Date: Sunday, December 10, 2017 @ 19:56:46 Author: arojas Revision: 273622
Update to 8.1 Added: sagemath-doc/trunk/jupyter-path.patch sagemath-doc/trunk/sagemath-detect-igraph.patch sagemath-doc/trunk/sagemath-env.patch sagemath-doc/trunk/sagemath-linbox-1.5.patch sagemath-doc/trunk/sagemath-networkx2.patch sagemath-doc/trunk/sagemath-pynac-0.7.14.patch sagemath-doc/trunk/sagemath-python3-notebook.patch sagemath-doc/trunk/sagemath-threejs.patch sagemath-doc/trunk/test-optional.patch Modified: sagemath-doc/trunk/PKGBUILD sagemath-doc/trunk/docbuild_main.patch sagemath-doc/trunk/fes02.patch sagemath-doc/trunk/latte-count.patch sagemath-doc/trunk/package.patch sagemath-doc/trunk/r-no-readline.patch Deleted: sagemath-doc/trunk/sagemath-sphinx-1.6.patch ---------------------------------+ PKGBUILD | 57 +++++-- docbuild_main.patch | 4 fes02.patch | 4 jupyter-path.patch | 22 +++ latte-count.patch | 14 - package.patch | 2 r-no-readline.patch | 2 sagemath-detect-igraph.patch | 21 ++ sagemath-env.patch | 105 ++++++++++++++ sagemath-linbox-1.5.patch | 272 ++++++++++++++++++++++++++++++++++++++ sagemath-networkx2.patch | 26 +++ sagemath-pynac-0.7.14.patch | 167 +++++++++++++++++++++++ sagemath-python3-notebook.patch | 27 +++ sagemath-sphinx-1.6.patch | 69 --------- sagemath-threejs.patch | 11 + test-optional.patch | 25 +++ 16 files changed, 728 insertions(+), 100 deletions(-) Modified: PKGBUILD =================================================================== --- PKGBUILD 2017-12-10 19:28:45 UTC (rev 273621) +++ PKGBUILD 2017-12-10 19:56:46 UTC (rev 273622) @@ -3,7 +3,7 @@ pkgbase=sagemath-doc pkgname=(sagemath-doc sagemath-src) -pkgver=8.0 +pkgver=8.1 pkgrel=1 arch=(any) url="http://www.sagemath.org"; @@ -10,17 +10,25 @@ license=(GPL) makedepends=(sagemath sage-notebook python2-pyzmq python2-pillow python2-docutils tachyon python2-jupyter_client python2-pkgconfig cython2 thebe python2-sphinx python2-ipywidgets) -source=("$pkgbase-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"; - package.patch fes02.patch docbuild_main.patch r-no-readline.patch latte-count.patch sagemath-ecl-no-sigfpe.patch - sagemath-sphinx-1.6.patch) -sha256sums=('91df3e303add71616e24b38c04789f66d57ada7b1017e5369e850c42d5e8753d' - '4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212' - 'a39da083c038ada797ffc5bedc9ba47455a3f77057d42f86484ae877ef9172ea' - '187b75d3ce202126012ff20b6316277b0a003ffdd7f15b820d3b88459d2753c8' - 'ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf' - 'c6836783251d94c00f0229c1e671de86c58c6c6fb0f6959725317817abc64ca8' - 'c31809f887bf9acc45c5bd9dd30bb93e73601d3efbf3016594c3c1d241731c8a' - '5358b4604dfab126a02bba6c9e436a5c41c66d5bc241ae3299e76ac1e9ae593d') +source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"; + sagemath-env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch + r-no-readline.patch fes02.patch sagemath-threejs.patch sagemath-detect-igraph.patch + sagemath-networkx2.patch sagemath-linbox-1.5.patch sagemath-pynac-0.7.14.patch docbuild_main.patch) +sha256sums=('a42b55c2c8ac244535dc9b87171b7d4dd7e1d498099518ab253354fbe2eaaa7b' + '6dc9b101310f80381c61c0312a3e5c648771bfe0de2e94ac46fafe7282a3e0ee' + 'c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107' + '0b680e674c11c47afa86162d8b49645620b8912722e08133d23357c29ca9310a' + '2cad308f8adbb6c54e6603fa22b2f0eb60f6f09248d5d015000c3932ac14f646' + '962ce805c87147212b21fc2ab0ac9af9bd0033942c7a6905b9906645b48e8a4f' + 'ef94908d4ab28d13af622e6e58ec191aa78817d17e4466c7bb6f64ee72a813b9' + 'afd0952b9bb8f52fd428eae36cf719a58ff85a894baae88cbb2124e043768cc7' + '7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94' + '514135b920a43f999571a15e97b41e14f5bed59f65b19643864dc23555a7b830' + '28d7789b8d777922ab8871ca43b6afab751428cae875c0343d3962e6a2030b88' + '37c5c1e694a2aca06c0f1c7d99622ff81fd2bc6a51e8745762294889fa4673f6' + 'a52d03e04c9d64bb957a1f8dcdae3280ebb9450a7fd76aaf5ae5de5c6f74774f' + '538f7b279d72f4b67edb445d386d267f3f7022c1079031ca7ea06f6ce392c906' + 'ea5e17bb7a7cb36a22e5e3872fcc2585852bc971c4b139b0b2cd69a36c1b009b') prepare() { cd sage-$pkgver @@ -28,21 +36,35 @@ # Arch-specific patches # assume all optional packages are installed patch -p0 -i ../package.patch +# set env variables + patch -p0 -i ../sagemath-env.patch +# don't list optional packages when running tests + patch -p0 -i ../test-optional.patch +# set jupyter path + patch -p0 -i ../jupyter-path.patch # fix freezes in R interface with readline 7 (Debian) patch -p1 -i ../r-no-readline.patch # use correct latte-count binary name patch -p1 -i ../latte-count.patch +# make 'sage -notebook=jupyter' work with our python3 jupyter-notebook package + patch -p1 -i ../sagemath-python3-notebook.patch # fix Cremona database detection sed -e "s|is_package_installed('database_cremona_ellcurve')|os.path.exists('/usr/share/cremona/cremona.db')|" \ -i src/sage/databases/cremona.py +# fix python-igraph detection + patch -p1 -i ../sagemath-detect-igraph.patch +# adapt to networkx 2 changes + patch -p1 -i ../sagemath-networkx2.patch +# fix three.js plotting backend + patch -p1 -i ../sagemath-threejs.patch -# Upstream patches +# Upstream patches # fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209 patch -p1 -i ../fes02.patch -# disable SIGFPE for ecl https://trac.sagemath.org/ticket/22191 - patch -p1 -i ../sagemath-ecl-no-sigfpe.patch -# fix doc build with Sphinx 1.6 https://trac.sagemath.org/ticket/23023 - patch -p1 -i ../sagemath-sphinx-1.6.patch +# fix build with linbox 1.5 https://trac.sagemath.org/ticket/24214 + patch -p1 -i ../sagemath-linbox-1.5.patch +# fix build with pynac 0.7.14 https://trac.sagemath.org/ticket/24329 + patch -p1 -i ../sagemath-pynac-0.7.14.patch # fix relative imports patch -p0 -i ../docbuild_main.patch @@ -58,6 +80,7 @@ cd sage-$pkgver/src export SAGE_LOCAL="/usr" + export SAGE_ROOT="/usr" export SAGE_SRC="$PWD" export SAGE_DOC_SRC="$SAGE_SRC"/doc export SAGE_DOC="$SAGE_SRC"/doc Modified: docbuild_main.patch =================================================================== --- docbuild_main.patch 2017-12-10 19:28:45 UTC (rev 273621) +++ docbuild_main.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -1,8 +1,6 @@ --- src/sage_setup/docbuild/__main__.py.orig +++ src/sage_setup/docbuild/__main__.py -@@ -1,3 +1,3 @@ +@@ -1,2 +1,2 @@ -from . import main +from sage_setup.docbuild import main main() - - # Remove old documentation Modified: fes02.patch =================================================================== --- fes02.patch 2017-12-10 19:28:45 UTC (rev 273621) +++ fes02.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -42,8 +42,8 @@ + void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose, int T) - include 'sage/ext/interrupt.pxi' #sig_on(), sig_off() -@@ -219,7 +221,7 @@ def exhaustive_search(eqs, max_sols=Infinity, verbose=False): + from sage.rings.integer import Integer +@@ -217,7 +217,7 @@ def exhaustive_search(eqs, max_sols=Infinity, verbose=False): # ------- runs the library sig_on() Added: jupyter-path.patch =================================================================== --- jupyter-path.patch (rev 0) +++ jupyter-path.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -0,0 +1,22 @@ +--- src/sage/repl/ipython_kernel/install.py.orig 2015-10-23 19:23:39.728456590 +0000 ++++ src/sage/repl/ipython_kernel/install.py 2015-10-23 19:24:00.965018978 +0000 +@@ -13,8 +13,7 @@ + SAGE_DOC, SAGE_LOCAL, SAGE_EXTCODE, + SAGE_VERSION + ) +-from jupyter_core.paths import ENV_JUPYTER_PATH +-JUPYTER_PATH = ENV_JUPYTER_PATH[0] ++JUPYTER_PATH = os.environ.get('JUPYTER_PATH') + + + class SageKernelSpec(object): +@@ -225,7 +225,7 @@ + sage: spec._symlink_resources() # not tested + """ + path = os.path.join(SAGE_EXTCODE, 'notebook-ipython') +- for filename in os.listdir(path): ++ for filename in os.listdir('ext/notebook-ipython'): + self.symlink( + os.path.join(path, filename), + os.path.join(self.kernel_dir, filename) + Modified: latte-count.patch =================================================================== --- latte-count.patch 2017-12-10 19:28:45 UTC (rev 273621) +++ latte-count.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -2,7 +2,7 @@ index 268af9db0d..70d41dfa30 100644 --- a/src/sage/geometry/polyhedron/base_ZZ.py +++ b/src/sage/geometry/polyhedron/base_ZZ.py -@@ -228,7 +228,7 @@ class Polyhedron_ZZ(Polyhedron_base): +@@ -171,7 +171,7 @@ class Polyhedron_ZZ(Polyhedron_base): sage: p = P.ehrhart_polynomial(maxdet=5, verbose=True) # optional - latte_int This is LattE integrale ... ... @@ -11,7 +11,7 @@ ... sage: p # optional - latte_int 1/2*t^2 + 3/2*t + 1 -@@ -236,7 +236,7 @@ class Polyhedron_ZZ(Polyhedron_base): +@@ -179,7 +179,7 @@ class Polyhedron_ZZ(Polyhedron_base): sage: p = P.ehrhart_polynomial(dual=True, verbose=True) # optional - latte_int This is LattE integrale ... ... @@ -20,7 +20,7 @@ ... sage: p # optional - latte_int 1/2*t^2 + 3/2*t + 1 -@@ -244,7 +244,7 @@ class Polyhedron_ZZ(Polyhedron_base): +@@ -187,7 +187,7 @@ class Polyhedron_ZZ(Polyhedron_base): sage: p = P.ehrhart_polynomial(irrational_primal=True, verbose=True) # optional - latte_int This is LattE integrale ... ... @@ -29,7 +29,7 @@ ... sage: p # optional - latte_int 1/2*t^2 + 3/2*t + 1 -@@ -252,7 +252,7 @@ class Polyhedron_ZZ(Polyhedron_base): +@@ -195,7 +195,7 @@ class Polyhedron_ZZ(Polyhedron_base): sage: p = P.ehrhart_polynomial(irrational_all_primal=True, verbose=True) # optional - latte_int This is LattE integrale ... ... @@ -38,7 +38,7 @@ ... sage: p # optional - latte_int 1/2*t^2 + 3/2*t + 1 -@@ -264,7 +264,7 @@ class Polyhedron_ZZ(Polyhedron_base): +@@ -207,7 +207,7 @@ class Polyhedron_ZZ(Polyhedron_base): ... RuntimeError: LattE integrale program failed (exit code 1): ... @@ -51,7 +51,7 @@ index 066cedd401..302b39910d 100644 --- a/src/sage/interfaces/latte.py +++ b/src/sage/interfaces/latte.py -@@ -86,7 +86,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False, +@@ -88,7 +88,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False, sage: n = count(cddin, cdd=True, verbose=True, raw_output=True) # optional - latte_int This is LattE integrale ... ... @@ -60,7 +60,7 @@ ... Total Unimodular Cones: ... Maximum number of simplicial cones in memory at once: ... -@@ -106,7 +106,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False, +@@ -108,7 +108,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False, from sage.misc.misc import SAGE_TMP from sage.rings.integer import Integer Modified: package.patch =================================================================== --- package.patch 2017-12-10 19:28:45 UTC (rev 273621) +++ package.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -1,6 +1,6 @@ --- src/sage/misc/package.py.orig 2014-11-23 15:58:13.000000000 +0100 +++ src/sage/misc/package.py 2015-01-22 20:32:25.651383902 +0100 -@@ -343,7 +343,7 @@ +@@ -320,7 +320,7 @@ sage: for pkg in list_packages('pip', local=True): ....: assert not is_package_installed(pkg) """ Modified: r-no-readline.patch =================================================================== --- r-no-readline.patch 2017-12-10 19:28:45 UTC (rev 273621) +++ r-no-readline.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -1,6 +1,6 @@ --- a/src/sage/interfaces/r.py +++ b/src/sage/interfaces/r.py -@@ -331,7 +331,7 @@ +@@ -332,7 +332,7 @@ prompt = '> ', #default, later comes the change # This is the command that starts up your program Added: sagemath-detect-igraph.patch =================================================================== --- sagemath-detect-igraph.patch (rev 0) +++ sagemath-detect-igraph.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -0,0 +1,21 @@ +diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py +index 252984f..ce19682 100644 +--- a/src/sage/graphs/generic_graph.py ++++ b/src/sage/graphs/generic_graph.py +@@ -8188,10 +8188,12 @@ class GenericGraph(GenericGraph_pyx): + if algorithm is None: + if vertex_bound: + algorithm = "LP" +- elif is_package_installed("python_igraph"): +- algorithm = "igraph" + else: +- algorithm = "FF" ++ algorithm = "igraph" ++ try: ++ import igraph ++ except ImportError: ++ algorithm = "FF" + + if (algorithm == "FF"): + return self._ford_fulkerson(x,y, value_only=value_only, integer=integer, use_edge_labels=use_edge_labels) + Added: sagemath-env.patch =================================================================== --- sagemath-env.patch (rev 0) +++ sagemath-env.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -0,0 +1,105 @@ +--- src/bin/sage-env.orig 2015-01-06 10:46:04.469687605 +0100 ++++ src/bin/sage-env 2015-01-06 10:49:59.547762019 +0100 +@@ -111,41 +111,7 @@ + } + + +-# New value for SAGE_ROOT: either SAGE_ROOT (if given) +-# or a guessed value based on pwd. +-if [ -n "$SAGE_ROOT" ]; then +- NEW_SAGE_ROOT="$SAGE_ROOT" +-elif [ -f sage -a -d build ]; then +- NEW_SAGE_ROOT="." +-elif [ -f ../../sage -a -d ../../build ]; then +- NEW_SAGE_ROOT="../.." +-else +- # No idea what SAGE_ROOT should be... +- echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this" +- echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory." +- return 1 +-fi +- +-# Make NEW_SAGE_ROOT absolute +-NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P` +- +-# Sanity check NEW_SAGE_ROOT +-if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then +- : +-else +- echo >&2 "Error: SAGE_ROOT is set to a bad value:" +- echo >&2 "SAGE_ROOT=$SAGE_ROOT" +- echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT" +- echo >&2 "or SAGE_ROOT/local/bin/ directory." +- return 1 +-fi +- +-# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT +-if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then +- echo >&2 "Warning: overwriting SAGE_ROOT environment variable:" +- echo >&2 "Old SAGE_ROOT=$SAGE_ROOT" +- echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT" +-fi ++NEW_SAGE_ROOT="/usr" + + # Display the Sage startup banner, used in src/bin/sage + sage_banner() { +@@ -185,6 +185,7 @@ + export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION + + export SAGE_ROOT="$NEW_SAGE_ROOT" ++export SAGE_LOCAL='/usr' + + + # sage-env must know where the Sage's script files are. +@@ -307,8 +307,9 @@ + export SAGE_EXTCODE="$SAGE_SHARE/sage/ext" + export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed" + export SAGE_LOGS="$SAGE_ROOT/logs/pkgs" +-export SAGE_SRC="$SAGE_ROOT/src" +-export SAGE_DOC_SRC="$SAGE_SRC/doc" ++export GAP_ROOT_DIR="/usr/lib/gap" ++export SAGE_SRC="$SAGE_SHARE/sage/source" ++export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage" + export SAGE_DOC="$SAGE_SHARE/doc/sage" + + if [ -z "${SAGE_ORIG_PATH_SET}" ]; then +@@ -414,6 +414,9 @@ + export SAGE_STARTUP_FILE + fi + ++export LIBMTX="$DOT_SAGE/meataxe" ++[[ -d $LIBMTX ]] || mkdir -p $LIBMTX # Create meataxe data dir ++ + if [ "$PYTHON_EGG_CACHE" = "" ]; then + PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs" + export PYTHON_EGG_CACHE +@@ -499,7 +499,6 @@ + fi + fi + fi +-export MAXIMA_PREFIX="$SAGE_LOCAL" + + PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB + +@@ -619,9 +619,6 @@ + LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH + fi + +-# See trac 7186 -- this is needed if ecl is moved +-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR +- + # Handle parallel building/testing/... + # See Trac Ticket #12016 + # First, figure out the right values for SAGE_NUM_THREADS (default +--- src/sage/env.py.orig 2017-12-07 19:51:25.554281539 +0000 ++++ src/sage/env.py 2017-12-07 19:51:42.787654650 +0000 +@@ -118,7 +118,7 @@ + + # bunch of sage directories and files + _add_variable_or_fallback('SAGE_ROOT', None) +-_add_variable_or_fallback('SAGE_LOCAL', None) ++_add_variable_or_fallback('SAGE_LOCAL', '/usr') + _add_variable_or_fallback('SAGE_ETC', opj('$SAGE_LOCAL', 'etc')) + _add_variable_or_fallback('SAGE_INC', opj('$SAGE_LOCAL', 'include')) + _add_variable_or_fallback('SAGE_SHARE', opj('$SAGE_LOCAL', 'share')) + Added: sagemath-linbox-1.5.patch =================================================================== --- sagemath-linbox-1.5.patch (rev 0) +++ sagemath-linbox-1.5.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -0,0 +1,272 @@ +diff --git a/src/sage/libs/linbox/fflas.pxd b/src/sage/libs/linbox/fflas.pxd +index ca23d71..03bbee9 100644 +--- a/src/sage/libs/linbox/fflas.pxd ++++ b/src/sage/libs/linbox/fflas.pxd +@@ -20,19 +20,29 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h" namespace "std": + iterator end() + size_t size() + +- cdef cppclass list[T]: +- cppclass iterator: +- T operator*() +- iterator operator++() +- bint operator==(iterator) +- bint operator!=(iterator) +- void push_back(T&) +- void pop_front() +- T& front() +- iterator begin() +- iterator end() ++cdef extern from "givaro/givpoly1.h": ++ ## template < typename T, typename A=std::allocator<T> > ++ ## class givvector : public __GIV_STANDARD_VECTOR<T,A> ++ cdef cppclass givvector "Givaro::givvector" [T,ALLOCATOR=*]: ++ T& operator[](size_t i) + size_t size() +- void clear() ++ ++ctypedef givvector[ModDoubleFieldElement] ModDoubleDensePolynomial ++ctypedef givvector[ModFloatFieldElement] ModFloatDensePolynomial ++ ++cdef extern from "givaro/givpoly1.h": ++ ## template <class Domain, class StorageTag= Givaro::Dense> ++ ## class GivPolynomialRing : public Givaro::Poly1FactorDom< Domain,StorageTag> ++ cdef cppclass ModDoublePolynomialRing "Givaro::Poly1Dom<Givaro::Modular<double>, Givaro::Dense>": ++ ctypedef givvector[ModDoubleField] Element ++ ctypedef givvector[ModDoubleField] Polynomial ++ ModDoublePolynomialRing(ModDoubleField& F) ++ ## template <class Domain, class StorageTag= Givaro::Dense> ++ ## class GivPolynomialRing : public Givaro::Poly1FactorDom< Domain,StorageTag> ++ cdef cppclass ModFloatPolynomialRing "Givaro::Poly1Dom<Givaro::Modular<float>, Givaro::Dense>": ++ ctypedef givvector[ModFloatField] Element ++ ctypedef givvector[ModFloatField] Polynomial ++ ModFloatPolynomialRing(ModFloatField& F) + + cdef extern from "fflas-ffpack/fflas-ffpack.h": + ctypedef enum fflas_trans_enum "FFLAS::FFLAS_TRANSPOSE": +@@ -105,13 +115,12 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h": + size_t nr, size_t foo, size_t r, + ModDoubleFieldElement* matrix, size_t nc, size_t* Q) + +- void ModDouble_MinPoly "FFPACK::MinPoly" ( ModDoubleField F, ++ void ModDouble_MinPoly "FFPACK::MinPoly" ( ModDoubleField& F, + vector[ModDoubleFieldElement] minP, size_t N, +- ModDoubleFieldElement* A, size_t lda, +- ModDoubleFieldElement* X, size_t ldx, size_t* P) ++ ModDoubleFieldElement*A, size_t lda) + +- void ModDouble_CharPoly "FFPACK::CharPoly" ( ModDoubleField F, +- list[vector[ModDoubleFieldElement]] charp, size_t N, ++ void ModDouble_CharPoly "FFPACK::CharPoly" ( ModDoublePolynomialRing& R, ++ ModDoubleDensePolynomial& charp, size_t N, + ModDoubleFieldElement* A, size_t lda) + + # float +@@ -142,9 +151,8 @@ cdef extern from "fflas-ffpack/fflas-ffpack.h": + + void ModFloat_MinPoly "FFPACK::MinPoly" ( ModFloatField F, + vector[ModFloatFieldElement] minP, size_t N, +- ModFloatFieldElement* A, size_t lda, +- ModFloatFieldElement* X, size_t ldx, size_t* P) ++ ModFloatFieldElement* A, size_t lda) + +- void ModFloat_CharPoly "FFPACK::CharPoly" ( ModFloatField F, +- list[vector[ModFloatFieldElement]] charp, size_t N, ++ void ModFloat_CharPoly "FFPACK::CharPoly" ( ModFloatPolynomialRing& F, ++ ModFloatDensePolynomial& charp, size_t N, + ModFloatFieldElement* A, size_t lda ) +diff --git a/src/sage/libs/linbox/linbox_flint_interface.pyx b/src/sage/libs/linbox/linbox_flint_interface.pyx +index 02a6151..a00d303 100644 +--- a/src/sage/libs/linbox/linbox_flint_interface.pyx ++++ b/src/sage/libs/linbox/linbox_flint_interface.pyx +@@ -76,19 +76,23 @@ cdef extern from "givaro/zring.h": + ctypedef GivaroInteger Element + + +-cdef extern from "givaro/givpoly1.h": +- ## template < typename T, typename A=std::allocator<T> > +- ## class givvector : public __GIV_STANDARD_VECTOR<T,A> +- cdef cppclass givvector "Givaro::givvector" [T,ALLOCATOR=*]: +- T& operator[](size_t i) ++cdef extern from "linbox/polynomial/dense-polynomial.h": ++ ## template<class Field> ++ ## class DensePolynomial : public Givaro::Poly1FactorDom<Field, Givaro::Dense>::Element ++ cdef cppclass LinBoxIntegerDensePolynomial "LinBox::DensePolynomial<Givaro::ZRing<Givaro::Integer> >": ++ ctypedef GivaroIntegerRing BaseRing ++ ctypedef GivaroInteger BaseRingElement ++ LinBoxIntegerDensePolynomial(BaseRing &F) ++ LinBoxIntegerDensePolynomial(BaseRing &F, size_t s) ++ BaseRingElement& operator[](size_t i) + size_t size() + +-cdef extern from "linbox/ring/givaro-polynomial.h": +- ## template <class Domain, class StorageTag= Givaro::Dense> +- ## class GivPolynomialRing : public Givaro::Poly1FactorDom< Domain,StorageTag> +- cdef cppclass LinBoxIntegerPolynomialRing "LinBox::GivPolynomialRing<Givaro::ZRing<Givaro::Integer>, Givaro::Dense>": +- ctypedef givvector[GivaroInteger] Element +- ctypedef givvector[GivaroInteger] Polynomial ++cdef extern from "linbox/ring/polynomial-ring.h": ++ ## template <class BaseRing, class StorageTag= Givaro::Dense> ++ ## class PolynomialRing : public Givaro::Poly1FactorDom<BaseRing,StorageTag> ++ cdef cppclass LinBoxIntegerPolynomialRing "LinBox::PolynomialRing<Givaro::ZRing<Givaro::Integer>, Givaro::Dense>": ++ ctypedef LinBoxIntegerDensePolynomial Element ++ ctypedef LinBoxIntegerDensePolynomial Polynomial + + cdef extern from "linbox/matrix/matrix-domain.h": + ## template <class Field_ > +@@ -190,40 +194,32 @@ cdef void linbox_fmpz_mat_mul(fmpz_mat_t C, fmpz_mat_t A, fmpz_mat_t B): + cdef void linbox_fmpz_mat_charpoly(fmpz_poly_t cp, fmpz_mat_t A): + cdef GivaroIntegerRing ZZ + cdef LinBoxIntegerDenseMatrix * LBA +- cdef LinBoxIntegerPolynomialRing.Element m_A +- +- # FIXME: bug in LinBox +- # see https://github.com/linbox-team/linbox/issues/51 +- if fmpz_mat_nrows(A) == 0: +- fmpz_poly_one(cp) +- return ++ cdef LinBoxIntegerDensePolynomial * m_A + + LBA = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(A), fmpz_mat_ncols(A)) + fmpz_mat_get_linbox(LBA[0], A) +- LinBoxIntegerDense_charpoly(m_A, LBA[0]) +- fmpz_poly_set_linbox(cp, m_A) ++ m_A = new LinBoxIntegerDensePolynomial(ZZ, fmpz_mat_nrows(A)) ++ LinBoxIntegerDense_charpoly(m_A[0], LBA[0]) ++ fmpz_poly_set_linbox(cp, m_A[0]) + + del LBA ++ del m_A + + + # set mp to the minimal polynomial of A + cdef void linbox_fmpz_mat_minpoly(fmpz_poly_t mp, fmpz_mat_t A): + cdef GivaroIntegerRing ZZ + cdef LinBoxIntegerDenseMatrix * LBA +- cdef LinBoxIntegerPolynomialRing.Element m_A +- +- # FIXME: bug in LinBox +- # see https://github.com/linbox-team/linbox/issues/51 +- if fmpz_mat_nrows(A) == 0: +- fmpz_poly_one(mp) +- return ++ cdef LinBoxIntegerDensePolynomial * m_A + + LBA = new LinBoxIntegerDenseMatrix(ZZ, fmpz_mat_nrows(A), fmpz_mat_ncols(A)) ++ m_A = new LinBoxIntegerDensePolynomial(ZZ) + fmpz_mat_get_linbox(LBA[0], A) +- LinBoxIntegerDense_minpoly(m_A, LBA[0]) +- fmpz_poly_set_linbox(mp, m_A) ++ LinBoxIntegerDense_minpoly(m_A[0], LBA[0]) ++ fmpz_poly_set_linbox(mp, m_A[0]) + + del LBA ++ del m_A + + + # return the rank of A +diff --git a/src/sage/matrix/matrix_modn_dense_double.pyx b/src/sage/matrix/matrix_modn_dense_double.pyx +index 15c35cb..b1f6154 100644 +--- a/src/sage/matrix/matrix_modn_dense_double.pyx ++++ b/src/sage/matrix/matrix_modn_dense_double.pyx +@@ -27,7 +27,9 @@ from sage.libs.linbox.fflas cimport ModDouble_fgemm as Mod_fgemm, ModDouble_fgem + ModDoubleRank as ModRank, ModDouble_echelon as Mod_echelon, \ + ModDouble_applyp as Mod_applyp, \ + ModDouble_MinPoly as Mod_MinPoly, \ +- ModDouble_CharPoly as Mod_CharPoly ++ ModDouble_CharPoly as Mod_CharPoly, \ ++ ModDoublePolynomialRing as ModDensePolyRing,\ ++ ModDoubleDensePolynomial as ModDensePoly + + # Limit for LinBox Modular<double> + MAX_MODULUS = 2**23 +diff --git a/src/sage/matrix/matrix_modn_dense_float.pyx b/src/sage/matrix/matrix_modn_dense_float.pyx +index 61457ce..eda8f0b 100644 +--- a/src/sage/matrix/matrix_modn_dense_float.pyx ++++ b/src/sage/matrix/matrix_modn_dense_float.pyx +@@ -25,7 +25,10 @@ from sage.libs.linbox.fflas cimport ModFloat_fgemm as Mod_fgemm, ModFloat_fgemv + ModFloatRank as ModRank, ModFloat_echelon as Mod_echelon, \ + ModFloat_applyp as Mod_applyp, \ + ModFloat_MinPoly as Mod_MinPoly, \ +- ModFloat_CharPoly as Mod_CharPoly ++ ModFloat_CharPoly as Mod_CharPoly, \ ++ ModFloatPolynomialRing as ModDensePolyRing,\ ++ ModFloatDensePolynomial as ModDensePoly ++ + + # LinBox supports up to 2^11 using float but that's double dog slow, + # so we pick a smaller value for crossover +diff --git a/src/sage/matrix/matrix_modn_dense_template.pxi b/src/sage/matrix/matrix_modn_dense_template.pxi +index 3da3e31..819ef2d 100644 +--- a/src/sage/matrix/matrix_modn_dense_template.pxi ++++ b/src/sage/matrix/matrix_modn_dense_template.pxi +@@ -306,23 +306,15 @@ cdef inline linbox_minpoly(celement modulus, Py_ssize_t nrows, celement* entries + cdef Py_ssize_t i + cdef ModField *F = new ModField(<long>modulus) + cdef vector[ModFieldElement] *minP = new vector[ModFieldElement]() +- cdef ModFieldElement *X = <ModFieldElement*>check_allocarray(nrows * (nrows+1), sizeof(ModFieldElement)) +- cdef size_t *P = <size_t*>check_allocarray(nrows, sizeof(size_t)) +- +- cdef celement *cpy = linbox_copy(modulus, entries, nrows, nrows) + + if nrows*nrows > 1000: sig_on() +- Mod_MinPoly(F[0], minP[0], nrows, <ModFieldElement*>cpy, nrows, X, nrows, P) ++ Mod_MinPoly(F[0], minP[0], nrows, <ModFieldElement*>entries, nrows) + if nrows*nrows > 1000: sig_off() + +- sig_free(cpy) +- + l = [] + for i in range(minP.size()): + l.append( <celement>minP.at(i) ) + +- sig_free(P) +- sig_free(X) + del F + return l + +@@ -332,27 +324,23 @@ cdef inline linbox_charpoly(celement modulus, Py_ssize_t nrows, celement* entrie + """ + cdef Py_ssize_t i + cdef ModField *F = new ModField(<long>modulus) +- cdef std_list[vector[ModFieldElement]] P_list +- P_list.clear() ++ cdef ModDensePolyRing * R = new ModDensePolyRing(F[0]) ++ cdef ModDensePoly P + + cdef celement *cpy = linbox_copy(modulus, entries, nrows, nrows) + + if nrows*nrows > 1000: sig_on() +- Mod_CharPoly(F[0], P_list, nrows, <ModFieldElement*>cpy, nrows) ++ Mod_CharPoly(R[0], P, nrows, <ModFieldElement*>cpy, nrows) + if nrows*nrows > 1000: sig_off() + + sig_free(cpy) + +- cdef vector[ModFieldElement] tmp + l = [] +- while P_list.size(): +- l.append([]) +- tmp = P_list.front() +- for i in range(tmp.size()): +- l[-1].append(<celement>tmp.at(i)) +- P_list.pop_front() ++ for i in range(P.size()): ++ l.append(<celement>P[i]) + + del F ++ del R + return l + + +@@ -1731,9 +1719,7 @@ cdef class Matrix_modn_dense_template(Matrix_dense): + R = self._base_ring[var] + # call linbox for charpoly + v = linbox_charpoly(self.p, self._nrows, self._entries) +- r = R(1) +- for e in v: +- r *= R(e) ++ r = R(v) + return r + + def echelonize(self, algorithm="linbox", **kwds): Added: sagemath-networkx2.patch =================================================================== --- sagemath-networkx2.patch (rev 0) +++ sagemath-networkx2.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -0,0 +1,26 @@ +diff --git a/src/sage/graphs/digraph.py b/src/sage/graphs/digraph.py +index 8c29602da6..e7a185d586 100644 +--- a/src/sage/graphs/digraph.py ++++ b/src/sage/graphs/digraph.py +@@ -755,7 +755,7 @@ class DiGraph(GenericGraph): + self.allow_multiple_edges(multiedges,check=False) + self.allow_loops(loops,check=False) + self.add_vertices(data.nodes()) +- self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True)) ++ self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True)) + elif format == 'igraph': + if not data.is_directed(): + raise ValueError("A *directed* igraph graph was expected. To "+ +diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py +index b63135d8e6..5775042976 100644 +--- a/src/sage/graphs/graph.py ++++ b/src/sage/graphs/graph.py +@@ -1199,7 +1199,7 @@ class Graph(GenericGraph): + self.allow_loops(loops, check=False) + self.allow_multiple_edges(multiedges, check=False) + self.add_vertices(data.nodes()) +- self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True)) ++ self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True)) + elif format == 'igraph': + if data.is_directed(): + raise ValueError("An *undirected* igraph graph was expected. "+ Added: sagemath-pynac-0.7.14.patch =================================================================== --- sagemath-pynac-0.7.14.patch (rev 0) +++ sagemath-pynac-0.7.14.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -0,0 +1,167 @@ +diff --git a/src/sage/libs/pynac/pynac.pxd b/src/sage/libs/pynac/pynac.pxd +index d4afc4e..6d1fcac 100644 +--- a/src/sage/libs/pynac/pynac.pxd ++++ b/src/sage/libs/pynac/pynac.pxd +@@ -481,22 +481,17 @@ cdef extern from "pynac_wrap.h": + ctypedef GParamSet const_paramset_ref "const GiNaC::paramset&" + + ctypedef struct py_funcs_struct: +- py_binomial(a, b) +- py_binomial_int(int n, unsigned int k) + py_gcd(a, b) + py_lcm(a, b) + py_real(a) + py_imag(a) + py_numer(a) + py_denom(a) +- py_conjugate(a) + bint py_is_rational(a) +- bint py_is_crational(a) + bint py_is_real(a) + bint py_is_integer(a) + bint py_is_equal(a, b) + bint py_is_even(a) +- bint py_is_cinteger(a) + bint py_is_prime(n) + bint py_is_exact(x) + +@@ -534,23 +529,14 @@ cdef extern from "pynac_wrap.h": + py_asinh(x) + py_acosh(x) + py_atanh(x) +- py_tgamma(x) +- py_lgamma(x) + py_isqrt(x) + py_sqrt(x) +- py_abs(x) + py_mod(x, y) + py_smod(x, y) + py_irem(x, y) +- py_iquo(x, y) +- py_iquo2(x, y) +- py_li(x, n, parent) +- py_li2(x) + py_psi(x) + py_psi2(n, x) + +- int py_int_length(x) except -1 +- + py_eval_constant(unsigned serial, parent) + py_eval_unsigned_infinity() + py_eval_infinity() +@@ -583,8 +569,6 @@ cdef extern from "pynac_wrap.h": + stdstring* py_latex_fderivative(unsigned id, params, args) + paramset_to_PyTuple(const_paramset_ref s) + +- py_rational_power_parts(basis, exp) +- + py_funcs_struct py_funcs "GiNaC::py_funcs" + + cdef extern from "pynac/order.h": +diff --git a/src/sage/libs/pynac/pynac.pyx b/src/sage/libs/pynac/pynac.pyx +index f303184..419cc47 100644 +--- a/src/sage/libs/pynac/pynac.pyx ++++ b/src/sage/libs/pynac/pynac.pyx +@@ -2432,23 +2432,18 @@ def init_function_table(): + called before Pynac is used; otherwise, there will be segfaults. + """ + +- py_funcs.py_binomial_int = &py_binomial_int +- py_funcs.py_binomial = &py_binomial + py_funcs.py_gcd = &py_gcd + py_funcs.py_lcm = &py_lcm + py_funcs.py_real = &py_real + py_funcs.py_imag = &py_imag + py_funcs.py_numer = &py_numer + py_funcs.py_denom = &py_denom +- py_funcs.py_conjugate = &py_conjugate + + py_funcs.py_is_rational = &py_is_rational +- py_funcs.py_is_crational = &py_is_crational + py_funcs.py_is_real = &py_is_real + py_funcs.py_is_integer = &py_is_integer + py_funcs.py_is_equal = &py_is_equal + py_funcs.py_is_even = &py_is_even +- py_funcs.py_is_cinteger = &py_is_cinteger + py_funcs.py_is_prime = &py_is_prime + py_funcs.py_is_exact = &py_is_exact + +@@ -2462,7 +2457,6 @@ def init_function_table(): + py_funcs.py_mpq_from_rational = &py_mpq_from_rational + + py_funcs.py_float = &py_float +- py_funcs.py_RDF_from_double = &py_RDF_from_double + + py_funcs.py_factorial = &py_factorial + py_funcs.py_doublefactorial = &py_doublefactorial +@@ -2486,23 +2480,14 @@ def init_function_table(): + py_funcs.py_asinh = &py_asinh + py_funcs.py_acosh = &py_acosh + py_funcs.py_atanh = &py_atanh +- py_funcs.py_tgamma = &py_tgamma +- py_funcs.py_lgamma = &py_lgamma + py_funcs.py_isqrt = &py_isqrt + py_funcs.py_sqrt = &py_sqrt +- py_funcs.py_abs = &py_abs + py_funcs.py_mod = &py_mod + py_funcs.py_smod = &py_smod + py_funcs.py_irem = &py_irem +- py_funcs.py_iquo = &py_iquo +- py_funcs.py_iquo2 = &py_iquo2 +- py_funcs.py_li = &py_li +- py_funcs.py_li2 = &py_li2 + py_funcs.py_psi = &py_psi + py_funcs.py_psi2 = &py_psi2 + +- py_funcs.py_int_length = &py_int_length +- + py_funcs.py_eval_constant = &py_eval_constant + py_funcs.py_eval_unsigned_infinity = &py_eval_unsigned_infinity + py_funcs.py_eval_infinity = &py_eval_infinity +@@ -2531,7 +2516,6 @@ def init_function_table(): + py_funcs.py_print_fderivative = &py_print_fderivative + py_funcs.py_latex_fderivative = &py_latex_fderivative + py_funcs.paramset_to_PyTuple = ¶mset_to_PyTuple +- py_funcs.py_rational_power_parts = &py_rational_power_parts + + init_function_table() + init_pynac_I() + +diff --git a/src/sage/functions/other.py b/src/sage/functions/other.py +index 81cd485..931cecc 100644 +--- a/src/sage/functions/other.py ++++ b/src/sage/functions/other.py +@@ -688,7 +688,6 @@ class Function_gamma(GinacFunction): + :meth:`sage.functions.other.gamma` + """ + GinacFunction.__init__(self, 'gamma', latex_name=r"\Gamma", +- ginac_name='tgamma', + conversions={'mathematica':'Gamma', + 'maple':'GAMMA', + 'sympy':'gamma', +diff --git a/src/sage/libs/pynac/pynac.pxd b/src/sage/libs/pynac/pynac.pxd +index 1739067..d4afc4e 100644 +--- a/src/sage/libs/pynac/pynac.pxd ++++ b/src/sage/libs/pynac/pynac.pxd +@@ -362,7 +362,7 @@ cdef extern from "pynac_wrap.h": + GEx g_zeta2 "GiNaC::zeta" (GEx m, GEx s) except + # alternating Euler sum + GEx g_stieltjes "GiNaC::stieltjes" (GEx m) except + # Stieltjes constants + GEx g_zetaderiv "GiNaC::zetaderiv" (GEx n, GEx x) except + # derivatives of Riemann's zeta function +- GEx g_tgamma "GiNaC::tgamma" (GEx x) except + # gamma function ++ GEx g_gamma "GiNaC::gamma" (GEx x) except + # gamma function + GEx g_lgamma "GiNaC::lgamma" (GEx x) except + # logarithm of gamma function + GEx g_beta "GiNaC::beta" (GEx x, GEx y) except + # beta function (tgamma(x)*tgamma(y)/tgamma(x+y)) + GEx g_psi "GiNaC::psi" (GEx x) except + # psi (digamma) function +diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx +index dfb8751..52303d1 100644 +--- a/src/sage/symbolic/expression.pyx ++++ b/src/sage/symbolic/expression.pyx +@@ -8917,7 +8917,7 @@ cdef class Expression(CommutativeRingElement): + cdef GEx x + sig_on() + try: +- x = g_hold_wrapper(g_tgamma, self._gobj, hold) ++ x = g_hold_wrapper(g_gamma, self._gobj, hold) + finally: + sig_off() + return new_Expression_from_GEx(self._parent, x) Added: sagemath-python3-notebook.patch =================================================================== --- sagemath-python3-notebook.patch (rev 0) +++ sagemath-python3-notebook.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -0,0 +1,27 @@ +diff --git a/src/bin/sage-notebook b/src/bin/sage-notebook +index 74192da240..0ede281aad 100755 +--- a/src/bin/sage-notebook ++++ b/src/bin/sage-notebook +@@ -96,8 +96,7 @@ class NotebookJupyter(object): + if not have_prerequisites(): + print(self.PREREQUISITE_ERROR) + raise SystemExit(1) +- from notebook.notebookapp import main +- main(argv) ++ os.execvp('jupyter-notebook', ['jupyter-notebook'] + argv) + + + class NotebookJupyterlab(object): +diff --git a/src/sage/repl/ipython_kernel/install.py b/src/sage/repl/ipython_kernel/install.py +index 3912b8cdf5..bd40cdadda 100644 +--- a/src/sage/repl/ipython_kernel/install.py ++++ b/src/sage/repl/ipython_kernel/install.py +@@ -280,7 +280,6 @@ def have_prerequisites(debug=True): + True + """ + try: +- from notebook.notebookapp import NotebookApp + return True + except ImportError: + if debug: + Deleted: sagemath-sphinx-1.6.patch =================================================================== --- sagemath-sphinx-1.6.patch 2017-12-10 19:28:45 UTC (rev 273621) +++ sagemath-sphinx-1.6.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -1,69 +0,0 @@ -diff --git a/src/sage_setup/docbuild/__init__.py b/src/sage_setup/docbuild/__init__.py -index 4315663..8618b86 100644 ---- a/src/sage_setup/docbuild/__init__.py -+++ b/src/sage_setup/docbuild/__init__.py -@@ -770,14 +770,16 @@ class ReferenceSubBuilder(DocBuilder): - Returns the Sphinx environment for this project. - """ - from sphinx.environment import BuildEnvironment -- class Foo(object): -- pass -- config = Foo() -- config.values = [] -+ class FakeConfig(object): -+ values = tuple() -+ class FakeApp(object): -+ def __init__(self, dir): -+ self.srcdir = dir -+ self.config = FakeConfig() - - env_pickle = os.path.join(self._doctrees_dir(), 'environment.pickle') - try: -- env = BuildEnvironment.frompickle(self.dir, config, env_pickle) -+ env = BuildEnvironment.frompickle(env_pickle, FakeApp(self.dir)) - logger.debug("Opened Sphinx environment: %s", env_pickle) - return env - except IOError as err: -diff --git a/src/sage_setup/docbuild/ext/multidocs.py b/src/sage_setup/docbuild/ext/multidocs.py -index 0a5457a..371546d 100644 ---- a/src/sage_setup/docbuild/ext/multidocs.py -+++ b/src/sage_setup/docbuild/ext/multidocs.py -@@ -86,9 +86,10 @@ def merge_environment(app, env): - env.metadata[ind] = md - # merge the citations - newcite = {} -- for ind, (path, tag) in six.iteritems(docenv.domaindata["std"]["citations"]): -+ citations = docenv.domaindata["std"]["citations"] -+ for ind, (path, tag, lineno) in six.iteritems(docenv.domaindata["std"]["citations"]): - # TODO: Warn on conflicts -- newcite[ind] = (fixpath(path), tag) -+ newcite[ind] = (fixpath(path), tag, lineno) - env.domaindata["std"]["citations"].update(newcite) - # merge the py:module indexes - newmodules = {} -@@ -247,9 +248,10 @@ def fetch_citation(app, env): - cache = cPickle.load(f) - app.builder.info("done (%s citations)."%len(cache)) - cite = env.domaindata["std"]["citations"] -- for ind, (path, tag) in six.iteritems(cache): -+ for ind, (path, tag, lineno) in six.iteritems(cache): - if ind not in cite: # don't override local citation -- cite[ind]=(os.path.join("..", path), tag) -+ cite[ind] = (os.path.join("..", path), tag, lineno) -+ - - def init_subdoc(app): - """ -diff --git a/src/sage_setup/docbuild/sphinxbuild.py b/src/sage_setup/docbuild/sphinxbuild.py -index c68292c..1deac3d 100644 ---- a/src/sage_setup/docbuild/sphinxbuild.py -+++ b/src/sage_setup/docbuild/sphinxbuild.py -@@ -55,6 +55,8 @@ class SageSphinxLogger(object): - re.compile('WARNING: html_static_path entry .* does not exist'), - re.compile('WARNING: while setting up extension'), - re.compile('WARNING: Any IDs not assiend for figure node'), -+ re.compile('WARNING: .* is not referenced'), -+ re.compile('language "hu" not supported'), - ) - - # replacements: pairs of regular expressions and their replacements, Added: sagemath-threejs.patch =================================================================== --- sagemath-threejs.patch (rev 0) +++ sagemath-threejs.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -0,0 +1,11 @@ +--- a/src/sage/repl/rich_output/display_manager.py ++++ b/src/sage/repl/rich_output/display_manager.py +@@ -744,7 +744,7 @@ class DisplayManager(SageObject): + """ + if online: + from sage.misc.package import installed_packages +- version = installed_packages()['threejs'] ++ version = 'r80' + return """ + <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/build/three.min.js";></script> + <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/examples/js/controls/OrbitControls.js";></script> Added: test-optional.patch =================================================================== --- test-optional.patch (rev 0) +++ test-optional.patch 2017-12-10 19:56:46 UTC (rev 273622) @@ -0,0 +1,25 @@ +--- src/sage/doctest/control.py.orig 2016-10-20 19:39:53.714618246 +0200 ++++ src/sage/doctest/control.py 2016-10-20 19:40:15.158049920 +0200 +@@ -320,22 +320,6 @@ + if "all" in options.optional: + # Special case to run all optional tests + options.optional = True +- else: +- # We replace the 'optional' tag by all optional +- # packages for which the installed version matches the +- # latest available version (this implies in particular +- # that the package is actually installed). +- if 'optional' in options.optional: +- options.optional.discard('optional') +- from sage.misc.package import list_packages +- for pkg in list_packages('optional', local=True).values(): +- if pkg['installed_version'] == pkg['remote_version']: +- options.optional.add(pkg['name']) +- +- # Check that all tags are valid +- for o in options.optional: +- if not optionaltag_regex.search(o): +- raise ValueError('invalid optional tag {!r}'.format(o)) + + self.options = options + self.files = args
