Date: Thursday, July 19, 2018 @ 18:26:41 Author: arojas Revision: 362431
archrelease: copy trunk to community-staging-x86_64 Added: sagemath/repos/community-staging-x86_64/ sagemath/repos/community-staging-x86_64/PKGBUILD (from rev 362430, sagemath/trunk/PKGBUILD) sagemath/repos/community-staging-x86_64/fes02.patch (from rev 362430, sagemath/trunk/fes02.patch) sagemath/repos/community-staging-x86_64/jupyter-path.patch (from rev 362430, sagemath/trunk/jupyter-path.patch) sagemath/repos/community-staging-x86_64/latte-count.patch (from rev 362430, sagemath/trunk/latte-count.patch) sagemath/repos/community-staging-x86_64/package.patch (from rev 362430, sagemath/trunk/package.patch) sagemath/repos/community-staging-x86_64/r-no-readline.patch (from rev 362430, sagemath/trunk/r-no-readline.patch) sagemath/repos/community-staging-x86_64/sagemath-cddlib-094j.patch (from rev 362430, sagemath/trunk/sagemath-cddlib-094j.patch) sagemath/repos/community-staging-x86_64/sagemath-detect-igraph.patch (from rev 362430, sagemath/trunk/sagemath-detect-igraph.patch) sagemath/repos/community-staging-x86_64/sagemath-eclib-20180710.patch (from rev 362430, sagemath/trunk/sagemath-eclib-20180710.patch) sagemath/repos/community-staging-x86_64/sagemath-env.patch (from rev 362430, sagemath/trunk/sagemath-env.patch) sagemath/repos/community-staging-x86_64/sagemath-gap-4.8.patch (from rev 362430, sagemath/trunk/sagemath-gap-4.8.patch) sagemath/repos/community-staging-x86_64/sagemath-ignore-warnings.patch (from rev 362430, sagemath/trunk/sagemath-ignore-warnings.patch) sagemath/repos/community-staging-x86_64/sagemath-lcalc-c++11.patch (from rev 362430, sagemath/trunk/sagemath-lcalc-c++11.patch) sagemath/repos/community-staging-x86_64/sagemath-lrs.patch (from rev 362430, sagemath/trunk/sagemath-lrs.patch) sagemath/repos/community-staging-x86_64/sagemath-networkx2.patch (from rev 362430, sagemath/trunk/sagemath-networkx2.patch) sagemath/repos/community-staging-x86_64/sagemath-python3-notebook.patch (from rev 362430, sagemath/trunk/sagemath-python3-notebook.patch) sagemath/repos/community-staging-x86_64/sagemath-scipy-1.0.patch (from rev 362430, sagemath/trunk/sagemath-scipy-1.0.patch) sagemath/repos/community-staging-x86_64/sagemath-singular-4.1.1.patch (from rev 362430, sagemath/trunk/sagemath-singular-4.1.1.patch) sagemath/repos/community-staging-x86_64/sagemath-threejs.patch (from rev 362430, sagemath/trunk/sagemath-threejs.patch) sagemath/repos/community-staging-x86_64/test-optional.patch (from rev 362430, sagemath/trunk/test-optional.patch) ---------------------------------+ PKGBUILD | 176 ++++++ fes02.patch | 57 ++ jupyter-path.patch | 22 latte-count.patch | 71 ++ package.patch | 38 + r-no-readline.patch | 11 sagemath-cddlib-094j.patch | 980 ++++++++++++++++++++++++++++++++++++++ sagemath-detect-igraph.patch | 21 sagemath-eclib-20180710.patch | 24 sagemath-env.patch | 149 +++++ sagemath-gap-4.8.patch | 31 + sagemath-ignore-warnings.patch | 25 sagemath-lcalc-c++11.patch | 10 sagemath-lrs.patch | 22 sagemath-networkx2.patch | 175 ++++++ sagemath-python3-notebook.patch | 27 + sagemath-scipy-1.0.patch | 16 sagemath-singular-4.1.1.patch | 108 ++++ sagemath-threejs.patch | 11 test-optional.patch | 27 + 20 files changed, 2001 insertions(+) Copied: sagemath/repos/community-staging-x86_64/PKGBUILD (from rev 362430, sagemath/trunk/PKGBUILD) =================================================================== --- community-staging-x86_64/PKGBUILD (rev 0) +++ community-staging-x86_64/PKGBUILD 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,176 @@ +# Maintainer: Antonio Rojas <aro...@archlinux.org> +# Contributor: Evgeniy Alekseev <arcanis.arch at gmail dot com> +# Contributor: Daniel Wallace <danielwallace at gtmanfred dot com> +# Contributor: Thomas Dziedzic <gostrc at gmail dot com> +# Contributor: Osman Ugus <ugus11 at yahoo dot com> +# Contributor: Stefan Husmann <stefan-husmann at t-online dot de> +# Special thanks to Nareto for moving the compile from the .install to the PKGBUILD + +pkgbase=sagemath +pkgname=(sagemath sagemath-jupyter) +pkgver=8.2 +pkgrel=14 +pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab" +arch=(x86_64) +url="http://www.sagemath.org" +license=(GPL) +depends=(ipython2 ppl palp brial cliquer maxima-ecl gfan sympow nauty python2-rpy2 python2-fpylll python2-psutil python2-cypari2 + python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow python2-future libgap flintqs lcalc lrcalc arb + eclib gmp-ecm zn_poly gd python2-cvxopt pynac linbox rubiks pari-galdata pari-seadata-small planarity rankwidth tachyon + sage-data-combinatorial_designs sage-data-elliptic_curves sage-data-graphs sage-data-polytopes_db sage-data-conway_polynomials) +optdepends=('cython2: to compile cython code' 'python2-pkgconfig: to compile cython code' + 'jmol: 3D plots' 'sage-notebook: Flask notebook interface (deprecated)' + 'sagemath-doc: Documentation and inline help' 'python2-igraph: igraph backend for graph theory' + 'coin-or-cbc: COIN backend for numerical computations' 'coin-or-csdp: for computing Lovász theta-function of graphs' + 'buckygen: for generating fullerene graphs' 'plantri: for generating some classes of graphs' 'benzene: for generating fusenes and benzenoids' + 'ffmpeg: to export animations to video' 'imagemagick: to show animations' + 'coxeter: Coxeter groups implementation' 'cryptominisat5: SAT solver' 'gap-4.8-data: for computing Galois groups' + 'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes' + 'libhomfly: for computing the homfly polynomial of links' 'libbraiding: for computing in braid groups' + 'libfes: exhaustive search of solutions for boolean equations' 'python2-pynormaliz: Normaliz backend for polyhedral computations' + 'latte-integrale: integral point count in polyhedra' 'polymake: polymake backend for polyhedral computations' + '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' + '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) +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-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' + '18edeafb01cc1ed7270c2dfb41a58717918680c98e8eada1858736acd65d92ba' + 'afd0952b9bb8f52fd428eae36cf719a58ff85a894baae88cbb2124e043768cc7' + '7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94' + '2d13b15ad2d1511bb3d752a261497060a8901882b1c2fa9813219781b7a71d83' + 'a4a6c87b46ff23b89608aca66d00427334502e8bfb5dfe68b94497d19be1c7ae' + 'bfe49f0168fe0824f0eaf4ea793b08d5b3e43c4e3634eb5f664c70644a793a59' + '8253730940687992dd29d90d95bea7e2685bb4854db004090c8196ce92859b64' + '17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a' + 'c0f65534a845ba802de6196229159fe67fcc3f72f0cb1ce57d4ae5c9fe10282c' + '507bf761df222d1961d53ebeaf8e6a5a3dc2d7b9cb78748d71ed8cb1ee1c4ac6' + '5114c912f821900e5bfae1e2cfeb7984de946d0b23e1182b0bf15be1d803dfd0' + '6917cb74e50ae965ea8d7c39577e5f0a5068e4b6a67b53fc6f219149a7d06584' + '94847fc033fd36bc59217c8484d4cf48d0640ff35bb5ca5ffba88a8158c6dd44' + '092a928b77c8bb1e23399f22be39f67797a0065954128b690ead6a09f9ce1e44' + '182b0765d58494978bf27628bada8b42c95ef7eb2671b91ddf9c67608560c662') + +prepare(){ + cd sage-$pkgver + +# Arch-specific patches +# assume all optional packages are installed + patch -p0 -i ../package.patch +# set env variables + patch -p0 -i ../sagemath-env.patch +# don't list optional packages when running tests + patch -p0 -i ../test-optional.patch +# set jupyter path + patch -p0 -i ../jupyter-path.patch +# fix freezes in R interface with readline 7 (Debian) + patch -p1 -i ../r-no-readline.patch +# use correct latte-count binary name + patch -p1 -i ../latte-count.patch +# make 'sage -notebook=jupyter' work with our python3 jupyter-notebook package + patch -p1 -i ../sagemath-python3-notebook.patch +# fix Cremona database detection + sed -e "s|is_package_installed('database_cremona_ellcurve')|os.path.exists('/usr/share/cremona/cremona.db')|" \ + -i src/sage/databases/cremona.py +# fix python-igraph detection + patch -p1 -i ../sagemath-detect-igraph.patch +# 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 + patch -p1 -i ../sagemath-singular-4.1.1.patch +# don't force c++98 for lcalc (fixes build with NTL 11) + patch -p1 -i ../sagemath-lcalc-c++11.patch +# Adjust paths for gap-4.8 + patch -p1 -i ../sagemath-gap-4.8.patch +# Fix build with eclib 20180710 + patch -p1 -i ../sagemath-eclib-20180710.patch + +# Upstream patches +# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209 + patch -p1 -i ../fes02.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 + +# 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|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 +} + + +build() { + cd sage-$pkgver/src + + export SAGE_ROOT="$PWD" + export SAGE_SRC="$PWD" + python2 setup.py build +} + +package_sagemath() { + optdepends+=('sagemath-jupyter: Jupyter kernel') + + cd sage-$pkgver/src + + export SAGE_ROOT="$PWD" + export SAGE_LOCAL="/usr" + export JUPYTER_PATH="$pkgdir"/usr/share/jupyter + python2 setup.py install --root="$pkgdir" --optimize=1 + + mkdir -p "$pkgdir"/usr/bin + cp bin/sage "$pkgdir"/usr/bin + for _i in arch-env cachegrind callgrind cleaner coverage coverageall cython env eval grep grepdoc inline-fortran \ + ipython massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2sws rst2txt run \ + run-cython runtests startuptime.py sws2rst valgrind version.sh + do + cp bin/sage-$_i "$pkgdir"/usr/bin + done + cp bin/math-readline "$pkgdir"/usr/bin + + mkdir -p "$pkgdir"/usr/share/sage + cp -r ext "$pkgdir"/usr/share/sage + +# Remove sage_setup + rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup + +# Split jupyter kernel + rm -r "$pkgdir"/usr/share/jupyter +} + +package_sagemath-jupyter() { + pkgdesc='Jupyter kernel for SageMath' + depends=(sagemath python2-jupyter_client python2-ipywidgets mathjax) + optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter') + + cd sage-$pkgver/src + + export SAGE_ROOT="$PWD" + export SAGE_LOCAL="/usr" + export JUPYTER_PATH="$pkgdir"/usr/share/jupyter + + python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update()" +} Copied: sagemath/repos/community-staging-x86_64/fes02.patch (from rev 362430, sagemath/trunk/fes02.patch) =================================================================== --- community-staging-x86_64/fes02.patch (rev 0) +++ community-staging-x86_64/fes02.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,57 @@ +From b1f5e3ecc789db674fe17552812f2d0e2ab84be0 Mon Sep 17 00:00:00 2001 +From: Charles Bouillaguet <charles.bouillag...@lifl.fr> +Date: Thu, 19 Sep 2013 10:31:11 +0200 +Subject: updating the libFES binding to match a change in the interface + +--- + src/sage/libs/fes.pyx | 12 +++++++----- + 1 file changed, 7 insertions(+), 5 deletions(-) + +diff --git a/src/sage/libs/fes.pyx b/src/sage/libs/fes.pyx +index 40b9c23..d188cf0 100644 +--- a/src/sage/libs/fes.pyx ++++ b/src/sage/libs/fes.pyx +@@ -1,17 +1,19 @@ + """ +-Binding for the FES library. ++Binding for the libFES library. + + Finding solutions of systems of boolean equations by exhaustive + search, via the fes library. This is usually (much) faster than + computing a Groebner basis, except in special cases where the latter + is particularly easy. + +-The FES library is presently only able to deal with polynomials in 64 ++More information is available at [http://www.lifl.fr/~bouillag/fes]. ++ ++The libFES library is presently only able to deal with polynomials in 64 + variables. Performing a full exhaustive search over 64 variables will + take a **long** time. The number of variables can be artificially + reduced to 64 by specializing some of them. + +-Note that the FES library **requires** at least of the equations to be ++Note that the libFES library **requires** at least of the equations to be + non-linear. + + AUTHORS: +@@ -71,7 +73,7 @@ from libc.stdint cimport uint64_t + cdef extern from "fes_interface.h": + ctypedef int (*solution_callback_t)(void *, uint64_t) + +- void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose) ++ void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose, int T) + + + from sage.rings.integer import Integer +@@ -217,7 +217,7 @@ def exhaustive_search(eqs, max_sols=Infinity, verbose=False): + + # ------- runs the library + sig_on() +- exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose) ++ exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose, 0) + sig_off() + + # ------- frees memory occupied by the dense representation of the equations +-- +cgit v1.0-1-gd88e + Copied: sagemath/repos/community-staging-x86_64/jupyter-path.patch (from rev 362430, sagemath/trunk/jupyter-path.patch) =================================================================== --- community-staging-x86_64/jupyter-path.patch (rev 0) +++ community-staging-x86_64/jupyter-path.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,22 @@ +--- src/sage/repl/ipython_kernel/install.py.orig 2015-10-23 19:23:39.728456590 +0000 ++++ src/sage/repl/ipython_kernel/install.py 2015-10-23 19:24:00.965018978 +0000 +@@ -13,8 +13,7 @@ + SAGE_DOC, SAGE_LOCAL, SAGE_EXTCODE, + SAGE_VERSION + ) +-from jupyter_core.paths import ENV_JUPYTER_PATH +-JUPYTER_PATH = ENV_JUPYTER_PATH[0] ++JUPYTER_PATH = os.environ.get('JUPYTER_PATH') + + + class SageKernelSpec(object): +@@ -225,7 +225,7 @@ + sage: spec._symlink_resources() # not tested + """ + path = os.path.join(SAGE_EXTCODE, 'notebook-ipython') +- for filename in os.listdir(path): ++ for filename in os.listdir('ext/notebook-ipython'): + self.symlink( + os.path.join(path, filename), + os.path.join(self.kernel_dir, filename) + Copied: sagemath/repos/community-staging-x86_64/latte-count.patch (from rev 362430, sagemath/trunk/latte-count.patch) =================================================================== --- community-staging-x86_64/latte-count.patch (rev 0) +++ community-staging-x86_64/latte-count.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,71 @@ +diff --git a/src/sage/geometry/polyhedron/base_ZZ.py b/src/sage/geometry/polyhedron/base_ZZ.py +index 268af9db0d..70d41dfa30 100644 +--- a/src/sage/geometry/polyhedron/base_ZZ.py ++++ b/src/sage/geometry/polyhedron/base_ZZ.py +@@ -171,7 +171,7 @@ class Polyhedron_ZZ(Polyhedron_base): + sage: p = P.ehrhart_polynomial(maxdet=5, verbose=True) # optional - latte_int + This is LattE integrale ... + ... +- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin ++ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin + ... + sage: p # optional - latte_int + 1/2*t^2 + 3/2*t + 1 +@@ -179,7 +179,7 @@ class Polyhedron_ZZ(Polyhedron_base): + sage: p = P.ehrhart_polynomial(dual=True, verbose=True) # optional - latte_int + This is LattE integrale ... + ... +- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin ++ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin + ... + sage: p # optional - latte_int + 1/2*t^2 + 3/2*t + 1 +@@ -187,7 +187,7 @@ class Polyhedron_ZZ(Polyhedron_base): + sage: p = P.ehrhart_polynomial(irrational_primal=True, verbose=True) # optional - latte_int + This is LattE integrale ... + ... +- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin ++ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin + ... + sage: p # optional - latte_int + 1/2*t^2 + 3/2*t + 1 +@@ -195,7 +195,7 @@ class Polyhedron_ZZ(Polyhedron_base): + sage: p = P.ehrhart_polynomial(irrational_all_primal=True, verbose=True) # optional - latte_int + This is LattE integrale ... + ... +- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin ++ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin + ... + sage: p # optional - latte_int + 1/2*t^2 + 3/2*t + 1 +@@ -207,7 +207,7 @@ class Polyhedron_ZZ(Polyhedron_base): + ... + RuntimeError: LattE integrale program failed (exit code 1): + ... +- Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin ++ Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin + Unknown command/option --bim-bam-boum=19 + """ + if self.is_empty(): +diff --git a/src/sage/interfaces/latte.py b/src/sage/interfaces/latte.py +index 066cedd401..302b39910d 100644 +--- a/src/sage/interfaces/latte.py ++++ b/src/sage/interfaces/latte.py +@@ -88,7 +88,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False, + sage: n = count(cddin, cdd=True, verbose=True, raw_output=True) # optional - latte_int + This is LattE integrale ... + ... +- Invocation: count '--redundancy-check=none' --cdd /dev/stdin ++ Invocation: latte-count '--redundancy-check=none' --cdd /dev/stdin + ... + Total Unimodular Cones: ... + Maximum number of simplicial cones in memory at once: ... +@@ -108,7 +108,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False, + from sage.misc.misc import SAGE_TMP + from sage.rings.integer import Integer + +- args = ['count'] ++ args = ['latte-count'] + if ehrhart_polynomial and multivariate_generating_function: + raise ValueError + if ehrhart_polynomial: Copied: sagemath/repos/community-staging-x86_64/package.patch (from rev 362430, sagemath/trunk/package.patch) =================================================================== --- community-staging-x86_64/package.patch (rev 0) +++ community-staging-x86_64/package.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,38 @@ +--- src/sage/misc/package.py.orig 2014-11-23 15:58:13.000000000 +0100 ++++ src/sage/misc/package.py 2015-01-22 20:32:25.651383902 +0100 +@@ -320,7 +320,7 @@ + sage: for pkg in list_packages('pip', local=True): + ....: assert not is_package_installed(pkg) + """ +- return any(p.split('-')[0] == package for p in installed_packages(exclude_pip)) ++ return True + + def package_versions(package_type, local=False): + r""" +--- src/sage_setup/optional_extension.py.orig 2016-10-19 18:35:10.092577510 +0000 ++++ src/sage_setup/optional_extension.py 2016-10-19 18:38:13.514765366 +0000 +@@ -21,8 +21,6 @@ + from distutils.extension import Extension + from sage.misc.package import is_package_installed, list_packages + +-all_packages = list_packages(local=True) +- + + class CythonizeExtension(Extension): + """ +@@ -76,14 +74,7 @@ + condition = kwds.pop("condition") + except KeyError: + pkg = kwds.pop("package") +- try: +- pkginfo = all_packages[pkg] +- except KeyError: +- # Might be an installed old-style package +- condition = is_package_installed(pkg) +- else: +- condition = (pkginfo["installed_version"] == pkginfo["remote_version"]) +- ++ condition = True + if condition: + return Extension(*args, **kwds) + else: Copied: sagemath/repos/community-staging-x86_64/r-no-readline.patch (from rev 362430, sagemath/trunk/r-no-readline.patch) =================================================================== --- community-staging-x86_64/r-no-readline.patch (rev 0) +++ community-staging-x86_64/r-no-readline.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,11 @@ +--- a/src/sage/interfaces/r.py ++++ b/src/sage/interfaces/r.py +@@ -332,7 +332,7 @@ + prompt = '> ', #default, later comes the change + + # This is the command that starts up your program +- command = "R --vanilla --quiet", ++ command = "R --no-readline --vanilla --quiet", + + server=server, + server_tmpdir=server_tmpdir, Copied: sagemath/repos/community-staging-x86_64/sagemath-cddlib-094j.patch (from rev 362430, sagemath/trunk/sagemath-cddlib-094j.patch) =================================================================== --- community-staging-x86_64/sagemath-cddlib-094j.patch (rev 0) +++ community-staging-x86_64/sagemath-cddlib-094j.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,980 @@ +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 Rüth <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 Copied: sagemath/repos/community-staging-x86_64/sagemath-detect-igraph.patch (from rev 362430, sagemath/trunk/sagemath-detect-igraph.patch) =================================================================== --- community-staging-x86_64/sagemath-detect-igraph.patch (rev 0) +++ community-staging-x86_64/sagemath-detect-igraph.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,21 @@ +diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py +index 252984f..ce19682 100644 +--- a/src/sage/graphs/generic_graph.py ++++ b/src/sage/graphs/generic_graph.py +@@ -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) + Copied: sagemath/repos/community-staging-x86_64/sagemath-eclib-20180710.patch (from rev 362430, sagemath/trunk/sagemath-eclib-20180710.patch) =================================================================== --- community-staging-x86_64/sagemath-eclib-20180710.patch (rev 0) +++ community-staging-x86_64/sagemath-eclib-20180710.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,24 @@ +diff --git a/src/sage/libs/eclib/wrap.cpp b/src/sage/libs/eclib/wrap.cpp +index 5fd5693b53..d12468faa8 100644 +--- a/src/sage/libs/eclib/wrap.cpp ++++ b/src/sage/libs/eclib/wrap.cpp +@@ -133,8 +133,8 @@ char* Curvedata_isogeny_class(struct Curvedata* E, int verbose) + + + int mw_process(struct Curvedata* curve, struct mw* m, +- const struct bigint* x, const struct bigint* y, +- const struct bigint* z, int sat) ++ const bigint* x, const bigint* y, ++ const bigint* z, int sat) + { + Point P(*curve, *x, *y, *z); + if (!P.isvalid()) +@@ -188,7 +188,7 @@ int mw_rank(struct mw* m) + } + + /* Returns index and unsat long array, which user must deallocate */ +-int mw_saturate(struct mw* m, struct bigint* index, char** unsat, ++int mw_saturate(struct mw* m, bigint* index, char** unsat, + long sat_bd, int odd_primes_only) + { + vector<long> v; Copied: sagemath/repos/community-staging-x86_64/sagemath-env.patch (from rev 362430, sagemath/trunk/sagemath-env.patch) =================================================================== --- community-staging-x86_64/sagemath-env.patch (rev 0) +++ community-staging-x86_64/sagemath-env.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,149 @@ +--- src/bin/sage-env.orig 2015-01-06 10:46:04.469687605 +0100 ++++ src/bin/sage-env 2015-01-06 10:49:59.547762019 +0100 +@@ -111,41 +111,7 @@ + } + + +-# New value for SAGE_ROOT: either SAGE_ROOT (if given) +-# or a guessed value based on pwd. +-if [ -n "$SAGE_ROOT" ]; then +- NEW_SAGE_ROOT="$SAGE_ROOT" +-elif [ -f sage -a -d build ]; then +- NEW_SAGE_ROOT="." +-elif [ -f ../../sage -a -d ../../build ]; then +- NEW_SAGE_ROOT="../.." +-else +- # No idea what SAGE_ROOT should be... +- echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this" +- echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory." +- return 1 +-fi +- +-# Make NEW_SAGE_ROOT absolute +-NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P` +- +-# Sanity check NEW_SAGE_ROOT +-if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then +- : +-else +- echo >&2 "Error: SAGE_ROOT is set to a bad value:" +- echo >&2 "SAGE_ROOT=$SAGE_ROOT" +- echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT" +- echo >&2 "or SAGE_ROOT/local/bin/ directory." +- return 1 +-fi +- +-# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT +-if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then +- echo >&2 "Warning: overwriting SAGE_ROOT environment variable:" +- echo >&2 "Old SAGE_ROOT=$SAGE_ROOT" +- echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT" +-fi ++NEW_SAGE_ROOT="/usr" + + + # Don't execute the commands more than once for the same version of +@@ -174,33 +174,9 @@ + export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION + + export SAGE_ROOT="$NEW_SAGE_ROOT" ++export SAGE_LOCAL='/usr' ++export SAGE_SCRIPTS_DIR='/usr/bin' + +- +-# sage-env must know where the Sage's script files are. +-# Note that SAGE_SCRIPTS_DIR is only used here, so it does not need to +-# be exported. +-if [ -z "$SAGE_SCRIPTS_DIR" ]; then +- if [ -n "$SAGE_LOCAL" ] && [ -f "$SAGE_LOCAL/bin/sage-env-config" ]; then +- SAGE_SCRIPTS_DIR="$SAGE_LOCAL/bin" +- elif [ -f "$SAGE_ROOT/src/bin/sage-env-config" ]; then +- SAGE_SCRIPTS_DIR="$SAGE_ROOT/src/bin" +- else +- echo >&2 "Error: You must set either the SAGE_LOCAL or SAGE_SCRIPTS_DIR environment variable to run this" +- return 1 +- fi +-elif [ ! -f "$SAGE_SCRIPTS_DIR/sage-env-config" ]; then +- echo >&2 "Error: SAGE_SCRIPTS_DIR is set to a bad value:" +- echo >&2 "SAGE_SCRIPTS_DIR=$SAGE_SCRIPTS_DIR" +- echo >&2 "You must correct it or erase it and rerun this script" +- return 1 +-fi +- +-# Set environment variables (like SAGE_LOCAL) depending on ./configure +-. "$SAGE_SCRIPTS_DIR/sage-env-config" +-if [ $? -ne 0 ]; then +- echo >&2 "Error: failed to source $SAGE_SCRIPTS_DIR/sage-env-config" +- return 1 +-fi + + # The compilers are set in order of priority by + # 1) environment variables +@@ -296,8 +296,9 @@ + export SAGE_EXTCODE="$SAGE_SHARE/sage/ext" + export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed" + export SAGE_LOGS="$SAGE_ROOT/logs/pkgs" +-export SAGE_SRC="$SAGE_ROOT/src" +-export SAGE_DOC_SRC="$SAGE_SRC/doc" ++export GAP_ROOT_DIR="/usr/lib/gap-4.8" ++export SAGE_SRC="$SAGE_LOCAL/lib/python2.7/site-packages" ++export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage" + export SAGE_DOC="$SAGE_SHARE/doc/sage" + + if [ -z "${SAGE_ORIG_PATH_SET}" ]; then +@@ -403,6 +403,9 @@ + export SAGE_STARTUP_FILE + fi + ++export LIBMTX="$DOT_SAGE/meataxe" ++[[ -d $LIBMTX ]] || mkdir -p $LIBMTX # Create meataxe data dir ++ + if [ "$PYTHON_EGG_CACHE" = "" ]; then + PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs" + export PYTHON_EGG_CACHE +@@ -488,7 +488,6 @@ + fi + fi + fi +-export MAXIMA_PREFIX="$SAGE_LOCAL" + + PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB + +@@ -608,9 +608,6 @@ + LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH + fi + +-# See trac 7186 -- this is needed if ecl is moved +-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR +- + # Handle parallel building/testing/... + # See Trac Ticket #12016 + # First, figure out the right values for SAGE_NUM_THREADS (default +--- src/sage/env.py.orig 2017-12-07 19:51:25.554281539 +0000 ++++ src/sage/env.py 2017-12-07 19:51:42.787654650 +0000 +@@ -117,13 +117,13 @@ + _add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid()) + + # bunch of sage directories and files +-_add_variable_or_fallback('SAGE_ROOT', None) +-_add_variable_or_fallback('SAGE_LOCAL', None) ++_add_variable_or_fallback('SAGE_ROOT', '') ++_add_variable_or_fallback('SAGE_LOCAL', '/usr') + _add_variable_or_fallback('SAGE_ETC', opj('$SAGE_LOCAL', 'etc')) + _add_variable_or_fallback('SAGE_INC', opj('$SAGE_LOCAL', 'include')) + _add_variable_or_fallback('SAGE_SHARE', opj('$SAGE_LOCAL', 'share')) + +-_add_variable_or_fallback('SAGE_SRC', opj('$SAGE_ROOT', 'src')) ++_add_variable_or_fallback('SAGE_SRC', opj('$SAGE_LOCAL', 'lib', 'python2.7', 'site-packages')) + + try: + sitepackages_dirs = site.getsitepackages() +@@ -163,7 +163,7 @@ + _add_variable_or_fallback('GRAPHS_DATA_DIR', opj('$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')) +-_add_variable_or_fallback('GAP_ROOT_DIR', opj('$SAGE_LOCAL','gap','latest')) ++_add_variable_or_fallback('GAP_ROOT_DIR', opj('$SAGE_LOCAL','lib','gap-4.8')) + _add_variable_or_fallback('THEBE_DIR', opj('$SAGE_SHARE','thebe')) + + # locate singular shared object Copied: sagemath/repos/community-staging-x86_64/sagemath-gap-4.8.patch (from rev 362430, sagemath/trunk/sagemath-gap-4.8.patch) =================================================================== --- community-staging-x86_64/sagemath-gap-4.8.patch (rev 0) +++ community-staging-x86_64/sagemath-gap-4.8.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,31 @@ +diff --git a/src/sage/interfaces/gap.py b/src/sage/interfaces/gap.py +index 177fc1b6eb..51c67bdd09 100644 +--- a/src/sage/interfaces/gap.py ++++ b/src/sage/interfaces/gap.py +@@ -197,11 +197,11 @@ import string + + WORKSPACE = gap_workspace_file() + +-GAP_BINARY = os.path.join(SAGE_LOCAL, 'bin', 'gap') ++GAP_BINARY = os.path.join(SAGE_LOCAL, 'bin', 'gap-4.8') + + first_try = True + +-gap_cmd = "gap -r" ++gap_cmd = "gap-4.8 -r" + if platform.processor() == 'ia64' and os.path.exists('/usr/bin/prctl'): + # suppress unaligned access to 0x..., ip=0x... warnings + gap_cmd = 'prctl --unaligned=silent ' + gap_cmd +diff --git a/src/sage/libs/gap/util.pyx b/src/sage/libs/gap/util.pyx +index 7bffcfc00d..51dad178d5 100644 +--- a/src/sage/libs/gap/util.pyx ++++ b/src/sage/libs/gap/util.pyx +@@ -166,7 +166,7 @@ def gap_root(): + if os.path.exists(GAP_ROOT_DIR): + return GAP_ROOT_DIR + print('The gap-4.5.5.spkg (or later) seems to be not installed!') +- gap_sh = open(os.path.join(SAGE_LOCAL, 'bin', 'gap')).read().splitlines() ++ gap_sh = open(os.path.join(SAGE_LOCAL, 'bin', 'gap-4.8')).read().splitlines() + gapdir = filter(lambda dir:dir.strip().startswith('GAP_DIR'), gap_sh)[0] + gapdir = gapdir.split('"')[1] + gapdir = gapdir.replace('$SAGE_LOCAL', SAGE_LOCAL) Copied: sagemath/repos/community-staging-x86_64/sagemath-ignore-warnings.patch (from rev 362430, sagemath/trunk/sagemath-ignore-warnings.patch) =================================================================== --- community-staging-x86_64/sagemath-ignore-warnings.patch (rev 0) +++ community-staging-x86_64/sagemath-ignore-warnings.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,25 @@ +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 Copied: sagemath/repos/community-staging-x86_64/sagemath-lcalc-c++11.patch (from rev 362430, sagemath/trunk/sagemath-lcalc-c++11.patch) =================================================================== --- community-staging-x86_64/sagemath-lcalc-c++11.patch (rev 0) +++ community-staging-x86_64/sagemath-lcalc-c++11.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,10 @@ +--- a/src/sage/libs/lcalc/lcalc_Lfunction.pxd ++++ b/src/sage/libs/lcalc/lcalc_Lfunction.pxd +@@ -1,6 +1,5 @@ + # Lcalc requires GNU extensions, it does not strictly conform to any + # C++ standard: https://trac.sagemath.org/ticket/23341 +-# distutils: extra_compile_args = -std=gnu++98 + + cdef extern from "lcalc_sage.h": + ctypedef struct doublevec "std::vector<double>": + Copied: sagemath/repos/community-staging-x86_64/sagemath-lrs.patch (from rev 362430, sagemath/trunk/sagemath-lrs.patch) =================================================================== --- community-staging-x86_64/sagemath-lrs.patch (rev 0) +++ community-staging-x86_64/sagemath-lrs.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,22 @@ +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" + Copied: sagemath/repos/community-staging-x86_64/sagemath-networkx2.patch (from rev 362430, sagemath/trunk/sagemath-networkx2.patch) =================================================================== --- community-staging-x86_64/sagemath-networkx2.patch (rev 0) +++ community-staging-x86_64/sagemath-networkx2.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,175 @@ +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): + Copied: sagemath/repos/community-staging-x86_64/sagemath-python3-notebook.patch (from rev 362430, sagemath/trunk/sagemath-python3-notebook.patch) =================================================================== --- community-staging-x86_64/sagemath-python3-notebook.patch (rev 0) +++ community-staging-x86_64/sagemath-python3-notebook.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,27 @@ +diff --git a/src/bin/sage-notebook b/src/bin/sage-notebook +index 74192da240..0ede281aad 100755 +--- a/src/bin/sage-notebook ++++ b/src/bin/sage-notebook +@@ -96,8 +96,7 @@ class NotebookJupyter(object): + if not have_prerequisites(): + print(self.PREREQUISITE_ERROR) + raise SystemExit(1) +- from notebook.notebookapp import main +- main(argv) ++ os.execvp('jupyter-notebook', ['jupyter-notebook'] + argv) + + + class NotebookJupyterlab(object): +diff --git a/src/sage/repl/ipython_kernel/install.py b/src/sage/repl/ipython_kernel/install.py +index 3912b8cdf5..bd40cdadda 100644 +--- a/src/sage/repl/ipython_kernel/install.py ++++ b/src/sage/repl/ipython_kernel/install.py +@@ -280,7 +280,6 @@ def have_prerequisites(debug=True): + True + """ + try: +- from notebook.notebookapp import NotebookApp + return True + except ImportError: + if debug: + Copied: sagemath/repos/community-staging-x86_64/sagemath-scipy-1.0.patch (from rev 362430, sagemath/trunk/sagemath-scipy-1.0.patch) =================================================================== --- community-staging-x86_64/sagemath-scipy-1.0.patch (rev 0) +++ community-staging-x86_64/sagemath-scipy-1.0.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,16 @@ +diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py +index 17b5ebb84b..7ce9055cba 100644 +--- a/src/sage/numerical/optimize.py ++++ b/src/sage/numerical/optimize.py +@@ -486,9 +486,9 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args) + else: + min = optimize.fmin_tnc(f, x0, approx_grad=True, bounds=cons, messages=0, **args)[0] + elif isinstance(cons[0], function_type) or isinstance(cons[0], Expression): +- min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args) ++ min = optimize.fmin_cobyla(f, x0, cons, **args) + elif isinstance(cons, function_type) or isinstance(cons, Expression): +- min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args) ++ min = optimize.fmin_cobyla(f, x0, cons, **args) + return vector(RDF, min) + + Copied: sagemath/repos/community-staging-x86_64/sagemath-singular-4.1.1.patch (from rev 362430, sagemath/trunk/sagemath-singular-4.1.1.patch) =================================================================== --- community-staging-x86_64/sagemath-singular-4.1.1.patch (rev 0) +++ community-staging-x86_64/sagemath-singular-4.1.1.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,108 @@ +diff --git a/src/sage/libs/singular/decl.pxd b/src/sage/libs/singular/decl.pxd +index 676544ab1e..5c8639d362 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": + + int n_NumberOfParameters(const n_Procs_s* r) + +- ctypedef struct poly "polyrec": ++ ctypedef struct poly "spolyrec": + poly *next + number *coef + unsigned long exp[1] +@@ -632,7 +632,7 @@ cdef extern from "singular/Singular/libsingular.h": + + # divide monomial p by monomial q, p,q const + +- poly *pDivide(poly *p,poly *q) ++ poly *pMDivide(poly *p,poly *q) + + # 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 +--- 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 ( + 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, pDivide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy, +- pDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy, ++ omFree, pMDivide, 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, + idLift, IDELEMS, On, Off, SW_USE_CHINREM_GCD, SW_USE_EZGCD, +@@ -1692,8 +1697,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic): + if not g._poly: + raise ZeroDivisionError + +- if r!=currRing: rChangeCurrRing(r) # pDivide +- res = pDivide(f._poly, g._poly) ++ if r!=currRing: rChangeCurrRing(r) # pMDivide ++ 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) +@@ -1852,8 +1857,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic): + and (<MPolynomial_libsingular>g) \ + and g.parent() is self \ + and p_LmDivisibleBy((<MPolynomial_libsingular>g)._poly, m, r): +- if r!=currRing: rChangeCurrRing(r) # pDivide +- flt = pDivide(f._poly, (<MPolynomial_libsingular>g)._poly) ++ 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 +@@ -4049,10 +4054,10 @@ cdef class MPolynomial_libsingular(MPolynomial): + if _right.is_monomial(): + p = _self._poly + quo = p_ISet(0,r) +- if r != currRing: rChangeCurrRing(r) # pDivide ++ if r != currRing: rChangeCurrRing(r) # pMDivide + while p: + if p_DivisibleBy(_right._poly, p, r): +- temp = pDivide(p, _right._poly) ++ temp = pMDivide(p, _right._poly) + p_SetCoeff0(temp, n_Copy(p_GetCoeff(p, r), r), r) + 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 +--- a/src/sage/rings/polynomial/plural.pyx ++++ b/src/sage/rings/polynomial/plural.pyx +@@ -999,7 +999,7 @@ cdef class NCPolynomialRing_plural(Ring): + if not g._poly: + raise ZeroDivisionError + +- res = pDivide(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) +@@ -1194,7 +1194,7 @@ cdef class NCPolynomialRing_plural(Ring): + if isinstance(g, NCPolynomial_plural) \ + and (<NCPolynomial_plural>g) \ + and p_LmDivisibleBy((<NCPolynomial_plural>g)._poly, m, r): +- flt = pDivide(f._poly, (<NCPolynomial_plural>g)._poly) ++ 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 +diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx +index 809ca72c76..9610ce125d 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): + if right.is_zero(): + raise ZeroDivisionError + +- if not self._parent._base.is_field() and not is_IntegerRing(self._parent._base): ++ if not self._parent._base.is_field(): + py_quo = self//right + py_rem = self - right*py_quo + return py_quo, py_rem + Copied: sagemath/repos/community-staging-x86_64/sagemath-threejs.patch (from rev 362430, sagemath/trunk/sagemath-threejs.patch) =================================================================== --- community-staging-x86_64/sagemath-threejs.patch (rev 0) +++ community-staging-x86_64/sagemath-threejs.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,11 @@ +--- a/src/sage/repl/rich_output/display_manager.py ++++ b/src/sage/repl/rich_output/display_manager.py +@@ -744,7 +744,7 @@ class DisplayManager(SageObject): + """ + if online: + from sage.misc.package import installed_packages +- version = installed_packages()['threejs'] ++ version = 'r90' + return """ + <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/build/three.min.js"></script> + <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/examples/js/controls/OrbitControls.js"></script> Copied: sagemath/repos/community-staging-x86_64/test-optional.patch (from rev 362430, sagemath/trunk/test-optional.patch) =================================================================== --- community-staging-x86_64/test-optional.patch (rev 0) +++ community-staging-x86_64/test-optional.patch 2018-07-19 18:26:41 UTC (rev 362431) @@ -0,0 +1,27 @@ +--- src/sage/doctest/control.py.orig 2016-10-20 19:39:53.714618246 +0200 ++++ src/sage/doctest/control.py 2016-10-20 19:40:15.158049920 +0200 +@@ -326,24 +326,6 @@ + if "all" in options.optional: + # Special case to run all optional tests + options.optional = True +- else: +- # We replace the 'optional' tag by all optional +- # packages for which the installed version matches the +- # latest available version (this implies in particular +- # that the package is actually installed). +- if 'optional' in options.optional: +- options.optional.discard('optional') +- from sage.misc.package import list_packages +- for pkg in list_packages('optional', local=True).values(): +- if pkg['installed_version'] == pkg['remote_version']: +- options.optional.add(pkg['name']) +- +- # Check that all tags are valid +- for o in options.optional: +- if not optionaltag_regex.search(o): +- raise ValueError('invalid optional tag {!r}'.format(o)) +- +- options.optional |= auto_optional_tags + + self.options = options + self.files = args