#9808: Upgrade numpy to 1.5.0 and scipy to 0.8
----------------------------------------------------------------------------------+
Reporter: maldun
| Owner: maldun
Type: task
| Status: needs_review
Priority: major
| Milestone: sage-4.6
Component: packages
| Keywords: numpy, scipy
Author: Stefan Reiterer, Francois Bissey
| Upstream: N/A
Reviewer: Karl-Dieter Crisman, David Kirkby, Leif Leonhardy, Francois
Bissey | Merged:
Work_issues:
|
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Comment(by jhpalmieri):
What do I need to do to install these? I did this: unpacked a
sage-4.6.alpha2 tarball, downloaded the new numpy and scipy spkg files,
applied the file "trac_9808_numpy_doctest_change.patch" to the main Sage
library spkg, and built Sage from scratch (with SAGE_CHECK=yes, except
when installing the python spkg, which always fails self-tests). On
taurus (a skynet linux machine, x86_64-Linux-nehalem-fc), I'm getting
doctest failures:
{{{
The following tests failed:
sage -t -long devel/sage/sage/plot/plot.py # 12 doctests failed
sage -t -long devel/sage/sage/misc/citation.pyx # 2 doctests
failed
sage -t -long devel/sage/sage/plot/misc.py # 4 doctests failed
}}}
For example:
{{{
sage -t -long devel/sage/sage/misc/citation.pyx
**********************************************************************
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/devel/sage-
main/sage/misc/citation.pyx", line 60\
:
sage: get_systems('integrate(x^2, x)')
Expected:
['ginac', 'Maxima']
Got:
['numpy', 'ginac', 'Maxima']
**********************************************************************
}}}
and
{{{
sage -t -long devel/sage/sage/plot/plot.py
**********************************************************************
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/devel/sage-
main/sage/plot/plot.py", line 207:
sage: (g1+g2).show(ticks=pi/6, tick_formatter=pi) # show their sum,
nicely formatted
Exception raised:
Traceback (most recent call last):
File
"/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/bin/ncadoctest.py",
line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File
"/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/bin/sagedoctest.py",
line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File
"/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/bin/ncadoctest.py",
line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_0[49]>", line 1, in <module>
(g1+g2).show(ticks=pi/Integer(6), tick_formatter=pi) # show their
sum, nicely formatted###line 207:
sage: (g1+g2).show(ticks=pi/6, tick_formatter=pi) # show their sum,
nicely formatted
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/sage/plot/plot.py", line 1546, in show
self.save(DOCTEST_MODE_FILE, **options)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/sage/plot/plot.py", line 2202, in save
figure.savefig(filename,dpi=dpi,bbox_inches='tight',**options)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/figure.py", line 1032, in savefig
self.canvas.print_figure(*args, **kwargs)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/backend_bases.py", line 1455, in print_figure
**kwargs)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/backends/backend_agg.py", line 358, in print_png
FigureCanvasAgg.draw(self)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/backends/backend_agg.py", line 314, in draw
self.figure.draw(self.renderer)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/artist.py", line 46, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/figure.py", line 773, in draw
for a in self.axes: a.draw(renderer)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/artist.py", line 46, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/axes.py", line 1735, in draw
a.draw(renderer)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/artist.py", line 46, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/axis.py", line 742, in draw
tick.draw(renderer)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/artist.py", line 46, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/axis.py", line 196, in draw
self.label1.draw(renderer)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/text.py", line 518, in draw
bbox, info = self._get_layout(renderer)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/text.py", line 280, in _get_layout
clean_line, self._fontproperties, ismath=ismath)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/backends/backend_agg.py", line 156, in
get_text_width_height_descent
self.mathtext_parser.parse(s, self.dpi, prop)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/mathtext.py", line 2797, in parse
font_output = fontset_class(prop, backend)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/mathtext.py", line 658, in __init__
self._stix_fallback = StixFonts(*args, **kwargs)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/mathtext.py", line 900, in __init__
fullpath = findfont(name)
File "/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python
/site-packages/matplotlib/font_manager.py", line 1306, in findfont
if not os.path.exists(font):
File
"/home/palmieri/taurus/numpy/sage-4.6.alpha2/local/lib/python2.6/genericpath.py",
line 18, in exists
st = os.stat(path)
TypeError: coercing to Unicode: need string or buffer, dict found
}}}
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/9808#comment:167>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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