Date: Wednesday, February 14, 2018 @ 17:16:04 Author: arojas Revision: 294438
archrelease: copy trunk to community-staging-x86_64 Added: sagemath/repos/community-staging-x86_64/ sagemath/repos/community-staging-x86_64/PKGBUILD (from rev 294437, sagemath/trunk/PKGBUILD) sagemath/repos/community-staging-x86_64/fes02.patch (from rev 294437, sagemath/trunk/fes02.patch) sagemath/repos/community-staging-x86_64/jupyter-path.patch (from rev 294437, sagemath/trunk/jupyter-path.patch) sagemath/repos/community-staging-x86_64/latte-count.patch (from rev 294437, sagemath/trunk/latte-count.patch) sagemath/repos/community-staging-x86_64/package.patch (from rev 294437, sagemath/trunk/package.patch) sagemath/repos/community-staging-x86_64/pari-stackwarn.patch (from rev 294437, sagemath/trunk/pari-stackwarn.patch) sagemath/repos/community-staging-x86_64/r-no-readline.patch (from rev 294437, sagemath/trunk/r-no-readline.patch) sagemath/repos/community-staging-x86_64/sagemath-detect-igraph.patch (from rev 294437, sagemath/trunk/sagemath-detect-igraph.patch) sagemath/repos/community-staging-x86_64/sagemath-env.patch (from rev 294437, sagemath/trunk/sagemath-env.patch) sagemath/repos/community-staging-x86_64/sagemath-ipython-prompt.patch (from rev 294437, sagemath/trunk/sagemath-ipython-prompt.patch) sagemath/repos/community-staging-x86_64/sagemath-linbox-1.5.patch (from rev 294437, sagemath/trunk/sagemath-linbox-1.5.patch) sagemath/repos/community-staging-x86_64/sagemath-lrs.patch (from rev 294437, sagemath/trunk/sagemath-lrs.patch) sagemath/repos/community-staging-x86_64/sagemath-matplotlib2.patch (from rev 294437, sagemath/trunk/sagemath-matplotlib2.patch) sagemath/repos/community-staging-x86_64/sagemath-networkx2.patch (from rev 294437, sagemath/trunk/sagemath-networkx2.patch) sagemath/repos/community-staging-x86_64/sagemath-pynac-0.7.14.patch (from rev 294437, sagemath/trunk/sagemath-pynac-0.7.14.patch) sagemath/repos/community-staging-x86_64/sagemath-python3-notebook.patch (from rev 294437, sagemath/trunk/sagemath-python3-notebook.patch) sagemath/repos/community-staging-x86_64/sagemath-scipy-1.0.patch (from rev 294437, sagemath/trunk/sagemath-scipy-1.0.patch) sagemath/repos/community-staging-x86_64/sagemath-singular-4.1.1.patch (from rev 294437, sagemath/trunk/sagemath-singular-4.1.1.patch) sagemath/repos/community-staging-x86_64/sagemath-threejs.patch (from rev 294437, sagemath/trunk/sagemath-threejs.patch) sagemath/repos/community-staging-x86_64/test-optional.patch (from rev 294437, sagemath/trunk/test-optional.patch) ---------------------------------+ PKGBUILD | 180 +++++++++++++++++++++++++ fes02.patch | 57 +++++++ jupyter-path.patch | 22 +++ latte-count.patch | 71 +++++++++ package.patch | 38 +++++ pari-stackwarn.patch | 23 +++ r-no-readline.patch | 11 + sagemath-detect-igraph.patch | 21 ++ sagemath-env.patch | 107 ++++++++++++++ sagemath-ipython-prompt.patch | 13 + sagemath-linbox-1.5.patch | 272 ++++++++++++++++++++++++++++++++++++++ sagemath-lrs.patch | 22 +++ sagemath-matplotlib2.patch | 253 +++++++++++++++++++++++++++++++++++ sagemath-networkx2.patch | 196 +++++++++++++++++++++++++++ sagemath-pynac-0.7.14.patch | 167 +++++++++++++++++++++++ sagemath-python3-notebook.patch | 27 +++ sagemath-scipy-1.0.patch | 16 ++ sagemath-singular-4.1.1.patch | 94 +++++++++++++ sagemath-threejs.patch | 11 + test-optional.patch | 25 +++ 20 files changed, 1626 insertions(+) Copied: sagemath/repos/community-staging-x86_64/PKGBUILD (from rev 294437, sagemath/trunk/PKGBUILD) =================================================================== --- community-staging-x86_64/PKGBUILD (rev 0) +++ community-staging-x86_64/PKGBUILD 2018-02-14 17:16:04 UTC (rev 294438) @@ -0,0 +1,180 @@ +# 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=8.1 +pkgrel=9 +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' + 'coxeter3: Coxeter groups implementation' 'cryptominisat5: SAT solver' 'gap-data: for computing Galois groups' + 'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes' + 'libhomfly: for computing the homfly polynomial of links' 'libbraiding: for computing in braid groups' + 'libfes: exhaustive search of solutions for boolean equations' 'python2-pynormaliz: Normaliz backend for polyhedral computations' + 'latte-integrale: integral point count in polyhedra' 'polymake: polymake backend for polyhedral computations' + 'shared_meataxe: faster matrix arithmetic over finite fields' + 'sirocco: for computing the fundamental group of the complement of a plane curve' + 'three.js: alternative 3D plots engine') +makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding sirocco + mcqd coxeter3 bliss-graphs tdlib python2-pkgconfig shared_meataxe libfes) +source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz" + sagemath-env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch + r-no-readline.patch fes02.patch sagemath-threejs.patch pari-stackwarn.patch + sagemath-detect-igraph.patch sagemath-networkx2.patch sagemath-linbox-1.5.patch sagemath-pynac-0.7.14.patch + sagemath-matplotlib2.patch sagemath-scipy-1.0.patch sagemath-lrs.patch sagemath-ipython-prompt.patch + sagemath-singular-4.1.1.patch) +sha256sums=('a42b55c2c8ac244535dc9b87171b7d4dd7e1d498099518ab253354fbe2eaaa7b' + '39b76a189365464998cab9355d177581bc2b15dff10858f316faa85f2efa0426' + 'c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107' + '0b680e674c11c47afa86162d8b49645620b8912722e08133d23357c29ca9310a' + '2cad308f8adbb6c54e6603fa22b2f0eb60f6f09248d5d015000c3932ac14f646' + '962ce805c87147212b21fc2ab0ac9af9bd0033942c7a6905b9906645b48e8a4f' + 'ef94908d4ab28d13af622e6e58ec191aa78817d17e4466c7bb6f64ee72a813b9' + 'afd0952b9bb8f52fd428eae36cf719a58ff85a894baae88cbb2124e043768cc7' + '7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94' + '514135b920a43f999571a15e97b41e14f5bed59f65b19643864dc23555a7b830' + 'bfd2a20a33ab19a8a8b216a77d07f62e809fe1e1879c4f171ce5dca62fd482e9' + '28d7789b8d777922ab8871ca43b6afab751428cae875c0343d3962e6a2030b88' + '1024f3a6a9a1a6ae96d9962bb7d1f5842f4a4a5ff5098afad81a60188b7d5160' + 'a52d03e04c9d64bb957a1f8dcdae3280ebb9450a7fd76aaf5ae5de5c6f74774f' + '538f7b279d72f4b67edb445d386d267f3f7022c1079031ca7ea06f6ce392c906' + 'b9ab2bb5f381ea425e8763b81b8b3a108a3951c594fb1f37f7df921e7c77e26d' + '17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a' + 'c0f65534a845ba802de6196229159fe67fcc3f72f0cb1ce57d4ae5c9fe10282c' + '937a0081e7aea56bda645ef5f0d34b8e356acd62a7dd128a35163f46e7836131' + 'cc679321c2968d5e74b0ec060979c74019df2995857906bdd1397695b1f24c5c') + +prepare(){ + cd sage-$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 warnings during doctesting (Debian) + patch -p1 -i ../pari-stackwarn.patch +# remove deprecated scipy parameters + patch -p1 -i ../sagemath-scipy-1.0.patch +# fix ipython prompt in pexpect interface + patch -p1 -i ../sagemath-ipython-prompt.patch +# fix build with Singular 4.1.1 + patch -p1 -i ../sagemath-singular-4.1.1.patch + +# Upstream patches +# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209 + patch -p1 -i ../fes02.patch +# fix build with linbox 1.5 https://trac.sagemath.org/ticket/24214 + patch -p1 -i ../sagemath-linbox-1.5.patch +# fix build with pynac 0.7.14 https://trac.sagemath.org/ticket/24329 + patch -p1 -i ../sagemath-pynac-0.7.14.patch +# port away from deprecated and removed functions in matplotlib 2 https://trac.sagemath.org/ticket/23696 + patch -p1 -i ../sagemath-matplotlib2.patch + +# use python2 + sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|\<exec python\>|exec python2|' -i src/bin/* + sed -e 's|cython {OPT}|cython2 {OPT}|' -e 's|python setup.py|python2 setup.py|' -i src/sage/misc/cython.py + sed -e 's|exec ipython|exec ipython2|' -e 's|cygdb|cygdb2|g' -i src/bin/sage + sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython + sed -e 's|bin/python|bin/python2|g' -i src/bin/sage-env +} + + +build() { + cd sage-$pkgver + autoreconf -vi + ./configure --prefix=/usr || true + + cd src + export SAGE_ROOT="$PWD" + export SAGE_SRC="$PWD" + + python2 setup.py build +} + +package_sagemath() { + optdepends+=('sagemath-jupyter: Jupyter kernel') + + cd sage-$pkgver/src + + export SAGE_ROOT="$PWD" + export SAGE_LOCAL="/usr" + export JUPYTER_PATH="$pkgdir"/usr/share/jupyter + + python2 setup.py install --root="$pkgdir" --optimize=1 + + mkdir -p "$pkgdir"/usr/bin + cp bin/sage "$pkgdir"/usr/bin + for _i in arch-env banner cachegrind callgrind cleaner coverage coverageall cython env env-config eval grep grepdoc inline-fortran \ + ipython massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2sws rst2txt run \ + run-cython runtests startuptime.py sws2rst valgrind version.sh + do + cp bin/sage-$_i "$pkgdir"/usr/bin + done + cp bin/math-readline "$pkgdir"/usr/bin + + mkdir -p "$pkgdir"/usr/share/sage + cp -r ext "$pkgdir"/usr/share/sage + +# Create SAGE_SRC, needed for the notebook and help + mkdir "$pkgdir"/usr/share/sage/source + ln -s /usr/share/doc/sage "$pkgdir"/usr/share/sage/source/doc + +# Remove sage_setup + rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup + +# Split jupyter kernel + rm -r "$pkgdir"/usr/share/jupyter +} + +package_sagemath-jupyter() { + pkgdesc='Jupyter kernel for SageMath' + depends=(sagemath python2-jupyter_client python2-ipywidgets mathjax) + optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter') + + cd sage-$pkgver/src + + export SAGE_ROOT="$PWD" + export SAGE_LOCAL="/usr" + export JUPYTER_PATH="$pkgdir"/usr/share/jupyter + + python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update()" +} Copied: sagemath/repos/community-staging-x86_64/fes02.patch (from rev 294437, sagemath/trunk/fes02.patch) =================================================================== --- community-staging-x86_64/fes02.patch (rev 0) +++ community-staging-x86_64/fes02.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -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 294437, sagemath/trunk/jupyter-path.patch) =================================================================== --- community-staging-x86_64/jupyter-path.patch (rev 0) +++ community-staging-x86_64/jupyter-path.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -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 294437, sagemath/trunk/latte-count.patch) =================================================================== --- community-staging-x86_64/latte-count.patch (rev 0) +++ community-staging-x86_64/latte-count.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -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 294437, sagemath/trunk/package.patch) =================================================================== --- community-staging-x86_64/package.patch (rev 0) +++ community-staging-x86_64/package.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -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/pari-stackwarn.patch (from rev 294437, sagemath/trunk/pari-stackwarn.patch) =================================================================== --- community-staging-x86_64/pari-stackwarn.patch (rev 0) +++ community-staging-x86_64/pari-stackwarn.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -0,0 +1,23 @@ +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 +@@ -39,6 +39,7 @@ + + float_regex = re.compile('\s*([+-]?\s*((\d*\.?\d+)|(\d+\.?))([eE][+-]?\d+)?)') + optional_regex = re.compile(r'(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+\.') + 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) +@@ -879,6 +880,7 @@ + 'you' + """ + got = self.human_readable_escape_sequences(got) ++ got = pari_stack_warning_regex.sub('', got) + if isinstance(want, MarkedOutput): + if want.random: + return True Copied: sagemath/repos/community-staging-x86_64/r-no-readline.patch (from rev 294437, sagemath/trunk/r-no-readline.patch) =================================================================== --- community-staging-x86_64/r-no-readline.patch (rev 0) +++ community-staging-x86_64/r-no-readline.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -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-detect-igraph.patch (from rev 294437, sagemath/trunk/sagemath-detect-igraph.patch) =================================================================== --- community-staging-x86_64/sagemath-detect-igraph.patch (rev 0) +++ community-staging-x86_64/sagemath-detect-igraph.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -0,0 +1,21 @@ +diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py +index 252984f..ce19682 100644 +--- a/src/sage/graphs/generic_graph.py ++++ b/src/sage/graphs/generic_graph.py +@@ -8188,10 +8188,12 @@ class GenericGraph(GenericGraph_pyx): + if algorithm is None: + if vertex_bound: + algorithm = "LP" +- elif is_package_installed("python_igraph"): +- algorithm = "igraph" + else: +- algorithm = "FF" ++ algorithm = "igraph" ++ try: ++ import igraph ++ except ImportError: ++ algorithm = "FF" + + if (algorithm == "FF"): + return self._ford_fulkerson(x,y, value_only=value_only, integer=integer, use_edge_labels=use_edge_labels) + Copied: sagemath/repos/community-staging-x86_64/sagemath-env.patch (from rev 294437, sagemath/trunk/sagemath-env.patch) =================================================================== --- community-staging-x86_64/sagemath-env.patch (rev 0) +++ community-staging-x86_64/sagemath-env.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -0,0 +1,107 @@ +--- src/bin/sage-env.orig 2015-01-06 10:46:04.469687605 +0100 ++++ src/bin/sage-env 2015-01-06 10:49:59.547762019 +0100 +@@ -111,41 +111,7 @@ + } + + +-# New value for SAGE_ROOT: either SAGE_ROOT (if given) +-# or a guessed value based on pwd. +-if [ -n "$SAGE_ROOT" ]; then +- NEW_SAGE_ROOT="$SAGE_ROOT" +-elif [ -f sage -a -d build ]; then +- NEW_SAGE_ROOT="." +-elif [ -f ../../sage -a -d ../../build ]; then +- NEW_SAGE_ROOT="../.." +-else +- # No idea what SAGE_ROOT should be... +- echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this" +- echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory." +- return 1 +-fi +- +-# Make NEW_SAGE_ROOT absolute +-NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P` +- +-# Sanity check NEW_SAGE_ROOT +-if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then +- : +-else +- echo >&2 "Error: SAGE_ROOT is set to a bad value:" +- echo >&2 "SAGE_ROOT=$SAGE_ROOT" +- echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT" +- echo >&2 "or SAGE_ROOT/local/bin/ directory." +- return 1 +-fi +- +-# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT +-if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then +- echo >&2 "Warning: overwriting SAGE_ROOT environment variable:" +- echo >&2 "Old SAGE_ROOT=$SAGE_ROOT" +- echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT" +-fi ++NEW_SAGE_ROOT="/usr" + + # Display the Sage startup banner, used in src/bin/sage + sage_banner() { +@@ -185,6 +185,7 @@ + export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION + + export SAGE_ROOT="$NEW_SAGE_ROOT" ++export SAGE_LOCAL='/usr' + + + # sage-env must know where the Sage's script files are. +@@ -307,8 +307,9 @@ + export SAGE_EXTCODE="$SAGE_SHARE/sage/ext" + export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed" + export SAGE_LOGS="$SAGE_ROOT/logs/pkgs" +-export SAGE_SRC="$SAGE_ROOT/src" +-export SAGE_DOC_SRC="$SAGE_SRC/doc" ++export GAP_ROOT_DIR="/usr/lib/gap" ++export SAGE_SRC="$SAGE_SHARE/sage/source" ++export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage" + export SAGE_DOC="$SAGE_SHARE/doc/sage" + + if [ -z "${SAGE_ORIG_PATH_SET}" ]; then +@@ -414,6 +414,9 @@ + export SAGE_STARTUP_FILE + fi + ++export LIBMTX="$DOT_SAGE/meataxe" ++[[ -d $LIBMTX ]] || mkdir -p $LIBMTX # Create meataxe data dir ++ + if [ "$PYTHON_EGG_CACHE" = "" ]; then + PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs" + export PYTHON_EGG_CACHE +@@ -499,7 +499,6 @@ + fi + fi + fi +-export MAXIMA_PREFIX="$SAGE_LOCAL" + + PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB + +@@ -619,9 +619,6 @@ + LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH + fi + +-# See trac 7186 -- this is needed if ecl is moved +-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR +- + # Handle parallel building/testing/... + # See Trac Ticket #12016 + # First, figure out the right values for SAGE_NUM_THREADS (default +--- src/sage/env.py.orig 2017-12-07 19:51:25.554281539 +0000 ++++ src/sage/env.py 2017-12-07 19:51:42.787654650 +0000 +@@ -117,8 +117,8 @@ + _add_variable_or_fallback('LOCAL_IDENTIFIER','$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')) + Copied: sagemath/repos/community-staging-x86_64/sagemath-ipython-prompt.patch (from rev 294437, sagemath/trunk/sagemath-ipython-prompt.patch) =================================================================== --- community-staging-x86_64/sagemath-ipython-prompt.patch (rev 0) +++ community-staging-x86_64/sagemath-ipython-prompt.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -0,0 +1,13 @@ +diff --git a/src/sage/interfaces/sage0.py b/src/sage/interfaces/sage0.py +index 4ba76ab0b8..e7740177f4 100644 +--- a/src/sage/interfaces/sage0.py ++++ b/src/sage/interfaces/sage0.py +@@ -161,7 +161,7 @@ class Sage(ExtraTabCompletion, Expect): + '--no-term-title', + '--simple-prompt', + ]) +- prompt = re.compile('In \[\d+\]: ') ++ prompt = re.compile('sage: ') + if init_code is None: + init_code = ['from six.moves import cPickle'] + Copied: sagemath/repos/community-staging-x86_64/sagemath-linbox-1.5.patch (from rev 294437, sagemath/trunk/sagemath-linbox-1.5.patch) =================================================================== --- community-staging-x86_64/sagemath-linbox-1.5.patch (rev 0) +++ community-staging-x86_64/sagemath-linbox-1.5.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -0,0 +1,272 @@ +diff --git a/src/sage/libs/linbox/fflas.pxd b/src/sage/libs/linbox/fflas.pxd +index ca23d71..03bbee9 100644 +--- a/src/sage/libs/linbox/fflas.pxd ++++ b/src/sage/libs/linbox/fflas.pxd +@@ -20,19 +20,29 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h" namespace "std": + iterator end() + size_t size() + +- cdef cppclass list[T]: +- cppclass iterator: +- T operator*() +- iterator operator++() +- bint operator==(iterator) +- bint operator!=(iterator) +- void push_back(T&) +- void pop_front() +- T& front() +- iterator begin() +- iterator end() ++cdef extern from "givaro/givpoly1.h": ++ ## template < typename T, typename A=std::allocator<T> > ++ ## class givvector : public __GIV_STANDARD_VECTOR<T,A> ++ cdef cppclass givvector "Givaro::givvector" [T,ALLOCATOR=*]: ++ T& operator[](size_t i) + size_t size() +- void clear() ++ ++ctypedef givvector[ModDoubleFieldElement] ModDoubleDensePolynomial ++ctypedef givvector[ModFloatFieldElement] ModFloatDensePolynomial ++ ++cdef extern from "givaro/givpoly1.h": ++ ## template <class Domain, class StorageTag= Givaro::Dense> ++ ## class GivPolynomialRing : public Givaro::Poly1FactorDom< Domain,StorageTag> ++ cdef cppclass ModDoublePolynomialRing "Givaro::Poly1Dom<Givaro::Modular<double>, Givaro::Dense>": ++ ctypedef givvector[ModDoubleField] Element ++ ctypedef givvector[ModDoubleField] Polynomial ++ ModDoublePolynomialRing(ModDoubleField& F) ++ ## template <class Domain, class StorageTag= Givaro::Dense> ++ ## class GivPolynomialRing : public Givaro::Poly1FactorDom< Domain,StorageTag> ++ cdef cppclass ModFloatPolynomialRing "Givaro::Poly1Dom<Givaro::Modular<float>, Givaro::Dense>": ++ ctypedef givvector[ModFloatField] Element ++ ctypedef givvector[ModFloatField] Polynomial ++ ModFloatPolynomialRing(ModFloatField& F) + + cdef extern from "fflas-ffpack/fflas-ffpack.h": + ctypedef enum fflas_trans_enum "FFLAS::FFLAS_TRANSPOSE": +@@ -105,13 +115,12 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h": + size_t nr, size_t foo, size_t r, + ModDoubleFieldElement* matrix, size_t nc, size_t* Q) + +- void ModDouble_MinPoly "FFPACK::MinPoly" ( ModDoubleField F, ++ void ModDouble_MinPoly "FFPACK::MinPoly" ( ModDoubleField& F, + vector[ModDoubleFieldElement] minP, size_t N, +- ModDoubleFieldElement* A, size_t lda, +- ModDoubleFieldElement* X, size_t ldx, size_t* P) ++ ModDoubleFieldElement*A, size_t lda) + +- void ModDouble_CharPoly "FFPACK::CharPoly" ( ModDoubleField F, +- list[vector[ModDoubleFieldElement]] charp, size_t N, ++ void ModDouble_CharPoly "FFPACK::CharPoly" ( ModDoublePolynomialRing& R, ++ ModDoubleDensePolynomial& charp, size_t N, + ModDoubleFieldElement* A, size_t lda) + + # float +@@ -142,9 +151,8 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h": + + void ModFloat_MinPoly "FFPACK::MinPoly" ( ModFloatField F, + vector[ModFloatFieldElement] minP, size_t N, +- ModFloatFieldElement* A, size_t lda, +- ModFloatFieldElement* X, size_t ldx, size_t* P) ++ ModFloatFieldElement* A, size_t lda) + +- void ModFloat_CharPoly "FFPACK::CharPoly" ( ModFloatField F, +- list[vector[ModFloatFieldElement]] charp, size_t N, ++ void ModFloat_CharPoly "FFPACK::CharPoly" ( ModFloatPolynomialRing& F, ++ ModFloatDensePolynomial& charp, size_t N, + ModFloatFieldElement* A, size_t lda ) +diff --git a/src/sage/libs/linbox/linbox_flint_interface.pyx b/src/sage/libs/linbox/linbox_flint_interface.pyx +index 02a6151..a00d303 100644 +--- a/src/sage/libs/linbox/linbox_flint_interface.pyx ++++ b/src/sage/libs/linbox/linbox_flint_interface.pyx +@@ -76,19 +76,23 @@ cdef extern from "givaro/zring.h": + ctypedef GivaroInteger Element + + +-cdef extern from "givaro/givpoly1.h": +- ## template < typename T, typename A=std::allocator<T> > +- ## class givvector : public __GIV_STANDARD_VECTOR<T,A> +- cdef cppclass givvector "Givaro::givvector" [T,ALLOCATOR=*]: +- T& operator[](size_t i) ++cdef extern from "linbox/polynomial/dense-polynomial.h": ++ ## template<class Field> ++ ## class DensePolynomial : public Givaro::Poly1FactorDom<Field, Givaro::Dense>::Element ++ cdef cppclass LinBoxIntegerDensePolynomial "LinBox::DensePolynomial<Givaro::ZRing<Givaro::Integer> >": ++ ctypedef GivaroIntegerRing BaseRing ++ ctypedef GivaroInteger BaseRingElement ++ LinBoxIntegerDensePolynomial(BaseRing &F) ++ LinBoxIntegerDensePolynomial(BaseRing &F, size_t s) ++ BaseRingElement& operator[](size_t i) + size_t size() + +-cdef extern from "linbox/ring/givaro-polynomial.h": +- ## template <class Domain, class StorageTag= Givaro::Dense> +- ## class GivPolynomialRing : public Givaro::Poly1FactorDom< Domain,StorageTag> +- cdef cppclass LinBoxIntegerPolynomialRing "LinBox::GivPolynomialRing<Givaro::ZRing<Givaro::Integer>, Givaro::Dense>": +- ctypedef givvector[GivaroInteger] Element +- ctypedef givvector[GivaroInteger] Polynomial ++cdef extern from "linbox/ring/polynomial-ring.h": ++ ## template <class BaseRing, class StorageTag= Givaro::Dense> ++ ## class PolynomialRing : public Givaro::Poly1FactorDom<BaseRing,StorageTag> ++ cdef cppclass LinBoxIntegerPolynomialRing "LinBox::PolynomialRing<Givaro::ZRing<Givaro::Integer>, Givaro::Dense>": ++ ctypedef LinBoxIntegerDensePolynomial Element ++ ctypedef LinBoxIntegerDensePolynomial Polynomial + + cdef extern from "linbox/matrix/matrix-domain.h": + ## template <class Field_ > +@@ -190,40 +194,32 @@ cdef void linbox_fmpz_mat_mul(fmpz_mat_t C, fmpz_mat_t A, fmpz_mat_t B): + cdef void linbox_fmpz_mat_charpoly(fmpz_poly_t cp, fmpz_mat_t A): + cdef GivaroIntegerRing ZZ + cdef LinBoxIntegerDenseMatrix * LBA +- cdef LinBoxIntegerPolynomialRing.Element m_A +- +- # FIXME: bug in LinBox +- # see https://github.com/linbox-team/linbox/issues/51 +- if fmpz_mat_nrows(A) == 0: +- fmpz_poly_one(cp) +- return ++ cdef LinBoxIntegerDensePolynomial * m_A + + LBA = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(A), fmpz_mat_ncols(A)) + fmpz_mat_get_linbox(LBA[0], A) +- LinBoxIntegerDense_charpoly(m_A, LBA[0]) +- fmpz_poly_set_linbox(cp, m_A) ++ m_A = new LinBoxIntegerDensePolynomial(ZZ, fmpz_mat_nrows(A)) ++ LinBoxIntegerDense_charpoly(m_A[0], LBA[0]) ++ fmpz_poly_set_linbox(cp, m_A[0]) + + del LBA ++ del m_A + + + # set mp to the minimal polynomial of A + cdef void linbox_fmpz_mat_minpoly(fmpz_poly_t mp, fmpz_mat_t A): + cdef GivaroIntegerRing ZZ + cdef LinBoxIntegerDenseMatrix * LBA +- cdef LinBoxIntegerPolynomialRing.Element m_A +- +- # FIXME: bug in LinBox +- # see https://github.com/linbox-team/linbox/issues/51 +- if fmpz_mat_nrows(A) == 0: +- fmpz_poly_one(mp) +- return ++ cdef LinBoxIntegerDensePolynomial * m_A + + LBA = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(A), fmpz_mat_ncols(A)) ++ m_A = new LinBoxIntegerDensePolynomial(ZZ) + fmpz_mat_get_linbox(LBA[0], A) +- LinBoxIntegerDense_minpoly(m_A, LBA[0]) +- fmpz_poly_set_linbox(mp, m_A) ++ LinBoxIntegerDense_minpoly(m_A[0], LBA[0]) ++ fmpz_poly_set_linbox(mp, m_A[0]) + + del LBA ++ del m_A + + + # return the rank of A +diff --git a/src/sage/matrix/matrix_modn_dense_double.pyx b/src/sage/matrix/matrix_modn_dense_double.pyx +index 15c35cb..b1f6154 100644 +--- a/src/sage/matrix/matrix_modn_dense_double.pyx ++++ b/src/sage/matrix/matrix_modn_dense_double.pyx +@@ -27,7 +27,9 @@ from sage.libs.linbox.fflas cimport ModDouble_fgemm as Mod_fgemm, ModDouble_fgem + ModDoubleRank as ModRank, ModDouble_echelon as Mod_echelon, \ + ModDouble_applyp as Mod_applyp, \ + ModDouble_MinPoly as Mod_MinPoly, \ +- ModDouble_CharPoly as Mod_CharPoly ++ ModDouble_CharPoly as Mod_CharPoly, \ ++ ModDoublePolynomialRing as ModDensePolyRing,\ ++ ModDoubleDensePolynomial as ModDensePoly + + # Limit for LinBox Modular<double> + MAX_MODULUS = 2**23 +diff --git a/src/sage/matrix/matrix_modn_dense_float.pyx b/src/sage/matrix/matrix_modn_dense_float.pyx +index 61457ce..eda8f0b 100644 +--- a/src/sage/matrix/matrix_modn_dense_float.pyx ++++ b/src/sage/matrix/matrix_modn_dense_float.pyx +@@ -25,7 +25,10 @@ from sage.libs.linbox.fflas cimport ModFloat_fgemm as Mod_fgemm, ModFloat_fgemv + ModFloatRank as ModRank, ModFloat_echelon as Mod_echelon, \ + ModFloat_applyp as Mod_applyp, \ + ModFloat_MinPoly as Mod_MinPoly, \ +- ModFloat_CharPoly as Mod_CharPoly ++ ModFloat_CharPoly as Mod_CharPoly, \ ++ ModFloatPolynomialRing as ModDensePolyRing,\ ++ ModFloatDensePolynomial as ModDensePoly ++ + + # LinBox supports up to 2^11 using float but that's double dog slow, + # so we pick a smaller value for crossover +diff --git a/src/sage/matrix/matrix_modn_dense_template.pxi b/src/sage/matrix/matrix_modn_dense_template.pxi +index 3da3e31..819ef2d 100644 +--- a/src/sage/matrix/matrix_modn_dense_template.pxi ++++ b/src/sage/matrix/matrix_modn_dense_template.pxi +@@ -306,23 +306,15 @@ cdef inline linbox_minpoly(celement modulus, Py_ssize_t nrows, celement* entries + cdef Py_ssize_t i + cdef ModField *F = new ModField(<long>modulus) + cdef vector[ModFieldElement] *minP = new vector[ModFieldElement]() +- cdef ModFieldElement *X = <ModFieldElement*>check_allocarray(nrows * (nrows+1), sizeof(ModFieldElement)) +- cdef size_t *P = <size_t*>check_allocarray(nrows, sizeof(size_t)) +- +- cdef celement *cpy = linbox_copy(modulus, entries, nrows, nrows) + + if nrows*nrows > 1000: sig_on() +- Mod_MinPoly(F[0], minP[0], nrows, <ModFieldElement*>cpy, nrows, X, nrows, P) ++ Mod_MinPoly(F[0], minP[0], nrows, <ModFieldElement*>entries, nrows) + if nrows*nrows > 1000: sig_off() + +- sig_free(cpy) +- + l = [] + for i in range(minP.size()): + l.append( <celement>minP.at(i) ) + +- sig_free(P) +- sig_free(X) + del F + return l + +@@ -332,27 +324,23 @@ cdef inline linbox_charpoly(celement modulus, Py_ssize_t nrows, celement* entrie + """ + cdef Py_ssize_t i + cdef ModField *F = new ModField(<long>modulus) +- cdef std_list[vector[ModFieldElement]] P_list +- P_list.clear() ++ cdef ModDensePolyRing * R = new ModDensePolyRing(F[0]) ++ cdef ModDensePoly P + + cdef celement *cpy = linbox_copy(modulus, entries, nrows, nrows) + + if nrows*nrows > 1000: sig_on() +- Mod_CharPoly(F[0], P_list, nrows, <ModFieldElement*>cpy, nrows) ++ Mod_CharPoly(R[0], P, nrows, <ModFieldElement*>cpy, nrows) + if nrows*nrows > 1000: sig_off() + + sig_free(cpy) + +- cdef vector[ModFieldElement] tmp + l = [] +- while P_list.size(): +- l.append([]) +- tmp = P_list.front() +- for i in range(tmp.size()): +- l[-1].append(<celement>tmp.at(i)) +- P_list.pop_front() ++ for i in range(P.size()): ++ l.append(<celement>P[i]) + + del F ++ del R + return l + + +@@ -1731,9 +1719,7 @@ cdef class Matrix_modn_dense_template(Matrix_dense): + R = self._base_ring[var] + # call linbox for charpoly + v = linbox_charpoly(self.p, self._nrows, self._entries) +- r = R(1) +- for e in v: +- r *= R(e) ++ r = R(v) + return r + + def echelonize(self, algorithm="linbox", **kwds): Copied: sagemath/repos/community-staging-x86_64/sagemath-lrs.patch (from rev 294437, sagemath/trunk/sagemath-lrs.patch) =================================================================== --- community-staging-x86_64/sagemath-lrs.patch (rev 0) +++ community-staging-x86_64/sagemath-lrs.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -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-matplotlib2.patch (from rev 294437, sagemath/trunk/sagemath-matplotlib2.patch) =================================================================== --- community-staging-x86_64/sagemath-matplotlib2.patch (rev 0) +++ community-staging-x86_64/sagemath-matplotlib2.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -0,0 +1,253 @@ +diff --git a/src/sage/all.py b/src/sage/all.py +index 300f519..19bc8ec 100644 +--- a/src/sage/all.py ++++ b/src/sage/all.py +@@ -313,8 +313,6 @@ warnings.filters.remove(('ignore', None, DeprecationWarning, None, 0)) + # Ignore all deprecations from IPython etc. + warnings.filterwarnings('ignore', + module='.*(IPython|ipykernel|jupyter_client|jupyter_core|nbformat|notebook|ipywidgets|storemagic)') +-# Ignore warnings due to matplotlib-1.5 together with numpy-1.13 +-warnings.filterwarnings('ignore', module='matplotlib[.]contour|numpy[.]ma[.]core') + # However, be sure to keep OUR deprecation warnings + warnings.filterwarnings('default', + '[\s\S]*See http://trac.sagemath.org/[0-9]* for details.') +diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py +index 98d6224..fbce029 100644 +--- a/src/sage/plot/arrow.py ++++ b/src/sage/plot/arrow.py +@@ -147,8 +147,8 @@ class CurveArrow(GraphicPrimitive): + bpath = Path(self.vertices, self.codes) + p = FancyArrowPatch(path=bpath, + lw=width, arrowstyle='%s,head_width=%s,head_length=%s' % (style, head_width, head_length), +- fc=color, ec=color) +- p.set_linestyle(get_matplotlib_linestyle(options['linestyle'], return_type='long')) ++ fc=color, ec=color, ++ linestyle=get_matplotlib_linestyle(options['linestyle'], return_type='long')) + p.set_zorder(options['zorder']) + p.set_label(options['legend_label']) + subplot.add_patch(p) +@@ -336,7 +336,7 @@ class Arrow(GraphicPrimitive): + this into account. See :trac:`12836`:: + + sage: fig = Graphics().matplotlib() +- sage: sp = fig.add_subplot(1,1,1) ++ sage: sp = fig.add_subplot(1,1,1, label='axis1') + sage: a = arrow((0,0), (1,1)) + sage: b = arrow((0,0), (1,1), width=20) + sage: p1 = a[0]._render_on_subplot(sp) +@@ -358,7 +358,7 @@ class Arrow(GraphicPrimitive): + sage: a.save(filename=filename) + sage: with open(filename, 'r') as f: + ....: contents = f.read().replace('\n', ' ') +- sage: two_stroke_pattern = r'setdash.*stroke.*stroke.*setdash' ++ sage: two_stroke_pattern = r'setdash.*setdash.*stroke.*stroke.*setdash' + sage: import re + sage: two_stroke_re = re.compile(two_stroke_pattern) + sage: two_stroke_re.search(contents) is None +@@ -383,8 +383,8 @@ class Arrow(GraphicPrimitive): + lw=width, + arrowstyle='%s,head_width=%s,head_length=%s' % (style, head_width, head_length), + shrinkA=arrowshorten_end, shrinkB=arrowshorten_end, +- fc=color, ec=color) +- p.set_linestyle(get_matplotlib_linestyle(options['linestyle'], return_type='long')) ++ fc=color, ec=color, ++ linestyle=get_matplotlib_linestyle(options['linestyle'], return_type='long')) + p.set_zorder(options['zorder']) + p.set_label(options['legend_label']) + +@@ -437,7 +437,7 @@ class Arrow(GraphicPrimitive): + pe1.draw_path(renderer, gc, tpath, affine, rgbFace) + + pe1 = ConditionalStroke(CheckNthSubPath(p, 0), [pe.Stroke()]) +- pe2 = ConditionalStroke(CheckNthSubPath(p, 1), [pe.Stroke(linestyle="solid")]) ++ pe2 = ConditionalStroke(CheckNthSubPath(p, 1), [pe.Stroke(dashes={'dash_offset': 0, 'dash_list': None})]) + p.set_path_effects([pe1, pe2]) + + subplot.add_patch(p) +diff --git a/src/sage/plot/contour_plot.py b/src/sage/plot/contour_plot.py +index 76077e3..efc1f2b 100644 +--- a/src/sage/plot/contour_plot.py ++++ b/src/sage/plot/contour_plot.py +@@ -178,12 +178,10 @@ class ContourPlot(GraphicPrimitive): + if fill: + if contours is None: + CSF = subplot.contourf(self.xy_data_array, cmap=cmap, +- extent=(x0, x1, y0, y1), +- label=options['legend_label']) ++ extent=(x0, x1, y0, y1)) + else: + CSF = subplot.contourf(self.xy_data_array, contours, cmap=cmap, +- extent=(x0, x1, y0, y1), extend='both', +- label=options['legend_label']) ++ extent=(x0, x1, y0, y1), extend='both') + + linewidths = options.get('linewidths', None) + if isinstance(linewidths, (int, Integer)): +@@ -200,13 +198,11 @@ class ContourPlot(GraphicPrimitive): + if contours is None: + CS = subplot.contour(self.xy_data_array, cmap=cmap, + extent=(x0, x1, y0, y1), +- linewidths=linewidths, linestyles=linestyles, +- label=options['legend_label']) ++ linewidths=linewidths, linestyles=linestyles) + else: + CS = subplot.contour(self.xy_data_array, contours, cmap=cmap, + extent=(x0, x1, y0, y1), +- linewidths=linewidths, linestyles=linestyles, +- label=options['legend_label']) ++ linewidths=linewidths, linestyles=linestyles) + if options.get('labels', False): + label_options = options['label_options'] + label_options['fontsize'] = int(label_options['fontsize']) +diff --git a/src/sage/plot/plot.py b/src/sage/plot/plot.py +index aa82eda..03a0f3a 100644 +--- a/src/sage/plot/plot.py ++++ b/src/sage/plot/plot.py +@@ -478,7 +478,7 @@ We test that ``imshow`` works as well, verifying that + + :: + +- sage: plt.imshow([[(0,0,0)]]) ++ sage: plt.imshow([[(0.0,0.0,0.0)]]) + <matplotlib.image.AxesImage object at ...> + sage: plt.savefig(os.path.join(SAGE_TMP, 'foo.png')) + +@@ -2908,11 +2908,14 @@ def list_plot(data, plotjoined=False, **kwargs): + If ``plotjoined`` is ``False`` then the axis that is in log scale + must have all points strictly positive. For instance, the following + plot will show no points in the figure since the points in the +- horizontal axis starts from `(0,1)`. ++ horizontal axis starts from `(0,1)`. Further, matplotlib will display ++ a user warning. + + :: + + sage: list_plot(yl, scale='loglog') # both axes are log ++ doctest:warning ++ ... + Graphics object consisting of 1 graphics primitive + + Instead this will work. We drop the point `(0,1)`.:: +@@ -3288,12 +3291,15 @@ def list_plot_semilogy(data, plotjoined=False, **kwds): + + If ``plotjoined`` is ``False`` then the vertical axis must have all + points strictly positive. Otherwise the plot will come up empty. +- For instance the following plot contains a point at `(1,0)`. ++ For instance the following plot contains a point at `(1,0)`. Further, ++ matplotlib will display a user warning. + + :: + + sage: xl = [2**k for k in range(12)]; yl = range(len(xl)) + sage: list_plot_semilogy(list(zip(xl,yl))) # plot empty due to (1,0) ++ doctest:warning ++ ... + Graphics object consisting of 1 graphics primitive + + We remove `(1,0)` to fix this.:: +diff --git a/src/sage/plot/plot3d/list_plot3d.py b/src/sage/plot/plot3d/list_plot3d.py +index c9f22dd..be87ff2 100644 +--- a/src/sage/plot/plot3d/list_plot3d.py ++++ b/src/sage/plot/plot3d/list_plot3d.py +@@ -29,21 +29,20 @@ def list_plot3d(v, interpolation_type='default', texture="automatic", point_list + + OPTIONAL KEYWORDS: + +- - ``interpolation_type`` - 'linear', 'nn' (natural neighbor), 'spline' ++ - ``interpolation_type`` - 'linear', 'clough' (CloughTocher2D), 'spline' + + 'linear' will perform linear interpolation + +- The option 'nn' An interpolation method for multivariate data in a +- Delaunay triangulation. The value for an interpolation point is +- estimated using weighted values of the closest surrounding points in +- the triangulation. These points, the natural neighbors, are the ones +- the interpolation point would connect to if inserted into the +- triangulation. ++ The option 'clough' will interpolate by using a piecewise cubic interpolating ++ Bezier polynomial on each triangle, using a Clough-Tocher scheme. ++ The interpolant is guaranteed to be continuously differentiable. ++ The gradients of the interpolant are chosen so that the curvature of the ++ interpolating surface is approximatively minimized. + + The option 'spline' interpolates using a bivariate B-spline. + + When v is a matrix the default is to use linear interpolation, when +- v is a list of points the default is nearest neighbor. ++ v is a list of points the default is 'clough'. + + - ``degree`` - an integer between 1 and 5, controls the degree of spline + used for spline interpolation. For data that is highly oscillatory +@@ -320,18 +319,18 @@ def list_plot3d_tuples(v, interpolation_type, texture, **kwds): + + OPTIONAL KEYWORDS: + +- - ``interpolation_type`` - 'linear', 'nn' (natural neighbor), 'spline' ++ - ``interpolation_type`` - 'linear', 'clough' (CloughTocher2D), 'spline' + + 'linear' will perform linear interpolation + +- The option 'nn' will interpolate by using natural neighbors. The +- value for an interpolation point is estimated using weighted values +- of the closest surrounding points in the triangulation. ++ The option 'clough' will interpolate by using a piecewise cubic interpolating ++ Bezier polynomial on each triangle, using a Clough-Tocher scheme. ++ The interpolant is guaranteed to be continuously differentiable. + + The option 'spline' interpolates using a bivariate B-spline. + + When v is a matrix the default is to use linear interpolation, when +- v is a list of points the default is nearest neighbor. ++ v is a list of points the default is 'clough'. + + - ``degree`` - an integer between 1 and 5, controls the degree of spline + used for spline interpolation. For data that is highly oscillatory +@@ -373,7 +372,7 @@ def list_plot3d_tuples(v, interpolation_type, texture, **kwds): + sage: list_plot3d([(1, 2, 3), (0, 1, 3), (2, 1, 4), (1, 0, -2)], texture='yellow', num_points=50) + Graphics3d Object + """ +- from matplotlib import tri, delaunay ++ from matplotlib import tri + import numpy + import scipy + from random import random +@@ -439,19 +438,15 @@ def list_plot3d_tuples(v, interpolation_type, texture, **kwds): + G._set_extra_kwds(kwds) + return G + +- if interpolation_type == 'nn' or interpolation_type =='default': ++ if interpolation_type == 'clough' or interpolation_type =='default': + +- T=delaunay.Triangulation(x,y) +- f=T.nn_interpolator(z) +- f.default_value=0.0 +- j=numpy.complex(0,1) +- vals=f[ymin:ymax:j*num_points,xmin:xmax:j*num_points] ++ points=[[x[i],y[i]] for i in range(len(x))] ++ j = numpy.complex(0, 1) ++ f = interpolate.CloughTocher2DInterpolator(points,z) + from .parametric_surface import ParametricSurface +- def g(x,y): +- i=round( (x-xmin)/(xmax-xmin)*(num_points-1) ) +- j=round( (y-ymin)/(ymax-ymin)*(num_points-1) ) +- z=vals[int(j),int(i)] +- return (x,y,z) ++ def g(x, y): ++ z = f([x, y]) ++ return (x, y, z) + G = ParametricSurface(g, (list(numpy.r_[xmin:xmax:num_points*j]), list(numpy.r_[ymin:ymax:num_points*j])), texture=texture, **kwds) + G._set_extra_kwds(kwds) + return G +diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx +index 3ce4642..f66cd89 100644 +--- a/src/sage/probability/probability_distribution.pyx ++++ b/src/sage/probability/probability_distribution.pyx +@@ -118,7 +118,7 @@ cdef class ProbabilityDistribution: + sage: P = [0.3, 0.4, 0.3] + sage: X = GeneralDiscreteDistribution(P) + sage: h, b = X.generate_histogram_data(bins = 10) +- sage: h ++ sage: h # rel tol 1e-08 + [1.6299999999999999, + 0.0, + 0.0, Copied: sagemath/repos/community-staging-x86_64/sagemath-networkx2.patch (from rev 294437, sagemath/trunk/sagemath-networkx2.patch) =================================================================== --- community-staging-x86_64/sagemath-networkx2.patch (rev 0) +++ community-staging-x86_64/sagemath-networkx2.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -0,0 +1,196 @@ +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 +@@ -1158,7 +1156,7 @@ 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 +@@ -1227,7 +1225,7 @@ 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)) +@@ -1416,7 +1414,7 @@ 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 "+ +@@ -2844,7 +2844,7 @@ 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 :: + +@@ -2870,9 +2870,7 @@ 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: +@@ -2895,10 +2893,7 @@ 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/basic.py b/src/sage/graphs/generators/basic.py +index 8777b95c4b..28ef7e48f2 100644 +--- a/src/sage/graphs/generators/basic.py ++++ b/src/sage/graphs/generators/basic.py +@@ -437,7 +437,7 @@ def CompleteBipartiteGraph(n1, n2): + + Compare the plotting:: + +- sage: n = networkx.complete_bipartite_graph(11,17) ++ sage: n = networkx.complete_bipartite_graph(11r,17r) + sage: spring_med = Graph(n) + sage: posdict_med = graphs.CompleteBipartiteGraph(11,17) + +@@ -469,7 +469,7 @@ def CompleteBipartiteGraph(n1, n2): + sage: g = [] + sage: j = [] + sage: for i in range(9): +- ....: spr = networkx.complete_bipartite_graph(i+1,4) ++ ....: spr = networkx.complete_bipartite_graph(int(i+1),4r) + ....: k = Graph(spr) + ....: g.append(k) + sage: for i in range(3): +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 +@@ -108,7 +108,7 @@ examples are covered here. + :: + + sage: import networkx +- sage: K = networkx.complete_bipartite_graph(12,7) ++ sage: K = networkx.complete_bipartite_graph(12r,7r) + sage: G = Graph(K) + sage: G.degree() + [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12] +@@ -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. "+ +@@ -4600,7 +4600,7 @@ 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)] + +@@ -6288,7 +6288,7 @@ 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): + """ + Returns a graph constructed with maximal cliques as vertices, and + edges between maximal cliques with common members in the original +@@ -6317,7 +6317,7 @@ 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-pynac-0.7.14.patch (from rev 294437, sagemath/trunk/sagemath-pynac-0.7.14.patch) =================================================================== --- community-staging-x86_64/sagemath-pynac-0.7.14.patch (rev 0) +++ community-staging-x86_64/sagemath-pynac-0.7.14.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -0,0 +1,167 @@ +diff --git a/src/sage/libs/pynac/pynac.pxd b/src/sage/libs/pynac/pynac.pxd +index d4afc4e..6d1fcac 100644 +--- a/src/sage/libs/pynac/pynac.pxd ++++ b/src/sage/libs/pynac/pynac.pxd +@@ -481,22 +481,17 @@ cdef extern from "pynac_wrap.h": + ctypedef GParamSet const_paramset_ref "const GiNaC::paramset&" + + ctypedef struct py_funcs_struct: +- py_binomial(a, b) +- py_binomial_int(int n, unsigned int k) + py_gcd(a, b) + py_lcm(a, b) + py_real(a) + py_imag(a) + py_numer(a) + py_denom(a) +- py_conjugate(a) + bint py_is_rational(a) +- bint py_is_crational(a) + bint py_is_real(a) + bint py_is_integer(a) + bint py_is_equal(a, b) + bint py_is_even(a) +- bint py_is_cinteger(a) + bint py_is_prime(n) + bint py_is_exact(x) + +@@ -534,23 +529,14 @@ cdef extern from "pynac_wrap.h": + py_asinh(x) + py_acosh(x) + py_atanh(x) +- py_tgamma(x) +- py_lgamma(x) + py_isqrt(x) + py_sqrt(x) +- py_abs(x) + py_mod(x, y) + py_smod(x, y) + py_irem(x, y) +- py_iquo(x, y) +- py_iquo2(x, y) +- py_li(x, n, parent) +- py_li2(x) + py_psi(x) + py_psi2(n, x) + +- int py_int_length(x) except -1 +- + py_eval_constant(unsigned serial, parent) + py_eval_unsigned_infinity() + py_eval_infinity() +@@ -583,8 +569,6 @@ cdef extern from "pynac_wrap.h": + stdstring* py_latex_fderivative(unsigned id, params, args) + paramset_to_PyTuple(const_paramset_ref s) + +- py_rational_power_parts(basis, exp) +- + py_funcs_struct py_funcs "GiNaC::py_funcs" + + cdef extern from "pynac/order.h": +diff --git a/src/sage/libs/pynac/pynac.pyx b/src/sage/libs/pynac/pynac.pyx +index f303184..419cc47 100644 +--- a/src/sage/libs/pynac/pynac.pyx ++++ b/src/sage/libs/pynac/pynac.pyx +@@ -2432,23 +2432,18 @@ def init_function_table(): + called before Pynac is used; otherwise, there will be segfaults. + """ + +- py_funcs.py_binomial_int = &py_binomial_int +- py_funcs.py_binomial = &py_binomial + py_funcs.py_gcd = &py_gcd + py_funcs.py_lcm = &py_lcm + py_funcs.py_real = &py_real + py_funcs.py_imag = &py_imag + py_funcs.py_numer = &py_numer + py_funcs.py_denom = &py_denom +- py_funcs.py_conjugate = &py_conjugate + + py_funcs.py_is_rational = &py_is_rational +- py_funcs.py_is_crational = &py_is_crational + py_funcs.py_is_real = &py_is_real + py_funcs.py_is_integer = &py_is_integer + py_funcs.py_is_equal = &py_is_equal + py_funcs.py_is_even = &py_is_even +- py_funcs.py_is_cinteger = &py_is_cinteger + py_funcs.py_is_prime = &py_is_prime + py_funcs.py_is_exact = &py_is_exact + +@@ -2462,7 +2457,6 @@ def init_function_table(): + py_funcs.py_mpq_from_rational = &py_mpq_from_rational + + py_funcs.py_float = &py_float +- py_funcs.py_RDF_from_double = &py_RDF_from_double + + py_funcs.py_factorial = &py_factorial + py_funcs.py_doublefactorial = &py_doublefactorial +@@ -2486,23 +2480,14 @@ def init_function_table(): + py_funcs.py_asinh = &py_asinh + py_funcs.py_acosh = &py_acosh + py_funcs.py_atanh = &py_atanh +- py_funcs.py_tgamma = &py_tgamma +- py_funcs.py_lgamma = &py_lgamma + py_funcs.py_isqrt = &py_isqrt + py_funcs.py_sqrt = &py_sqrt +- py_funcs.py_abs = &py_abs + py_funcs.py_mod = &py_mod + py_funcs.py_smod = &py_smod + py_funcs.py_irem = &py_irem +- py_funcs.py_iquo = &py_iquo +- py_funcs.py_iquo2 = &py_iquo2 +- py_funcs.py_li = &py_li +- py_funcs.py_li2 = &py_li2 + py_funcs.py_psi = &py_psi + py_funcs.py_psi2 = &py_psi2 + +- py_funcs.py_int_length = &py_int_length +- + py_funcs.py_eval_constant = &py_eval_constant + py_funcs.py_eval_unsigned_infinity = &py_eval_unsigned_infinity + py_funcs.py_eval_infinity = &py_eval_infinity +@@ -2531,7 +2516,6 @@ def init_function_table(): + py_funcs.py_print_fderivative = &py_print_fderivative + py_funcs.py_latex_fderivative = &py_latex_fderivative + py_funcs.paramset_to_PyTuple = ¶mset_to_PyTuple +- py_funcs.py_rational_power_parts = &py_rational_power_parts + + init_function_table() + init_pynac_I() + +diff --git a/src/sage/functions/other.py b/src/sage/functions/other.py +index 81cd485..931cecc 100644 +--- a/src/sage/functions/other.py ++++ b/src/sage/functions/other.py +@@ -688,7 +688,6 @@ class Function_gamma(GinacFunction): + :meth:`sage.functions.other.gamma` + """ + GinacFunction.__init__(self, 'gamma', latex_name=r"\Gamma", +- ginac_name='tgamma', + conversions={'mathematica':'Gamma', + 'maple':'GAMMA', + 'sympy':'gamma', +diff --git a/src/sage/libs/pynac/pynac.pxd b/src/sage/libs/pynac/pynac.pxd +index 1739067..d4afc4e 100644 +--- a/src/sage/libs/pynac/pynac.pxd ++++ b/src/sage/libs/pynac/pynac.pxd +@@ -362,7 +362,7 @@ cdef extern from "pynac_wrap.h": + GEx g_zeta2 "GiNaC::zeta" (GEx m, GEx s) except + # alternating Euler sum + GEx g_stieltjes "GiNaC::stieltjes" (GEx m) except + # Stieltjes constants + GEx g_zetaderiv "GiNaC::zetaderiv" (GEx n, GEx x) except + # derivatives of Riemann's zeta function +- GEx g_tgamma "GiNaC::tgamma" (GEx x) except + # gamma function ++ GEx g_gamma "GiNaC::gamma" (GEx x) except + # gamma function + GEx g_lgamma "GiNaC::lgamma" (GEx x) except + # logarithm of gamma function + GEx g_beta "GiNaC::beta" (GEx x, GEx y) except + # beta function (tgamma(x)*tgamma(y)/tgamma(x+y)) + GEx g_psi "GiNaC::psi" (GEx x) except + # psi (digamma) function +diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx +index dfb8751..52303d1 100644 +--- a/src/sage/symbolic/expression.pyx ++++ b/src/sage/symbolic/expression.pyx +@@ -8917,7 +8917,7 @@ cdef class Expression(CommutativeRingElement): + cdef GEx x + sig_on() + try: +- x = g_hold_wrapper(g_tgamma, self._gobj, hold) ++ x = g_hold_wrapper(g_gamma, self._gobj, hold) + finally: + sig_off() + return new_Expression_from_GEx(self._parent, x) Copied: sagemath/repos/community-staging-x86_64/sagemath-python3-notebook.patch (from rev 294437, sagemath/trunk/sagemath-python3-notebook.patch) =================================================================== --- community-staging-x86_64/sagemath-python3-notebook.patch (rev 0) +++ community-staging-x86_64/sagemath-python3-notebook.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -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 294437, 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 2018-02-14 17:16:04 UTC (rev 294438) @@ -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 294437, 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 2018-02-14 17:16:04 UTC (rev 294438) @@ -0,0 +1,94 @@ +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 +@@ -188,7 +188,7 @@ 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] +@@ -650,7 +650,7 @@ 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 +@@ -188,8 +188,8 @@ 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, +@@ -1690,8 +1695,8 @@ 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) +@@ -1850,8 +1855,8 @@ 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 +@@ -4046,10 +4051,10 @@ 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 Copied: sagemath/repos/community-staging-x86_64/sagemath-threejs.patch (from rev 294437, sagemath/trunk/sagemath-threejs.patch) =================================================================== --- community-staging-x86_64/sagemath-threejs.patch (rev 0) +++ community-staging-x86_64/sagemath-threejs.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -0,0 +1,11 @@ +--- a/src/sage/repl/rich_output/display_manager.py ++++ b/src/sage/repl/rich_output/display_manager.py +@@ -744,7 +744,7 @@ class DisplayManager(SageObject): + """ + if online: + from sage.misc.package import installed_packages +- version = installed_packages()['threejs'] ++ version = 'r80' + return """ + <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/build/three.min.js"></script> + <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/examples/js/controls/OrbitControls.js"></script> Copied: sagemath/repos/community-staging-x86_64/test-optional.patch (from rev 294437, sagemath/trunk/test-optional.patch) =================================================================== --- community-staging-x86_64/test-optional.patch (rev 0) +++ community-staging-x86_64/test-optional.patch 2018-02-14 17:16:04 UTC (rev 294438) @@ -0,0 +1,25 @@ +--- src/sage/doctest/control.py.orig 2016-10-20 19:39:53.714618246 +0200 ++++ src/sage/doctest/control.py 2016-10-20 19:40:15.158049920 +0200 +@@ -320,22 +320,6 @@ + if "all" in options.optional: + # Special case to run all optional tests + options.optional = True +- else: +- # We replace the 'optional' tag by all optional +- # packages for which the installed version matches the +- # latest available version (this implies in particular +- # that the package is actually installed). +- if 'optional' in options.optional: +- options.optional.discard('optional') +- from sage.misc.package import list_packages +- for pkg in list_packages('optional', local=True).values(): +- if pkg['installed_version'] == pkg['remote_version']: +- options.optional.add(pkg['name']) +- +- # Check that all tags are valid +- for o in options.optional: +- if not optionaltag_regex.search(o): +- raise ValueError('invalid optional tag {!r}'.format(o)) + + self.options = options + self.files = args