[arch-commits] Commit in sagemath/trunk (6 files)
Antonio Rojas
arojas at archlinux.org
Fri Dec 15 21:39:14 UTC 2017
Date: Friday, December 15, 2017 @ 21:39:13
Author: arojas
Revision: 274537
Add some fixes for new scipy, matplotlib and networkx
Added:
sagemath/trunk/pari-stackwarn.patch
sagemath/trunk/sagemath-lrs.patch
sagemath/trunk/sagemath-matplotlib2.patch
sagemath/trunk/sagemath-scipy-1.0.patch
Modified:
sagemath/trunk/PKGBUILD
sagemath/trunk/sagemath-networkx2.patch
----------------------------+
PKGBUILD | 30 +++--
pari-stackwarn.patch | 23 +++
sagemath-lrs.patch | 22 +++
sagemath-matplotlib2.patch | 253 +++++++++++++++++++++++++++++++++++++++++++
sagemath-networkx2.patch | 174 +++++++++++++++++++++++++++++
sagemath-scipy-1.0.patch | 16 ++
6 files changed, 506 insertions(+), 12 deletions(-)
Modified: PKGBUILD
===================================================================
--- PKGBUILD 2017-12-15 18:00:54 UTC (rev 274536)
+++ PKGBUILD 2017-12-15 21:39:13 UTC (rev 274537)
@@ -9,7 +9,7 @@
pkgbase=sagemath
pkgname=(sagemath sagemath-jupyter)
pkgver=8.1
-pkgrel=1
+pkgrel=2
pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"
arch=(x86_64)
url="http://www.sagemath.org"
@@ -16,7 +16,7 @@
license=(GPL)
depends=(ipython2 ppl palp brial cliquer maxima-ecl gfan sympow nauty python2-rpy2 python2-fpylll python2-psutil python2-cypari2
python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow python2-future libgap flintqs lcalc lrcalc arb
- eclib gmp-ecm zn_poly gd python2-cvxopt pynac linbox rubiks pari-galdata pari-seadata-small planarity rankwidth
+ eclib gmp-ecm zn_poly gd python2-cvxopt pynac linbox rubiks pari-galdata pari-seadata-small planarity rankwidth tachyon
sage-data-combinatorial_designs sage-data-elliptic_curves sage-data-graphs sage-data-polytopes_db sage-data-conway_polynomials)
optdepends=('cython2: to compile cython code' 'python2-pkgconfig: to compile cython code'
'jmol: 3D plots' 'sage-notebook: Flask notebook interface (deprecated)'
@@ -31,13 +31,14 @@
'latte-integrale: integral point count in polyhedra' 'polymake: polymake backend for polyhedral computations'
'meataxe: faster matrix arithmetic over finite fields'
'sirocco: for computing the fundamental group of the complement of a plane curve'
- 'three.js: alternative 3D plots engine' 'tachyon: alternative 3D plots engine')
+ '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 meataxe libfes)
source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
sagemath-env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch
- r-no-readline.patch fes02.patch sagemath-ecl-no-sigfpe.patch sagemath-threejs.patch
- sagemath-detect-igraph.patch sagemath-networkx2.patch sagemath-linbox-1.5.patch sagemath-pynac-0.7.14.patch)
+ r-no-readline.patch fes02.patch sagemath-ecl-no-sigfpe.patch sagemath-threejs.patch pari-stackwarn.patch
+ sagemath-detect-igraph.patch sagemath-networkx2.patch sagemath-linbox-1.5.patch sagemath-pynac-0.7.14.patch
+ sagemath-matplotlib2.patch sagemath-scipy-1.0.patch sagemath-lrs.patch)
sha256sums=('a42b55c2c8ac244535dc9b87171b7d4dd7e1d498099518ab253354fbe2eaaa7b'
'6dc9b101310f80381c61c0312a3e5c648771bfe0de2e94ac46fafe7282a3e0ee'
'c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107'
@@ -49,10 +50,14 @@
'7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94'
'c31809f887bf9acc45c5bd9dd30bb93e73601d3efbf3016594c3c1d241731c8a'
'514135b920a43f999571a15e97b41e14f5bed59f65b19643864dc23555a7b830'
+ 'bfd2a20a33ab19a8a8b216a77d07f62e809fe1e1879c4f171ce5dca62fd482e9'
'28d7789b8d777922ab8871ca43b6afab751428cae875c0343d3962e6a2030b88'
- '37c5c1e694a2aca06c0f1c7d99622ff81fd2bc6a51e8745762294889fa4673f6'
+ '1024f3a6a9a1a6ae96d9962bb7d1f5842f4a4a5ff5098afad81a60188b7d5160'
'a52d03e04c9d64bb957a1f8dcdae3280ebb9450a7fd76aaf5ae5de5c6f74774f'
- '538f7b279d72f4b67edb445d386d267f3f7022c1079031ca7ea06f6ce392c906')
+ '538f7b279d72f4b67edb445d386d267f3f7022c1079031ca7ea06f6ce392c906'
+ 'b9ab2bb5f381ea425e8763b81b8b3a108a3951c594fb1f37f7df921e7c77e26d'
+ '17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a'
+ 'c0f65534a845ba802de6196229159fe67fcc3f72f0cb1ce57d4ae5c9fe10282c')
prepare(){
cd sage-$pkgver
@@ -77,20 +82,26 @@
-i src/sage/databases/cremona.py
# fix python-igraph detection
patch -p1 -i ../sagemath-detect-igraph.patch
+# fix lrs detection
+ patch -p1 -i ../sagemath-lrs.patch
# adapt to networkx 2 changes
patch -p1 -i ../sagemath-networkx2.patch
# fix three.js plotting backend
patch -p1 -i ../sagemath-threejs.patch
+# don't show PARI stack size increase warnings during doctesting (Debian)
+ patch -p1 -i ../pari-stackwarn.patch
+# remove deprecated scipy parameters
+ patch -p1 -i ../sagemath-scipy-1.0.patch
# Upstream patches
# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
patch -p1 -i ../fes02.patch
-# disable SIGFPE for ecl https://trac.sagemath.org/ticket/22191
-# patch -p1 -i ../sagemath-ecl-no-sigfpe.patch
# 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
# use python2
sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' -e 's|exec python|exec python2|' -i src/bin/*
@@ -107,7 +118,6 @@
./configure --prefix=/usr || true
cd src
- export SAGE_LOCAL="/usr"
export SAGE_ROOT="$PWD"
export SAGE_SRC="$PWD"
Added: pari-stackwarn.patch
===================================================================
--- pari-stackwarn.patch (rev 0)
+++ pari-stackwarn.patch 2017-12-15 21:39:13 UTC (rev 274537)
@@ -0,0 +1,23 @@
+Description: Ignore warnings of PARI increasing the stack size when parsing doctests
+ Since we can't patch PARI to not produce the warnings and we don't want to
+ patch tons of doctests to expect the warnings, we patch the doctest parser
+ to ignore them.
+Author: Tobias Hansen <thansen at debian.org>
+--- sage/src/sage/doctest/parsing.py
++++ sage/src/sage/doctest/parsing.py
+@@ -39,6 +39,7 @@
+
+ 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)*))')
++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'
+ """
+ got = self.human_readable_escape_sequences(got)
++ got = pari_stack_warning_regex.sub('', got)
+ if isinstance(want, MarkedOutput):
+ if want.random:
+ return True
Added: sagemath-lrs.patch
===================================================================
--- sagemath-lrs.patch (rev 0)
+++ sagemath-lrs.patch 2017-12-15 21:39:13 UTC (rev 274537)
@@ -0,0 +1,22 @@
+diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/normal_form_game.py
+index 2115de6800..da94aa5d45 100644
+--- a/src/sage/game_theory/normal_form_game.py
++++ b/src/sage/game_theory/normal_form_game.py
+@@ -621,6 +621,7 @@ from sage.matrix.constructor import vector
+ from sage.misc.package import is_package_installed, PackageNotFoundError
+ from sage.misc.temporary_file import tmp_filename
+ from sage.numerical.mip import MixedIntegerLinearProgram
++import os
+
+ try:
+ from gambit import Game
+@@ -1636,7 +1637,7 @@ class NormalFormGame(SageObject, MutableMapping):
+ if not algorithm:
+ if self.is_constant_sum():
+ algorithm = "lp"
+- elif is_package_installed('lrslib'):
++ elif os.path.exists('/usr/bin/lrsnash'):
+ algorithm = "lrs"
+ else:
+ algorithm = "enumeration"
+
Added: sagemath-matplotlib2.patch
===================================================================
--- sagemath-matplotlib2.patch (rev 0)
+++ sagemath-matplotlib2.patch 2017-12-15 21:39:13 UTC (rev 274537)
@@ -0,0 +1,253 @@
+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 2017-12-15 18:00:54 UTC (rev 274536)
+++ sagemath-networkx2.patch 2017-12-15 21:39:13 UTC (rev 274537)
@@ -1,5 +1,62 @@
+diff --git a/src/sage/graphs/base/graph_backends.pyx b/src/sage/graphs/base/graph_backends.pyx
+index ff1d02900a..bad4a18539 100644
+--- a/src/sage/graphs/base/graph_backends.pyx
++++ b/src/sage/graphs/base/graph_backends.pyx
+@@ -800,9 +800,9 @@ class NetworkXGraphDeprecated(SageObject):
+ sage: X.multiedges = True
+ sage: G = X.mutate()
+ sage: G.edges()
+- [(1, 2), (2, 3)]
++ MultiEdgeDataView([(1, 2), (2, 3)])
+ sage: G.edges(data=True)
+- [(1, 2, {'weight': 7}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})]
++ MultiEdgeDataView([(1, 2, {'weight': 7}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})])
+
+ """
+ import networkx
+@@ -868,11 +868,9 @@ class NetworkXDiGraphDeprecated(SageObject):
+ sage: X.multiedges = True
+ sage: G = X.mutate()
+ sage: G.edges()
+- [(1, 2), (2, 1), (2, 3)]
++ OutMultiEdgeDataView([(1, 2), (2, 1), (2, 3)])
+ sage: G.edges(data=True)
+- [(1, 2, {'weight': 7}),
+- (2, 1, {7: {}, 8: {}}),
+- (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})]
++ OutMultiEdgeDataView([(1, 2, {'weight': 7}), (2, 1, {8: {}, 7: {}}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})])
+
+ """
+ import networkx
+@@ -1158,7 +1156,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
+ import networkx
+ try:
+ if self._nxg.is_multigraph():
+- for k,d in self._nxg.edge[u][v].iteritems():
++ for u0,v0,k,d in self._nxg.edges([u,v],True,keys=True):
+ if d.get('weight',None) == l:
+ self._nxg.remove_edge(u,v,k)
+ break
+@@ -1227,7 +1225,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
+ """
+ cdef dict E
+ try:
+- E = self._nxg.edge[u][v]
++ E = self._nxg.edges[u,v,0]
+ 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):
+ sage: G.iterator_nbrs(0)
+ <dictionary-keyiterator object at ...>
+ """
+- return self._nxg.neighbors_iter(v)
++ return self._nxg.neighbors(v)
+
+ def iterator_in_nbrs(self, v):
+ """
diff --git a/src/sage/graphs/digraph.py b/src/sage/graphs/digraph.py
-index 8c29602da6..e7a185d586 100644
+index 003a8d6bcb..986137a9b0 100644
--- a/src/sage/graphs/digraph.py
+++ b/src/sage/graphs/digraph.py
@@ -755,7 +755,7 @@ class DiGraph(GenericGraph):
@@ -11,10 +68,96 @@
elif format == 'igraph':
if not data.is_directed():
raise ValueError("A *directed* igraph graph was expected. To "+
+@@ -2844,7 +2844,7 @@ class DiGraph(GenericGraph):
+ Using the NetworkX implementation ::
+
+ sage: D.topological_sort(implementation = "NetworkX")
+- [4, 5, 6, 9, 0, 1, 2, 3, 7, 8, 10]
++ [4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10]
+
+ Using the NetworkX recursive implementation ::
+
+@@ -2870,9 +2870,7 @@ 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()
+- sage: networkx.topological_sort(N)
+- [4, 5, 6, 9, 0, 1, 2, 3, 7, 8, 10]
+- sage: networkx.topological_sort_recursive(N)
++ sage: list(networkx.topological_sort(N))
+ [4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10]
+
+ TESTS:
+@@ -2895,10 +2893,7 @@ class DiGraph(GenericGraph):
+
+ elif implementation == "NetworkX" or implementation == "recursive":
+ import networkx
+- if implementation == "NetworkX":
+- S = networkx.topological_sort(self.networkx_graph(copy=False))
+- else:
+- S = networkx.topological_sort_recursive(self.networkx_graph(copy=False))
++ S = list(networkx.topological_sort(self.networkx_graph(copy=False)))
+ 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
++++ b/src/sage/graphs/generators/families.py
+@@ -197,7 +197,7 @@ def BalancedTree(r, h):
+ gracefully::
+
+ sage: graphs.BalancedTree(1, 10)
+- Balanced tree: Graph on 2 vertices
++ Balanced tree: Graph on 11 vertices
+
+ sage: graphs.BalancedTree(-1, 10)
+ Balanced tree: Graph on 1 vertex
+@@ -208,9 +208,6 @@ def BalancedTree(r, h):
+ sage: graphs.BalancedTree(3, 0)
+ Balanced tree: Graph on 1 vertex
+
+- sage: graphs.BalancedTree(5, -2)
+- Balanced tree: Graph on 0 vertices
+-
+ sage: graphs.BalancedTree(-2,-2)
+ Balanced tree: Graph on 0 vertices
+ """
diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py
-index b63135d8e6..5775042976 100644
+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)
@@ -24,3 +167,30 @@
elif format == 'igraph':
if data.is_directed():
raise ValueError("An *undirected* igraph graph was expected. "+
+@@ -4600,7 +4600,7 @@ class Graph(GenericGraph):
+
+ sage: g = Graph([(0,1,0), (1,2,999), (2,3,-5)])
+ sage: g.matching(use_edge_labels=True)
+- [(1, 2, 999)]
++ [(0, 1, 0), (2, 3, -5)]
+ sage: g.matching(algorithm="LP", use_edge_labels=True)
+ [(1, 2, 999)]
+
+@@ -6288,7 +6288,7 @@ class Graph(GenericGraph):
+ return networkx.number_of_cliques(self.networkx_graph(copy=False), vertices, cliques)
+
+ @doc_index("Clique-related methods")
+- 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):
+ sage: (G.cliques_get_max_clique_graph()).show(figsize=[2,2])
+ """
+ import networkx
+- return Graph(networkx.make_max_clique_graph(self.networkx_graph(copy=False), name=name, create_using=networkx.MultiGraph()))
++ return Graph(networkx.make_max_clique_graph(self.networkx_graph(copy=False), create_using=networkx.MultiGraph()))
+
+ @doc_index("Clique-related methods")
+ def cliques_get_clique_bipartite(self, **kwds):
Added: sagemath-scipy-1.0.patch
===================================================================
--- sagemath-scipy-1.0.patch (rev 0)
+++ sagemath-scipy-1.0.patch 2017-12-15 21:39:13 UTC (rev 274537)
@@ -0,0 +1,16 @@
+diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
+index 17b5ebb84b..7ce9055cba 100644
+--- a/src/sage/numerical/optimize.py
++++ b/src/sage/numerical/optimize.py
+@@ -486,9 +486,9 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
+ else:
+ min = optimize.fmin_tnc(f, x0, approx_grad=True, bounds=cons, messages=0, **args)[0]
+ elif isinstance(cons[0], function_type) or isinstance(cons[0], Expression):
+- min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args)
++ min = optimize.fmin_cobyla(f, x0, cons, **args)
+ elif isinstance(cons, function_type) or isinstance(cons, Expression):
+- min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args)
++ min = optimize.fmin_cobyla(f, x0, cons, **args)
+ return vector(RDF, min)
+
+
More information about the arch-commits
mailing list