- +cgit v1.0-1-gd88e + + +From 0f55b763c775bb0d652b53d50dc26f11e9f472a0 Mon Sep 17 00:00:00 2001 +From: Antonio Rojas <aro...@archlinux.org> +Date: Tue, 24 Jul 2018 19:16:20 +0200 +Subject: More real -> Float porting + +--- + src/sage/interfaces/singular.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/sage/interfaces/singular.py b/src/sage/interfaces/singular.py +index 3815951..0447920 100644 +--- a/src/sage/interfaces/singular.py ++++ b/src/sage/interfaces/singular.py +@@ -1750,7 +1750,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement): + + # Singular 4 puts parentheses around floats and sign outside them + charstr = self.parent().eval('charstr(basering)').split(',',1) +- if charstr[0] in ['real', 'complex']: ++ if charstr[0]=='complex' or charstr[0].startswith('Float'): + for i in range(coeff_start, 2 * coeff_start): + singular_poly_list[i] = singular_poly_list[i].replace('(','').replace(')','') + +-- +cgit v1.0-1-gd88e + + +From aea054407a41a517070eb06e8efcd02d6356269f Mon Sep 17 00:00:00 2001 +From: Antonio Rojas <aro...@archlinux.org> +Date: Tue, 24 Jul 2018 19:38:55 +0200 +Subject: Don't check for exact Singular version + +Should improve testing future Singular upgrades on distributions +--- + src/sage/interfaces/singular.py | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/src/sage/interfaces/singular.py b/src/sage/interfaces/singular.py +index 0447920..a028bbe 100644 +--- a/src/sage/interfaces/singular.py ++++ b/src/sage/interfaces/singular.py +@@ -1183,7 +1183,7 @@ class Singular(ExtraTabCompletion, Expect): + EXAMPLES:: + + sage: singular.version() +- "Singular ... version 4.1.1 ... ++ "Singular ... version 4... + """ + return singular_version() + +@@ -2358,7 +2358,7 @@ def singular_version(): + EXAMPLES:: + + sage: singular.version() +- "Singular ... version 4.1.1 ... ++ "Singular ... version 4... + """ + return singular.eval('system("--version");') + +-- +cgit v1.0-1-gd88e + + +From 4e52b5e3ca6bbb34666c25decbf9bab3e2b46e82 Mon Sep 17 00:00:00 2001 +From: Antonio Rojas <aro...@archlinux.org> +Date: Wed, 25 Jul 2018 16:17:38 +0200 +Subject: Use p_Divide for lcm as suggested by upstream + +See https://www.singular.uni-kl.de/forum/viewtopic.php?f=10&t=2768 +--- + src/sage/libs/singular/decl.pxd | 4 ++++ + src/sage/rings/polynomial/multi_polynomial_libsingular.pyx | 12 ++---------- + 2 files changed, 6 insertions(+), 10 deletions(-) + +diff --git a/src/sage/libs/singular/decl.pxd b/src/sage/libs/singular/decl.pxd +index 84476a9..d863740 100644 +--- a/src/sage/libs/singular/decl.pxd ++++ b/src/sage/libs/singular/decl.pxd +@@ -630,6 +630,10 @@ cdef extern from "singular/Singular/libsingular.h": + # return p*q, destroys p and q + poly *p_Mult_q(poly *p, poly *q, ring *r) + ++ # polynomial division, ignoring the rest ++ # via singclap_pdivide resp. idLift, destroys p,q ++ poly *p_Divide(poly *p, poly *q, ring *r) ++ + # divide monomial p by monomial q, p,q const + + poly *pMDivide(poly *p,poly *q) +diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +index 619e7f0..aeff53a 100644 +--- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx ++++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +@@ -190,7 +190,7 @@ from sage.libs.singular.decl cimport ( + n_IsUnit, n_Invers, + p_ISet, rChangeCurrRing, p_Copy, p_Init, p_SetCoeff, p_Setm, p_SetExp, p_Add_q, + p_NSet, p_GetCoeff, p_Delete, p_GetExp, pNext, rRingVar, omAlloc0, omStrDup, +- omFree, pMDivide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy, ++ omFree, pMDivide, p_Divide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy, + pMDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy, + p_IsUnit, p_Series, p_Head, idInit, fast_map_common_subexp, id_Delete, + p_IsHomogeneous, p_Homogen, p_Totaldegree,pLDeg1_Totaldegree, singclap_pdivide, singclap_factorize, +@@ -4802,12 +4802,6 @@ cdef class MPolynomial_libsingular(MPolynomial): + if _ring.cf.type != n_unknown: + if _ring.cf.type == n_Znm or _ring.cf.type == n_Zn or _ring.cf.type == n_Z2m : + raise TypeError("LCM over non-integral domains not available.") +- if _ring.cf.type == n_Z: +- f_content = self.content() +- g_content = g.content() +- f_primitivepart = self / f_content +- g_primitivepart = g / g_content +- return f_primitivepart.change_ring(RationalField()).lcm(g_primitivepart.change_ring(RationalField())) * f_content.lcm(g_content) + + if self._parent is not g._parent: + _g = self._parent._coerce_c(g) +@@ -4824,9 +4818,7 @@ cdef class MPolynomial_libsingular(MPolynomial): + if _ring!=currRing: rChangeCurrRing(_ring) # singclap_gcd + gcd = singclap_gcd(p_Copy(self._poly, _ring), p_Copy(_g._poly, _ring), _ring ) + prod = pp_Mult_qq(self._poly, _g._poly, _ring) +- ret = singclap_pdivide(prod , gcd , _ring) +- p_Delete(&prod, _ring) +- p_Delete(&gcd, _ring) ++ ret = p_Divide(prod, gcd, _ring) + if count >= 20: + sig_off() + return new_MP(self._parent, ret) +-- +cgit v1.0-1-gd88e + +From 930ba2eb1cacaf4e1e43733feb560dd105d531be Mon Sep 17 00:00:00 2001 +From: Antonio Rojas <aro...@archlinux.org> +Date: Wed, 25 Jul 2018 22:45:15 +0200 +Subject: Remove duplicate cimport + +--- + src/sage/rings/polynomial/multi_polynomial_libsingular.pyx | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +index aeff53a..f0a174f 100644 +--- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx ++++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +@@ -190,7 +190,7 @@ from sage.libs.singular.decl cimport ( + n_IsUnit, n_Invers, + p_ISet, rChangeCurrRing, p_Copy, p_Init, p_SetCoeff, p_Setm, p_SetExp, p_Add_q, + p_NSet, p_GetCoeff, p_Delete, p_GetExp, pNext, rRingVar, omAlloc0, omStrDup, +- omFree, pMDivide, p_Divide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy, ++ omFree, p_Divide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy, + pMDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy, + p_IsUnit, p_Series, p_Head, idInit, fast_map_common_subexp, id_Delete, + p_IsHomogeneous, p_Homogen, p_Totaldegree,pLDeg1_Totaldegree, singclap_pdivide, singclap_factorize, +-- +cgit v1.0-1-gd88e + +From 07ef11b3209f498dc771bf5cb02f1b3ce1264cbb Mon Sep 17 00:00:00 2001 +From: Antonio Rojas <aro...@archlinux.org> +Date: Thu, 26 Jul 2018 15:25:57 +0200 +Subject: rest -> reminder + +--- + src/sage/libs/singular/decl.pxd | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/sage/libs/singular/decl.pxd b/src/sage/libs/singular/decl.pxd +index d863740..7f09aaf 100644 +--- a/src/sage/libs/singular/decl.pxd ++++ b/src/sage/libs/singular/decl.pxd +@@ -630,7 +630,7 @@ cdef extern from "singular/Singular/libsingular.h": + # return p*q, destroys p and q + poly *p_Mult_q(poly *p, poly *q, ring *r) + +- # polynomial division, ignoring the rest ++ # polynomial division, ignoring the remainder + # via singclap_pdivide resp. idLift, destroys p,q + poly *p_Divide(poly *p, poly *q, ring *r) + +-- +cgit v1.0-1-gd88e + + +From a9e5aed9215175f8cf49327c790ae153648a2513 Mon Sep 17 00:00:00 2001 +From: Jeroen Demeyer <jdeme...@cage.ugent.be> +Date: Sat, 28 Jul 2018 15:09:54 +0200 +Subject: Minor fixes to Singular interface + +--- + src/sage/interfaces/singular.py | 4 +- + .../polynomial/multi_polynomial_libsingular.pyx | 79 ++++++++++++---------- + src/sage/rings/polynomial/plural.pyx | 19 +++--- + 3 files changed, 55 insertions(+), 47 deletions(-) + +diff --git a/src/sage/interfaces/singular.py b/src/sage/interfaces/singular.py +index a028bbe..3d563ff 100644 +--- a/src/sage/interfaces/singular.py ++++ b/src/sage/interfaces/singular.py +@@ -654,6 +654,8 @@ class Singular(ExtraTabCompletion, Expect): + + s = Expect.eval(self, x, **kwds) + ++ # "Segment fault" is not a typo: ++ # Singular actually does use that string + if s.find("error occurred") != -1 or s.find("Segment fault") != -1: + raise SingularError('Singular error:\n%s'%s) + +@@ -1750,7 +1752,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement): + + # Singular 4 puts parentheses around floats and sign outside them + charstr = self.parent().eval('charstr(basering)').split(',',1) +- if charstr[0]=='complex' or charstr[0].startswith('Float'): ++ if charstr[0].startswith('Float') or charstr[0] == 'complex': + for i in range(coeff_start, 2 * coeff_start): + singular_poly_list[i] = singular_poly_list[i].replace('(','').replace(')','') + +diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +index f0a174f..043696e 100644 +--- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx ++++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +@@ -181,8 +181,8 @@ from cysignals.signals cimport sig_on, sig_off + from sage.cpython.string cimport char_to_str, str_to_bytes + + # singular types +-from sage.libs.singular.decl cimport ring, poly, ideal, intvec, number, currRing +-from sage.libs.singular.decl cimport n_unknown, n_Zp, n_Q, n_R, n_GF, n_long_R, n_algExt,n_transExt,n_long_C, n_Z, n_Zn, n_Znm, n_Z2m, n_CF ++from sage.libs.singular.decl cimport (ring, poly, ideal, intvec, number, ++ currRing, n_unknown, n_Z, n_Zn, n_Znm, n_Z2m) + + # singular functions + from sage.libs.singular.decl cimport ( +@@ -198,7 +198,7 @@ from sage.libs.singular.decl cimport ( + p_LmIsConstant, pTakeOutComp1, singclap_gcd, pp_Mult_qq, p_GetMaxExp, + pLength, kNF, p_Neg, p_Minus_mm_Mult_qq, p_Plus_mm_Mult_qq, + pDiff, singclap_resultant, p_Normalize, +- prCopyR, prCopyR_NoSort ) ++ prCopyR, prCopyR_NoSort) + + # singular conversion routines + from sage.libs.singular.singular cimport si2sa, sa2si, overflow_check +@@ -225,7 +225,7 @@ from sage.rings.polynomial.polynomial_ring import is_PolynomialRing + # base ring imports + from sage.rings.finite_rings.finite_field_prime_modn import FiniteField_prime_modn + from sage.rings.rational cimport Rational +-from sage.rings.rational_field import RationalField ++from sage.rings.rational_field import QQ + from sage.rings.complex_field import is_ComplexField + from sage.rings.real_mpfr import is_RealField + from sage.rings.integer_ring import is_IntegerRing, ZZ +@@ -1693,7 +1693,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_base): + if not g._poly: + raise ZeroDivisionError + +- if r!=currRing: rChangeCurrRing(r) # pMDivide ++ if r is not currRing: ++ rChangeCurrRing(r) + res = pMDivide(f._poly, g._poly) + if coeff: + if r.cf.type == n_unknown or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf): +@@ -1846,19 +1847,18 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_base): + cdef poly *flt + + if not m: +- return f,f ++ return (f, f) + + for g in G: +- if isinstance(g, MPolynomial_libsingular) \ +- and (<MPolynomial_libsingular>g) \ +- and g.parent() is self \ +- and p_LmDivisibleBy((<MPolynomial_libsingular>g)._poly, m, r): +- if r!=currRing: rChangeCurrRing(r) # pMDivide +- flt = pMDivide(f._poly, (<MPolynomial_libsingular>g)._poly) +- #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<MPolynomial_libsingular>g)._poly, r), r), r) +- p_SetCoeff(flt, n_Init(1, r), r) +- return new_MP(self,flt), g +- return self._zero_element,self._zero_element ++ if isinstance(g, MPolynomial_libsingular) and g: ++ h = <MPolynomial_libsingular>g ++ if h._parent is self and p_LmDivisibleBy(h._poly, m, r): ++ if r is not currRing: ++ rChangeCurrRing(r) ++ flt = pMDivide(f._poly, h._poly) ++ p_SetCoeff(flt, n_Init(1, r), r) ++ return (new_MP(self, flt), h) ++ return (self._zero_element, self._zero_element) + + def monomial_pairwise_prime(self, MPolynomial_libsingular g, MPolynomial_libsingular h): + """ +@@ -4023,11 +4023,19 @@ cdef class MPolynomial_libsingular(MPolynomial): + Traceback (most recent call last): + ... + NotImplementedError: Division of multivariate polynomials over non fields by non-monomials not implemented. ++ ++ TESTS:: ++ ++ sage: P.<x,y> = ZZ[] ++ sage: p = 3*(-x^8*y^2 - x*y^9 + 6*x^8*y + 17*x^2*y^6 - x^3*y^2) ++ sage: q = 7*(x^2 + x*y + y^2 + 1) ++ sage: p*q//q == p ++ True ++ sage: p*q//p == q ++ True + """ + cdef MPolynomialRing_libsingular parent = self._parent + cdef ring *r = self._parent_ring +- if(r != currRing): rChangeCurrRing(r) +- cdef MPolynomial_libsingular _self, _right + cdef poly *quo + cdef poly *temp + cdef poly *p +@@ -4038,19 +4046,19 @@ cdef class MPolynomial_libsingular(MPolynomial): + if self._parent._base.is_finite() and self._parent._base.characteristic() > 1<<29: + raise NotImplementedError("Division of multivariate polynomials over prime fields with characteristic > 2^29 is not implemented.") + +- _self = <MPolynomial_libsingular>self + _right = <MPolynomial_libsingular>right + ++ if r is not currRing: ++ rChangeCurrRing(r) ++ + if r.cf.type != n_unknown: + if r.cf.type == n_Z: +- P = parent.change_ring(RationalField()) +- f = P(self)//P(right) +- CM = list(f) +- return parent(sum([c.floor()*m for c,m in CM])) ++ P = parent.change_ring(QQ) ++ f = (<MPolynomial_libsingular>P(self))._floordiv_(P(right)) ++ return parent(sum([c.floor() * m for c, m in f])) + if _right.is_monomial(): +- p = _self._poly ++ p = self._poly + quo = p_ISet(0,r) +- if r != currRing: rChangeCurrRing(r) # pMDivide + while p: + if p_DivisibleBy(_right._poly, p, r): + temp = pMDivide(p, _right._poly) +@@ -4061,16 +4069,13 @@ cdef class MPolynomial_libsingular(MPolynomial): + if r.cf.type == n_Znm or r.cf.type == n_Zn or r.cf.type == n_Z2m : + raise NotImplementedError("Division of multivariate polynomials over non fields by non-monomials not implemented.") + +- cdef int count = singular_polynomial_length_bounded(_self._poly,15) ++ count = singular_polynomial_length_bounded(self._poly, 15) + if count >= 15: # note that _right._poly must be of shorter length than self._poly for us to care about this call + sig_on() +- if r!=currRing: rChangeCurrRing(r) # singclap_pdivide +- quo = singclap_pdivide( _self._poly, _right._poly, r ) ++ quo = singclap_pdivide(self._poly, _right._poly, r) + if count >= 15: + sig_off() +- f = new_MP(parent, quo) +- +- return f ++ return new_MP(parent, quo) + + def factor(self, proof=True): + """ +@@ -4789,7 +4794,9 @@ cdef class MPolynomial_libsingular(MPolynomial): + sage: p = -x*y + x*z + 54*x - 2 + sage: (5*p^2).lcm(3*p) == 15*p^2 + True +- sage: lcm(2*x,2*x*y) ++ sage: lcm(2*x, 2*y) ++ 2*x*y ++ sage: lcm(2*x, 2*x*y) + 2*x*y + """ + cdef ring *_ring = self._parent_ring +@@ -5222,7 +5229,7 @@ cdef class MPolynomial_libsingular(MPolynomial): + if ambient_ring is not self._parent: + raise TypeError("the variable is not in the same ring as self") + +- if not ambient_ring.has_coerce_map_from(RationalField()): ++ if not ambient_ring.has_coerce_map_from(QQ): + raise TypeError("the ring must contain the rational numbers") + + gens = ambient_ring.gens() +@@ -5325,8 +5332,8 @@ cdef class MPolynomial_libsingular(MPolynomial): + raise NotImplementedError("Resultants of multivariate polynomials over prime fields with characteristic > 2^29 is not implemented.") + + if is_IntegerRing(self._parent._base): +- ret = self.change_ring(RationalField()).resultant(other.change_ring(RationalField()), +- variable.change_ring(RationalField())) ++ ret = self.change_ring(QQ).resultant(other.change_ring(QQ), ++ variable.change_ring(QQ)) + return ret.change_ring(ZZ) + elif not self._parent._base.is_field(): + raise ValueError("Resultants require base fields or integer base ring.") +@@ -5457,7 +5464,7 @@ cdef class MPolynomial_libsingular(MPolynomial): + sage: f.numerator().parent() is P + True + """ +- if self.base_ring() == RationalField(): ++ if self.base_ring() is QQ: + #This part is for compatibility with the univariate case, + #where the numerator of a polynomial over RationalField + #is a polynomial over IntegerRing +diff --git a/src/sage/rings/polynomial/plural.pyx b/src/sage/rings/polynomial/plural.pyx +index ad20ebc..6dfcb47 100644 +--- a/src/sage/rings/polynomial/plural.pyx ++++ b/src/sage/rings/polynomial/plural.pyx +@@ -998,7 +998,7 @@ cdef class NCPolynomialRing_plural(Ring): + if not g._poly: + raise ZeroDivisionError + +- res = pMDivide(f._poly,g._poly) ++ res = pMDivide(f._poly, g._poly) + if coeff: + if (r.cf.type == n_unknown) or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf): + n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf) +@@ -1187,17 +1187,16 @@ cdef class NCPolynomialRing_plural(Ring): + cdef poly *flt + + if not m: +- return f,f ++ return (f, f) + + for g in G: +- if isinstance(g, NCPolynomial_plural) \ +- and (<NCPolynomial_plural>g) \ +- and p_LmDivisibleBy((<NCPolynomial_plural>g)._poly, m, r): +- flt = pMDivide(f._poly, (<NCPolynomial_plural>g)._poly) +- #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<NCPolynomial_plural>g)._poly, r), r), r) +- p_SetCoeff(flt, n_Init(1, r), r) +- return new_NCP(self,flt), g +- return self._zero_element,self._zero_element ++ if isinstance(g, NCPolynomial_plural) and g: ++ h = <NCPolynomial_plural>g ++ if p_LmDivisibleBy(h._poly, m, r): ++ flt = pMDivide(f._poly, h._poly) ++ p_SetCoeff(flt, n_Init(1, r), r) ++ return (new_NCP(self,flt), h) ++ return (self._zero_element, self._zero_element) + + def monomial_pairwise_prime(self, NCPolynomial_plural g, NCPolynomial_plural h): + """ +-- +cgit v1.0-1-gd88e + + +From 45ff3719d4f9059a0e85d142cd1e31cb87efa11c Mon Sep 17 00:00:00 2001 +From: Jeroen Demeyer <jdeme...@cage.ugent.be> +Date: Wed, 8 Aug 2018 10:31:27 +0200 +Subject: Fix debug build of Singular + +--- + build/pkgs/singular/spkg-install | 10 ++-------- + 1 file changed, 2 insertions(+), 8 deletions(-) + +diff --git a/build/pkgs/singular/spkg-install b/build/pkgs/singular/spkg-install +index 41dcad1..5a4d8de 100644 +--- a/build/pkgs/singular/spkg-install ++++ b/build/pkgs/singular/spkg-install +@@ -6,16 +6,10 @@ SRC=`pwd`/src + cd "$SRC" + + if [ "x$SAGE_DEBUG" = "xyes" ]; then ++ # This used to disable omalloc but that is not really supported ++ # by upstream + SINGULAR_CONFIGURE="$SINGULAR_CONFIGURE --enable-debug --disable-optimizationflags" + +- # --disable-omalloc is broken: linking fails because of missing flags +- #SINGULAR_CONFIGURE="$SINGULAR_CONFIGURE --disable-omalloc" +- +- # Replace omalloc by xalloc in places unaffected by --disable-omalloc +- # See xalloc/README, altough here we just replace the folder for simplicity +- rm -rf "$SRC/omalloc" +- mv "$SRC/xalloc" "$SRC/omalloc" +- + CFLAGS="$CFLAGS -O0 -g" + CXXFLAGS="$CXXFLAGS -O0 -g" + else +-- +cgit v1.0-1-gd88e + Modified: sagemath-threejs.patch =================================================================== --- sagemath-threejs.patch 2018-08-17 21:06:27 UTC (rev 372567) +++ sagemath-threejs.patch 2018-08-17 22:28:57 UTC (rev 372568) @@ -1,11 +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): +@@ -746,7 +746,7 @@ class DisplayManager(SageObject): """ if online: from sage.misc.package import installed_packages -- version = installed_packages()['threejs'] -+ version = 'r90' +- version = installed_packages()['threejs'].split('.')[0] ++ version = 'r95' 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>