Date: Monday, February 19, 2018 @ 23:18:25 Author: arojas Revision: 296440
archrelease: copy trunk to community-any Added: sagemath-doc/repos/community-any/PKGBUILD (from rev 296439, sagemath-doc/trunk/PKGBUILD) sagemath-doc/repos/community-any/docbuild_main.patch (from rev 296439, sagemath-doc/trunk/docbuild_main.patch) sagemath-doc/repos/community-any/sagemath-doc-no-sagenb.patch (from rev 296439, sagemath-doc/trunk/sagemath-doc-no-sagenb.patch) Deleted: sagemath-doc/repos/community-any/PKGBUILD sagemath-doc/repos/community-any/docbuild_main.patch sagemath-doc/repos/community-any/fes02.patch sagemath-doc/repos/community-any/jupyter-path.patch sagemath-doc/repos/community-any/latte-count.patch sagemath-doc/repos/community-any/package.patch sagemath-doc/repos/community-any/pari-stackwarn.patch sagemath-doc/repos/community-any/r-no-readline.patch sagemath-doc/repos/community-any/sagemath-detect-igraph.patch sagemath-doc/repos/community-any/sagemath-doc-no-sagenb.patch sagemath-doc/repos/community-any/sagemath-ecl-no-sigfpe.patch sagemath-doc/repos/community-any/sagemath-env.patch sagemath-doc/repos/community-any/sagemath-linbox-1.5.patch sagemath-doc/repos/community-any/sagemath-lrs.patch sagemath-doc/repos/community-any/sagemath-matplotlib2.patch sagemath-doc/repos/community-any/sagemath-networkx2.patch sagemath-doc/repos/community-any/sagemath-pynac-0.7.14.patch sagemath-doc/repos/community-any/sagemath-python3-notebook.patch sagemath-doc/repos/community-any/sagemath-scipy-1.0.patch sagemath-doc/repos/community-any/sagemath-threejs.patch sagemath-doc/repos/community-any/test-optional.patch ---------------------------------+ PKGBUILD | 208 +++++++++-------------------- docbuild_main.patch | 12 - 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-doc-no-sagenb.patch | 56 +++---- sagemath-ecl-no-sigfpe.patch | 12 - sagemath-env.patch | 105 -------------- sagemath-linbox-1.5.patch | 272 -------------------------------------- sagemath-lrs.patch | 22 --- sagemath-matplotlib2.patch | 253 ----------------------------------- sagemath-networkx2.patch | 26 --- sagemath-pynac-0.7.14.patch | 167 ----------------------- sagemath-python3-notebook.patch | 27 --- sagemath-scipy-1.0.patch | 16 -- sagemath-threejs.patch | 11 - test-optional.patch | 25 --- 21 files changed, 101 insertions(+), 1354 deletions(-) Deleted: PKGBUILD =================================================================== --- PKGBUILD 2018-02-19 23:17:44 UTC (rev 296439) +++ PKGBUILD 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,141 +0,0 @@ -# $Id$ -# Maintainer: Antonio Rojas <aro...@archlinux.org> - -pkgbase=sagemath-doc -pkgname=(sagemath-doc sagemath-src) -pkgver=8.1 -pkgrel=2 -arch=(any) -url="http://www.sagemath.org" -license=(GPL) -makedepends=(sage-notebook python2-pyzmq python2-pillow python2-docutils tachyon - python2-jupyter_client python2-pkgconfig cython2 thebe python2-sphinx python2-ipywidgets) -source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz" - sagemath-env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch - r-no-readline.patch fes02.patch sagemath-threejs.patch sagemath-detect-igraph.patch pari-stackwarn.patch - sagemath-detect-igraph.patch sagemath-networkx2.patch sagemath-linbox-1.5.patch sagemath-pynac-0.7.14.patch - sagemath-matplotlib2.patch sagemath-scipy-1.0.patch sagemath-lrs.patch - docbuild_main.patch sagemath-doc-no-sagenb.patch) -sha256sums=('a42b55c2c8ac244535dc9b87171b7d4dd7e1d498099518ab253354fbe2eaaa7b' - '6dc9b101310f80381c61c0312a3e5c648771bfe0de2e94ac46fafe7282a3e0ee' - 'c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107' - '0b680e674c11c47afa86162d8b49645620b8912722e08133d23357c29ca9310a' - '2cad308f8adbb6c54e6603fa22b2f0eb60f6f09248d5d015000c3932ac14f646' - '962ce805c87147212b21fc2ab0ac9af9bd0033942c7a6905b9906645b48e8a4f' - 'ef94908d4ab28d13af622e6e58ec191aa78817d17e4466c7bb6f64ee72a813b9' - 'afd0952b9bb8f52fd428eae36cf719a58ff85a894baae88cbb2124e043768cc7' - '7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94' - '514135b920a43f999571a15e97b41e14f5bed59f65b19643864dc23555a7b830' - '28d7789b8d777922ab8871ca43b6afab751428cae875c0343d3962e6a2030b88' - 'bfd2a20a33ab19a8a8b216a77d07f62e809fe1e1879c4f171ce5dca62fd482e9' - '28d7789b8d777922ab8871ca43b6afab751428cae875c0343d3962e6a2030b88' - '37c5c1e694a2aca06c0f1c7d99622ff81fd2bc6a51e8745762294889fa4673f6' - 'a52d03e04c9d64bb957a1f8dcdae3280ebb9450a7fd76aaf5ae5de5c6f74774f' - '538f7b279d72f4b67edb445d386d267f3f7022c1079031ca7ea06f6ce392c906' - 'b9ab2bb5f381ea425e8763b81b8b3a108a3951c594fb1f37f7df921e7c77e26d' - '17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a' - 'c0f65534a845ba802de6196229159fe67fcc3f72f0cb1ce57d4ae5c9fe10282c' - 'ea5e17bb7a7cb36a22e5e3872fcc2585852bc971c4b139b0b2cd69a36c1b009b' - '261bdb5c24e67fb34f537e29bdf35af655162de3fea7d05abc72f85a864720fe') - -prepare() { - cd sage-$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 - -# 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 -# drop sage-notebook dependency from sagemath-doc https://trac.sagemath.org/ticket/24250 - patch -p1 -i ../sagemath-doc-no-sagenb.patch - -# fix relative imports - patch -p0 -i ../docbuild_main.patch - -# use python2 - sed -e 's|cython %s %s|cython2 %s %s|' -e 's|python setup.py|python2 setup.py|' -i src/sage/misc/cython.py - -# use sage_setup imports from sagemath source, but use system sage ones (which include compiled modules) - mkdir -p local-python - ln -sr src/sage_setup local-python -} - -build() { - cd sage-$pkgver/src - - export SAGE_LOCAL="/usr" - export SAGE_ROOT="/usr" - export SAGE_SRC="$PWD" - export SAGE_DOC_SRC="$SAGE_SRC"/doc - export SAGE_DOC="$SAGE_SRC"/doc - export SAGE_DOC_MATHJAX=yes - export PYTHONPATH="$srcdir"/sage-$pkgver/local-python - python2 sage_setup/docbuild --no-pdf-links -k all html -} - -package_sagemath-doc() { - pkgdesc="HTML documentation and inline help for SageMath" - depends=(python2-sphinx gap-doc thebe) - conflicts=(sage-mathematics-doc) - replaces=(sage-mathematics-doc) - - cd sage-$pkgver/src/doc - - mkdir -p "$pkgdir"/usr/share/doc/sage/en - cp -r en/introspect "$pkgdir"/usr/share/doc/sage/en - cp -r common "$pkgdir"/usr/share/doc/sage - cp -r html "$pkgdir"/usr/share/doc/sage - -# Replace duplicated files by symlinks (Gentoo) - cd "$pkgdir"/usr/share/doc/sage - mv html/en/_static{,.tmp} - for _dir in `find -name _static` ; do - rm -r $_dir - ln -s /usr/share/doc/sage/html/en/_static $_dir - done - mv html/en/_static{.tmp,} -} - -package_sagemath-src() { - pkgdesc="Source files for SageMath" - conflicts=(sage-mathematics-src) - replaces=(sage-mathematics-src) - - mkdir -p "$pkgdir"/usr/share/sage/source - cp -r sage-$pkgver/src/{sage,sage_setup} "$pkgdir"/usr/share/sage/source -} Copied: sagemath-doc/repos/community-any/PKGBUILD (from rev 296439, sagemath-doc/trunk/PKGBUILD) =================================================================== --- PKGBUILD (rev 0) +++ PKGBUILD 2018-02-19 23:18:25 UTC (rev 296440) @@ -0,0 +1,67 @@ +# $Id$ +# Maintainer: Antonio Rojas <aro...@archlinux.org> + +pkgname=sagemath-doc +pkgver=8.1 +pkgrel=3 +pkgdesc="HTML documentation and inline help for SageMath" +arch=(any) +url="http://www.sagemath.org" +license=(GPL) +depends=(python2-sphinx gap-doc thebe) +makedepends=(sage-notebook python2-pyzmq python2-pillow python2-docutils tachyon + python2-jupyter_client python2-pkgconfig cython2 python2-ipywidgets) +source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz" + docbuild_main.patch sagemath-doc-no-sagenb.patch) +sha256sums=('a42b55c2c8ac244535dc9b87171b7d4dd7e1d498099518ab253354fbe2eaaa7b' + 'ea5e17bb7a7cb36a22e5e3872fcc2585852bc971c4b139b0b2cd69a36c1b009b' + '261bdb5c24e67fb34f537e29bdf35af655162de3fea7d05abc72f85a864720fe') + +prepare() { + cd sage-$pkgver + +# drop sage-notebook dependency from sagemath-doc https://trac.sagemath.org/ticket/24250 + patch -p1 -i ../sagemath-doc-no-sagenb.patch +# fix relative imports + patch -p0 -i ../docbuild_main.patch + +# use sage_setup imports from sagemath source, but use system sage ones (which include compiled modules) + mkdir -p local-python + ln -sr src/sage_setup local-python +} + +build() { + cd sage-$pkgver/src + + export SAGE_LOCAL="/usr" + export SAGE_ROOT="/usr" + export SAGE_SRC="$PWD" + export SAGE_DOC_SRC="$SAGE_SRC"/doc + export SAGE_DOC="$SAGE_SRC"/doc + export SAGE_DOC_MATHJAX=yes + export PYTHONPATH="$srcdir"/sage-$pkgver/local-python + python2 sage_setup/docbuild --no-pdf-links -k all html +} + +package() { + pkgdesc="HTML documentation and inline help for SageMath" + depends=(python2-sphinx gap-doc thebe) + conflicts=(sage-mathematics-doc) + replaces=(sage-mathematics-doc) + + cd sage-$pkgver/src/doc + + mkdir -p "$pkgdir"/usr/share/doc/sage/en + cp -r en/introspect "$pkgdir"/usr/share/doc/sage/en + cp -r common "$pkgdir"/usr/share/doc/sage + cp -r html "$pkgdir"/usr/share/doc/sage + +# Replace duplicated files by symlinks (Gentoo) + cd "$pkgdir"/usr/share/doc/sage + mv html/en/_static{,.tmp} + for _dir in `find -name _static` ; do + rm -r $_dir + ln -s /usr/share/doc/sage/html/en/_static $_dir + done + mv html/en/_static{.tmp,} +} Deleted: docbuild_main.patch =================================================================== --- docbuild_main.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ docbuild_main.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,6 +0,0 @@ ---- src/sage_setup/docbuild/__main__.py.orig -+++ src/sage_setup/docbuild/__main__.py -@@ -1,2 +1,2 @@ --from . import main -+from sage_setup.docbuild import main - main() Copied: sagemath-doc/repos/community-any/docbuild_main.patch (from rev 296439, sagemath-doc/trunk/docbuild_main.patch) =================================================================== --- docbuild_main.patch (rev 0) +++ docbuild_main.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -0,0 +1,6 @@ +--- src/sage_setup/docbuild/__main__.py.orig ++++ src/sage_setup/docbuild/__main__.py +@@ -1,2 +1,2 @@ +-from . import main ++from sage_setup.docbuild import main + main() Deleted: fes02.patch =================================================================== --- fes02.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ fes02.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,57 +0,0 @@ -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 - Deleted: jupyter-path.patch =================================================================== --- jupyter-path.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ jupyter-path.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,22 +0,0 @@ ---- src/sage/repl/ipython_kernel/install.py.orig 2015-10-23 19:23:39.728456590 +0000 -+++ src/sage/repl/ipython_kernel/install.py 2015-10-23 19:24:00.965018978 +0000 -@@ -13,8 +13,7 @@ - SAGE_DOC, SAGE_LOCAL, SAGE_EXTCODE, - SAGE_VERSION - ) --from jupyter_core.paths import ENV_JUPYTER_PATH --JUPYTER_PATH = ENV_JUPYTER_PATH[0] -+JUPYTER_PATH = os.environ.get('JUPYTER_PATH') - - - class SageKernelSpec(object): -@@ -225,7 +225,7 @@ - sage: spec._symlink_resources() # not tested - """ - path = os.path.join(SAGE_EXTCODE, 'notebook-ipython') -- for filename in os.listdir(path): -+ for filename in os.listdir('ext/notebook-ipython'): - self.symlink( - os.path.join(path, filename), - os.path.join(self.kernel_dir, filename) - Deleted: latte-count.patch =================================================================== --- latte-count.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ latte-count.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,71 +0,0 @@ -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: Deleted: package.patch =================================================================== --- package.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ package.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,38 +0,0 @@ ---- 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: Deleted: pari-stackwarn.patch =================================================================== --- pari-stackwarn.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ pari-stackwarn.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,23 +0,0 @@ -Description: Ignore warnings of PARI increasing the stack size when parsing doctests - Since we can't patch PARI to not produce the warnings and we don't want to - patch tons of doctests to expect the warnings, we patch the doctest parser - to ignore them. -Author: Tobias Hansen <than...@debian.org> ---- sage/src/sage/doctest/parsing.py -+++ sage/src/sage/doctest/parsing.py -@@ -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 Deleted: r-no-readline.patch =================================================================== --- r-no-readline.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ r-no-readline.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,11 +0,0 @@ ---- 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, Deleted: sagemath-detect-igraph.patch =================================================================== --- sagemath-detect-igraph.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ sagemath-detect-igraph.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,21 +0,0 @@ -diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py -index 252984f..ce19682 100644 ---- a/src/sage/graphs/generic_graph.py -+++ b/src/sage/graphs/generic_graph.py -@@ -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) - Deleted: sagemath-doc-no-sagenb.patch =================================================================== --- sagemath-doc-no-sagenb.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ sagemath-doc-no-sagenb.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,28 +0,0 @@ -diff --git a/src/doc/common/conf.py b/src/doc/common/conf.py -index 2e115fa..c4dfbf5 100644 ---- a/src/doc/common/conf.py -+++ b/src/doc/common/conf.py -@@ -1,5 +1,5 @@ - import sys, os, sphinx --from sage.env import SAGE_DOC_SRC, SAGE_DOC, SAGE_SRC, THEBE_DIR -+from sage.env import SAGE_DOC_SRC, SAGE_DOC, SAGE_SRC, THEBE_DIR, SAGE_SHARE - from datetime import date - from six import iteritems - -@@ -219,14 +219,12 @@ if (os.environ.get('SAGE_DOC_MATHJAX', 'no') != 'no' - from sage.misc.latex_macros import sage_mathjax_macros - html_theme_options['mathjax_macros'] = sage_mathjax_macros() - -- from pkg_resources import Requirement, working_set -- sagenb_path = working_set.find(Requirement.parse('sagenb')).location -- mathjax_relative = os.path.join('sagenb','data','mathjax') -+ mathjax_relative = 'mathjax' - - # It would be really nice if sphinx would copy the entire mathjax directory, - # (so we could have a _static/mathjax directory), rather than the contents of the directory - -- mathjax_static = os.path.join(sagenb_path, mathjax_relative) -+ mathjax_static = os.path.join(SAGE_SHARE, mathjax_relative) - html_static_path.append(mathjax_static) - exclude_patterns += ['**/'+os.path.join(mathjax_relative, i) - for i in ('docs', 'README*', 'test', Copied: sagemath-doc/repos/community-any/sagemath-doc-no-sagenb.patch (from rev 296439, sagemath-doc/trunk/sagemath-doc-no-sagenb.patch) =================================================================== --- sagemath-doc-no-sagenb.patch (rev 0) +++ sagemath-doc-no-sagenb.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -0,0 +1,28 @@ +diff --git a/src/doc/common/conf.py b/src/doc/common/conf.py +index 2e115fa..c4dfbf5 100644 +--- a/src/doc/common/conf.py ++++ b/src/doc/common/conf.py +@@ -1,5 +1,5 @@ + import sys, os, sphinx +-from sage.env import SAGE_DOC_SRC, SAGE_DOC, SAGE_SRC, THEBE_DIR ++from sage.env import SAGE_DOC_SRC, SAGE_DOC, SAGE_SRC, THEBE_DIR, SAGE_SHARE + from datetime import date + from six import iteritems + +@@ -219,14 +219,12 @@ if (os.environ.get('SAGE_DOC_MATHJAX', 'no') != 'no' + from sage.misc.latex_macros import sage_mathjax_macros + html_theme_options['mathjax_macros'] = sage_mathjax_macros() + +- from pkg_resources import Requirement, working_set +- sagenb_path = working_set.find(Requirement.parse('sagenb')).location +- mathjax_relative = os.path.join('sagenb','data','mathjax') ++ mathjax_relative = 'mathjax' + + # It would be really nice if sphinx would copy the entire mathjax directory, + # (so we could have a _static/mathjax directory), rather than the contents of the directory + +- mathjax_static = os.path.join(sagenb_path, mathjax_relative) ++ mathjax_static = os.path.join(SAGE_SHARE, mathjax_relative) + html_static_path.append(mathjax_static) + exclude_patterns += ['**/'+os.path.join(mathjax_relative, i) + for i in ('docs', 'README*', 'test', Deleted: sagemath-ecl-no-sigfpe.patch =================================================================== --- sagemath-ecl-no-sigfpe.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ sagemath-ecl-no-sigfpe.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,12 +0,0 @@ -diff --git a/src/sage/libs/ecl.pyx b/src/sage/libs/ecl.pyx -index 1fafb6c..4f730ad 100644 ---- a/src/sage/libs/ecl.pyx -+++ b/src/sage/libs/ecl.pyx -@@ -314,6 +314,7 @@ def init_ecl(): - """)) - safe_funcall_clobj=cl_eval(string_to_object("(symbol-function 'sage-safe-funcall)")) - -+ cl_eval(string_to_object("(si::trap-fpe T NIL)")) - ecl_has_booted = 1 - - cdef cl_object ecl_safe_eval(cl_object form) except NULL: Deleted: sagemath-env.patch =================================================================== --- sagemath-env.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ sagemath-env.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,105 +0,0 @@ ---- src/bin/sage-env.orig 2015-01-06 10:46:04.469687605 +0100 -+++ src/bin/sage-env 2015-01-06 10:49:59.547762019 +0100 -@@ -111,41 +111,7 @@ - } - - --# New value for SAGE_ROOT: either SAGE_ROOT (if given) --# or a guessed value based on pwd. --if [ -n "$SAGE_ROOT" ]; then -- NEW_SAGE_ROOT="$SAGE_ROOT" --elif [ -f sage -a -d build ]; then -- NEW_SAGE_ROOT="." --elif [ -f ../../sage -a -d ../../build ]; then -- NEW_SAGE_ROOT="../.." --else -- # No idea what SAGE_ROOT should be... -- echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this" -- echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory." -- return 1 --fi -- --# Make NEW_SAGE_ROOT absolute --NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P` -- --# Sanity check NEW_SAGE_ROOT --if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then -- : --else -- echo >&2 "Error: SAGE_ROOT is set to a bad value:" -- echo >&2 "SAGE_ROOT=$SAGE_ROOT" -- echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT" -- echo >&2 "or SAGE_ROOT/local/bin/ directory." -- return 1 --fi -- --# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT --if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then -- echo >&2 "Warning: overwriting SAGE_ROOT environment variable:" -- echo >&2 "Old SAGE_ROOT=$SAGE_ROOT" -- echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT" --fi -+NEW_SAGE_ROOT="/usr" - - # Display the Sage startup banner, used in src/bin/sage - sage_banner() { -@@ -185,6 +185,7 @@ - export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION - - export SAGE_ROOT="$NEW_SAGE_ROOT" -+export SAGE_LOCAL='/usr' - - - # sage-env must know where the Sage's script files are. -@@ -307,8 +307,9 @@ - export SAGE_EXTCODE="$SAGE_SHARE/sage/ext" - export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed" - export SAGE_LOGS="$SAGE_ROOT/logs/pkgs" --export SAGE_SRC="$SAGE_ROOT/src" --export SAGE_DOC_SRC="$SAGE_SRC/doc" -+export GAP_ROOT_DIR="/usr/lib/gap" -+export SAGE_SRC="$SAGE_SHARE/sage/source" -+export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage" - export SAGE_DOC="$SAGE_SHARE/doc/sage" - - if [ -z "${SAGE_ORIG_PATH_SET}" ]; then -@@ -414,6 +414,9 @@ - export SAGE_STARTUP_FILE - fi - -+export LIBMTX="$DOT_SAGE/meataxe" -+[[ -d $LIBMTX ]] || mkdir -p $LIBMTX # Create meataxe data dir -+ - if [ "$PYTHON_EGG_CACHE" = "" ]; then - PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs" - export PYTHON_EGG_CACHE -@@ -499,7 +499,6 @@ - fi - fi - fi --export MAXIMA_PREFIX="$SAGE_LOCAL" - - PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB - -@@ -619,9 +619,6 @@ - LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH - fi - --# See trac 7186 -- this is needed if ecl is moved --ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR -- - # Handle parallel building/testing/... - # See Trac Ticket #12016 - # First, figure out the right values for SAGE_NUM_THREADS (default ---- src/sage/env.py.orig 2017-12-07 19:51:25.554281539 +0000 -+++ src/sage/env.py 2017-12-07 19:51:42.787654650 +0000 -@@ -118,7 +118,7 @@ - - # bunch of sage directories and files - _add_variable_or_fallback('SAGE_ROOT', None) --_add_variable_or_fallback('SAGE_LOCAL', None) -+_add_variable_or_fallback('SAGE_LOCAL', '/usr') - _add_variable_or_fallback('SAGE_ETC', opj('$SAGE_LOCAL', 'etc')) - _add_variable_or_fallback('SAGE_INC', opj('$SAGE_LOCAL', 'include')) - _add_variable_or_fallback('SAGE_SHARE', opj('$SAGE_LOCAL', 'share')) - Deleted: sagemath-linbox-1.5.patch =================================================================== --- sagemath-linbox-1.5.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ sagemath-linbox-1.5.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,272 +0,0 @@ -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): Deleted: sagemath-lrs.patch =================================================================== --- sagemath-lrs.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ sagemath-lrs.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,22 +0,0 @@ -diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/normal_form_game.py -index 2115de6800..da94aa5d45 100644 ---- a/src/sage/game_theory/normal_form_game.py -+++ b/src/sage/game_theory/normal_form_game.py -@@ -621,6 +621,7 @@ from sage.matrix.constructor import vector - from sage.misc.package import is_package_installed, PackageNotFoundError - from sage.misc.temporary_file import tmp_filename - from sage.numerical.mip import MixedIntegerLinearProgram -+import os - - try: - from gambit import Game -@@ -1636,7 +1637,7 @@ class NormalFormGame(SageObject, MutableMapping): - if not algorithm: - if self.is_constant_sum(): - algorithm = "lp" -- elif is_package_installed('lrslib'): -+ elif os.path.exists('/usr/bin/lrsnash'): - algorithm = "lrs" - else: - algorithm = "enumeration" - Deleted: sagemath-matplotlib2.patch =================================================================== --- sagemath-matplotlib2.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ sagemath-matplotlib2.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,253 +0,0 @@ -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, Deleted: sagemath-networkx2.patch =================================================================== --- sagemath-networkx2.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ sagemath-networkx2.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,26 +0,0 @@ -diff --git a/src/sage/graphs/digraph.py b/src/sage/graphs/digraph.py -index 8c29602da6..e7a185d586 100644 ---- a/src/sage/graphs/digraph.py -+++ b/src/sage/graphs/digraph.py -@@ -755,7 +755,7 @@ class DiGraph(GenericGraph): - self.allow_multiple_edges(multiedges,check=False) - self.allow_loops(loops,check=False) - self.add_vertices(data.nodes()) -- self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True)) -+ self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True)) - elif format == 'igraph': - if not data.is_directed(): - raise ValueError("A *directed* igraph graph was expected. To "+ -diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py -index b63135d8e6..5775042976 100644 ---- a/src/sage/graphs/graph.py -+++ b/src/sage/graphs/graph.py -@@ -1199,7 +1199,7 @@ class Graph(GenericGraph): - self.allow_loops(loops, check=False) - self.allow_multiple_edges(multiedges, check=False) - self.add_vertices(data.nodes()) -- self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True)) -+ self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True)) - elif format == 'igraph': - if data.is_directed(): - raise ValueError("An *undirected* igraph graph was expected. "+ Deleted: sagemath-pynac-0.7.14.patch =================================================================== --- sagemath-pynac-0.7.14.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ sagemath-pynac-0.7.14.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,167 +0,0 @@ -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) Deleted: sagemath-python3-notebook.patch =================================================================== --- sagemath-python3-notebook.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ sagemath-python3-notebook.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,27 +0,0 @@ -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: - Deleted: sagemath-scipy-1.0.patch =================================================================== --- sagemath-scipy-1.0.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ sagemath-scipy-1.0.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,16 +0,0 @@ -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) - - Deleted: sagemath-threejs.patch =================================================================== --- sagemath-threejs.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ sagemath-threejs.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,11 +0,0 @@ ---- 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> Deleted: test-optional.patch =================================================================== --- test-optional.patch 2018-02-19 23:17:44 UTC (rev 296439) +++ test-optional.patch 2018-02-19 23:18:25 UTC (rev 296440) @@ -1,25 +0,0 @@ ---- 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