[arch-commits] Commit in sagemath/trunk (12 files)
Antonio Rojas
arojas at archlinux.org
Sun May 6 12:07:53 UTC 2018
Date: Sunday, May 6, 2018 @ 12:07:52
Author: arojas
Revision: 319013
Update to 8.2
Modified:
sagemath/trunk/PKGBUILD
sagemath/trunk/pari-stackwarn.patch
sagemath/trunk/sagemath-detect-igraph.patch
sagemath/trunk/sagemath-env.patch
sagemath/trunk/sagemath-networkx2.patch
sagemath/trunk/sagemath-singular-4.1.1.patch
sagemath/trunk/test-optional.patch
Deleted:
sagemath/trunk/sagemath-cython-0.28c.patch
sagemath/trunk/sagemath-ipython-prompt.patch
sagemath/trunk/sagemath-linbox-1.5.patch
sagemath/trunk/sagemath-matplotlib2.patch
sagemath/trunk/sagemath-pynac-0.7.14.patch
-------------------------------+
PKGBUILD | 70 ++--------
pari-stackwarn.patch | 8 -
sagemath-cython-0.28c.patch | 59 --------
sagemath-detect-igraph.patch | 2
sagemath-env.patch | 62 +++++----
sagemath-ipython-prompt.patch | 13 -
sagemath-linbox-1.5.patch | 272 ----------------------------------------
sagemath-matplotlib2.patch | 253 -------------------------------------
sagemath-networkx2.patch | 53 +------
sagemath-pynac-0.7.14.patch | 167 ------------------------
sagemath-singular-4.1.1.patch | 12 -
test-optional.patch | 6
12 files changed, 84 insertions(+), 893 deletions(-)
Modified: PKGBUILD
===================================================================
--- PKGBUILD 2018-05-06 10:44:48 UTC (rev 319012)
+++ PKGBUILD 2018-05-06 12:07:52 UTC (rev 319013)
@@ -8,8 +8,8 @@
pkgbase=sagemath
pkgname=(sagemath sagemath-jupyter)
-pkgver=8.1
-pkgrel=12
+pkgver=8.2
+pkgrel=1
pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"
arch=(x86_64)
url="http://www.sagemath.org"
@@ -24,7 +24,7 @@
'coin-or-cbc: COIN backend for numerical computations' 'coin-or-csdp: for computing Lovász theta-function of graphs'
'buckygen: for generating fullerene graphs' 'plantri: for generating some classes of graphs' 'benzene: for generating fusenes and benzenoids'
'ffmpeg: to export animations to video' 'imagemagick: to show animations'
- 'coxeter3: Coxeter groups implementation' 'cryptominisat5: SAT solver' 'gap-data: for computing Galois groups'
+ 'coxeter: 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'
@@ -33,44 +33,31 @@
'sirocco: for computing the fundamental group of the complement of a plane curve'
'three.js: alternative 3D plots engine')
makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding sirocco
- mcqd coxeter3 bliss-graphs tdlib python2-pkgconfig shared_meataxe libfes)
+ mcqd coxeter bliss-graphs tdlib python2-pkgconfig shared_meataxe libfes)
source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
sagemath-env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch
r-no-readline.patch fes02.patch sagemath-threejs.patch pari-stackwarn.patch
- sagemath-detect-igraph.patch sagemath-networkx2.patch sagemath-linbox-1.5.patch sagemath-pynac-0.7.14.patch
- sagemath-matplotlib2.patch sagemath-scipy-1.0.patch sagemath-lrs.patch sagemath-ipython-prompt.patch
+ sagemath-detect-igraph.patch sagemath-networkx2.patch sagemath-scipy-1.0.patch sagemath-lrs.patch
sagemath-singular-4.1.1.patch sagemath-lcalc-c++11.patch
- sagemath-cython-source.patch::"https://github.com/sagemath/sage/commit/fccaf230.patch"
- sagemath-cython-0.28a.patch::"https://github.com/sagemath/sage/commit/348432f7.patch"
- sagemath-cython-0.28b.patch::"https://github.com/sagemath/sage/commit/609a04de.patch"
- sagemath-cython-0.28c.patch
- sagemath-cython-0.28d.patch::"https://github.com/sagemath/sage/commit/c331d9bb.patch")
-sha256sums=('a42b55c2c8ac244535dc9b87171b7d4dd7e1d498099518ab253354fbe2eaaa7b'
- '9593f49ac3f73bc7106f661bdaa484d22c12b889964986f5a99b75a605a2359b'
+ pari-ratpoints.patch::"https://github.com/sagemath/sage/commit/83458400.patch")
+sha256sums=('41ba2c2dde7a02e1bb6880ae875d37ab058567cc26e760efe87eeb12188cd65b'
+ 'ad1ce89c624b848c5908e34851e4b765d1ba85819bb3626eedfd0cab6157c5e4'
'c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107'
'0b680e674c11c47afa86162d8b49645620b8912722e08133d23357c29ca9310a'
'2cad308f8adbb6c54e6603fa22b2f0eb60f6f09248d5d015000c3932ac14f646'
'962ce805c87147212b21fc2ab0ac9af9bd0033942c7a6905b9906645b48e8a4f'
- 'ef94908d4ab28d13af622e6e58ec191aa78817d17e4466c7bb6f64ee72a813b9'
+ '18edeafb01cc1ed7270c2dfb41a58717918680c98e8eada1858736acd65d92ba'
'afd0952b9bb8f52fd428eae36cf719a58ff85a894baae88cbb2124e043768cc7'
'7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94'
'2d13b15ad2d1511bb3d752a261497060a8901882b1c2fa9813219781b7a71d83'
- 'bfd2a20a33ab19a8a8b216a77d07f62e809fe1e1879c4f171ce5dca62fd482e9'
- '28d7789b8d777922ab8871ca43b6afab751428cae875c0343d3962e6a2030b88'
- '1024f3a6a9a1a6ae96d9962bb7d1f5842f4a4a5ff5098afad81a60188b7d5160'
- 'a52d03e04c9d64bb957a1f8dcdae3280ebb9450a7fd76aaf5ae5de5c6f74774f'
- '538f7b279d72f4b67edb445d386d267f3f7022c1079031ca7ea06f6ce392c906'
- 'b9ab2bb5f381ea425e8763b81b8b3a108a3951c594fb1f37f7df921e7c77e26d'
+ 'eaf252b2c9b397a0db8fb8cbf45f0b56a21910b5f632d59709f41eff30c5eaab'
+ 'bfe49f0168fe0824f0eaf4ea793b08d5b3e43c4e3634eb5f664c70644a793a59'
+ '54bb6de642cbc07c24904016546f42de5d5aa040e67014884cbfa20e35e52cbd'
'17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a'
'c0f65534a845ba802de6196229159fe67fcc3f72f0cb1ce57d4ae5c9fe10282c'
- '937a0081e7aea56bda645ef5f0d34b8e356acd62a7dd128a35163f46e7836131'
- 'cc679321c2968d5e74b0ec060979c74019df2995857906bdd1397695b1f24c5c'
+ '369f1483e0364031d73d43d9e63b7bf2b0929c8a1d470c1596f98f9f1aa80750'
'5114c912f821900e5bfae1e2cfeb7984de946d0b23e1182b0bf15be1d803dfd0'
- '447a616937e5c43da5f72aeb186fb649e2b3756f7683967380c66b9b1448875e'
- '8b88c72495c47c400a63cd2c6b3998cd6de649f653b6f5acbd506e2fc158f062'
- '6deaa988737f670f27f174c838501248004d9ce029c29d3e643a93cd1c500894'
- '7cfca93a35bc0ad4608286fae477195c7bee94787a3655021e55055d0adfe224'
- 'a46f60c3df77f95e9b0e65573a281d6f9980b218a9dbea1417fa51ea7af2558d')
+ 'e24ad879f6b2eb970778fc5e867bcbe0a6d393feca8f11f5cb8d07da1f024be9')
prepare(){
cd sage-$pkgver
@@ -105,10 +92,10 @@
patch -p1 -i ../pari-stackwarn.patch
# remove deprecated scipy parameters
patch -p1 -i ../sagemath-scipy-1.0.patch
-# fix ipython prompt in pexpect interface
- patch -p1 -i ../sagemath-ipython-prompt.patch
# fix build with Singular 4.1.1
patch -p1 -i ../sagemath-singular-4.1.1.patch
+# revert usage of development PARI features
+ patch -Rp1 -i ../pari-ratpoints.patch
# don't force c++98 for lcalc (fixes build with NTL 11)
patch -p1 -i ../sagemath-lcalc-c++11.patch
@@ -115,22 +102,10 @@
# Upstream patches
# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
patch -p1 -i ../fes02.patch
-# fix build with linbox 1.5 https://trac.sagemath.org/ticket/24214
- patch -p1 -i ../sagemath-linbox-1.5.patch
-# fix build with pynac 0.7.14 https://trac.sagemath.org/ticket/24329
- patch -p1 -i ../sagemath-pynac-0.7.14.patch
-# port away from deprecated and removed functions in matplotlib 2 https://trac.sagemath.org/ticket/23696
- patch -p1 -i ../sagemath-matplotlib2.patch
-# install cython source files https://trac.sagemath.org/24690
- patch -p1 -i ../sagemath-cython-source.patch
-# fix build with cython 0.28
- patch -p1 -i ../sagemath-cython-0.28a.patch
- patch -p1 -i ../sagemath-cython-0.28b.patch
- patch -p1 -i ../sagemath-cython-0.28c.patch
- patch -p1 -i ../sagemath-cython-0.28d.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|#!/usr/bin/env sage-python23|#!/usr/bin/env python2|' -e 's|\<#!/usr/bin/env sage-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
@@ -139,14 +114,10 @@
build() {
- cd sage-$pkgver
- autoreconf -vi
- ./configure --prefix=/usr || true
+ cd sage-$pkgver/src
- cd src
export SAGE_ROOT="$PWD"
export SAGE_SRC="$PWD"
-
python2 setup.py build
}
@@ -158,12 +129,11 @@
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 \
+ for _i in arch-env cachegrind callgrind cleaner coverage coverageall cython env eval grep grepdoc inline-fortran \
ipython massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2sws rst2txt run \
run-cython runtests startuptime.py sws2rst valgrind version.sh
do
Modified: pari-stackwarn.patch
===================================================================
--- pari-stackwarn.patch 2018-05-06 10:44:48 UTC (rev 319012)
+++ pari-stackwarn.patch 2018-05-06 12:07:52 UTC (rev 319013)
@@ -5,16 +5,16 @@
Author: Tobias Hansen <thansen at debian.org>
--- sage/src/sage/doctest/parsing.py
+++ sage/src/sage/doctest/parsing.py
-@@ -39,6 +39,7 @@
+@@ -40,6 +40,7 @@
float_regex = re.compile('\s*([+-]?\s*((\d*\.?\d+)|(\d+\.?))([eE][+-]?\d+)?)')
- optional_regex = re.compile(r'(long time|not implemented|not tested|known bug)|([^ a-z]\s*optional\s*[:-]*((\s|\w)*))')
+ optional_regex = re.compile(r'(py2|py3|long time|not implemented|not tested|known bug)|([^ a-z]\s*optional\s*[:-]*((\s|\w)*))')
+pari_stack_warning_regex = re.compile(r'\s*\*\*\*.*(Warning: increasing stack size to )\d+\.')
find_sage_prompt = re.compile(r"^(\s*)sage: ", re.M)
find_sage_continuation = re.compile(r"^(\s*)\.\.\.\.:", re.M)
random_marker = re.compile('.*random', re.I)
-@@ -879,6 +880,7 @@
- 'you'
+@@ -935,6 +936,7 @@
+ <type 'float'>
"""
got = self.human_readable_escape_sequences(got)
+ got = pari_stack_warning_regex.sub('', got)
Deleted: sagemath-cython-0.28c.patch
===================================================================
--- sagemath-cython-0.28c.patch 2018-05-06 10:44:48 UTC (rev 319012)
+++ sagemath-cython-0.28c.patch 2018-05-06 12:07:52 UTC (rev 319013)
@@ -1,59 +0,0 @@
-From e9efe88316733178b9330b21eee2c207f01132fd Mon Sep 17 00:00:00 2001
-From: Jeroen Demeyer <jdemeyer at cage.ugent.be>
-Date: Tue, 6 Mar 2018 12:43:46 +0100
-Subject: [PATCH 2/2] Use late includes
-
----
- src/sage_setup/autogen/interpreters/generator.py | 26 ------------------------
- src/setup.py | 1 +
- 2 files changed, 1 insertion(+), 26 deletions(-)
-
-diff --git a/src/sage_setup/autogen/interpreters/generator.py b/src/sage_setup/autogen/interpreters/generator.py
-index feefd9ee2f3..d1db4557784 100644
---- a/src/sage_setup/autogen/interpreters/generator.py
-+++ b/src/sage_setup/autogen/interpreters/generator.py
-@@ -277,32 +277,6 @@ def write_interpreter(self, write):
- /* {{ warn }} */
- #include <Python.h>
-
-- /* Some interpreter files (for example interp_el.c) need access
-- * to functions defined in the Cython wrapper. This is done by
-- * including a file wrapper_X.h which is auto-generated by
-- * Cython. It contains declarations for functions declared in
-- * wrapper_X.pyx as cdef public. Including wrapper_X.h allows
-- * interp_X.c to call those functions.
-- *
-- * The file interp_X.c is in turn included by wrapper_X.c,
-- * which is the compilation of wrapper_X.pyx.
-- *
-- * Now, for some reason, Cython puts include guards in wrapper_X.h
-- * and it also defines those guards in the wrapper_X.c file.
-- * This way, including the wrapper_X.h file from the wrapper_X.c file
-- * (indirectly through interp_X.c) has no effect. But we really want
-- * that header file to be included, so we #undef those include guards.
-- * This way, the functions will be declared twice (once in wrapper_X.h
-- * and once in wrapper_X.c) but that is legal in C.
-- *
-- * See https://trac.sagemath.org/ticket/21459 for why this hack is
-- * needed. If Cython merges https://github.com/cython/cython/pull/1650
-- * this hack could be replaced by using a late include for
-- * cdef extern from "sage/ext/interpreters/interp_{{ s.name }}.c"
-- */
-- #undef __PYX_HAVE__sage__ext__interpreters__wrapper_{{ s.name }}
-- #undef __PYX_HAVE_API__sage__ext__interpreters__wrapper_{{ s.name }}
--
- {% print(s.c_header) %}
-
- {{ myself.func_header() }} {
-diff --git a/src/setup.py b/src/setup.py
-index 5abd6dc5939..b706310a1de 100755
---- a/src/setup.py
-+++ b/src/setup.py
-@@ -284,6 +284,7 @@ def finalize_options(self):
- cdivision=True,
- embedsignature=True,
- fast_getattr=True,
-+ preliminary_late_includes_cy28=True,
- profile=self.profile,
- )
- self.compile_time_env = dict(
Modified: sagemath-detect-igraph.patch
===================================================================
--- sagemath-detect-igraph.patch 2018-05-06 10:44:48 UTC (rev 319012)
+++ sagemath-detect-igraph.patch 2018-05-06 12:07:52 UTC (rev 319013)
@@ -2,7 +2,7 @@
index 252984f..ce19682 100644
--- a/src/sage/graphs/generic_graph.py
+++ b/src/sage/graphs/generic_graph.py
-@@ -8188,10 +8188,12 @@ class GenericGraph(GenericGraph_pyx):
+@@ -8480,10 +8480,12 @@ class GenericGraph(GenericGraph_pyx):
if algorithm is None:
if vertex_bound:
algorithm = "LP"
Modified: sagemath-env.patch
===================================================================
--- sagemath-env.patch 2018-05-06 10:44:48 UTC (rev 319012)
+++ sagemath-env.patch 2018-05-06 12:07:52 UTC (rev 319013)
@@ -41,17 +41,45 @@
-fi
+NEW_SAGE_ROOT="/usr"
- # Display the Sage startup banner, used in src/bin/sage
- sage_banner() {
-@@ -185,6 +185,7 @@
+
+ # Don't execute the commands more than once for the same version of
+@@ -174,33 +174,9 @@
export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION
export SAGE_ROOT="$NEW_SAGE_ROOT"
+export SAGE_LOCAL='/usr'
++export SAGE_SCRIPTS_DIR='/usr/bin'
+-
+-# sage-env must know where the Sage's script files are.
+-# Note that SAGE_SCRIPTS_DIR is only used here, so it does not need to
+-# be exported.
+-if [ -z "$SAGE_SCRIPTS_DIR" ]; then
+- if [ -n "$SAGE_LOCAL" ] && [ -f "$SAGE_LOCAL/bin/sage-env-config" ]; then
+- SAGE_SCRIPTS_DIR="$SAGE_LOCAL/bin"
+- elif [ -f "$SAGE_ROOT/src/bin/sage-env-config" ]; then
+- SAGE_SCRIPTS_DIR="$SAGE_ROOT/src/bin"
+- else
+- echo >&2 "Error: You must set either the SAGE_LOCAL or SAGE_SCRIPTS_DIR environment variable to run this"
+- return 1
+- fi
+-elif [ ! -f "$SAGE_SCRIPTS_DIR/sage-env-config" ]; then
+- echo >&2 "Error: SAGE_SCRIPTS_DIR is set to a bad value:"
+- echo >&2 "SAGE_SCRIPTS_DIR=$SAGE_SCRIPTS_DIR"
+- echo >&2 "You must correct it or erase it and rerun this script"
+- return 1
+-fi
+-
+-# Set environment variables (like SAGE_LOCAL) depending on ./configure
+-. "$SAGE_SCRIPTS_DIR/sage-env-config"
+-if [ $? -ne 0 ]; then
+- echo >&2 "Error: failed to source $SAGE_SCRIPTS_DIR/sage-env-config"
+- return 1
+-fi
- # sage-env must know where the Sage's script files are.
-@@ -307,8 +307,9 @@
+ # The compilers are set in order of priority by
+ # 1) environment variables
+@@ -296,8 +296,9 @@
export SAGE_EXTCODE="$SAGE_SHARE/sage/ext"
export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
@@ -58,12 +86,12 @@
-export SAGE_SRC="$SAGE_ROOT/src"
-export SAGE_DOC_SRC="$SAGE_SRC/doc"
+export GAP_ROOT_DIR="/usr/lib/gap"
-+export SAGE_SRC="$SAGE_LOCAL/lib/python2.7/site-packages"
++export SAGE_SRC="$SAGE_SHARE/sage/source"
+export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
export SAGE_DOC="$SAGE_SHARE/doc/sage"
if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
-@@ -414,6 +414,9 @@
+@@ -403,6 +403,9 @@
export SAGE_STARTUP_FILE
fi
@@ -73,7 +101,7 @@
if [ "$PYTHON_EGG_CACHE" = "" ]; then
PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs"
export PYTHON_EGG_CACHE
-@@ -499,7 +499,6 @@
+@@ -488,7 +488,6 @@
fi
fi
fi
@@ -81,7 +109,7 @@
PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
-@@ -619,9 +619,6 @@
+@@ -608,9 +608,6 @@
LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH
fi
@@ -104,18 +132,4 @@
_add_variable_or_fallback('SAGE_ETC', opj('$SAGE_LOCAL', 'etc'))
_add_variable_or_fallback('SAGE_INC', opj('$SAGE_LOCAL', 'include'))
_add_variable_or_fallback('SAGE_SHARE', opj('$SAGE_LOCAL', 'share'))
-
--_add_variable_or_fallback('SAGE_SRC', opj('$SAGE_ROOT', 'src'))
-+_add_variable_or_fallback('SAGE_SRC', opj('$SAGE_LOCAL', 'lib', 'python2.7', 'site-packages'))
-
- try:
- sitepackages_dirs = site.getsitepackages()
-@@ -163,7 +163,7 @@
- _add_variable_or_fallback('GRAPHS_DATA_DIR', opj('$SAGE_SHARE','graphs'))
- _add_variable_or_fallback('ELLCURVE_DATA_DIR',opj('$SAGE_SHARE','ellcurves'))
- _add_variable_or_fallback('POLYTOPE_DATA_DIR',opj('$SAGE_SHARE','reflexive_polytopes'))
--_add_variable_or_fallback('GAP_ROOT_DIR', opj('$SAGE_LOCAL','gap','latest'))
-+_add_variable_or_fallback('GAP_ROOT_DIR', opj('$SAGE_LOCAL','lib','gap'))
- _add_variable_or_fallback('THEBE_DIR', opj('$SAGE_SHARE','thebe'))
-
- # locate singular shared object
+
Deleted: sagemath-ipython-prompt.patch
===================================================================
--- sagemath-ipython-prompt.patch 2018-05-06 10:44:48 UTC (rev 319012)
+++ sagemath-ipython-prompt.patch 2018-05-06 12:07:52 UTC (rev 319013)
@@ -1,13 +0,0 @@
-diff --git a/src/sage/interfaces/sage0.py b/src/sage/interfaces/sage0.py
-index 4ba76ab0b8..e7740177f4 100644
---- a/src/sage/interfaces/sage0.py
-+++ b/src/sage/interfaces/sage0.py
-@@ -161,7 +161,7 @@ class Sage(ExtraTabCompletion, Expect):
- '--no-term-title',
- '--simple-prompt',
- ])
-- prompt = re.compile('In \[\d+\]: ')
-+ prompt = re.compile('sage: ')
- if init_code is None:
- init_code = ['from six.moves import cPickle']
-
Deleted: sagemath-linbox-1.5.patch
===================================================================
--- sagemath-linbox-1.5.patch 2018-05-06 10:44:48 UTC (rev 319012)
+++ sagemath-linbox-1.5.patch 2018-05-06 12:07:52 UTC (rev 319013)
@@ -1,272 +0,0 @@
-diff --git a/src/sage/libs/linbox/fflas.pxd b/src/sage/libs/linbox/fflas.pxd
-index ca23d71..03bbee9 100644
---- a/src/sage/libs/linbox/fflas.pxd
-+++ b/src/sage/libs/linbox/fflas.pxd
-@@ -20,19 +20,29 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h" namespace "std":
- iterator end()
- size_t size()
-
-- cdef cppclass list[T]:
-- cppclass iterator:
-- T operator*()
-- iterator operator++()
-- bint operator==(iterator)
-- bint operator!=(iterator)
-- void push_back(T&)
-- void pop_front()
-- T& front()
-- iterator begin()
-- iterator end()
-+cdef extern from "givaro/givpoly1.h":
-+ ## template < typename T, typename A=std::allocator<T> >
-+ ## class givvector : public __GIV_STANDARD_VECTOR<T,A>
-+ cdef cppclass givvector "Givaro::givvector" [T,ALLOCATOR=*]:
-+ T& operator[](size_t i)
- size_t size()
-- void clear()
-+
-+ctypedef givvector[ModDoubleFieldElement] ModDoubleDensePolynomial
-+ctypedef givvector[ModFloatFieldElement] ModFloatDensePolynomial
-+
-+cdef extern from "givaro/givpoly1.h":
-+ ## template <class Domain, class StorageTag= Givaro::Dense>
-+ ## class GivPolynomialRing : public Givaro::Poly1FactorDom< Domain,StorageTag>
-+ cdef cppclass ModDoublePolynomialRing "Givaro::Poly1Dom<Givaro::Modular<double>, Givaro::Dense>":
-+ ctypedef givvector[ModDoubleField] Element
-+ ctypedef givvector[ModDoubleField] Polynomial
-+ ModDoublePolynomialRing(ModDoubleField& F)
-+ ## template <class Domain, class StorageTag= Givaro::Dense>
-+ ## class GivPolynomialRing : public Givaro::Poly1FactorDom< Domain,StorageTag>
-+ cdef cppclass ModFloatPolynomialRing "Givaro::Poly1Dom<Givaro::Modular<float>, Givaro::Dense>":
-+ ctypedef givvector[ModFloatField] Element
-+ ctypedef givvector[ModFloatField] Polynomial
-+ ModFloatPolynomialRing(ModFloatField& F)
-
- cdef extern from "fflas-ffpack/fflas-ffpack.h":
- ctypedef enum fflas_trans_enum "FFLAS::FFLAS_TRANSPOSE":
-@@ -105,13 +115,12 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h":
- size_t nr, size_t foo, size_t r,
- ModDoubleFieldElement* matrix, size_t nc, size_t* Q)
-
-- void ModDouble_MinPoly "FFPACK::MinPoly" ( ModDoubleField F,
-+ void ModDouble_MinPoly "FFPACK::MinPoly" ( ModDoubleField& F,
- vector[ModDoubleFieldElement] minP, size_t N,
-- ModDoubleFieldElement* A, size_t lda,
-- ModDoubleFieldElement* X, size_t ldx, size_t* P)
-+ ModDoubleFieldElement*A, size_t lda)
-
-- void ModDouble_CharPoly "FFPACK::CharPoly" ( ModDoubleField F,
-- list[vector[ModDoubleFieldElement]] charp, size_t N,
-+ void ModDouble_CharPoly "FFPACK::CharPoly" ( ModDoublePolynomialRing& R,
-+ ModDoubleDensePolynomial& charp, size_t N,
- ModDoubleFieldElement* A, size_t lda)
-
- # float
-@@ -142,9 +151,8 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h":
-
- void ModFloat_MinPoly "FFPACK::MinPoly" ( ModFloatField F,
- vector[ModFloatFieldElement] minP, size_t N,
-- ModFloatFieldElement* A, size_t lda,
-- ModFloatFieldElement* X, size_t ldx, size_t* P)
-+ ModFloatFieldElement* A, size_t lda)
-
-- void ModFloat_CharPoly "FFPACK::CharPoly" ( ModFloatField F,
-- list[vector[ModFloatFieldElement]] charp, size_t N,
-+ void ModFloat_CharPoly "FFPACK::CharPoly" ( ModFloatPolynomialRing& F,
-+ ModFloatDensePolynomial& charp, size_t N,
- ModFloatFieldElement* A, size_t lda )
-diff --git a/src/sage/libs/linbox/linbox_flint_interface.pyx b/src/sage/libs/linbox/linbox_flint_interface.pyx
-index 02a6151..a00d303 100644
---- a/src/sage/libs/linbox/linbox_flint_interface.pyx
-+++ b/src/sage/libs/linbox/linbox_flint_interface.pyx
-@@ -76,19 +76,23 @@ cdef extern from "givaro/zring.h":
- ctypedef GivaroInteger Element
-
-
--cdef extern from "givaro/givpoly1.h":
-- ## template < typename T, typename A=std::allocator<T> >
-- ## class givvector : public __GIV_STANDARD_VECTOR<T,A>
-- cdef cppclass givvector "Givaro::givvector" [T,ALLOCATOR=*]:
-- T& operator[](size_t i)
-+cdef extern from "linbox/polynomial/dense-polynomial.h":
-+ ## template<class Field>
-+ ## class DensePolynomial : public Givaro::Poly1FactorDom<Field, Givaro::Dense>::Element
-+ cdef cppclass LinBoxIntegerDensePolynomial "LinBox::DensePolynomial<Givaro::ZRing<Givaro::Integer> >":
-+ ctypedef GivaroIntegerRing BaseRing
-+ ctypedef GivaroInteger BaseRingElement
-+ LinBoxIntegerDensePolynomial(BaseRing &F)
-+ LinBoxIntegerDensePolynomial(BaseRing &F, size_t s)
-+ BaseRingElement& operator[](size_t i)
- size_t size()
-
--cdef extern from "linbox/ring/givaro-polynomial.h":
-- ## template <class Domain, class StorageTag= Givaro::Dense>
-- ## class GivPolynomialRing : public Givaro::Poly1FactorDom< Domain,StorageTag>
-- cdef cppclass LinBoxIntegerPolynomialRing "LinBox::GivPolynomialRing<Givaro::ZRing<Givaro::Integer>, Givaro::Dense>":
-- ctypedef givvector[GivaroInteger] Element
-- ctypedef givvector[GivaroInteger] Polynomial
-+cdef extern from "linbox/ring/polynomial-ring.h":
-+ ## template <class BaseRing, class StorageTag= Givaro::Dense>
-+ ## class PolynomialRing : public Givaro::Poly1FactorDom<BaseRing,StorageTag>
-+ cdef cppclass LinBoxIntegerPolynomialRing "LinBox::PolynomialRing<Givaro::ZRing<Givaro::Integer>, Givaro::Dense>":
-+ ctypedef LinBoxIntegerDensePolynomial Element
-+ ctypedef LinBoxIntegerDensePolynomial Polynomial
-
- cdef extern from "linbox/matrix/matrix-domain.h":
- ## template <class Field_ >
-@@ -190,40 +194,32 @@ cdef void linbox_fmpz_mat_mul(fmpz_mat_t C, fmpz_mat_t A, fmpz_mat_t B):
- cdef void linbox_fmpz_mat_charpoly(fmpz_poly_t cp, fmpz_mat_t A):
- cdef GivaroIntegerRing ZZ
- cdef LinBoxIntegerDenseMatrix * LBA
-- cdef LinBoxIntegerPolynomialRing.Element m_A
--
-- # FIXME: bug in LinBox
-- # see https://github.com/linbox-team/linbox/issues/51
-- if fmpz_mat_nrows(A) == 0:
-- fmpz_poly_one(cp)
-- return
-+ cdef LinBoxIntegerDensePolynomial * m_A
-
- LBA = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(A), fmpz_mat_ncols(A))
- fmpz_mat_get_linbox(LBA[0], A)
-- LinBoxIntegerDense_charpoly(m_A, LBA[0])
-- fmpz_poly_set_linbox(cp, m_A)
-+ m_A = new LinBoxIntegerDensePolynomial(ZZ, fmpz_mat_nrows(A))
-+ LinBoxIntegerDense_charpoly(m_A[0], LBA[0])
-+ fmpz_poly_set_linbox(cp, m_A[0])
-
- del LBA
-+ del m_A
-
-
- # set mp to the minimal polynomial of A
- cdef void linbox_fmpz_mat_minpoly(fmpz_poly_t mp, fmpz_mat_t A):
- cdef GivaroIntegerRing ZZ
- cdef LinBoxIntegerDenseMatrix * LBA
-- cdef LinBoxIntegerPolynomialRing.Element m_A
--
-- # FIXME: bug in LinBox
-- # see https://github.com/linbox-team/linbox/issues/51
-- if fmpz_mat_nrows(A) == 0:
-- fmpz_poly_one(mp)
-- return
-+ cdef LinBoxIntegerDensePolynomial * m_A
-
- LBA = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(A), fmpz_mat_ncols(A))
-+ m_A = new LinBoxIntegerDensePolynomial(ZZ)
- fmpz_mat_get_linbox(LBA[0], A)
-- LinBoxIntegerDense_minpoly(m_A, LBA[0])
-- fmpz_poly_set_linbox(mp, m_A)
-+ LinBoxIntegerDense_minpoly(m_A[0], LBA[0])
-+ fmpz_poly_set_linbox(mp, m_A[0])
-
- del LBA
-+ del m_A
-
-
- # return the rank of A
-diff --git a/src/sage/matrix/matrix_modn_dense_double.pyx b/src/sage/matrix/matrix_modn_dense_double.pyx
-index 15c35cb..b1f6154 100644
---- a/src/sage/matrix/matrix_modn_dense_double.pyx
-+++ b/src/sage/matrix/matrix_modn_dense_double.pyx
-@@ -27,7 +27,9 @@ from sage.libs.linbox.fflas cimport ModDouble_fgemm as Mod_fgemm, ModDouble_fgem
- ModDoubleRank as ModRank, ModDouble_echelon as Mod_echelon, \
- ModDouble_applyp as Mod_applyp, \
- ModDouble_MinPoly as Mod_MinPoly, \
-- ModDouble_CharPoly as Mod_CharPoly
-+ ModDouble_CharPoly as Mod_CharPoly, \
-+ ModDoublePolynomialRing as ModDensePolyRing,\
-+ ModDoubleDensePolynomial as ModDensePoly
-
- # Limit for LinBox Modular<double>
- MAX_MODULUS = 2**23
-diff --git a/src/sage/matrix/matrix_modn_dense_float.pyx b/src/sage/matrix/matrix_modn_dense_float.pyx
-index 61457ce..eda8f0b 100644
---- a/src/sage/matrix/matrix_modn_dense_float.pyx
-+++ b/src/sage/matrix/matrix_modn_dense_float.pyx
-@@ -25,7 +25,10 @@ from sage.libs.linbox.fflas cimport ModFloat_fgemm as Mod_fgemm, ModFloat_fgemv
- ModFloatRank as ModRank, ModFloat_echelon as Mod_echelon, \
- ModFloat_applyp as Mod_applyp, \
- ModFloat_MinPoly as Mod_MinPoly, \
-- ModFloat_CharPoly as Mod_CharPoly
-+ ModFloat_CharPoly as Mod_CharPoly, \
-+ ModFloatPolynomialRing as ModDensePolyRing,\
-+ ModFloatDensePolynomial as ModDensePoly
-+
-
- # LinBox supports up to 2^11 using float but that's double dog slow,
- # so we pick a smaller value for crossover
-diff --git a/src/sage/matrix/matrix_modn_dense_template.pxi b/src/sage/matrix/matrix_modn_dense_template.pxi
-index 3da3e31..819ef2d 100644
---- a/src/sage/matrix/matrix_modn_dense_template.pxi
-+++ b/src/sage/matrix/matrix_modn_dense_template.pxi
-@@ -306,23 +306,15 @@ cdef inline linbox_minpoly(celement modulus, Py_ssize_t nrows, celement* entries
- cdef Py_ssize_t i
- cdef ModField *F = new ModField(<long>modulus)
- cdef vector[ModFieldElement] *minP = new vector[ModFieldElement]()
-- cdef ModFieldElement *X = <ModFieldElement*>check_allocarray(nrows * (nrows+1), sizeof(ModFieldElement))
-- cdef size_t *P = <size_t*>check_allocarray(nrows, sizeof(size_t))
--
-- cdef celement *cpy = linbox_copy(modulus, entries, nrows, nrows)
-
- if nrows*nrows > 1000: sig_on()
-- Mod_MinPoly(F[0], minP[0], nrows, <ModFieldElement*>cpy, nrows, X, nrows, P)
-+ Mod_MinPoly(F[0], minP[0], nrows, <ModFieldElement*>entries, nrows)
- if nrows*nrows > 1000: sig_off()
-
-- sig_free(cpy)
--
- l = []
- for i in range(minP.size()):
- l.append( <celement>minP.at(i) )
-
-- sig_free(P)
-- sig_free(X)
- del F
- return l
-
-@@ -332,27 +324,23 @@ cdef inline linbox_charpoly(celement modulus, Py_ssize_t nrows, celement* entrie
- """
- cdef Py_ssize_t i
- cdef ModField *F = new ModField(<long>modulus)
-- cdef std_list[vector[ModFieldElement]] P_list
-- P_list.clear()
-+ cdef ModDensePolyRing * R = new ModDensePolyRing(F[0])
-+ cdef ModDensePoly P
-
- cdef celement *cpy = linbox_copy(modulus, entries, nrows, nrows)
-
- if nrows*nrows > 1000: sig_on()
-- Mod_CharPoly(F[0], P_list, nrows, <ModFieldElement*>cpy, nrows)
-+ Mod_CharPoly(R[0], P, nrows, <ModFieldElement*>cpy, nrows)
- if nrows*nrows > 1000: sig_off()
-
- sig_free(cpy)
-
-- cdef vector[ModFieldElement] tmp
- l = []
-- while P_list.size():
-- l.append([])
-- tmp = P_list.front()
-- for i in range(tmp.size()):
-- l[-1].append(<celement>tmp.at(i))
-- P_list.pop_front()
-+ for i in range(P.size()):
-+ l.append(<celement>P[i])
-
- del F
-+ del R
- return l
-
-
-@@ -1731,9 +1719,7 @@ cdef class Matrix_modn_dense_template(Matrix_dense):
- R = self._base_ring[var]
- # call linbox for charpoly
- v = linbox_charpoly(self.p, self._nrows, self._entries)
-- r = R(1)
-- for e in v:
-- r *= R(e)
-+ r = R(v)
- return r
-
- def echelonize(self, algorithm="linbox", **kwds):
Deleted: sagemath-matplotlib2.patch
===================================================================
--- sagemath-matplotlib2.patch 2018-05-06 10:44:48 UTC (rev 319012)
+++ sagemath-matplotlib2.patch 2018-05-06 12:07:52 UTC (rev 319013)
@@ -1,253 +0,0 @@
-diff --git a/src/sage/all.py b/src/sage/all.py
-index 300f519..19bc8ec 100644
---- a/src/sage/all.py
-+++ b/src/sage/all.py
-@@ -313,8 +313,6 @@ warnings.filters.remove(('ignore', None, DeprecationWarning, None, 0))
- # Ignore all deprecations from IPython etc.
- warnings.filterwarnings('ignore',
- module='.*(IPython|ipykernel|jupyter_client|jupyter_core|nbformat|notebook|ipywidgets|storemagic)')
--# Ignore warnings due to matplotlib-1.5 together with numpy-1.13
--warnings.filterwarnings('ignore', module='matplotlib[.]contour|numpy[.]ma[.]core')
- # However, be sure to keep OUR deprecation warnings
- warnings.filterwarnings('default',
- '[\s\S]*See http://trac.sagemath.org/[0-9]* for details.')
-diff --git a/src/sage/plot/arrow.py b/src/sage/plot/arrow.py
-index 98d6224..fbce029 100644
---- a/src/sage/plot/arrow.py
-+++ b/src/sage/plot/arrow.py
-@@ -147,8 +147,8 @@ class CurveArrow(GraphicPrimitive):
- bpath = Path(self.vertices, self.codes)
- p = FancyArrowPatch(path=bpath,
- lw=width, arrowstyle='%s,head_width=%s,head_length=%s' % (style, head_width, head_length),
-- fc=color, ec=color)
-- p.set_linestyle(get_matplotlib_linestyle(options['linestyle'], return_type='long'))
-+ fc=color, ec=color,
-+ linestyle=get_matplotlib_linestyle(options['linestyle'], return_type='long'))
- p.set_zorder(options['zorder'])
- p.set_label(options['legend_label'])
- subplot.add_patch(p)
-@@ -336,7 +336,7 @@ class Arrow(GraphicPrimitive):
- this into account. See :trac:`12836`::
-
- sage: fig = Graphics().matplotlib()
-- sage: sp = fig.add_subplot(1,1,1)
-+ sage: sp = fig.add_subplot(1,1,1, label='axis1')
- sage: a = arrow((0,0), (1,1))
- sage: b = arrow((0,0), (1,1), width=20)
- sage: p1 = a[0]._render_on_subplot(sp)
-@@ -358,7 +358,7 @@ class Arrow(GraphicPrimitive):
- sage: a.save(filename=filename)
- sage: with open(filename, 'r') as f:
- ....: contents = f.read().replace('\n', ' ')
-- sage: two_stroke_pattern = r'setdash.*stroke.*stroke.*setdash'
-+ sage: two_stroke_pattern = r'setdash.*setdash.*stroke.*stroke.*setdash'
- sage: import re
- sage: two_stroke_re = re.compile(two_stroke_pattern)
- sage: two_stroke_re.search(contents) is None
-@@ -383,8 +383,8 @@ class Arrow(GraphicPrimitive):
- lw=width,
- arrowstyle='%s,head_width=%s,head_length=%s' % (style, head_width, head_length),
- shrinkA=arrowshorten_end, shrinkB=arrowshorten_end,
-- fc=color, ec=color)
-- p.set_linestyle(get_matplotlib_linestyle(options['linestyle'], return_type='long'))
-+ fc=color, ec=color,
-+ linestyle=get_matplotlib_linestyle(options['linestyle'], return_type='long'))
- p.set_zorder(options['zorder'])
- p.set_label(options['legend_label'])
-
-@@ -437,7 +437,7 @@ class Arrow(GraphicPrimitive):
- pe1.draw_path(renderer, gc, tpath, affine, rgbFace)
-
- pe1 = ConditionalStroke(CheckNthSubPath(p, 0), [pe.Stroke()])
-- pe2 = ConditionalStroke(CheckNthSubPath(p, 1), [pe.Stroke(linestyle="solid")])
-+ pe2 = ConditionalStroke(CheckNthSubPath(p, 1), [pe.Stroke(dashes={'dash_offset': 0, 'dash_list': None})])
- p.set_path_effects([pe1, pe2])
-
- subplot.add_patch(p)
-diff --git a/src/sage/plot/contour_plot.py b/src/sage/plot/contour_plot.py
-index 76077e3..efc1f2b 100644
---- a/src/sage/plot/contour_plot.py
-+++ b/src/sage/plot/contour_plot.py
-@@ -178,12 +178,10 @@ class ContourPlot(GraphicPrimitive):
- if fill:
- if contours is None:
- CSF = subplot.contourf(self.xy_data_array, cmap=cmap,
-- extent=(x0, x1, y0, y1),
-- label=options['legend_label'])
-+ extent=(x0, x1, y0, y1))
- else:
- CSF = subplot.contourf(self.xy_data_array, contours, cmap=cmap,
-- extent=(x0, x1, y0, y1), extend='both',
-- label=options['legend_label'])
-+ extent=(x0, x1, y0, y1), extend='both')
-
- linewidths = options.get('linewidths', None)
- if isinstance(linewidths, (int, Integer)):
-@@ -200,13 +198,11 @@ class ContourPlot(GraphicPrimitive):
- if contours is None:
- CS = subplot.contour(self.xy_data_array, cmap=cmap,
- extent=(x0, x1, y0, y1),
-- linewidths=linewidths, linestyles=linestyles,
-- label=options['legend_label'])
-+ linewidths=linewidths, linestyles=linestyles)
- else:
- CS = subplot.contour(self.xy_data_array, contours, cmap=cmap,
- extent=(x0, x1, y0, y1),
-- linewidths=linewidths, linestyles=linestyles,
-- label=options['legend_label'])
-+ linewidths=linewidths, linestyles=linestyles)
- if options.get('labels', False):
- label_options = options['label_options']
- label_options['fontsize'] = int(label_options['fontsize'])
-diff --git a/src/sage/plot/plot.py b/src/sage/plot/plot.py
-index aa82eda..03a0f3a 100644
---- a/src/sage/plot/plot.py
-+++ b/src/sage/plot/plot.py
-@@ -478,7 +478,7 @@ We test that ``imshow`` works as well, verifying that
-
- ::
-
-- sage: plt.imshow([[(0,0,0)]])
-+ sage: plt.imshow([[(0.0,0.0,0.0)]])
- <matplotlib.image.AxesImage object at ...>
- sage: plt.savefig(os.path.join(SAGE_TMP, 'foo.png'))
-
-@@ -2908,11 +2908,14 @@ def list_plot(data, plotjoined=False, **kwargs):
- If ``plotjoined`` is ``False`` then the axis that is in log scale
- must have all points strictly positive. For instance, the following
- plot will show no points in the figure since the points in the
-- horizontal axis starts from `(0,1)`.
-+ horizontal axis starts from `(0,1)`. Further, matplotlib will display
-+ a user warning.
-
- ::
-
- sage: list_plot(yl, scale='loglog') # both axes are log
-+ doctest:warning
-+ ...
- Graphics object consisting of 1 graphics primitive
-
- Instead this will work. We drop the point `(0,1)`.::
-@@ -3288,12 +3291,15 @@ def list_plot_semilogy(data, plotjoined=False, **kwds):
-
- If ``plotjoined`` is ``False`` then the vertical axis must have all
- points strictly positive. Otherwise the plot will come up empty.
-- For instance the following plot contains a point at `(1,0)`.
-+ For instance the following plot contains a point at `(1,0)`. Further,
-+ matplotlib will display a user warning.
-
- ::
-
- sage: xl = [2**k for k in range(12)]; yl = range(len(xl))
- sage: list_plot_semilogy(list(zip(xl,yl))) # plot empty due to (1,0)
-+ doctest:warning
-+ ...
- Graphics object consisting of 1 graphics primitive
-
- We remove `(1,0)` to fix this.::
-diff --git a/src/sage/plot/plot3d/list_plot3d.py b/src/sage/plot/plot3d/list_plot3d.py
-index c9f22dd..be87ff2 100644
---- a/src/sage/plot/plot3d/list_plot3d.py
-+++ b/src/sage/plot/plot3d/list_plot3d.py
-@@ -29,21 +29,20 @@ def list_plot3d(v, interpolation_type='default', texture="automatic", point_list
-
- OPTIONAL KEYWORDS:
-
-- - ``interpolation_type`` - 'linear', 'nn' (natural neighbor), 'spline'
-+ - ``interpolation_type`` - 'linear', 'clough' (CloughTocher2D), 'spline'
-
- 'linear' will perform linear interpolation
-
-- The option 'nn' An interpolation method for multivariate data in a
-- Delaunay triangulation. The value for an interpolation point is
-- estimated using weighted values of the closest surrounding points in
-- the triangulation. These points, the natural neighbors, are the ones
-- the interpolation point would connect to if inserted into the
-- triangulation.
-+ The option 'clough' will interpolate by using a piecewise cubic interpolating
-+ Bezier polynomial on each triangle, using a Clough-Tocher scheme.
-+ The interpolant is guaranteed to be continuously differentiable.
-+ The gradients of the interpolant are chosen so that the curvature of the
-+ interpolating surface is approximatively minimized.
-
- The option 'spline' interpolates using a bivariate B-spline.
-
- When v is a matrix the default is to use linear interpolation, when
-- v is a list of points the default is nearest neighbor.
-+ v is a list of points the default is 'clough'.
-
- - ``degree`` - an integer between 1 and 5, controls the degree of spline
- used for spline interpolation. For data that is highly oscillatory
-@@ -320,18 +319,18 @@ def list_plot3d_tuples(v, interpolation_type, texture, **kwds):
-
- OPTIONAL KEYWORDS:
-
-- - ``interpolation_type`` - 'linear', 'nn' (natural neighbor), 'spline'
-+ - ``interpolation_type`` - 'linear', 'clough' (CloughTocher2D), 'spline'
-
- 'linear' will perform linear interpolation
-
-- The option 'nn' will interpolate by using natural neighbors. The
-- value for an interpolation point is estimated using weighted values
-- of the closest surrounding points in the triangulation.
-+ The option 'clough' will interpolate by using a piecewise cubic interpolating
-+ Bezier polynomial on each triangle, using a Clough-Tocher scheme.
-+ The interpolant is guaranteed to be continuously differentiable.
-
- The option 'spline' interpolates using a bivariate B-spline.
-
- When v is a matrix the default is to use linear interpolation, when
-- v is a list of points the default is nearest neighbor.
-+ v is a list of points the default is 'clough'.
-
- - ``degree`` - an integer between 1 and 5, controls the degree of spline
- used for spline interpolation. For data that is highly oscillatory
-@@ -373,7 +372,7 @@ def list_plot3d_tuples(v, interpolation_type, texture, **kwds):
- sage: list_plot3d([(1, 2, 3), (0, 1, 3), (2, 1, 4), (1, 0, -2)], texture='yellow', num_points=50)
- Graphics3d Object
- """
-- from matplotlib import tri, delaunay
-+ from matplotlib import tri
- import numpy
- import scipy
- from random import random
-@@ -439,19 +438,15 @@ def list_plot3d_tuples(v, interpolation_type, texture, **kwds):
- G._set_extra_kwds(kwds)
- return G
-
-- if interpolation_type == 'nn' or interpolation_type =='default':
-+ if interpolation_type == 'clough' or interpolation_type =='default':
-
-- T=delaunay.Triangulation(x,y)
-- f=T.nn_interpolator(z)
-- f.default_value=0.0
-- j=numpy.complex(0,1)
-- vals=f[ymin:ymax:j*num_points,xmin:xmax:j*num_points]
-+ points=[[x[i],y[i]] for i in range(len(x))]
-+ j = numpy.complex(0, 1)
-+ f = interpolate.CloughTocher2DInterpolator(points,z)
- from .parametric_surface import ParametricSurface
-- def g(x,y):
-- i=round( (x-xmin)/(xmax-xmin)*(num_points-1) )
-- j=round( (y-ymin)/(ymax-ymin)*(num_points-1) )
-- z=vals[int(j),int(i)]
-- return (x,y,z)
-+ def g(x, y):
-+ z = f([x, y])
-+ return (x, y, z)
- G = ParametricSurface(g, (list(numpy.r_[xmin:xmax:num_points*j]), list(numpy.r_[ymin:ymax:num_points*j])), texture=texture, **kwds)
- G._set_extra_kwds(kwds)
- return G
-diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index 3ce4642..f66cd89 100644
---- a/src/sage/probability/probability_distribution.pyx
-+++ b/src/sage/probability/probability_distribution.pyx
-@@ -118,7 +118,7 @@ cdef class ProbabilityDistribution:
- sage: P = [0.3, 0.4, 0.3]
- sage: X = GeneralDiscreteDistribution(P)
- sage: h, b = X.generate_histogram_data(bins = 10)
-- sage: h
-+ sage: h # rel tol 1e-08
- [1.6299999999999999,
- 0.0,
- 0.0,
Modified: sagemath-networkx2.patch
===================================================================
--- sagemath-networkx2.patch 2018-05-06 10:44:48 UTC (rev 319012)
+++ sagemath-networkx2.patch 2018-05-06 12:07:52 UTC (rev 319013)
@@ -28,7 +28,7 @@
"""
import networkx
-@@ -1158,7 +1156,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
+@@ -1154,7 +1152,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
import networkx
try:
if self._nxg.is_multigraph():
@@ -37,7 +37,7 @@
if d.get('weight',None) == l:
self._nxg.remove_edge(u,v,k)
break
-@@ -1227,7 +1225,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
+@@ -1223,7 +1221,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
"""
cdef dict E
try:
@@ -46,7 +46,7 @@
except KeyError:
from networkx import NetworkXError
raise NetworkXError("Edge (%s,%s) requested via get_edge_label does not exist."%(u,v))
-@@ -1416,7 +1414,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
+@@ -1412,7 +1410,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
sage: G.iterator_nbrs(0)
<dictionary-keyiterator object at ...>
"""
@@ -68,7 +68,7 @@
elif format == 'igraph':
if not data.is_directed():
raise ValueError("A *directed* igraph graph was expected. To "+
-@@ -2844,7 +2844,7 @@ class DiGraph(GenericGraph):
+@@ -2846,7 +2846,7 @@ class DiGraph(GenericGraph):
Using the NetworkX implementation ::
sage: D.topological_sort(implementation = "NetworkX")
@@ -77,7 +77,7 @@
Using the NetworkX recursive implementation ::
-@@ -2870,9 +2870,7 @@ class DiGraph(GenericGraph):
+@@ -2872,9 +2872,7 @@ class DiGraph(GenericGraph):
sage: D = DiGraph({ 0:[1,2,3], 4:[2,5], 1:[8], 2:[7], 3:[7],
....: 5:[6,7], 7:[8], 6:[9], 8:[10], 9:[10] })
sage: N = D.networkx_graph()
@@ -88,7 +88,7 @@
[4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10]
TESTS:
-@@ -2895,10 +2893,7 @@ class DiGraph(GenericGraph):
+@@ -2897,10 +2895,7 @@ class DiGraph(GenericGraph):
elif implementation == "NetworkX" or implementation == "recursive":
import networkx
@@ -100,28 +100,6 @@
if S is None:
raise TypeError('Digraph is not acyclic; there is no topological sort.')
else:
-diff --git a/src/sage/graphs/generators/basic.py b/src/sage/graphs/generators/basic.py
-index 8777b95c4b..28ef7e48f2 100644
---- a/src/sage/graphs/generators/basic.py
-+++ b/src/sage/graphs/generators/basic.py
-@@ -437,7 +437,7 @@ def CompleteBipartiteGraph(n1, n2):
-
- Compare the plotting::
-
-- sage: n = networkx.complete_bipartite_graph(11,17)
-+ sage: n = networkx.complete_bipartite_graph(11r,17r)
- sage: spring_med = Graph(n)
- sage: posdict_med = graphs.CompleteBipartiteGraph(11,17)
-
-@@ -469,7 +469,7 @@ def CompleteBipartiteGraph(n1, n2):
- sage: g = []
- sage: j = []
- sage: for i in range(9):
-- ....: spr = networkx.complete_bipartite_graph(i+1,4)
-+ ....: spr = networkx.complete_bipartite_graph(int(i+1),4r)
- ....: k = Graph(spr)
- ....: g.append(k)
- sage: for i in range(3):
diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
index 8f81333685..1540ec0dcc 100644
--- a/src/sage/graphs/generators/families.py
@@ -149,15 +127,6 @@
index 3550f990ef..490813e619 100644
--- a/src/sage/graphs/graph.py
+++ b/src/sage/graphs/graph.py
-@@ -108,7 +108,7 @@ examples are covered here.
- ::
-
- sage: import networkx
-- sage: K = networkx.complete_bipartite_graph(12,7)
-+ sage: K = networkx.complete_bipartite_graph(12r,7r)
- sage: G = Graph(K)
- sage: G.degree()
- [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12]
@@ -1199,7 +1199,7 @@ class Graph(GenericGraph):
self.allow_loops(loops, check=False)
self.allow_multiple_edges(multiedges, check=False)
@@ -167,7 +136,7 @@
elif format == 'igraph':
if data.is_directed():
raise ValueError("An *undirected* igraph graph was expected. "+
-@@ -4600,7 +4600,7 @@ class Graph(GenericGraph):
+@@ -4621,7 +4621,7 @@ class Graph(GenericGraph):
sage: g = Graph([(0,1,0), (1,2,999), (2,3,-5)])
sage: g.matching(use_edge_labels=True)
@@ -176,7 +145,7 @@
sage: g.matching(algorithm="LP", use_edge_labels=True)
[(1, 2, 999)]
-@@ -6288,7 +6288,7 @@ class Graph(GenericGraph):
+@@ -6305,7 +6305,7 @@ class Graph(GenericGraph):
return networkx.number_of_cliques(self.networkx_graph(copy=False), vertices, cliques)
@doc_index("Clique-related methods")
@@ -183,9 +152,9 @@
- def cliques_get_max_clique_graph(self, name=''):
+ def cliques_get_max_clique_graph(self):
"""
- Returns a graph constructed with maximal cliques as vertices, and
- edges between maximal cliques with common members in the original
-@@ -6317,7 +6317,7 @@ class Graph(GenericGraph):
+ Return the clique graph.
+
+@@ -6336,7 +6336,7 @@ class Graph(GenericGraph):
sage: (G.cliques_get_max_clique_graph()).show(figsize=[2,2])
"""
import networkx
Deleted: sagemath-pynac-0.7.14.patch
===================================================================
--- sagemath-pynac-0.7.14.patch 2018-05-06 10:44:48 UTC (rev 319012)
+++ sagemath-pynac-0.7.14.patch 2018-05-06 12:07:52 UTC (rev 319013)
@@ -1,167 +0,0 @@
-diff --git a/src/sage/libs/pynac/pynac.pxd b/src/sage/libs/pynac/pynac.pxd
-index d4afc4e..6d1fcac 100644
---- a/src/sage/libs/pynac/pynac.pxd
-+++ b/src/sage/libs/pynac/pynac.pxd
-@@ -481,22 +481,17 @@ cdef extern from "pynac_wrap.h":
- ctypedef GParamSet const_paramset_ref "const GiNaC::paramset&"
-
- ctypedef struct py_funcs_struct:
-- py_binomial(a, b)
-- py_binomial_int(int n, unsigned int k)
- py_gcd(a, b)
- py_lcm(a, b)
- py_real(a)
- py_imag(a)
- py_numer(a)
- py_denom(a)
-- py_conjugate(a)
- bint py_is_rational(a)
-- bint py_is_crational(a)
- bint py_is_real(a)
- bint py_is_integer(a)
- bint py_is_equal(a, b)
- bint py_is_even(a)
-- bint py_is_cinteger(a)
- bint py_is_prime(n)
- bint py_is_exact(x)
-
-@@ -534,23 +529,14 @@ cdef extern from "pynac_wrap.h":
- py_asinh(x)
- py_acosh(x)
- py_atanh(x)
-- py_tgamma(x)
-- py_lgamma(x)
- py_isqrt(x)
- py_sqrt(x)
-- py_abs(x)
- py_mod(x, y)
- py_smod(x, y)
- py_irem(x, y)
-- py_iquo(x, y)
-- py_iquo2(x, y)
-- py_li(x, n, parent)
-- py_li2(x)
- py_psi(x)
- py_psi2(n, x)
-
-- int py_int_length(x) except -1
--
- py_eval_constant(unsigned serial, parent)
- py_eval_unsigned_infinity()
- py_eval_infinity()
-@@ -583,8 +569,6 @@ cdef extern from "pynac_wrap.h":
- stdstring* py_latex_fderivative(unsigned id, params, args)
- paramset_to_PyTuple(const_paramset_ref s)
-
-- py_rational_power_parts(basis, exp)
--
- py_funcs_struct py_funcs "GiNaC::py_funcs"
-
- cdef extern from "pynac/order.h":
-diff --git a/src/sage/libs/pynac/pynac.pyx b/src/sage/libs/pynac/pynac.pyx
-index f303184..419cc47 100644
---- a/src/sage/libs/pynac/pynac.pyx
-+++ b/src/sage/libs/pynac/pynac.pyx
-@@ -2432,23 +2432,18 @@ def init_function_table():
- called before Pynac is used; otherwise, there will be segfaults.
- """
-
-- py_funcs.py_binomial_int = &py_binomial_int
-- py_funcs.py_binomial = &py_binomial
- py_funcs.py_gcd = &py_gcd
- py_funcs.py_lcm = &py_lcm
- py_funcs.py_real = &py_real
- py_funcs.py_imag = &py_imag
- py_funcs.py_numer = &py_numer
- py_funcs.py_denom = &py_denom
-- py_funcs.py_conjugate = &py_conjugate
-
- py_funcs.py_is_rational = &py_is_rational
-- py_funcs.py_is_crational = &py_is_crational
- py_funcs.py_is_real = &py_is_real
- py_funcs.py_is_integer = &py_is_integer
- py_funcs.py_is_equal = &py_is_equal
- py_funcs.py_is_even = &py_is_even
-- py_funcs.py_is_cinteger = &py_is_cinteger
- py_funcs.py_is_prime = &py_is_prime
- py_funcs.py_is_exact = &py_is_exact
-
-@@ -2462,7 +2457,6 @@ def init_function_table():
- py_funcs.py_mpq_from_rational = &py_mpq_from_rational
-
- py_funcs.py_float = &py_float
-- py_funcs.py_RDF_from_double = &py_RDF_from_double
-
- py_funcs.py_factorial = &py_factorial
- py_funcs.py_doublefactorial = &py_doublefactorial
-@@ -2486,23 +2480,14 @@ def init_function_table():
- py_funcs.py_asinh = &py_asinh
- py_funcs.py_acosh = &py_acosh
- py_funcs.py_atanh = &py_atanh
-- py_funcs.py_tgamma = &py_tgamma
-- py_funcs.py_lgamma = &py_lgamma
- py_funcs.py_isqrt = &py_isqrt
- py_funcs.py_sqrt = &py_sqrt
-- py_funcs.py_abs = &py_abs
- py_funcs.py_mod = &py_mod
- py_funcs.py_smod = &py_smod
- py_funcs.py_irem = &py_irem
-- py_funcs.py_iquo = &py_iquo
-- py_funcs.py_iquo2 = &py_iquo2
-- py_funcs.py_li = &py_li
-- py_funcs.py_li2 = &py_li2
- py_funcs.py_psi = &py_psi
- py_funcs.py_psi2 = &py_psi2
-
-- py_funcs.py_int_length = &py_int_length
--
- py_funcs.py_eval_constant = &py_eval_constant
- py_funcs.py_eval_unsigned_infinity = &py_eval_unsigned_infinity
- py_funcs.py_eval_infinity = &py_eval_infinity
-@@ -2531,7 +2516,6 @@ def init_function_table():
- py_funcs.py_print_fderivative = &py_print_fderivative
- py_funcs.py_latex_fderivative = &py_latex_fderivative
- py_funcs.paramset_to_PyTuple = ¶mset_to_PyTuple
-- py_funcs.py_rational_power_parts = &py_rational_power_parts
-
- init_function_table()
- init_pynac_I()
-
-diff --git a/src/sage/functions/other.py b/src/sage/functions/other.py
-index 81cd485..931cecc 100644
---- a/src/sage/functions/other.py
-+++ b/src/sage/functions/other.py
-@@ -688,7 +688,6 @@ class Function_gamma(GinacFunction):
- :meth:`sage.functions.other.gamma`
- """
- GinacFunction.__init__(self, 'gamma', latex_name=r"\Gamma",
-- ginac_name='tgamma',
- conversions={'mathematica':'Gamma',
- 'maple':'GAMMA',
- 'sympy':'gamma',
-diff --git a/src/sage/libs/pynac/pynac.pxd b/src/sage/libs/pynac/pynac.pxd
-index 1739067..d4afc4e 100644
---- a/src/sage/libs/pynac/pynac.pxd
-+++ b/src/sage/libs/pynac/pynac.pxd
-@@ -362,7 +362,7 @@ cdef extern from "pynac_wrap.h":
- GEx g_zeta2 "GiNaC::zeta" (GEx m, GEx s) except + # alternating Euler sum
- GEx g_stieltjes "GiNaC::stieltjes" (GEx m) except + # Stieltjes constants
- GEx g_zetaderiv "GiNaC::zetaderiv" (GEx n, GEx x) except + # derivatives of Riemann's zeta function
-- GEx g_tgamma "GiNaC::tgamma" (GEx x) except + # gamma function
-+ GEx g_gamma "GiNaC::gamma" (GEx x) except + # gamma function
- GEx g_lgamma "GiNaC::lgamma" (GEx x) except + # logarithm of gamma function
- GEx g_beta "GiNaC::beta" (GEx x, GEx y) except + # beta function (tgamma(x)*tgamma(y)/tgamma(x+y))
- GEx g_psi "GiNaC::psi" (GEx x) except + # psi (digamma) function
-diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
-index dfb8751..52303d1 100644
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -8917,7 +8917,7 @@ cdef class Expression(CommutativeRingElement):
- cdef GEx x
- sig_on()
- try:
-- x = g_hold_wrapper(g_tgamma, self._gobj, hold)
-+ x = g_hold_wrapper(g_gamma, self._gobj, hold)
- finally:
- sig_off()
- return new_Expression_from_GEx(self._parent, x)
Modified: sagemath-singular-4.1.1.patch
===================================================================
--- sagemath-singular-4.1.1.patch 2018-05-06 10:44:48 UTC (rev 319012)
+++ sagemath-singular-4.1.1.patch 2018-05-06 12:07:52 UTC (rev 319013)
@@ -2,7 +2,7 @@
index 676544ab1e..5c8639d362 100644
--- a/src/sage/libs/singular/decl.pxd
+++ b/src/sage/libs/singular/decl.pxd
-@@ -188,7 +188,7 @@ cdef extern from "singular/Singular/libsingular.h":
+@@ -170,7 +170,7 @@ cdef extern from "singular/Singular/libsingular.h":
int n_NumberOfParameters(const n_Procs_s* r)
@@ -11,7 +11,7 @@
poly *next
number *coef
unsigned long exp[1]
-@@ -650,7 +650,7 @@ cdef extern from "singular/Singular/libsingular.h":
+@@ -632,7 +632,7 @@ cdef extern from "singular/Singular/libsingular.h":
# divide monomial p by monomial q, p,q const
@@ -24,7 +24,7 @@
index 089524d6b4..ce6d58fc6f 100644
--- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
+++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
-@@ -188,8 +188,8 @@ from sage.libs.singular.decl cimport (
+@@ -190,8 +190,8 @@ from sage.libs.singular.decl cimport (
n_IsUnit, n_Invers,
p_ISet, rChangeCurrRing, p_Copy, p_Init, p_SetCoeff, p_Setm, p_SetExp, p_Add_q,
p_NSet, p_GetCoeff, p_Delete, p_GetExp, pNext, rRingVar, omAlloc0, omStrDup,
@@ -35,7 +35,7 @@
p_IsUnit, p_Series, p_Head, idInit, fast_map_common_subexp, id_Delete,
p_IsHomogeneous, p_Homogen, p_Totaldegree,pLDeg1_Totaldegree, singclap_pdivide, singclap_factorize,
idLift, IDELEMS, On, Off, SW_USE_CHINREM_GCD, SW_USE_EZGCD,
-@@ -1690,8 +1695,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic):
+@@ -1692,8 +1697,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic):
if not g._poly:
raise ZeroDivisionError
@@ -46,7 +46,7 @@
if coeff:
if r.cf.type == n_unknown or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf):
n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf)
-@@ -1850,8 +1855,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic):
+@@ -1852,8 +1857,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic):
and (<MPolynomial_libsingular>g) \
and g.parent() is self \
and p_LmDivisibleBy((<MPolynomial_libsingular>g)._poly, m, r):
@@ -57,7 +57,7 @@
#p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<MPolynomial_libsingular>g)._poly, r), r), r)
p_SetCoeff(flt, n_Init(1, r), r)
return new_MP(self,flt), g
-@@ -4046,10 +4051,10 @@ cdef class MPolynomial_libsingular(MPolynomial):
+@@ -4049,10 +4054,10 @@ cdef class MPolynomial_libsingular(MPolynomial):
if _right.is_monomial():
p = _self._poly
quo = p_ISet(0,r)
Modified: test-optional.patch
===================================================================
--- test-optional.patch 2018-05-06 10:44:48 UTC (rev 319012)
+++ test-optional.patch 2018-05-06 12:07:52 UTC (rev 319013)
@@ -1,6 +1,6 @@
--- src/sage/doctest/control.py.orig 2016-10-20 19:39:53.714618246 +0200
+++ src/sage/doctest/control.py 2016-10-20 19:40:15.158049920 +0200
-@@ -320,22 +320,6 @@
+@@ -326,24 +326,6 @@
if "all" in options.optional:
# Special case to run all optional tests
options.optional = True
@@ -20,6 +20,8 @@
- for o in options.optional:
- if not optionaltag_regex.search(o):
- raise ValueError('invalid optional tag {!r}'.format(o))
-
+-
+- options.optional |= auto_optional_tags
+
self.options = options
self.files = args
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