[arch-commits] Commit in sagemath-doc/trunk (16 files)
Antonio Rojas
arojas at archlinux.org
Sun Dec 10 19:56:46 UTC 2017
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
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