matplotlib-devel Mailing List for matplotlib

Hi,
I noticed several tracebacks during doc building, so I'm adding them
here so we can get them fixed; let's start:
reading sources... [ 54%] examples/pylab_examples/geo_demo
/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/sphinxext/plot_directive.p
y:322: PlotWarning: Exception running plot
/home/morph/deb/build-area/matplotlib-1.0.1-test/doc/mpl_examples/pyla
b_examples/geo_demo.py
Traceback (most recent call last):
 File "/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/sphinxext/plot_directive.py",
line 319, in render_figures
 run_code(plot_path, function_name, plot_code, context=context)
 File "/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/sphinxext/plot_directive.py",
line 230, in run_code
 "__plot__", fd, fname, ('py', 'r', imp.PY_SOURCE))
 File "geo_demo.py", line 10, in <module>
 File "/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/pyplot.py",
line 658, in subplot
 a = fig.add_subplot(*args, **kwargs)
 File "/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/figure.py",
line 687, in add_subplot
 a = subplot_class_factory(projection_class)(self, *args, **kwargs)
 File "/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/axes.py",
line 8380, in __init__
 self._axes_class.__init__(self, fig, self.figbox, **kwargs)
 File "custom_projection_example.py", line 33, in __init__
TypeError: expected string or Unicode object, NoneType found
 warnings.warn(s, PlotWarning)
---
reading sources... [ 57%] examples/pylab_examples/image_demo2
/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/sphinxext/plot_directive.py:322:
PlotWarning: Exception running plot
/home/morph/deb/build-area/matplotlib-1.0.1-test/doc/mpl_examples/pylab_examples/image_demo2.py
Traceback (most recent call last):
 File "/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/sphinxext/plot_directive.py",
line 319, in render_figures
 run_code(plot_path, function_name, plot_code, context=context)
 File "/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/sphinxext/plot_directive.py",
line 230, in run_code
 "__plot__", fd, fname, ('py', 'r', imp.PY_SOURCE))
 File "image_demo2.py", line 9, in <module>
IOError: [Errno 2] No such file or directory:
'/home/morph/deb/build-area/matplotlib-1.0.1-test/sampledata/ct.raw'
 warnings.warn(s, PlotWarning)
(see other email about missing ct.raw in sampledata tarball)
---
reading sources... [ 61%] examples/pylab_examples/loadrec
/usr/lib/pymodules/python2.6/xlwt/Cell.py:17: DeprecationWarning:
struct integer overflow masking is deprecated
 return pack('<5HL', 0x00FD, 10, self.rowx, self.colx, self.xf_idx,
self.sst_idx)
/usr/lib/pymodules/python2.6/xlwt/Cell.py:225: DeprecationWarning:
struct integer overflow masking is deprecated
 pieces.append(pack('<4H', 0x00BD, 6 * nc + 6, rowx, icolx))
/usr/lib/pymodules/python2.6/xlwt/Cell.py:227: DeprecationWarning:
struct integer overflow masking is deprecated
 pieces.append(pack('<H', lastcolx))
---
reading sources... [ 81%] examples/units/artist_tests
/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/sphinxext/plot_directive.p
y:322: PlotWarning: Exception running plot
/home/morph/deb/build-area/matplotlib-1.0.1-test/doc/mpl_examples/unit
s/artist_tests.py
Traceback (most recent call last):
 File "/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/sphinxext/plot_directive.py",
line 319, in render_figures
 run_code(plot_path, function_name, plot_code, context=context)
 File "/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/sphinxext/plot_directive.py",
line 230, in run_code
 "__plot__", fd, fname, ('py', 'r', imp.PY_SOURCE))
 File "artist_tests.py", line 30, in <module>
 File "/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/collections.py",
line 836, in __init__
 self.set_segments(segments)
 File "/home/morph/deb/build-area/matplotlib-1.0.1-test/build/lib.linux-x86_64-2.6/matplotlib/collections.py",
line 845, in set_segments
 seg = np.asarray(seg, np.float_)
 File "/usr/lib/pymodules/python2.6/numpy/core/numeric.py", line 261,
in asarray
 return array(a, dtype, copy=False, order=order)
ValueError: setting an array element with a sequence.
 warnings.warn(s, PlotWarning)
---
Severals:
* (WARNING/2) Block quote ends without a blank line; unexpected unindent.
* (ERROR/3) Unexpected indentation.
* (WARNING/2) malformed hyperlink target.
* WARNING: document isn't included in any toctree
* WARNING: unusable reference target found
Cheers,
-- 
Sandro Tosi (aka morph, morpheus, matrixhasu)
My website: http://matrixhasu.altervista.org/
Me at Debian: http://wiki.debian.org/SandroTosi

Hi,
I noticed some erroneous behaviour when using a
LinearSegmentedColormap with an "under" color and different numbers of
color levels. The attached script replicates the behaviour, whereby
lowering the number of colors causes less of the values to be
considered "under" the vmin. I tracked the problem back to the
Colormap class where the results of Normalize are multiplied by the
number of color levels (N) and casted as an int to be used as indices
in the color array. The expected behaviour would be that all negative
values should be considered "under", however the results of the cast
means that anything between 0 and -0.5 will be set to 0 and therefore
will be in the normal color range for the colormap. The attached patch
overcomes this by setting all negative values to -1 before applying
the cast.
Thanks for your help,
Eoghan

Hi,
On Tue, Jan 4, 2011 at 19:11, Jakub Wilk <jw...@de...> wrote:
> Package: python-matplotlib-doc
> Version: 0.99.3-1
> Severity: minor
>
> There are several "Exception occurred rendering plot" warnings in the
> generated documentation:
>
> $ cd /usr/share/doc/python-matplotlib-doc/html/ && grep -r 'Exception
> occurred' .
> ./users/screenshots.html:[<a class="reference external"
> href="../plot_directive/mpl_examples/pylab_examples/scatter_demo2.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./users/screenshots.html:[<a class="reference external"
> href="../plot_directive/mpl_examples/api/date_demo.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./users/screenshots.html:[<a class="reference external"
> href="../plot_directive/mpl_examples/pylab_examples/finance_work2.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./users/screenshots.html:[<a class="reference external"
> href="../plot_directive/pyplots/plotmap.py">source code</a>]<p>Exception
> occurred rendering plot.</p>
> ./examples/units/date_support.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/units/date_support.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/units/basic_units.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/units/basic_units.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/units/artist_tests.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/units/artist_tests.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/axes_grid/demo_image.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/axes_grid/demo_image.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/pylab_examples/data_helper.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/pylab_examples/data_helper.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/pylab_examples/date_demo2.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/pylab_examples/date_demo2.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/pylab_examples/geo_demo.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/pylab_examples/geo_demo.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/pylab_examples/centered_ticklabels.html:[<a class="reference
> external"
> href="../../plot_directive/mpl_examples/pylab_examples/centered_ticklabels.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/pylab_examples/finance_demo.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/pylab_examples/finance_demo.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/pylab_examples/date_demo1.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/pylab_examples/date_demo1.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/pylab_examples/finance_work2.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/pylab_examples/finance_work2.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/pylab_examples/loadrec.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/pylab_examples/loadrec.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/pylab_examples/scatter_demo2.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/pylab_examples/scatter_demo2.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/pylab_examples/multipage_pdf.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/pylab_examples/multipage_pdf.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
> ./examples/api/date_demo.html:[<a class="reference external"
> href="../../plot_directive/mpl_examples/api/date_demo.py">source
> code</a>]<p>Exception occurred rendering plot.</p>
The updated list is:
api/axes_api.html
api/pyplot_api.html
examples/api/hinton_demo.html
examples/api/radar_chart.html
examples/api/sankey_demo.html
examples/pylab_examples/anchored_artists.html
examples/pylab_examples/arrow_demo.html
examples/pylab_examples/axes_zoom_effect.html
examples/pylab_examples/data_helper.html
examples/pylab_examples/demo_bboximage.html
examples/pylab_examples/geo_demo.html
examples/pylab_examples/image_demo2.html
examples/pylab_examples/legend_auto.html
examples/pylab_examples/multipage_pdf.html
examples/units/artist_tests.html
examples/units/basic_units.html
users/annotations_guide.html
users/screenshots.html
But I have some problems debugging these issues, since when I run the
code by-hand, it works fine but in the html file it's not shown. How
can I debug that? in the log there's nothing about these problems (but
other error, I'll follow them up in another mail).
Thanks in advance,
-- 
Sandro Tosi (aka morph, morpheus, matrixhasu)
My website: http://matrixhasu.altervista.org/
Me at Debian: http://wiki.debian.org/SandroTosi

Message for matplotlib developers
I have posted a message on the matplotlib-users list, but it may be of interest to some in the -devel list as well. Here is an excerpt describing an installation problem, and workaround, that affects Mac OS X and matplotlib.
I am new to Python, and have tried installing matplotlib on a Mac OS X 10.6 (Snow Leopard). In spite of excellent tools and documentation provided, the installation was unsuccessful:
- my computer is 10.6.6 (fully updated Snow Leopard)
- with full Xcode (c developers) code installed
- it reports Python 2.6.1 installed
- it installs packages such as numpy and biopython ok (which gives me a little confidence that I am doing things correctly)
But when I tried to install matplotlib 1.0.1, I encountered the following problems:
- the matplotlib mkpg .dmg files will not run as they advise Python 2.6 is required (but which is already installed!)
- upgrading to Python 2.7 did not fix this problem and the error message continued
- using tar and then installing via Python install files resulted in an unsatisfied compiler reference from "lipo"
- installing Python easy-install and using .egg scripts produced the same error message
A call for help on the matplotlib-users list produced a suggestion to go back to matplotlib 1.0.0 (not 1.0.1). This worked on one Mac, but did not work on a second Mac (with what I thought was identical configuration).
Finally, a general solution was found using MacPorts, as follows:
> **update** matplotlib 1.0.0 setup worked on one but did not work on a second Mac OS X 10.6.6. The second one again failed with a missing dependency. It seems to depend on what previous packages may have been installed.
> The following seems to be a complete fix:
> 1. On Mac OS X 10.6.x (in my case...6)
> 2. Install Apple Xcode (requires registration as an Apple developer)
> 3. Install MacPorts http://www.macports.org/
> 4. Check that all library dependencies for matplotlib in Python 2.6 have been satisfied by first running (with Administrator privileges):
> 	sudo port install py26-matplotlib
> (this will use MacPorts script to install matplotlib 1.0.0)
> 5. (optional) you can reinstall now matplotlib from http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.0/matplotlib-1.0.0.tar.gz/download
> **now** it works :-)
The above may suggest that matplotlib may have a dependency that is not present on a virgin OSX Xcode machine but which is incidentally installed by some other package usually present on a developer's machine and so whose absence is not noticed when preparing the installation script.
I hope the above report is of assistance to the devel community. I am a newbie to this so won't be of much help to you other than having found and documented the problem.
Many thanks for bringing matplotlib to the world!
Leslie Burnett
Sydney University

Hi Ben,
thanks for the fast reply!
On Mon, Jan 17, 2011 at 20:35, Benjamin Root <ben...@ou...> wrote:
> I have seen this before, and I think it was discussed once before.
> Visually, there is very little difference,
indeed, looking at the 2 images, I can't see any difference.
> but supposedly there is some sort
> of issue with different PIL versions. What version of PIL do you have?
1.1.7
Cheers,
-- 
Sandro Tosi (aka morph, morpheus, matrixhasu)
My website: http://matrixhasu.altervista.org/
Me at Debian: http://wiki.debian.org/SandroTosi

On Mon, Jan 17, 2011 at 1:28 PM, Sandro Tosi <mo...@de...> wrote:
> Hi,
> I was playing with test suite and I noticed that :
>
> morph@zion:~/deb/build-area/matplotlib-1.0.1$
> PYTHONPATH=build/lib.linux-x86_64-2.6 python -c "import matplotlib as
> m ; m.test(verbosity=1)"
> /usr/lib/pymodules/python2.6/nose/plugins/manager.py:391: UserWarning:
> Module matplotlib was already imported from
>
> /home/morph/deb/build-area/matplotlib-1.0.1/build/lib.linux-x86_64-2.6/matplotlib/__init__.pyc,
> but /usr/lib/pymodules/python2.6 is being added to sys.path
> import pkg_resources
>
> ..K........K..K..K..K..K..K..K..K..K..K..K..K..K..K..K..K..K..K..K..K..KE.K..K..K..K..K..K/home/morph/deb/build-area/matplotlib-1.0.1/build/lib.linux-x86_64-2.6/matplotlib/axes.py:2381:
> UserWarning: Attempting to set identical left==right results
> in singular transformations; automatically expanding.
> left=730139.0, right=730139.0
> + 'left=%s, right=%s') % (left, right))
> ...K..KK..K..K.....K..K..K..K..K....K..K..K....K..K..K..K..K
> ======================================================================
> ERROR: matplotlib.tests.test_axes.test_pcolormesh
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/pymodules/python2.6/nose/case.py", line 183, in runTest
> self.test(*self.arg)
> File
> "/home/morph/deb/build-area/matplotlib-1.0.1/build/lib.linux-x86_64-2.6/matplotlib/testing/decorators.py",
> line 32, in failer
> result = f(*args, **kwargs)
> File
> "/home/morph/deb/build-area/matplotlib-1.0.1/build/lib.linux-x86_64-2.6/matplotlib/testing/decorators.py",
> line 126, in decorated_compare_images
> '(RMS %(rms).3f)'%err)
> ImageComparisonFailure: images not close:
>
> /home/morph/deb/build-area/matplotlib-1.0.1/result_images/test_axes/pcolormesh.png
> vs.
> /home/morph/deb/build-area/matplotlib-1.0.1/result_images/test_axes/expected-pcolormesh.png
> (RMS 116.512)
>
> ----------------------------------------------------------------------
> Ran 150 tests in 107.607s
>
> FAILED (KNOWNFAIL=46, errors=1)
>
> Except for the UserWarning, there is an error in the suite: is someone
> else able to replicate it? is it another KNOWNFAIL?
>
> Cheers,
> --
> Sandro Tosi (aka morph, morpheus, matrixhasu)
> My website: http://matrixhasu.altervista.org/
> Me at Debian: http://wiki.debian.org/SandroTosi
>
>
I have seen this before, and I think it was discussed once before.
Visually, there is very little difference, but supposedly there is some sort
of issue with different PIL versions. What version of PIL do you have?
Ben Root

Hi everyone,
I just committed a big typos fix to trunk (r8925), should changes
like this be backported to the maintenance branch?
best,
-- 
Paul Ivanov
314 address only used for lists, off-list direct email at:
http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7 

Hi,
I was playing with test suite and I noticed that :
morph@zion:~/deb/build-area/matplotlib-1.0.1$
PYTHONPATH=build/lib.linux-x86_64-2.6 python -c "import matplotlib as
m ; m.test(verbosity=1)"
/usr/lib/pymodules/python2.6/nose/plugins/manager.py:391: UserWarning:
Module matplotlib was already imported from
/home/morph/deb/build-area/matplotlib-1.0.1/build/lib.linux-x86_64-2.6/matplotlib/__init__.pyc,
but /usr/lib/pymodules/python2.6 is being added to sys.path
 import pkg_resources
..K........K..K..K..K..K..K..K..K..K..K..K..K..K..K..K..K..K..K..K..K..KE.K..K..K..K..K..K/home/morph/deb/build-area/matplotlib-1.0.1/build/lib.linux-x86_64-2.6/matplotlib/axes.py:2381:
UserWarning: Attempting to set identical left==right results
in singular transformations; automatically expanding.
left=730139.0, right=730139.0
 + 'left=%s, right=%s') % (left, right))
...K..KK..K..K.....K..K..K..K..K....K..K..K....K..K..K..K..K
======================================================================
ERROR: matplotlib.tests.test_axes.test_pcolormesh
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/usr/lib/pymodules/python2.6/nose/case.py", line 183, in runTest
 self.test(*self.arg)
 File "/home/morph/deb/build-area/matplotlib-1.0.1/build/lib.linux-x86_64-2.6/matplotlib/testing/decorators.py",
line 32, in failer
 result = f(*args, **kwargs)
 File "/home/morph/deb/build-area/matplotlib-1.0.1/build/lib.linux-x86_64-2.6/matplotlib/testing/decorators.py",
line 126, in decorated_compare_images
 '(RMS %(rms).3f)'%err)
ImageComparisonFailure: images not close:
/home/morph/deb/build-area/matplotlib-1.0.1/result_images/test_axes/pcolormesh.png
vs. /home/morph/deb/build-area/matplotlib-1.0.1/result_images/test_axes/expected-pcolormesh.png
(RMS 116.512)
----------------------------------------------------------------------
Ran 150 tests in 107.607s
FAILED (KNOWNFAIL=46, errors=1)
Except for the UserWarning, there is an error in the suite: is someone
else able to replicate it? is it another KNOWNFAIL?
Cheers,
-- 
Sandro Tosi (aka morph, morpheus, matrixhasu)
My website: http://matrixhasu.altervista.org/
Me at Debian: http://wiki.debian.org/SandroTosi