Date: Sunday, October 1, 2017 @ 16:47:03 Author: arojas Revision: 261181
archrelease: copy trunk to community-staging-i686, community-staging-x86_64 Added: sagemath/repos/community-staging-i686/ sagemath/repos/community-staging-i686/PKGBUILD (from rev 261180, sagemath/trunk/PKGBUILD) sagemath/repos/community-staging-i686/env.patch (from rev 261180, sagemath/trunk/env.patch) sagemath/repos/community-staging-i686/fes02.patch (from rev 261180, sagemath/trunk/fes02.patch) sagemath/repos/community-staging-i686/jupyter-path.patch (from rev 261180, sagemath/trunk/jupyter-path.patch) sagemath/repos/community-staging-i686/latte-count.patch (from rev 261180, sagemath/trunk/latte-count.patch) sagemath/repos/community-staging-i686/package.patch (from rev 261180, sagemath/trunk/package.patch) sagemath/repos/community-staging-i686/r-no-readline.patch (from rev 261180, sagemath/trunk/r-no-readline.patch) sagemath/repos/community-staging-i686/sagemath-cython-0.26.patch (from rev 261180, sagemath/trunk/sagemath-cython-0.26.patch) sagemath/repos/community-staging-i686/sagemath-detect-igraph.patch (from rev 261180, sagemath/trunk/sagemath-detect-igraph.patch) sagemath/repos/community-staging-i686/sagemath-ecl-no-sigfpe.patch (from rev 261180, sagemath/trunk/sagemath-ecl-no-sigfpe.patch) sagemath/repos/community-staging-i686/sagemath-networkx2.patch (from rev 261180, sagemath/trunk/sagemath-networkx2.patch) sagemath/repos/community-staging-i686/sagemath-pynac-0.7.11.patch (from rev 261180, sagemath/trunk/sagemath-pynac-0.7.11.patch) sagemath/repos/community-staging-i686/sagemath-pynac-0.7.12.patch (from rev 261180, sagemath/trunk/sagemath-pynac-0.7.12.patch) sagemath/repos/community-staging-i686/sagemath-python3-notebook.patch (from rev 261180, sagemath/trunk/sagemath-python3-notebook.patch) sagemath/repos/community-staging-i686/test-optional.patch (from rev 261180, sagemath/trunk/test-optional.patch) sagemath/repos/community-staging-x86_64/ sagemath/repos/community-staging-x86_64/PKGBUILD (from rev 261180, sagemath/trunk/PKGBUILD) sagemath/repos/community-staging-x86_64/env.patch (from rev 261180, sagemath/trunk/env.patch) sagemath/repos/community-staging-x86_64/fes02.patch (from rev 261180, sagemath/trunk/fes02.patch) sagemath/repos/community-staging-x86_64/jupyter-path.patch (from rev 261180, sagemath/trunk/jupyter-path.patch) sagemath/repos/community-staging-x86_64/latte-count.patch (from rev 261180, sagemath/trunk/latte-count.patch) sagemath/repos/community-staging-x86_64/package.patch (from rev 261180, sagemath/trunk/package.patch) sagemath/repos/community-staging-x86_64/r-no-readline.patch (from rev 261180, sagemath/trunk/r-no-readline.patch) sagemath/repos/community-staging-x86_64/sagemath-cython-0.26.patch (from rev 261180, sagemath/trunk/sagemath-cython-0.26.patch) sagemath/repos/community-staging-x86_64/sagemath-detect-igraph.patch (from rev 261180, sagemath/trunk/sagemath-detect-igraph.patch) sagemath/repos/community-staging-x86_64/sagemath-ecl-no-sigfpe.patch (from rev 261180, sagemath/trunk/sagemath-ecl-no-sigfpe.patch) sagemath/repos/community-staging-x86_64/sagemath-networkx2.patch (from rev 261180, sagemath/trunk/sagemath-networkx2.patch) sagemath/repos/community-staging-x86_64/sagemath-pynac-0.7.11.patch (from rev 261180, sagemath/trunk/sagemath-pynac-0.7.11.patch) sagemath/repos/community-staging-x86_64/sagemath-pynac-0.7.12.patch (from rev 261180, sagemath/trunk/sagemath-pynac-0.7.12.patch) sagemath/repos/community-staging-x86_64/sagemath-python3-notebook.patch (from rev 261180, sagemath/trunk/sagemath-python3-notebook.patch) sagemath/repos/community-staging-x86_64/test-optional.patch (from rev 261180, sagemath/trunk/test-optional.patch) ----------------------------------------------------------+ community-staging-i686/PKGBUILD | 168 +++++ community-staging-i686/env.patch | 93 +++ community-staging-i686/fes02.patch | 57 + community-staging-i686/jupyter-path.patch | 22 community-staging-i686/latte-count.patch | 71 ++ community-staging-i686/package.patch | 38 + community-staging-i686/r-no-readline.patch | 11 community-staging-i686/sagemath-cython-0.26.patch | 26 community-staging-i686/sagemath-detect-igraph.patch | 21 community-staging-i686/sagemath-ecl-no-sigfpe.patch | 12 community-staging-i686/sagemath-networkx2.patch | 26 community-staging-i686/sagemath-pynac-0.7.11.patch | 21 community-staging-i686/sagemath-pynac-0.7.12.patch | 390 +++++++++++++ community-staging-i686/sagemath-python3-notebook.patch | 27 community-staging-i686/test-optional.patch | 25 community-staging-x86_64/PKGBUILD | 168 +++++ community-staging-x86_64/env.patch | 93 +++ community-staging-x86_64/fes02.patch | 57 + community-staging-x86_64/jupyter-path.patch | 22 community-staging-x86_64/latte-count.patch | 71 ++ community-staging-x86_64/package.patch | 38 + community-staging-x86_64/r-no-readline.patch | 11 community-staging-x86_64/sagemath-cython-0.26.patch | 26 community-staging-x86_64/sagemath-detect-igraph.patch | 21 community-staging-x86_64/sagemath-ecl-no-sigfpe.patch | 12 community-staging-x86_64/sagemath-networkx2.patch | 26 community-staging-x86_64/sagemath-pynac-0.7.11.patch | 21 community-staging-x86_64/sagemath-pynac-0.7.12.patch | 390 +++++++++++++ community-staging-x86_64/sagemath-python3-notebook.patch | 27 community-staging-x86_64/test-optional.patch | 25 30 files changed, 2016 insertions(+) Copied: sagemath/repos/community-staging-i686/PKGBUILD (from rev 261180, sagemath/trunk/PKGBUILD) =================================================================== --- community-staging-i686/PKGBUILD (rev 0) +++ community-staging-i686/PKGBUILD 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,168 @@ +# 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=8.0 +pkgrel=6 +pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab" +arch=(i686 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 + 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' + 'modular_decomposition: modular decomposition of graphs' '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' + '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' 'tachyon: alternative 3D plots engine') +makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding sirocco + mcqd coxeter3 modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe libfes) +source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz" + env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch + r-no-readline.patch fes02.patch sagemath-ecl-no-sigfpe.patch sagemath-cython-0.26.patch + sagemath-pynac-0.7.11.patch sagemath-pynac-0.7.12.patch sagemath-detect-igraph.patch sagemath-networkx2.patch) +sha256sums=('91df3e303add71616e24b38c04789f66d57ada7b1017e5369e850c42d5e8753d' + 'e0b5b8673300857fde823209a7e90faecf9e754ab812cc5e54297eddc0c79571' + '4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212' + 'c6836783251d94c00f0229c1e671de86c58c6c6fb0f6959725317817abc64ca8' + '775051aa9076ebf631c8a291af38b6ec4a13c904740dc9da831641d592d8bcd8' + '27aa73d427d92aeb2c181a233aa3a574a4158cd7dee33832808f69edaec55ea2' + '81d08c6a760f171f3381455b66a6c84789c9f0eefddbe6ca5794075514ad8c3a' + 'ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf' + 'a39da083c038ada797ffc5bedc9ba47455a3f77057d42f86484ae877ef9172ea' + 'c31809f887bf9acc45c5bd9dd30bb93e73601d3efbf3016594c3c1d241731c8a' + '2953ef15d957a2f3304a5584c154bf4777bcb4b461414d3a2178423257539755' + '3e23ff449a5a3a032684287722455633762636b93ecfc35fb00e875c69eff240' + '719bb39c9c2cd1c6e75be0969000ba5ffcd2875bb5190fce6bb6a6feaa76b96f' + '90be1d1a90120bd5bd3620769480106ba809dd23e896bc4a3f8931e5340f3cda' + 'a1a0ab5b794136b518f5f66fe9f1689411fabb3b81560b159eae81f6f69000e3') + +prepare(){ + cd sage-$pkgver + +# Arch-specific patches +# assume all optional packages are installed + patch -p0 -i ../package.patch +# set env variables + patch -p0 -i ../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 +# adapt to networkx 2 changes + patch -p1 -i ../sagemath-networkx2.patch + +# Upstream patches +# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209 + patch -p1 -i ../fes02.patch +# disable SIGFPE for ecl https://trac.sagemath.org/ticket/22191 + patch -p1 -i ../sagemath-ecl-no-sigfpe.patch +# disable auto_picke for cython 0.26 https://trac.sagemath.org/ticket/23360 + patch -p1 -i ../sagemath-cython-0.26.patch +# fix build with pynac 0.7.11 https://trac.sagemath.org/ticket/23820 + patch -p1 -i ../sagemath-pynac-0.7.11.patch +# fix build with pynac 0.7.12 https://trac.sagemath.org/ticket/23950 + patch -p1 -i ../sagemath-pynac-0.7.12.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-$pkgver + autoreconf -vi + ./configure --prefix=/usr || true + + cd src + export SAGE_LOCAL="/usr" + export SAGE_ROOT="$PWD" + export SAGE_SRC="$PWD" + export CC=gcc + + python2 setup.py build +} + +package_sagemath() { + optdepends+=('sagemath-jupyter: Jupyter kernel') + conflicts=(sage-mathematics) + replaces=(sage-mathematics) + provides=(sage-mathematics) + + cd sage-$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 "$pkgdir"/usr/bin + for _i in arch-env banner cachegrind callgrind cleaner coverage coverageall cython env env-config eval grep grepdoc inline-fortran \ + ipython massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2ipynb rst2sws rst2txt run \ + run-cython runtests startuptime.py sws2rst valgrind version.sh + do + cp bin/sage-$_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="$pkgdir"/usr/share/jupyter + + python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update()" +} Copied: sagemath/repos/community-staging-i686/env.patch (from rev 261180, sagemath/trunk/env.patch) =================================================================== --- community-staging-i686/env.patch (rev 0) +++ community-staging-i686/env.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,93 @@ +--- src/bin/sage-env.orig 2015-01-06 10:46:04.469687605 +0100 ++++ src/bin/sage-env 2015-01-06 10:49:59.547762019 +0100 +@@ -111,41 +111,7 @@ + } + + +-# New value for SAGE_ROOT: either SAGE_ROOT (if given) +-# or a guessed value based on pwd. +-if [ -n "$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() { +@@ -151,6 +151,7 @@ + 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. + +@@ -233,8 +233,9 @@ + 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 "${SAGE_ORIG_PATH_SET}" ]; then +@@ -374,6 +337,9 @@ + export SAGE_STARTUP_FILE + fi + ++export LIBMTX="$DOT_SAGE/meataxe" ++[[ -d $LIBMTX ]] || mkdir -p $LIBMTX # Create meataxe data dir ++ + if [ -z "$IPYTHONDIR" ]; then + # We hardcode a version number in the directory name. The idea is + # that we keep using the same version number as long as that is +@@ -468,7 +400,6 @@ + fi + fi + fi +-export MAXIMA_PREFIX="$SAGE_LOCAL" + + PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB + +@@ -629,9 +608,6 @@ + LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH + fi + +-# See trac 7186 -- this is needed if ecl is moved +-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR +- + # Handle parallel building/testing/... + # See Trac Ticket #12016 + # First, figure out the right values for SAGE_NUM_THREADS (default Copied: sagemath/repos/community-staging-i686/fes02.patch (from rev 261180, sagemath/trunk/fes02.patch) =================================================================== --- community-staging-i686/fes02.patch (rev 0) +++ community-staging-i686/fes02.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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) + + + include 'sage/ext/interrupt.pxi' #sig_on(), sig_off() +@@ -219,7 +221,7 @@ 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-i686/jupyter-path.patch (from rev 261180, sagemath/trunk/jupyter-path.patch) =================================================================== --- community-staging-i686/jupyter-path.patch (rev 0) +++ community-staging-i686/jupyter-path.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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_ROOT, 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): + +@@ -208,7 +208,7 @@ + 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-i686/latte-count.patch (from rev 261180, sagemath/trunk/latte-count.patch) =================================================================== --- community-staging-i686/latte-count.patch (rev 0) +++ community-staging-i686/latte-count.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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 +@@ -228,7 +228,7 @@ 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 +@@ -236,7 +236,7 @@ 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 +@@ -244,7 +244,7 @@ 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 +@@ -252,7 +252,7 @@ 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 +@@ -264,7 +264,7 @@ 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 +@@ -86,7 +86,7 @@ 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: ... +@@ -106,7 +106,7 @@ 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-i686/package.patch (from rev 261180, sagemath/trunk/package.patch) =================================================================== --- community-staging-i686/package.patch (rev 0) +++ community-staging-i686/package.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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 +@@ -343,7 +343,7 @@ + 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-i686/r-no-readline.patch (from rev 261180, sagemath/trunk/r-no-readline.patch) =================================================================== --- community-staging-i686/r-no-readline.patch (rev 0) +++ community-staging-i686/r-no-readline.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,11 @@ +--- a/src/sage/interfaces/r.py ++++ b/src/sage/interfaces/r.py +@@ -331,7 +331,7 @@ + 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-i686/sagemath-cython-0.26.patch (from rev 261180, sagemath/trunk/sagemath-cython-0.26.patch) =================================================================== --- community-staging-i686/sagemath-cython-0.26.patch (rev 0) +++ community-staging-i686/sagemath-cython-0.26.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,26 @@ +diff --git a/src/setup.py b/src/setup.py +index 2215379..ddca1eb 100755 +--- a/src/setup.py ++++ b/src/setup.py +@@ -95,7 +95,12 @@ library_dirs = [os.path.join(SAGE_LOCAL, "lib")] + + # Manually add -fno-strict-aliasing, which is needed to compile Cython + # and disappears from the default flags if the user has set CFLAGS. +-extra_compile_args = [ "-fno-strict-aliasing" ] ++# ++# Add -DCYTHON_CLINE_IN_TRACEBACK=1 which causes the .c line number to ++# always appear in exception tracebacks (by default, this is a runtime ++# setting in Cython which causes some overhead every time an exception ++# is raised). ++extra_compile_args = ["-fno-strict-aliasing", "-DCYTHON_CLINE_IN_TRACEBACK=1"] + extra_link_args = [ ] + + DEVEL = False +@@ -336,6 +341,7 @@ class sage_build_cython(Command): + + # Cython compiler directives + self.cython_directives = dict( ++ auto_pickle=False, + autotestdict=False, + cdivision=True, + embedsignature=True, Copied: sagemath/repos/community-staging-i686/sagemath-detect-igraph.patch (from rev 261180, sagemath/trunk/sagemath-detect-igraph.patch) =================================================================== --- community-staging-i686/sagemath-detect-igraph.patch (rev 0) +++ community-staging-i686/sagemath-detect-igraph.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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 +@@ -7876,10 +7875,12 @@ 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-i686/sagemath-ecl-no-sigfpe.patch (from rev 261180, sagemath/trunk/sagemath-ecl-no-sigfpe.patch) =================================================================== --- community-staging-i686/sagemath-ecl-no-sigfpe.patch (rev 0) +++ community-staging-i686/sagemath-ecl-no-sigfpe.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,12 @@ +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: Copied: sagemath/repos/community-staging-i686/sagemath-networkx2.patch (from rev 261180, sagemath/trunk/sagemath-networkx2.patch) =================================================================== --- community-staging-i686/sagemath-networkx2.patch (rev 0) +++ community-staging-i686/sagemath-networkx2.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,26 @@ +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 +@@ -751,7 +751,7 @@ 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. "+ Copied: sagemath/repos/community-staging-i686/sagemath-pynac-0.7.11.patch (from rev 261180, sagemath/trunk/sagemath-pynac-0.7.11.patch) =================================================================== --- community-staging-i686/sagemath-pynac-0.7.11.patch (rev 0) +++ community-staging-i686/sagemath-pynac-0.7.11.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,21 @@ +--- a/src/sage/libs/pynac/pynac.pxd ++++ b/src/sage/libs/pynac/pynac.pxd +@@ -302,7 +302,6 @@ cdef extern from "sage/libs/pynac/wrap.h": + bint is_a_fderivative "is_a<GiNaC::fderivative>" (GEx e) + bint is_a_function "is_a<GiNaC::function>" (GEx e) + bint is_exactly_a_function "is_exactly_a<GiNaC::function>" (GEx e) +- bint is_a_ncmul "is_a<GiNaC::ncmul>" (GEx e) + + # Arithmetic + int ginac_error() +--- a/src/sage/symbolic/expression.pyx ++++ b/src/sage/symbolic/expression.pyx +@@ -5536,7 +5536,7 @@ cdef class Expression(CommutativeRingElement): + cdef unsigned serial + if is_a_add(self._gobj): + return add_vararg +- elif is_a_mul(self._gobj) or is_a_ncmul(self._gobj): ++ elif is_a_mul(self._gobj): + return mul_vararg + elif is_a_power(self._gobj): + return operator.pow Copied: sagemath/repos/community-staging-i686/sagemath-pynac-0.7.12.patch (from rev 261180, sagemath/trunk/sagemath-pynac-0.7.12.patch) =================================================================== --- community-staging-i686/sagemath-pynac-0.7.12.patch (rev 0) +++ community-staging-i686/sagemath-pynac-0.7.12.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,390 @@ +diff --git a/src/doc/de/thematische_anleitungen/sage_gymnasium.rst b/src/doc/de/thematische_anleitungen/sage_gymnasium.rst +index 5a150a0..f9ede06 100644 +--- a/src/doc/de/thematische_anleitungen/sage_gymnasium.rst ++++ b/src/doc/de/thematische_anleitungen/sage_gymnasium.rst +@@ -716,7 +716,7 @@ die ähnliche Funktion ``canonicalize_radical``:: + Diese Gesetze können auch umgekehrt verwendet werden, wie in diesem Beispiel:: + + sage: (5*log(2) + 5*log(5)).simplify_log() +- log(100000) ++ 5*log(10) + + Es geben weitere mögliche Vereinfachungen, die wir hier nicht weiter erwähnen. + +diff --git a/src/sage/coding/code_bounds.py b/src/sage/coding/code_bounds.py +index 7935bbf..64ac455 100644 +--- a/src/sage/coding/code_bounds.py ++++ b/src/sage/coding/code_bounds.py +@@ -577,8 +577,8 @@ def entropy(x, q=2): + + sage: codes.bounds.entropy(0, 2) + 0 +- sage: codes.bounds.entropy(1/5,4) +- 1/5*log(3)/log(4) - 4/5*log(4/5)/log(4) - 1/5*log(1/5)/log(4) ++ sage: codes.bounds.entropy(1/5,4).factor() ++ 1/10*(log(3) - 4*log(4/5) - log(1/5))/log(2) + sage: codes.bounds.entropy(1, 3) + log(2)/log(3) + +diff --git a/src/sage/functions/log.py b/src/sage/functions/log.py +index 15e3dbf..64d898c 100644 +--- a/src/sage/functions/log.py ++++ b/src/sage/functions/log.py +@@ -121,12 +121,12 @@ class Function_exp(GinacFunction): + sage: model_exp = exp(II)**a*(b) + sage: sol1_l={b: 5.0, a: 1.1} + sage: model_exp.subs(sol1_l) +- 5.00000000000000*(e^II)^1.10000000000000 ++ 5.00000000000000*e^(1.10000000000000*II) + + :: + + sage: exp(3)^II*exp(x) +- (e^3)^II*e^x ++ e^(3*II + x) + sage: exp(x)*exp(x) + e^(2*x) + sage: exp(x)*exp(a) +@@ -137,7 +137,7 @@ class Function_exp(GinacFunction): + Another instance of the same problem (:trac:`7394`):: + + sage: 2*sqrt(e) +- 2*sqrt(e) ++ 2*e^(1/2) + + Check that :trac:`19918` is fixed:: + +@@ -271,7 +271,7 @@ class Function_log(GinacFunction): + sage: RDF(log(1024, 2)) + 10.0 + sage: log(10, 4) +- log(10)/log(4) ++ 1/2*log(10)/log(2) + sage: RDF(log(10, 4)) + 1.6609640474436813 + sage: log(10, 2) +diff --git a/src/sage/functions/orthogonal_polys.py b/src/sage/functions/orthogonal_polys.py +index 5db9871..c877454 100644 +--- a/src/sage/functions/orthogonal_polys.py ++++ b/src/sage/functions/orthogonal_polys.py +@@ -1666,7 +1666,7 @@ class Func_assoc_legendre_Q(BuiltinFunction): + EXAMPLES:: + + sage: gen_legendre_Q(2,1,3) +- -1/4*sqrt(-2)*(-36*I*pi + 36*log(4) - 36*log(2) - 25) ++ -1/4*sqrt(-2)*(-36*I*pi + 36*log(2) - 25) + """ + ret = self._eval_special_values_(n, m, x) + if ret is not None: +diff --git a/src/sage/libs/pynac/pynac.pxd b/src/sage/libs/pynac/pynac.pxd +index 9e37f08..1d19fdd 100644 +--- a/src/sage/libs/pynac/pynac.pxd ++++ b/src/sage/libs/pynac/pynac.pxd +@@ -97,6 +97,7 @@ cdef extern from "sage/libs/pynac/wrap.h": + + cdef cppclass GEx "ex": + GEx() ++ GEx(GNumeric o) + GEx(GSymbol m) + GEx(GEx m) + GEx(long n) +@@ -127,8 +128,8 @@ cdef extern from "sage/libs/pynac/wrap.h": + GEx numer() except + + GEx denom() except + + GEx numer_denom() except + +- int degree(GEx expr) except + +- int ldegree(GEx expr) except + ++ GNumeric degree(GEx expr) except + ++ GNumeric ldegree(GEx expr) except + + GEx unit(GEx expr) except + + GEx content(GEx expr) except + + GEx primpart(GEx expr) except + +@@ -161,6 +162,7 @@ cdef extern from "sage/libs/pynac/wrap.h": + + # Algorithms + GEx g_gcd "gcd"(GEx a, GEx b) except + ++ bint g_factor "factor"(GEx expr, GEx res) except + + GEx g_gosper_term "gosper_term"(GEx the_ex, GEx n) except + + GEx g_gosper_sum_definite "gosper_sum_definite"(GEx the_ex, + GEx n, GEx a, GEx b, int* p) except + +diff --git a/src/sage/rings/asymptotic/asymptotic_ring.py b/src/sage/rings/asymptotic/asymptotic_ring.py +index 0b03a4a..9de56a6 100644 +--- a/src/sage/rings/asymptotic/asymptotic_ring.py ++++ b/src/sage/rings/asymptotic/asymptotic_ring.py +@@ -2485,7 +2485,7 @@ class AsymptoticExpansion(CommutativeAlgebraElement): + :: + + sage: (x^2 + log(x)).subs(x=4*x+2).truncate(5) +- 16*x^2 + 16*x + log(x) + log(4) + 4 + 1/2*x^(-1) + O(x^(-2)) ++ 16*x^2 + 16*x + log(x) + 2*log(2) + 4 + 1/2*x^(-1) + O(x^(-2)) + sage: _.parent() + Asymptotic Ring <(e^x)^QQ * x^ZZ * log(x)^ZZ> over Symbolic Ring + +diff --git a/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py +b/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py +index 9a6f67a..de61ed3 100644 +--- a/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py ++++ b/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py +@@ -60,9 +60,15 @@ A univariate smooth point example:: + sage: decomp = F.asymptotic_decomposition(alpha) + sage: decomp + (0, []) + +- (-1/2*(x^2 + 6*x + 9)*r^2/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) +- - 1/2*(5*x^2 + 24*x + 27)*r/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) +- - 3*(x^2 + 3*x + 3)/(x^5 + 9*x^4 + 27*x^3 + 27*x^2), ++ (-1/2*r^2*(x^2/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) ++ + 6*x/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) ++ + 9/(x^5 + 9*x^4 + 27*x^3 + 27*x^2)) ++ - 1/2*r*(5*x^2/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) ++ + 24*x/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) ++ + 27/(x^5 + 9*x^4 + 27*x^3 + 27*x^2)) ++ - 3*x^2/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) ++ - 9*x/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) ++ - 9/(x^5 + 9*x^4 + 27*x^3 + 27*x^2), + [(x - 1/2, 1)]) + sage: F1 = decomp[1] + sage: p = {x: 1/2} +@@ -139,9 +145,9 @@ A multiple point example (Example 6.5 of [RaWi2012]_):: + sage: alpha = (var('a'), var('b')) + sage: decomp = F.asymptotic_decomposition(alpha); decomp + (0, []) + +- (-1/9*(2*b^2*x^2 - 5*a*b*x*y + 2*a^2*y^2)*r^2/(x^2*y^2) +- - 1/9*(6*b*x^2 - 5*(a + b)*x*y + 6*a*y^2)*r/(x^2*y^2) +- - 1/9*(4*x^2 - 5*x*y + 4*y^2)/(x^2*y^2), ++ (-1/9*r^2*(2*a^2/x^2 + 2*b^2/y^2 - 5*a*b/(x*y)) ++ - 1/9*r*(6*a/x^2 + 6*b/y^2 - 5*a/(x*y) - 5*b/(x*y)) ++ - 4/9/x^2 - 4/9/y^2 + 5/9/(x*y), + [(x + 2*y - 1, 1), (2*x + y - 1, 1)]) + sage: F1 = decomp[1] + sage: F1.asymptotics(p, alpha, 2) +@@ -1480,9 +1486,9 @@ class FractionWithFactoredDenominator(RingElement): + sage: alpha = [var('a')] + sage: F.asymptotic_decomposition(alpha) + (0, []) + +- (1/54*(5*a^2*x^2 + 2*a^2*x + 11*a^2)*r^2/x^2 +- - 1/54*(5*a*x^2 - 2*a*x - 33*a)*r/x^2 + 11/27/x^2, [(x - 1, 1)]) + +- (-5/27, [(x + 2, 1)]) ++ (1/54*(5*a^2 + 2*a^2/x + 11*a^2/x^2)*r^2 ++ - 1/54*(5*a - 2*a/x - 33*a/x^2)*r + 11/27/x^2, ++ [(x - 1, 1)]) + (-5/27, [(x + 2, 1)]) + + :: + +@@ -1495,7 +1501,7 @@ class FractionWithFactoredDenominator(RingElement): + sage: alpha = var('a, b') + sage: F.asymptotic_decomposition(alpha) + (0, []) + +- (1/3*(2*b*x - a*y)*r/(x*y) + 1/3*(2*x - y)/(x*y), ++ (-1/3*r*(a/x - 2*b/y) - 1/3/x + 2/3/y, + [(x + 2*y - 1, 1), (2*x + y - 1, 1)]) + """ + R = self.denominator_ring +@@ -1600,7 +1606,7 @@ class FractionWithFactoredDenominator(RingElement): + (1, [(x*y + x + y - 1, 2)]) + sage: alpha = [4, 3] + sage: decomp = F.asymptotic_decomposition(alpha); decomp +- (0, []) + (-3/2*r*(y + 1)/y - 1/2*(y + 1)/y, [(x*y + x + y - 1, 1)]) ++ (0, []) + (-3/2*r*(1/y + 1) - 1/2/y - 1/2, [(x*y + x + y - 1, 1)]) + sage: F1 = decomp[1] + sage: p = {y: 1/3, x: 1/2} + sage: asy = F1.asymptotics(p, alpha, 2, verbose=True) +@@ -1634,7 +1640,7 @@ class FractionWithFactoredDenominator(RingElement): + sage: alpha = [3, 3, 2] + sage: decomp = F.asymptotic_decomposition(alpha); decomp + (0, []) + +- (16*r*(4*y - 3*z)/(y*z) + 16*(2*y - z)/(y*z), ++ (-16*r*(3/y - 4/z) - 16/y + 32/z, + [(x + 2*y + z - 4, 1), (2*x + y + z - 4, 1)]) + sage: F1 = decomp[1] + sage: p = {x: 1, y: 1, z: 1} +diff --git a/src/sage/rings/asymptotic/term_monoid.py b/src/sage/rings/asymptotic/term_monoid.py +index b879639..ded7f02 100644 +--- a/src/sage/rings/asymptotic/term_monoid.py ++++ b/src/sage/rings/asymptotic/term_monoid.py +@@ -3339,7 +3339,7 @@ class ExactTerm(TermWithCoefficient): + sage: T(x^1234).log_term() + (1234*log(x),) + sage: T(49*x^7).log_term(base=7) +- (log(49)/log(7), 7/log(7)*log(x)) ++ (2, 7/log(7)*log(x)) + + :: + +@@ -3347,7 +3347,7 @@ class ExactTerm(TermWithCoefficient): + sage: T('x * y').log_term() + (log(x), log(y)) + sage: T('4 * x * y').log_term(base=2) +- (log(4)/log(2), 1/log(2)*log(x), 1/log(2)*log(y)) ++ (2, 1/log(2)*log(x), 1/log(2)*log(y)) + + .. SEEALSO:: + +diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx +index 0b8a3bd..cdc34a2 100644 +--- a/src/sage/rings/integer.pyx ++++ b/src/sage/rings/integer.pyx +@@ -2532,7 +2532,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement): + sage: Integer(125).log(5,prec=53) + 3.00000000000000 + sage: log(Integer(125)) +- log(125) ++ 3*log(5) + + For extremely large numbers, this works:: + +diff --git a/src/sage/rings/rational.pyx b/src/sage/rings/rational.pyx +index 36af3a5..857081b 100644 +--- a/src/sage/rings/rational.pyx ++++ b/src/sage/rings/rational.pyx +@@ -3075,11 +3075,11 @@ cdef class Rational(sage.structure.element.FieldElement): + sage: (124/345).log(5,100) + -0.63578895682825611710391773754 + sage: log(QQ(125)) +- log(125) ++ 3*log(5) + sage: log(QQ(125), 5) + 3 + sage: log(QQ(125), 3) +- log(125)/log(3) ++ 3*log(5)/log(3) + sage: QQ(8).log(1/2) + -3 + sage: (1/8).log(1/2) +diff --git a/src/sage/schemes/elliptic_curves/ell_point.py b/src/sage/schemes/elliptic_curves/ell_point.py +index 8009421..9ec892e 100644 +--- a/src/sage/schemes/elliptic_curves/ell_point.py ++++ b/src/sage/schemes/elliptic_curves/ell_point.py +@@ -2886,7 +2886,7 @@ class EllipticCurvePoint_number_field(EllipticCurvePoint_field): + sage: Q.non_archimedean_local_height(K.ideal(1-2*i)) + 0 + sage: Q.non_archimedean_local_height() +- 1/2*log(16) ++ 2*log(2) + + An example over the rational numbers:: + +diff --git a/src/sage/symbolic/constants_c.pyx b/src/sage/symbolic/constants_c.pyx +index 8eb61f5..38e8db6 100644 +--- a/src/sage/symbolic/constants_c.pyx ++++ b/src/sage/symbolic/constants_c.pyx +@@ -145,14 +145,14 @@ cdef class E(Expression): + sage: t.operands() + [a] + +- As opposed to:: ++ This applies to the unit argument as well:: + + sage: u = SR(1).exp()^a; u + e^a + sage: u.operator() +- <built-in function pow> ++ exp + sage: u.operands() +- [e, a] ++ [a] + + It also works with matrices (see :trac:`4735`):: + +diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx +index 94252ea..3e06201 100644 +--- a/src/sage/symbolic/expression.pyx ++++ b/src/sage/symbolic/expression.pyx +@@ -3247,11 +3247,8 @@ cdef class Expression(CommutativeRingElement): + -1 + sage: b = -x*A; c = b*b; c + 1/4*x^2*(sqrt(5) + I*sqrt(2*sqrt(5) + 10) - 1) +- +- Products of non integer powers of exp are not simplified:: +- + sage: exp(x)^I*exp(z)^(2.5) +- (e^x)^I*(e^z)^2.50000000000000 ++ e^(I*x + 2.50000000000000*z) + + :: + +@@ -3925,7 +3922,7 @@ cdef class Expression(CommutativeRingElement): + sage: 0^1.0 + 0.000000000000000 + sage: exp(x)^1.0 +- (e^x)^1.00000000000000 ++ e^(1.00000000000000*x) + """ + cdef Expression base, nexp + +@@ -6311,7 +6308,7 @@ cdef class Expression(CommutativeRingElement): + 0 + """ + cdef Expression ss = self.coerce_in(s) +- return self._gobj.ldegree(ss._gobj) ++ return new_Expression_from_GEx(self._parent, GEx(self._gobj.ldegree(ss._gobj))) + + def degree(self, s): + """ +@@ -6337,7 +6334,7 @@ cdef class Expression(CommutativeRingElement): + 0 + """ + cdef Expression ss = self.coerce_in(s) +- return self._gobj.degree(ss._gobj) ++ return new_Expression_from_GEx(self._parent, GEx(self._gobj.degree(ss._gobj))) + + def unit(self, s): + """ +@@ -7185,12 +7182,12 @@ cdef class Expression(CommutativeRingElement): + sage: f.collect(z) + (x^2*y^2 + 4)*z^2 + 4*x*y + 20*y^2 + (x + 21*y)*z + +- Sometimes, we do have to call :meth:`expand()` on the +- expression first to achieve the desired result:: ++ The terms are collected, whether the expression ++ is expanded or not:: + + sage: f = (x + y)*(x - z) + sage: f.collect(x) +- x^2 + x*y - x*z - y*z ++ x^2 + x*(y - z) - y*z + sage: f.expand().collect(x) + x^2 + x*(y - z) - y*z + +@@ -10433,9 +10430,9 @@ cdef class Expression(CommutativeRingElement): + ``x*log(9)`` is contracted only if ``algorithm`` is ``'all'``:: + + sage: (x*log(9)).simplify_log() +- x*log(9) ++ 2*x*log(3) + sage: (x*log(9)).simplify_log('all') +- log(9^x) ++ log(3^(2*x)) + + TESTS: + +@@ -10550,7 +10547,7 @@ cdef class Expression(CommutativeRingElement): + To expand also log(3/4) use ``algorithm='all'``:: + + sage: (log(3/4*x^pi)).log_expand('all') +- pi*log(x) - log(4) + log(3) ++ pi*log(x) + log(3) - 2*log(2) + + To expand only the power use ``algorithm='powers'``.:: + +@@ -10573,7 +10570,7 @@ cdef class Expression(CommutativeRingElement): + pi*log(x) + log(3/4) + + sage: (log(3/4*x^pi)).log_expand('all') +- pi*log(x) - log(4) + log(3) ++ pi*log(x) + log(3) - 2*log(2) + + sage: (log(3/4*x^pi)).log_expand() + pi*log(x) + log(3/4) +diff --git a/src/sage/tests/french_book/calculus_doctest.py b/src/sage/tests/french_book/calculus_doctest.py +index 0d40cae..ffe5d4b 100644 +--- a/src/sage/tests/french_book/calculus_doctest.py ++++ b/src/sage/tests/french_book/calculus_doctest.py +@@ -331,7 +331,7 @@ Sage example in ./calculus.tex, line 914:: + Sage example in ./calculus.tex, line 929:: + + sage: v(x) = diff(u(x), x); sol = solve(v(x) == 0, x); sol +- [x == 100/log(100), x == 0] ++ [x == 50/log(10), x == 0] + sage: floor(sol[0].rhs()) + 21 + Copied: sagemath/repos/community-staging-i686/sagemath-python3-notebook.patch (from rev 261180, sagemath/trunk/sagemath-python3-notebook.patch) =================================================================== --- community-staging-i686/sagemath-python3-notebook.patch (rev 0) +++ community-staging-i686/sagemath-python3-notebook.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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 SageNBExport(NotebookJupyter): +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 +@@ -281,7 +281,6 @@ def have_prerequisites(debug=True): + True + """ + try: +- from notebook.notebookapp import NotebookApp + return True + except ImportError: + if debug: + Copied: sagemath/repos/community-staging-i686/test-optional.patch (from rev 261180, sagemath/trunk/test-optional.patch) =================================================================== --- community-staging-i686/test-optional.patch (rev 0) +++ community-staging-i686/test-optional.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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 +@@ -307,22 +307,6 @@ + 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 Copied: sagemath/repos/community-staging-x86_64/PKGBUILD (from rev 261180, sagemath/trunk/PKGBUILD) =================================================================== --- community-staging-x86_64/PKGBUILD (rev 0) +++ community-staging-x86_64/PKGBUILD 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,168 @@ +# 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=8.0 +pkgrel=6 +pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab" +arch=(i686 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 + 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' + 'modular_decomposition: modular decomposition of graphs' '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' + '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' 'tachyon: alternative 3D plots engine') +makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding sirocco + mcqd coxeter3 modular_decomposition bliss-graphs tdlib python2-pkgconfig meataxe libfes) +source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz" + env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch + r-no-readline.patch fes02.patch sagemath-ecl-no-sigfpe.patch sagemath-cython-0.26.patch + sagemath-pynac-0.7.11.patch sagemath-pynac-0.7.12.patch sagemath-detect-igraph.patch sagemath-networkx2.patch) +sha256sums=('91df3e303add71616e24b38c04789f66d57ada7b1017e5369e850c42d5e8753d' + 'e0b5b8673300857fde823209a7e90faecf9e754ab812cc5e54297eddc0c79571' + '4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212' + 'c6836783251d94c00f0229c1e671de86c58c6c6fb0f6959725317817abc64ca8' + '775051aa9076ebf631c8a291af38b6ec4a13c904740dc9da831641d592d8bcd8' + '27aa73d427d92aeb2c181a233aa3a574a4158cd7dee33832808f69edaec55ea2' + '81d08c6a760f171f3381455b66a6c84789c9f0eefddbe6ca5794075514ad8c3a' + 'ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf' + 'a39da083c038ada797ffc5bedc9ba47455a3f77057d42f86484ae877ef9172ea' + 'c31809f887bf9acc45c5bd9dd30bb93e73601d3efbf3016594c3c1d241731c8a' + '2953ef15d957a2f3304a5584c154bf4777bcb4b461414d3a2178423257539755' + '3e23ff449a5a3a032684287722455633762636b93ecfc35fb00e875c69eff240' + '719bb39c9c2cd1c6e75be0969000ba5ffcd2875bb5190fce6bb6a6feaa76b96f' + '90be1d1a90120bd5bd3620769480106ba809dd23e896bc4a3f8931e5340f3cda' + 'a1a0ab5b794136b518f5f66fe9f1689411fabb3b81560b159eae81f6f69000e3') + +prepare(){ + cd sage-$pkgver + +# Arch-specific patches +# assume all optional packages are installed + patch -p0 -i ../package.patch +# set env variables + patch -p0 -i ../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 +# adapt to networkx 2 changes + patch -p1 -i ../sagemath-networkx2.patch + +# Upstream patches +# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209 + patch -p1 -i ../fes02.patch +# disable SIGFPE for ecl https://trac.sagemath.org/ticket/22191 + patch -p1 -i ../sagemath-ecl-no-sigfpe.patch +# disable auto_picke for cython 0.26 https://trac.sagemath.org/ticket/23360 + patch -p1 -i ../sagemath-cython-0.26.patch +# fix build with pynac 0.7.11 https://trac.sagemath.org/ticket/23820 + patch -p1 -i ../sagemath-pynac-0.7.11.patch +# fix build with pynac 0.7.12 https://trac.sagemath.org/ticket/23950 + patch -p1 -i ../sagemath-pynac-0.7.12.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-$pkgver + autoreconf -vi + ./configure --prefix=/usr || true + + cd src + export SAGE_LOCAL="/usr" + export SAGE_ROOT="$PWD" + export SAGE_SRC="$PWD" + export CC=gcc + + python2 setup.py build +} + +package_sagemath() { + optdepends+=('sagemath-jupyter: Jupyter kernel') + conflicts=(sage-mathematics) + replaces=(sage-mathematics) + provides=(sage-mathematics) + + cd sage-$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 "$pkgdir"/usr/bin + for _i in arch-env banner cachegrind callgrind cleaner coverage coverageall cython env env-config eval grep grepdoc inline-fortran \ + ipython massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2ipynb rst2sws rst2txt run \ + run-cython runtests startuptime.py sws2rst valgrind version.sh + do + cp bin/sage-$_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="$pkgdir"/usr/share/jupyter + + python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update()" +} Copied: sagemath/repos/community-staging-x86_64/env.patch (from rev 261180, sagemath/trunk/env.patch) =================================================================== --- community-staging-x86_64/env.patch (rev 0) +++ community-staging-x86_64/env.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,93 @@ +--- src/bin/sage-env.orig 2015-01-06 10:46:04.469687605 +0100 ++++ src/bin/sage-env 2015-01-06 10:49:59.547762019 +0100 +@@ -111,41 +111,7 @@ + } + + +-# New value for SAGE_ROOT: either SAGE_ROOT (if given) +-# or a guessed value based on pwd. +-if [ -n "$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() { +@@ -151,6 +151,7 @@ + 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. + +@@ -233,8 +233,9 @@ + 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 "${SAGE_ORIG_PATH_SET}" ]; then +@@ -374,6 +337,9 @@ + export SAGE_STARTUP_FILE + fi + ++export LIBMTX="$DOT_SAGE/meataxe" ++[[ -d $LIBMTX ]] || mkdir -p $LIBMTX # Create meataxe data dir ++ + if [ -z "$IPYTHONDIR" ]; then + # We hardcode a version number in the directory name. The idea is + # that we keep using the same version number as long as that is +@@ -468,7 +400,6 @@ + fi + fi + fi +-export MAXIMA_PREFIX="$SAGE_LOCAL" + + PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB + +@@ -629,9 +608,6 @@ + LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH + fi + +-# See trac 7186 -- this is needed if ecl is moved +-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR +- + # Handle parallel building/testing/... + # See Trac Ticket #12016 + # First, figure out the right values for SAGE_NUM_THREADS (default Copied: sagemath/repos/community-staging-x86_64/fes02.patch (from rev 261180, sagemath/trunk/fes02.patch) =================================================================== --- community-staging-x86_64/fes02.patch (rev 0) +++ community-staging-x86_64/fes02.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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) + + + include 'sage/ext/interrupt.pxi' #sig_on(), sig_off() +@@ -219,7 +221,7 @@ 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 261180, sagemath/trunk/jupyter-path.patch) =================================================================== --- community-staging-x86_64/jupyter-path.patch (rev 0) +++ community-staging-x86_64/jupyter-path.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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_ROOT, 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): + +@@ -208,7 +208,7 @@ + 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 261180, sagemath/trunk/latte-count.patch) =================================================================== --- community-staging-x86_64/latte-count.patch (rev 0) +++ community-staging-x86_64/latte-count.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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 +@@ -228,7 +228,7 @@ 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 +@@ -236,7 +236,7 @@ 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 +@@ -244,7 +244,7 @@ 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 +@@ -252,7 +252,7 @@ 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 +@@ -264,7 +264,7 @@ 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 +@@ -86,7 +86,7 @@ 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: ... +@@ -106,7 +106,7 @@ 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 261180, sagemath/trunk/package.patch) =================================================================== --- community-staging-x86_64/package.patch (rev 0) +++ community-staging-x86_64/package.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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 +@@ -343,7 +343,7 @@ + sage: for pkg in list_packages('pip', local=True): + ....: assert not is_package_installed(pkg) + """ +- return any(p.split('-')[0] == package for p in installed_packages(exclude_pip)) ++ return True + + def package_versions(package_type, local=False): + r""" +--- src/sage_setup/optional_extension.py.orig 2016-10-19 18:35:10.092577510 +0000 ++++ src/sage_setup/optional_extension.py 2016-10-19 18:38:13.514765366 +0000 +@@ -21,8 +21,6 @@ + from distutils.extension import Extension + from sage.misc.package import is_package_installed, list_packages + +-all_packages = list_packages(local=True) +- + + class CythonizeExtension(Extension): + """ +@@ -76,14 +74,7 @@ + condition = kwds.pop("condition") + except KeyError: + pkg = kwds.pop("package") +- try: +- pkginfo = all_packages[pkg] +- except KeyError: +- # Might be an installed old-style package +- condition = is_package_installed(pkg) +- else: +- condition = (pkginfo["installed_version"] == pkginfo["remote_version"]) +- ++ condition = True + if condition: + return Extension(*args, **kwds) + else: Copied: sagemath/repos/community-staging-x86_64/r-no-readline.patch (from rev 261180, sagemath/trunk/r-no-readline.patch) =================================================================== --- community-staging-x86_64/r-no-readline.patch (rev 0) +++ community-staging-x86_64/r-no-readline.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,11 @@ +--- a/src/sage/interfaces/r.py ++++ b/src/sage/interfaces/r.py +@@ -331,7 +331,7 @@ + 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-cython-0.26.patch (from rev 261180, sagemath/trunk/sagemath-cython-0.26.patch) =================================================================== --- community-staging-x86_64/sagemath-cython-0.26.patch (rev 0) +++ community-staging-x86_64/sagemath-cython-0.26.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,26 @@ +diff --git a/src/setup.py b/src/setup.py +index 2215379..ddca1eb 100755 +--- a/src/setup.py ++++ b/src/setup.py +@@ -95,7 +95,12 @@ library_dirs = [os.path.join(SAGE_LOCAL, "lib")] + + # Manually add -fno-strict-aliasing, which is needed to compile Cython + # and disappears from the default flags if the user has set CFLAGS. +-extra_compile_args = [ "-fno-strict-aliasing" ] ++# ++# Add -DCYTHON_CLINE_IN_TRACEBACK=1 which causes the .c line number to ++# always appear in exception tracebacks (by default, this is a runtime ++# setting in Cython which causes some overhead every time an exception ++# is raised). ++extra_compile_args = ["-fno-strict-aliasing", "-DCYTHON_CLINE_IN_TRACEBACK=1"] + extra_link_args = [ ] + + DEVEL = False +@@ -336,6 +341,7 @@ class sage_build_cython(Command): + + # Cython compiler directives + self.cython_directives = dict( ++ auto_pickle=False, + autotestdict=False, + cdivision=True, + embedsignature=True, Copied: sagemath/repos/community-staging-x86_64/sagemath-detect-igraph.patch (from rev 261180, sagemath/trunk/sagemath-detect-igraph.patch) =================================================================== --- community-staging-x86_64/sagemath-detect-igraph.patch (rev 0) +++ community-staging-x86_64/sagemath-detect-igraph.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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 +@@ -7876,10 +7875,12 @@ 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-ecl-no-sigfpe.patch (from rev 261180, sagemath/trunk/sagemath-ecl-no-sigfpe.patch) =================================================================== --- community-staging-x86_64/sagemath-ecl-no-sigfpe.patch (rev 0) +++ community-staging-x86_64/sagemath-ecl-no-sigfpe.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,12 @@ +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: Copied: sagemath/repos/community-staging-x86_64/sagemath-networkx2.patch (from rev 261180, sagemath/trunk/sagemath-networkx2.patch) =================================================================== --- community-staging-x86_64/sagemath-networkx2.patch (rev 0) +++ community-staging-x86_64/sagemath-networkx2.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,26 @@ +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 +@@ -751,7 +751,7 @@ 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. "+ Copied: sagemath/repos/community-staging-x86_64/sagemath-pynac-0.7.11.patch (from rev 261180, sagemath/trunk/sagemath-pynac-0.7.11.patch) =================================================================== --- community-staging-x86_64/sagemath-pynac-0.7.11.patch (rev 0) +++ community-staging-x86_64/sagemath-pynac-0.7.11.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,21 @@ +--- a/src/sage/libs/pynac/pynac.pxd ++++ b/src/sage/libs/pynac/pynac.pxd +@@ -302,7 +302,6 @@ cdef extern from "sage/libs/pynac/wrap.h": + bint is_a_fderivative "is_a<GiNaC::fderivative>" (GEx e) + bint is_a_function "is_a<GiNaC::function>" (GEx e) + bint is_exactly_a_function "is_exactly_a<GiNaC::function>" (GEx e) +- bint is_a_ncmul "is_a<GiNaC::ncmul>" (GEx e) + + # Arithmetic + int ginac_error() +--- a/src/sage/symbolic/expression.pyx ++++ b/src/sage/symbolic/expression.pyx +@@ -5536,7 +5536,7 @@ cdef class Expression(CommutativeRingElement): + cdef unsigned serial + if is_a_add(self._gobj): + return add_vararg +- elif is_a_mul(self._gobj) or is_a_ncmul(self._gobj): ++ elif is_a_mul(self._gobj): + return mul_vararg + elif is_a_power(self._gobj): + return operator.pow Copied: sagemath/repos/community-staging-x86_64/sagemath-pynac-0.7.12.patch (from rev 261180, sagemath/trunk/sagemath-pynac-0.7.12.patch) =================================================================== --- community-staging-x86_64/sagemath-pynac-0.7.12.patch (rev 0) +++ community-staging-x86_64/sagemath-pynac-0.7.12.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -0,0 +1,390 @@ +diff --git a/src/doc/de/thematische_anleitungen/sage_gymnasium.rst b/src/doc/de/thematische_anleitungen/sage_gymnasium.rst +index 5a150a0..f9ede06 100644 +--- a/src/doc/de/thematische_anleitungen/sage_gymnasium.rst ++++ b/src/doc/de/thematische_anleitungen/sage_gymnasium.rst +@@ -716,7 +716,7 @@ die ähnliche Funktion ``canonicalize_radical``:: + Diese Gesetze können auch umgekehrt verwendet werden, wie in diesem Beispiel:: + + sage: (5*log(2) + 5*log(5)).simplify_log() +- log(100000) ++ 5*log(10) + + Es geben weitere mögliche Vereinfachungen, die wir hier nicht weiter erwähnen. + +diff --git a/src/sage/coding/code_bounds.py b/src/sage/coding/code_bounds.py +index 7935bbf..64ac455 100644 +--- a/src/sage/coding/code_bounds.py ++++ b/src/sage/coding/code_bounds.py +@@ -577,8 +577,8 @@ def entropy(x, q=2): + + sage: codes.bounds.entropy(0, 2) + 0 +- sage: codes.bounds.entropy(1/5,4) +- 1/5*log(3)/log(4) - 4/5*log(4/5)/log(4) - 1/5*log(1/5)/log(4) ++ sage: codes.bounds.entropy(1/5,4).factor() ++ 1/10*(log(3) - 4*log(4/5) - log(1/5))/log(2) + sage: codes.bounds.entropy(1, 3) + log(2)/log(3) + +diff --git a/src/sage/functions/log.py b/src/sage/functions/log.py +index 15e3dbf..64d898c 100644 +--- a/src/sage/functions/log.py ++++ b/src/sage/functions/log.py +@@ -121,12 +121,12 @@ class Function_exp(GinacFunction): + sage: model_exp = exp(II)**a*(b) + sage: sol1_l={b: 5.0, a: 1.1} + sage: model_exp.subs(sol1_l) +- 5.00000000000000*(e^II)^1.10000000000000 ++ 5.00000000000000*e^(1.10000000000000*II) + + :: + + sage: exp(3)^II*exp(x) +- (e^3)^II*e^x ++ e^(3*II + x) + sage: exp(x)*exp(x) + e^(2*x) + sage: exp(x)*exp(a) +@@ -137,7 +137,7 @@ class Function_exp(GinacFunction): + Another instance of the same problem (:trac:`7394`):: + + sage: 2*sqrt(e) +- 2*sqrt(e) ++ 2*e^(1/2) + + Check that :trac:`19918` is fixed:: + +@@ -271,7 +271,7 @@ class Function_log(GinacFunction): + sage: RDF(log(1024, 2)) + 10.0 + sage: log(10, 4) +- log(10)/log(4) ++ 1/2*log(10)/log(2) + sage: RDF(log(10, 4)) + 1.6609640474436813 + sage: log(10, 2) +diff --git a/src/sage/functions/orthogonal_polys.py b/src/sage/functions/orthogonal_polys.py +index 5db9871..c877454 100644 +--- a/src/sage/functions/orthogonal_polys.py ++++ b/src/sage/functions/orthogonal_polys.py +@@ -1666,7 +1666,7 @@ class Func_assoc_legendre_Q(BuiltinFunction): + EXAMPLES:: + + sage: gen_legendre_Q(2,1,3) +- -1/4*sqrt(-2)*(-36*I*pi + 36*log(4) - 36*log(2) - 25) ++ -1/4*sqrt(-2)*(-36*I*pi + 36*log(2) - 25) + """ + ret = self._eval_special_values_(n, m, x) + if ret is not None: +diff --git a/src/sage/libs/pynac/pynac.pxd b/src/sage/libs/pynac/pynac.pxd +index 9e37f08..1d19fdd 100644 +--- a/src/sage/libs/pynac/pynac.pxd ++++ b/src/sage/libs/pynac/pynac.pxd +@@ -97,6 +97,7 @@ cdef extern from "sage/libs/pynac/wrap.h": + + cdef cppclass GEx "ex": + GEx() ++ GEx(GNumeric o) + GEx(GSymbol m) + GEx(GEx m) + GEx(long n) +@@ -127,8 +128,8 @@ cdef extern from "sage/libs/pynac/wrap.h": + GEx numer() except + + GEx denom() except + + GEx numer_denom() except + +- int degree(GEx expr) except + +- int ldegree(GEx expr) except + ++ GNumeric degree(GEx expr) except + ++ GNumeric ldegree(GEx expr) except + + GEx unit(GEx expr) except + + GEx content(GEx expr) except + + GEx primpart(GEx expr) except + +@@ -161,6 +162,7 @@ cdef extern from "sage/libs/pynac/wrap.h": + + # Algorithms + GEx g_gcd "gcd"(GEx a, GEx b) except + ++ bint g_factor "factor"(GEx expr, GEx res) except + + GEx g_gosper_term "gosper_term"(GEx the_ex, GEx n) except + + GEx g_gosper_sum_definite "gosper_sum_definite"(GEx the_ex, + GEx n, GEx a, GEx b, int* p) except + +diff --git a/src/sage/rings/asymptotic/asymptotic_ring.py b/src/sage/rings/asymptotic/asymptotic_ring.py +index 0b03a4a..9de56a6 100644 +--- a/src/sage/rings/asymptotic/asymptotic_ring.py ++++ b/src/sage/rings/asymptotic/asymptotic_ring.py +@@ -2485,7 +2485,7 @@ class AsymptoticExpansion(CommutativeAlgebraElement): + :: + + sage: (x^2 + log(x)).subs(x=4*x+2).truncate(5) +- 16*x^2 + 16*x + log(x) + log(4) + 4 + 1/2*x^(-1) + O(x^(-2)) ++ 16*x^2 + 16*x + log(x) + 2*log(2) + 4 + 1/2*x^(-1) + O(x^(-2)) + sage: _.parent() + Asymptotic Ring <(e^x)^QQ * x^ZZ * log(x)^ZZ> over Symbolic Ring + +diff --git a/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py +b/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py +index 9a6f67a..de61ed3 100644 +--- a/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py ++++ b/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py +@@ -60,9 +60,15 @@ A univariate smooth point example:: + sage: decomp = F.asymptotic_decomposition(alpha) + sage: decomp + (0, []) + +- (-1/2*(x^2 + 6*x + 9)*r^2/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) +- - 1/2*(5*x^2 + 24*x + 27)*r/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) +- - 3*(x^2 + 3*x + 3)/(x^5 + 9*x^4 + 27*x^3 + 27*x^2), ++ (-1/2*r^2*(x^2/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) ++ + 6*x/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) ++ + 9/(x^5 + 9*x^4 + 27*x^3 + 27*x^2)) ++ - 1/2*r*(5*x^2/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) ++ + 24*x/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) ++ + 27/(x^5 + 9*x^4 + 27*x^3 + 27*x^2)) ++ - 3*x^2/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) ++ - 9*x/(x^5 + 9*x^4 + 27*x^3 + 27*x^2) ++ - 9/(x^5 + 9*x^4 + 27*x^3 + 27*x^2), + [(x - 1/2, 1)]) + sage: F1 = decomp[1] + sage: p = {x: 1/2} +@@ -139,9 +145,9 @@ A multiple point example (Example 6.5 of [RaWi2012]_):: + sage: alpha = (var('a'), var('b')) + sage: decomp = F.asymptotic_decomposition(alpha); decomp + (0, []) + +- (-1/9*(2*b^2*x^2 - 5*a*b*x*y + 2*a^2*y^2)*r^2/(x^2*y^2) +- - 1/9*(6*b*x^2 - 5*(a + b)*x*y + 6*a*y^2)*r/(x^2*y^2) +- - 1/9*(4*x^2 - 5*x*y + 4*y^2)/(x^2*y^2), ++ (-1/9*r^2*(2*a^2/x^2 + 2*b^2/y^2 - 5*a*b/(x*y)) ++ - 1/9*r*(6*a/x^2 + 6*b/y^2 - 5*a/(x*y) - 5*b/(x*y)) ++ - 4/9/x^2 - 4/9/y^2 + 5/9/(x*y), + [(x + 2*y - 1, 1), (2*x + y - 1, 1)]) + sage: F1 = decomp[1] + sage: F1.asymptotics(p, alpha, 2) +@@ -1480,9 +1486,9 @@ class FractionWithFactoredDenominator(RingElement): + sage: alpha = [var('a')] + sage: F.asymptotic_decomposition(alpha) + (0, []) + +- (1/54*(5*a^2*x^2 + 2*a^2*x + 11*a^2)*r^2/x^2 +- - 1/54*(5*a*x^2 - 2*a*x - 33*a)*r/x^2 + 11/27/x^2, [(x - 1, 1)]) + +- (-5/27, [(x + 2, 1)]) ++ (1/54*(5*a^2 + 2*a^2/x + 11*a^2/x^2)*r^2 ++ - 1/54*(5*a - 2*a/x - 33*a/x^2)*r + 11/27/x^2, ++ [(x - 1, 1)]) + (-5/27, [(x + 2, 1)]) + + :: + +@@ -1495,7 +1501,7 @@ class FractionWithFactoredDenominator(RingElement): + sage: alpha = var('a, b') + sage: F.asymptotic_decomposition(alpha) + (0, []) + +- (1/3*(2*b*x - a*y)*r/(x*y) + 1/3*(2*x - y)/(x*y), ++ (-1/3*r*(a/x - 2*b/y) - 1/3/x + 2/3/y, + [(x + 2*y - 1, 1), (2*x + y - 1, 1)]) + """ + R = self.denominator_ring +@@ -1600,7 +1606,7 @@ class FractionWithFactoredDenominator(RingElement): + (1, [(x*y + x + y - 1, 2)]) + sage: alpha = [4, 3] + sage: decomp = F.asymptotic_decomposition(alpha); decomp +- (0, []) + (-3/2*r*(y + 1)/y - 1/2*(y + 1)/y, [(x*y + x + y - 1, 1)]) ++ (0, []) + (-3/2*r*(1/y + 1) - 1/2/y - 1/2, [(x*y + x + y - 1, 1)]) + sage: F1 = decomp[1] + sage: p = {y: 1/3, x: 1/2} + sage: asy = F1.asymptotics(p, alpha, 2, verbose=True) +@@ -1634,7 +1640,7 @@ class FractionWithFactoredDenominator(RingElement): + sage: alpha = [3, 3, 2] + sage: decomp = F.asymptotic_decomposition(alpha); decomp + (0, []) + +- (16*r*(4*y - 3*z)/(y*z) + 16*(2*y - z)/(y*z), ++ (-16*r*(3/y - 4/z) - 16/y + 32/z, + [(x + 2*y + z - 4, 1), (2*x + y + z - 4, 1)]) + sage: F1 = decomp[1] + sage: p = {x: 1, y: 1, z: 1} +diff --git a/src/sage/rings/asymptotic/term_monoid.py b/src/sage/rings/asymptotic/term_monoid.py +index b879639..ded7f02 100644 +--- a/src/sage/rings/asymptotic/term_monoid.py ++++ b/src/sage/rings/asymptotic/term_monoid.py +@@ -3339,7 +3339,7 @@ class ExactTerm(TermWithCoefficient): + sage: T(x^1234).log_term() + (1234*log(x),) + sage: T(49*x^7).log_term(base=7) +- (log(49)/log(7), 7/log(7)*log(x)) ++ (2, 7/log(7)*log(x)) + + :: + +@@ -3347,7 +3347,7 @@ class ExactTerm(TermWithCoefficient): + sage: T('x * y').log_term() + (log(x), log(y)) + sage: T('4 * x * y').log_term(base=2) +- (log(4)/log(2), 1/log(2)*log(x), 1/log(2)*log(y)) ++ (2, 1/log(2)*log(x), 1/log(2)*log(y)) + + .. SEEALSO:: + +diff --git a/src/sage/rings/integer.pyx b/src/sage/rings/integer.pyx +index 0b8a3bd..cdc34a2 100644 +--- a/src/sage/rings/integer.pyx ++++ b/src/sage/rings/integer.pyx +@@ -2532,7 +2532,7 @@ cdef class Integer(sage.structure.element.EuclideanDomainElement): + sage: Integer(125).log(5,prec=53) + 3.00000000000000 + sage: log(Integer(125)) +- log(125) ++ 3*log(5) + + For extremely large numbers, this works:: + +diff --git a/src/sage/rings/rational.pyx b/src/sage/rings/rational.pyx +index 36af3a5..857081b 100644 +--- a/src/sage/rings/rational.pyx ++++ b/src/sage/rings/rational.pyx +@@ -3075,11 +3075,11 @@ cdef class Rational(sage.structure.element.FieldElement): + sage: (124/345).log(5,100) + -0.63578895682825611710391773754 + sage: log(QQ(125)) +- log(125) ++ 3*log(5) + sage: log(QQ(125), 5) + 3 + sage: log(QQ(125), 3) +- log(125)/log(3) ++ 3*log(5)/log(3) + sage: QQ(8).log(1/2) + -3 + sage: (1/8).log(1/2) +diff --git a/src/sage/schemes/elliptic_curves/ell_point.py b/src/sage/schemes/elliptic_curves/ell_point.py +index 8009421..9ec892e 100644 +--- a/src/sage/schemes/elliptic_curves/ell_point.py ++++ b/src/sage/schemes/elliptic_curves/ell_point.py +@@ -2886,7 +2886,7 @@ class EllipticCurvePoint_number_field(EllipticCurvePoint_field): + sage: Q.non_archimedean_local_height(K.ideal(1-2*i)) + 0 + sage: Q.non_archimedean_local_height() +- 1/2*log(16) ++ 2*log(2) + + An example over the rational numbers:: + +diff --git a/src/sage/symbolic/constants_c.pyx b/src/sage/symbolic/constants_c.pyx +index 8eb61f5..38e8db6 100644 +--- a/src/sage/symbolic/constants_c.pyx ++++ b/src/sage/symbolic/constants_c.pyx +@@ -145,14 +145,14 @@ cdef class E(Expression): + sage: t.operands() + [a] + +- As opposed to:: ++ This applies to the unit argument as well:: + + sage: u = SR(1).exp()^a; u + e^a + sage: u.operator() +- <built-in function pow> ++ exp + sage: u.operands() +- [e, a] ++ [a] + + It also works with matrices (see :trac:`4735`):: + +diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx +index 94252ea..3e06201 100644 +--- a/src/sage/symbolic/expression.pyx ++++ b/src/sage/symbolic/expression.pyx +@@ -3247,11 +3247,8 @@ cdef class Expression(CommutativeRingElement): + -1 + sage: b = -x*A; c = b*b; c + 1/4*x^2*(sqrt(5) + I*sqrt(2*sqrt(5) + 10) - 1) +- +- Products of non integer powers of exp are not simplified:: +- + sage: exp(x)^I*exp(z)^(2.5) +- (e^x)^I*(e^z)^2.50000000000000 ++ e^(I*x + 2.50000000000000*z) + + :: + +@@ -3925,7 +3922,7 @@ cdef class Expression(CommutativeRingElement): + sage: 0^1.0 + 0.000000000000000 + sage: exp(x)^1.0 +- (e^x)^1.00000000000000 ++ e^(1.00000000000000*x) + """ + cdef Expression base, nexp + +@@ -6311,7 +6308,7 @@ cdef class Expression(CommutativeRingElement): + 0 + """ + cdef Expression ss = self.coerce_in(s) +- return self._gobj.ldegree(ss._gobj) ++ return new_Expression_from_GEx(self._parent, GEx(self._gobj.ldegree(ss._gobj))) + + def degree(self, s): + """ +@@ -6337,7 +6334,7 @@ cdef class Expression(CommutativeRingElement): + 0 + """ + cdef Expression ss = self.coerce_in(s) +- return self._gobj.degree(ss._gobj) ++ return new_Expression_from_GEx(self._parent, GEx(self._gobj.degree(ss._gobj))) + + def unit(self, s): + """ +@@ -7185,12 +7182,12 @@ cdef class Expression(CommutativeRingElement): + sage: f.collect(z) + (x^2*y^2 + 4)*z^2 + 4*x*y + 20*y^2 + (x + 21*y)*z + +- Sometimes, we do have to call :meth:`expand()` on the +- expression first to achieve the desired result:: ++ The terms are collected, whether the expression ++ is expanded or not:: + + sage: f = (x + y)*(x - z) + sage: f.collect(x) +- x^2 + x*y - x*z - y*z ++ x^2 + x*(y - z) - y*z + sage: f.expand().collect(x) + x^2 + x*(y - z) - y*z + +@@ -10433,9 +10430,9 @@ cdef class Expression(CommutativeRingElement): + ``x*log(9)`` is contracted only if ``algorithm`` is ``'all'``:: + + sage: (x*log(9)).simplify_log() +- x*log(9) ++ 2*x*log(3) + sage: (x*log(9)).simplify_log('all') +- log(9^x) ++ log(3^(2*x)) + + TESTS: + +@@ -10550,7 +10547,7 @@ cdef class Expression(CommutativeRingElement): + To expand also log(3/4) use ``algorithm='all'``:: + + sage: (log(3/4*x^pi)).log_expand('all') +- pi*log(x) - log(4) + log(3) ++ pi*log(x) + log(3) - 2*log(2) + + To expand only the power use ``algorithm='powers'``.:: + +@@ -10573,7 +10570,7 @@ cdef class Expression(CommutativeRingElement): + pi*log(x) + log(3/4) + + sage: (log(3/4*x^pi)).log_expand('all') +- pi*log(x) - log(4) + log(3) ++ pi*log(x) + log(3) - 2*log(2) + + sage: (log(3/4*x^pi)).log_expand() + pi*log(x) + log(3/4) +diff --git a/src/sage/tests/french_book/calculus_doctest.py b/src/sage/tests/french_book/calculus_doctest.py +index 0d40cae..ffe5d4b 100644 +--- a/src/sage/tests/french_book/calculus_doctest.py ++++ b/src/sage/tests/french_book/calculus_doctest.py +@@ -331,7 +331,7 @@ Sage example in ./calculus.tex, line 914:: + Sage example in ./calculus.tex, line 929:: + + sage: v(x) = diff(u(x), x); sol = solve(v(x) == 0, x); sol +- [x == 100/log(100), x == 0] ++ [x == 50/log(10), x == 0] + sage: floor(sol[0].rhs()) + 21 + Copied: sagemath/repos/community-staging-x86_64/sagemath-python3-notebook.patch (from rev 261180, sagemath/trunk/sagemath-python3-notebook.patch) =================================================================== --- community-staging-x86_64/sagemath-python3-notebook.patch (rev 0) +++ community-staging-x86_64/sagemath-python3-notebook.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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 SageNBExport(NotebookJupyter): +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 +@@ -281,7 +281,6 @@ 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/test-optional.patch (from rev 261180, sagemath/trunk/test-optional.patch) =================================================================== --- community-staging-x86_64/test-optional.patch (rev 0) +++ community-staging-x86_64/test-optional.patch 2017-10-01 16:47:03 UTC (rev 261181) @@ -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 +@@ -307,22 +307,6 @@ + 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