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 <[email protected]> --- 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 <[email protected]> -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
