matplotlib-users Mailing List for matplotlib

Sharaf Al-Sharif wrote:
> Hi,
> Is there a way to specify the number of ticks on an axis? Say, I want 
> the y-axes on all my subplots to have 5 ticks, for example.
import matplotlib.ticker as mticker
ax.yaxis.set_major_locator(mticker.MaxNLocator(4,steps=[1, 2, 5, 10]))

As far as I can see, this happens when there are obsolete rst files
(related with the Gallery I guess), created during the doc. build with
previous svn checkout.
For example, I recently removed
mpl_examples/axes_grid/demo_fixed_size_axes.py from the svn. But if
you ever have built the documentation with previous svn checkout
(before that file is removed), then you already have some associated
rst files under the doc/examples directory. And the errors are raised
when these obsolete files are processed with sphinx.
I think removing doc/examples directory will solve the problem, or
build the doc from the completely new checkout.
We may delete the "doc/examples" directory within the "make.py", but
I'm not sure how much this will slow down the build time.
Please let me know if there still is a problem.
Regards,
-JJ
On Tue, Dec 22, 2009 at 4:32 PM, Michael Droettboom <md...@st...> wrote:
> I get the same errors as you (which seem to indicate a bug in the
> axis_grid toolkit), but it's not catastrophic -- the documentation is
> ultimately built anyway, missing a couple of figures. (I tried with
> both Sphinx 0.6.3 and Sphinx hg latest).
>
> Have you tried a clean rebuild? (By removing the doc/build directory?)
>
> Mike
>
> Nils Wagner wrote:
>> Hi all,
>>
>> I cannot build the documentation of matplotlib.
>> I am using the latest svn of numpy and matplotlib.
>>
>> How can I fix the problem ?
>>
>>
>>        Nils
>>
>> python make.py html
>> Running Sphinx v1.0
>> loading pickled environment... not found
>> animation, api, axes_grid, event_handling, misc, mplot3d,
>> pngsuite, pylab_examples, tests, units, user_interfaces,
>> widgets,
>> building [html]: targets for 494 source files that are out
>> of date
>> updating environment: 494 added, 0 changed, 0 removed
>> /home/nwagner/local/lib64/python2.6/site-packages/numpy/core/numeric.py:692:
>> DeprecationWarning:
>> The current behavior of correlate is deprecated for 1.4.0,
>> and will be removed
>> for NumPy 1.5.0.
>>
>> The new behavior fits the conventional definition of
>> correlation: inputs are
>> never swapped, and the second argument is conjugated for
>> complex arrays.
>>  DeprecationWarning)
>> /home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py:273:
>> UserWarning: Exception running plot
>> /home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_axes_divider.py
>> Traceback (most recent call last):
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py",
>> line 270, in render_figures
>>   run_code(plot_path, function_name, plot_code)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py",
>> line 182, in run_code
>>   "__plot__", fd, fname, ('py', 'r', imp.PY_SOURCE))
>>  File "demo_axes_divider.py", line 129, in <module>
>>  File "demo_axes_divider.py", line 125, in demo
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/pyplot.py",
>> line 350, in draw
>>   get_current_fig_manager().canvas.draw()
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/backends/backend_agg.py",
>> line 388, in draw
>>   self.figure.draw(self.renderer)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py",
>> line 55, in draw_wrapper
>>   draw(artist, renderer, *kl)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/figure.py",
>> line 802, in draw
>>   func(*args)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axes_divider.py",
>> line 582, in draw
>>   self._axes_class.draw(self, renderer, inframe)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axislines.py",
>> line 710, in draw
>>   super(Axes, self).draw(renderer, inframe)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py",
>> line 55, in draw_wrapper
>>   draw(artist, renderer, *kl)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/axes.py",
>> line 1775, in draw
>>   a.draw(renderer)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py",
>> line 55, in draw_wrapper
>>   draw(artist, renderer, *kl)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 1343, in draw
>>   self._draw_ticks(renderer)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 1209, in _draw_ticks
>>   self.major_ticks.draw(renderer)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 309, in draw
>>   gc.set_foreground(self.get_markeredgecolor())
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 236, in get_markeredgecolor
>>   return self.get_color()
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 232, in get_color
>>   return self.get_attribute_from_ref_artist("color",
>> "k")
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 187, in get_attribute_from_ref_artist
>>   ref_artist = self.get_ref_artist()
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 229, in get_ref_artist
>>   return self._ref_artist.get_ticklines()[0]
>> IndexError: list index out of range
>>
>>  warnings.warn(s)
>> /home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py:273:
>> UserWarning: Exception running plot
>> /home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_axes_rgb.py
>> Traceback (most recent call last):
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py",
>> line 270, in render_figures
>>   run_code(plot_path, function_name, plot_code)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py",
>> line 182, in run_code
>>   "__plot__", fd, fname, ('py', 'r', imp.PY_SOURCE))
>>  File "demo_axes_rgb.py", line 4, in <module>
>>  File
>> "/home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_axes_divider.py",
>> line 129, in <module>
>>   demo()
>>  File
>> "/home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_axes_divider.py",
>> line 125, in demo
>>   plt.draw()
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/pyplot.py",
>> line 350, in draw
>>   get_current_fig_manager().canvas.draw()
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/backends/backend_agg.py",
>> line 388, in draw
>>   self.figure.draw(self.renderer)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py",
>> line 55, in draw_wrapper
>>   draw(artist, renderer, *kl)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/figure.py",
>> line 802, in draw
>>   func(*args)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axes_divider.py",
>> line 582, in draw
>>   self._axes_class.draw(self, renderer, inframe)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axislines.py",
>> line 710, in draw
>>   super(Axes, self).draw(renderer, inframe)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py",
>> line 55, in draw_wrapper
>>   draw(artist, renderer, *kl)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/axes.py",
>> line 1775, in draw
>>   a.draw(renderer)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py",
>> line 55, in draw_wrapper
>>   draw(artist, renderer, *kl)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 1343, in draw
>>   self._draw_ticks(renderer)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 1209, in _draw_ticks
>>   self.major_ticks.draw(renderer)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 309, in draw
>>   gc.set_foreground(self.get_markeredgecolor())
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 236, in get_markeredgecolor
>>   return self.get_color()
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 232, in get_color
>>   return self.get_attribute_from_ref_artist("color",
>> "k")
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 187, in get_attribute_from_ref_artist
>>   ref_artist = self.get_ref_artist()
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py",
>> line 229, in get_ref_artist
>>   return self._ref_artist.get_ticklines()[0]
>> IndexError: list index out of range
>>
>>  warnings.warn(s)
>> /home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py:273:
>> UserWarning: Exception running plot
>> /home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_fixed_size_axes.py
>> Traceback (most recent call last):
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py",
>> line 270, in render_figures
>>   run_code(plot_path, function_name, plot_code)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py",
>> line 180, in run_code
>>   fd = open(fname)
>> IOError: [Errno 2] No such file or directory:
>> 'demo_fixed_size_axes.py'
>>
>>  warnings.warn(s)
>> Exception occurred while building, starting debugger:
>> Traceback (most recent call last):
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/cmdline.py",
>> line 172, in main
>>   app.build(all_files, filenames)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/application.py",
>> line 130, in build
>>   self.builder.build_update()
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/builders/__init__.py",
>> line 265, in build_update
>>   'out of date' % len(to_build))
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/builders/__init__.py",
>> line 285, in build
>>   purple, length):
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/builders/__init__.py",
>> line 131, in status_iterator
>>   for item in iterable:
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/environment.py",
>> line 513, in update_generator
>>   self.read_doc(docname, app=app)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/environment.py",
>> line 604, in read_doc
>>   pub.publish()
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/core.py",
>> line 204, in publish
>>   self.settings)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/readers/__init__.py",
>> line 69, in read
>>   self.parse()
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/readesphinx repositoryrs/__init__.py",
>> line 75, in parse
>>   self.parser.parse(self.input, document)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/__init__.py",
>> line 157, in parse
>>   self.statemachine.run(inputlines, document,
>> inliner=self.inliner)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py",
>> line 170, in run
>>   input_source=document['source'])
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/statemachine.py",
>> line 232, in run
>>   context, state, transitions)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/statemachine.py",
>> line 420, in check_line
>>   return method(match, context, next_state)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py",
>> line 2658, in underline
>>   self.section(title, source, style, lineno - 1,
>> messages)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py",
>> line 308, in section
>>   self.new_subsection(title, lineno, messages)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py",
>> line 376, in new_subsection
>>   node=section_node, match_titles=1)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py",
>> line 266, in nested_parse
>>   node=node, match_titles=match_titles)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py",
>> line 195, in run
>>   results = StateMachineWS.run(self, input_lines,
>> input_offset)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/statemachine.py",
>> line 232, in run
>>   context, state, transitions)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/statemachine.py",
>> line 420, in check_line
>>   return method(match, context, next_state)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py",
>> line 2239, in explicit_markup
>>   nodelist, blank_finish =
>> self.explicit_construct(match)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py",
>> line 2251, in explicit_construct
>>   return method(self, expmatch)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py",
>> line 1994, in directive
>>   directive_class, match, type_name, option_presets)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py",
>> line 2043, in run_directive
>>   result = directive_instance.run()
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/__init__.py",
>> line 364, in run
>>   self.state, self.state_machine)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py",
>> line 414, in plot_directive
>>   options, state_machine)
>>  File
>> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py",
>> line 337, in _plot_directive
>>   shutil.copyfile(plot_path, os.path.join(destdir,
>> fname))
>>  File "/usr/lib64/python2.6/shutil.py", line 52, in
>> copyfile
>>   fsrc = open(src, 'rb')
>> IOError: [Errno 2] No such file or directory:
>> u'/home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_fixed_size_axes.py'
>>
>>> /usr/lib64/python2.6/shutil.py(52)copyfile()
>>>
>> -> fsrc = open(src, 'rb')
>>
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>
> --
> Michael Droettboom
> Science Software Branch
> Operations and Engineering Division
> Space Telescope Science Institute
> Operated by AURA for NASA
>
>
> ------------------------------------------------------------------------------
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>

Hi,
Is there a way to specify the number of ticks on an axis? Say, I want the
y-axes on all my subplots to have 5 ticks, for example.
Thanks.
Sharaf

I get the same errors as you (which seem to indicate a bug in the 
axis_grid toolkit), but it's not catastrophic -- the documentation is 
ultimately built anyway, missing a couple of figures. (I tried with 
both Sphinx 0.6.3 and Sphinx hg latest).
Have you tried a clean rebuild? (By removing the doc/build directory?)
Mike
Nils Wagner wrote:
> Hi all,
>
> I cannot build the documentation of matplotlib.
> I am using the latest svn of numpy and matplotlib.
>
> How can I fix the problem ?
>
>
> Nils
>
> python make.py html
> Running Sphinx v1.0
> loading pickled environment... not found
> animation, api, axes_grid, event_handling, misc, mplot3d, 
> pngsuite, pylab_examples, tests, units, user_interfaces, 
> widgets,
> building [html]: targets for 494 source files that are out 
> of date
> updating environment: 494 added, 0 changed, 0 removed
> /home/nwagner/local/lib64/python2.6/site-packages/numpy/core/numeric.py:692: 
> DeprecationWarning:
> The current behavior of correlate is deprecated for 1.4.0, 
> and will be removed
> for NumPy 1.5.0.
>
> The new behavior fits the conventional definition of 
> correlation: inputs are
> never swapped, and the second argument is conjugated for 
> complex arrays.
> DeprecationWarning)
> /home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py:273: 
> UserWarning: Exception running plot 
> /home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_axes_divider.py
> Traceback (most recent call last):
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
> line 270, in render_figures
> run_code(plot_path, function_name, plot_code)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
> line 182, in run_code
> "__plot__", fd, fname, ('py', 'r', imp.PY_SOURCE))
> File "demo_axes_divider.py", line 129, in <module>
> File "demo_axes_divider.py", line 125, in demo
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/pyplot.py", 
> line 350, in draw
> get_current_fig_manager().canvas.draw()
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/backends/backend_agg.py", 
> line 388, in draw
> self.figure.draw(self.renderer)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py", 
> line 55, in draw_wrapper
> draw(artist, renderer, *kl)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/figure.py", 
> line 802, in draw
> func(*args)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axes_divider.py", 
> line 582, in draw
> self._axes_class.draw(self, renderer, inframe)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axislines.py", 
> line 710, in draw
> super(Axes, self).draw(renderer, inframe)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py", 
> line 55, in draw_wrapper
> draw(artist, renderer, *kl)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/axes.py", 
> line 1775, in draw
> a.draw(renderer)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py", 
> line 55, in draw_wrapper
> draw(artist, renderer, *kl)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 1343, in draw
> self._draw_ticks(renderer)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 1209, in _draw_ticks
> self.major_ticks.draw(renderer)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 309, in draw
> gc.set_foreground(self.get_markeredgecolor())
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 236, in get_markeredgecolor
> return self.get_color()
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 232, in get_color
> return self.get_attribute_from_ref_artist("color", 
> "k")
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 187, in get_attribute_from_ref_artist
> ref_artist = self.get_ref_artist()
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 229, in get_ref_artist
> return self._ref_artist.get_ticklines()[0]
> IndexError: list index out of range
>
> warnings.warn(s)
> /home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py:273: 
> UserWarning: Exception running plot 
> /home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_axes_rgb.py
> Traceback (most recent call last):
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
> line 270, in render_figures
> run_code(plot_path, function_name, plot_code)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
> line 182, in run_code
> "__plot__", fd, fname, ('py', 'r', imp.PY_SOURCE))
> File "demo_axes_rgb.py", line 4, in <module>
> File 
> "/home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_axes_divider.py", 
> line 129, in <module>
> demo()
> File 
> "/home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_axes_divider.py", 
> line 125, in demo
> plt.draw()
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/pyplot.py", 
> line 350, in draw
> get_current_fig_manager().canvas.draw()
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/backends/backend_agg.py", 
> line 388, in draw
> self.figure.draw(self.renderer)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py", 
> line 55, in draw_wrapper
> draw(artist, renderer, *kl)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/figure.py", 
> line 802, in draw
> func(*args)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axes_divider.py", 
> line 582, in draw
> self._axes_class.draw(self, renderer, inframe)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axislines.py", 
> line 710, in draw
> super(Axes, self).draw(renderer, inframe)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py", 
> line 55, in draw_wrapper
> draw(artist, renderer, *kl)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/axes.py", 
> line 1775, in draw
> a.draw(renderer)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py", 
> line 55, in draw_wrapper
> draw(artist, renderer, *kl)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 1343, in draw
> self._draw_ticks(renderer)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 1209, in _draw_ticks
> self.major_ticks.draw(renderer)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 309, in draw
> gc.set_foreground(self.get_markeredgecolor())
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 236, in get_markeredgecolor
> return self.get_color()
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 232, in get_color
> return self.get_attribute_from_ref_artist("color", 
> "k")
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 187, in get_attribute_from_ref_artist
> ref_artist = self.get_ref_artist()
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
> line 229, in get_ref_artist
> return self._ref_artist.get_ticklines()[0]
> IndexError: list index out of range
>
> warnings.warn(s)
> /home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py:273: 
> UserWarning: Exception running plot 
> /home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_fixed_size_axes.py
> Traceback (most recent call last):
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
> line 270, in render_figures
> run_code(plot_path, function_name, plot_code)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
> line 180, in run_code
> fd = open(fname)
> IOError: [Errno 2] No such file or directory: 
> 'demo_fixed_size_axes.py'
>
> warnings.warn(s)
> Exception occurred while building, starting debugger:
> Traceback (most recent call last):
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/cmdline.py", 
> line 172, in main
> app.build(all_files, filenames)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/application.py", 
> line 130, in build
> self.builder.build_update()
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/builders/__init__.py", 
> line 265, in build_update
> 'out of date' % len(to_build))
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/builders/__init__.py", 
> line 285, in build
> purple, length):
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/builders/__init__.py", 
> line 131, in status_iterator
> for item in iterable:
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/environment.py", 
> line 513, in update_generator
> self.read_doc(docname, app=app)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/environment.py", 
> line 604, in read_doc
> pub.publish()
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/core.py", 
> line 204, in publish
> self.settings)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/readers/__init__.py", 
> line 69, in read
> self.parse()
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/readesphinx repositoryrs/__init__.py", 
> line 75, in parse
> self.parser.parse(self.input, document)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/__init__.py", 
> line 157, in parse
> self.statemachine.run(inputlines, document, 
> inliner=self.inliner)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
> line 170, in run
> input_source=document['source'])
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/statemachine.py", 
> line 232, in run
> context, state, transitions)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/statemachine.py", 
> line 420, in check_line
> return method(match, context, next_state)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
> line 2658, in underline
> self.section(title, source, style, lineno - 1, 
> messages)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
> line 308, in section
> self.new_subsection(title, lineno, messages)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
> line 376, in new_subsection
> node=section_node, match_titles=1)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
> line 266, in nested_parse
> node=node, match_titles=match_titles)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
> line 195, in run
> results = StateMachineWS.run(self, input_lines, 
> input_offset)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/statemachine.py", 
> line 232, in run
> context, state, transitions)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/statemachine.py", 
> line 420, in check_line
> return method(match, context, next_state)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
> line 2239, in explicit_markup
> nodelist, blank_finish = 
> self.explicit_construct(match)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
> line 2251, in explicit_construct
> return method(self, expmatch)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
> line 1994, in directive
> directive_class, match, type_name, option_presets)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
> line 2043, in run_directive
> result = directive_instance.run()
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/__init__.py", 
> line 364, in run
> self.state, self.state_machine)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
> line 414, in plot_directive
> options, state_machine)
> File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
> line 337, in _plot_directive
> shutil.copyfile(plot_path, os.path.join(destdir, 
> fname))
> File "/usr/lib64/python2.6/shutil.py", line 52, in 
> copyfile
> fsrc = open(src, 'rb')
> IOError: [Errno 2] No such file or directory: 
> u'/home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_fixed_size_axes.py'
> 
>> /usr/lib64/python2.6/shutil.py(52)copyfile()
>> 
> -> fsrc = open(src, 'rb')
>
> ------------------------------------------------------------------------------
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> 
-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Hi all,
I cannot build the documentation of matplotlib.
I am using the latest svn of numpy and matplotlib.
How can I fix the problem ?
 Nils
python make.py html
Running Sphinx v1.0
loading pickled environment... not found
animation, api, axes_grid, event_handling, misc, mplot3d, 
pngsuite, pylab_examples, tests, units, user_interfaces, 
widgets,
building [html]: targets for 494 source files that are out 
of date
updating environment: 494 added, 0 changed, 0 removed
/home/nwagner/local/lib64/python2.6/site-packages/numpy/core/numeric.py:692: 
DeprecationWarning:
The current behavior of correlate is deprecated for 1.4.0, 
and will be removed
for NumPy 1.5.0.
The new behavior fits the conventional definition of 
correlation: inputs are
never swapped, and the second argument is conjugated for 
complex arrays.
 DeprecationWarning)
/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py:273: 
UserWarning: Exception running plot 
/home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_axes_divider.py
Traceback (most recent call last):
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
line 270, in render_figures
 run_code(plot_path, function_name, plot_code)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
line 182, in run_code
 "__plot__", fd, fname, ('py', 'r', imp.PY_SOURCE))
 File "demo_axes_divider.py", line 129, in <module>
 File "demo_axes_divider.py", line 125, in demo
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/pyplot.py", 
line 350, in draw
 get_current_fig_manager().canvas.draw()
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/backends/backend_agg.py", 
line 388, in draw
 self.figure.draw(self.renderer)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py", 
line 55, in draw_wrapper
 draw(artist, renderer, *kl)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/figure.py", 
line 802, in draw
 func(*args)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axes_divider.py", 
line 582, in draw
 self._axes_class.draw(self, renderer, inframe)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axislines.py", 
line 710, in draw
 super(Axes, self).draw(renderer, inframe)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py", 
line 55, in draw_wrapper
 draw(artist, renderer, *kl)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/axes.py", 
line 1775, in draw
 a.draw(renderer)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py", 
line 55, in draw_wrapper
 draw(artist, renderer, *kl)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 1343, in draw
 self._draw_ticks(renderer)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 1209, in _draw_ticks
 self.major_ticks.draw(renderer)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 309, in draw
 gc.set_foreground(self.get_markeredgecolor())
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 236, in get_markeredgecolor
 return self.get_color()
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 232, in get_color
 return self.get_attribute_from_ref_artist("color", 
"k")
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 187, in get_attribute_from_ref_artist
 ref_artist = self.get_ref_artist()
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 229, in get_ref_artist
 return self._ref_artist.get_ticklines()[0]
IndexError: list index out of range
 warnings.warn(s)
/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py:273: 
UserWarning: Exception running plot 
/home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_axes_rgb.py
Traceback (most recent call last):
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
line 270, in render_figures
 run_code(plot_path, function_name, plot_code)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
line 182, in run_code
 "__plot__", fd, fname, ('py', 'r', imp.PY_SOURCE))
 File "demo_axes_rgb.py", line 4, in <module>
 File 
"/home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_axes_divider.py", 
line 129, in <module>
 demo()
 File 
"/home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_axes_divider.py", 
line 125, in demo
 plt.draw()
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/pyplot.py", 
line 350, in draw
 get_current_fig_manager().canvas.draw()
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/backends/backend_agg.py", 
line 388, in draw
 self.figure.draw(self.renderer)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py", 
line 55, in draw_wrapper
 draw(artist, renderer, *kl)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/figure.py", 
line 802, in draw
 func(*args)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axes_divider.py", 
line 582, in draw
 self._axes_class.draw(self, renderer, inframe)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axislines.py", 
line 710, in draw
 super(Axes, self).draw(renderer, inframe)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py", 
line 55, in draw_wrapper
 draw(artist, renderer, *kl)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/axes.py", 
line 1775, in draw
 a.draw(renderer)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/artist.py", 
line 55, in draw_wrapper
 draw(artist, renderer, *kl)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 1343, in draw
 self._draw_ticks(renderer)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 1209, in _draw_ticks
 self.major_ticks.draw(renderer)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 309, in draw
 gc.set_foreground(self.get_markeredgecolor())
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 236, in get_markeredgecolor
 return self.get_color()
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 232, in get_color
 return self.get_attribute_from_ref_artist("color", 
"k")
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 187, in get_attribute_from_ref_artist
 ref_artist = self.get_ref_artist()
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/axes_grid/axis_artist.py", 
line 229, in get_ref_artist
 return self._ref_artist.get_ticklines()[0]
IndexError: list index out of range
 warnings.warn(s)
/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py:273: 
UserWarning: Exception running plot 
/home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_fixed_size_axes.py
Traceback (most recent call last):
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
line 270, in render_figures
 run_code(plot_path, function_name, plot_code)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
line 180, in run_code
 fd = open(fname)
IOError: [Errno 2] No such file or directory: 
'demo_fixed_size_axes.py'
 warnings.warn(s)
Exception occurred while building, starting debugger:
Traceback (most recent call last):
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/cmdline.py", 
line 172, in main
 app.build(all_files, filenames)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/application.py", 
line 130, in build
 self.builder.build_update()
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/builders/__init__.py", 
line 265, in build_update
 'out of date' % len(to_build))
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/builders/__init__.py", 
line 285, in build
 purple, length):
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/builders/__init__.py", 
line 131, in status_iterator
 for item in iterable:
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/environment.py", 
line 513, in update_generator
 self.read_doc(docname, app=app)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/Sphinx-1.0dev_20091204-py2.6.egg/sphinx/environment.py", 
line 604, in read_doc
 pub.publish()
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/core.py", 
line 204, in publish
 self.settings)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/readers/__init__.py", 
line 69, in read
 self.parse()
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/readers/__init__.py", 
line 75, in parse
 self.parser.parse(self.input, document)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/__init__.py", 
line 157, in parse
 self.statemachine.run(inputlines, document, 
inliner=self.inliner)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
line 170, in run
 input_source=document['source'])
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/statemachine.py", 
line 232, in run
 context, state, transitions)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/statemachine.py", 
line 420, in check_line
 return method(match, context, next_state)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
line 2658, in underline
 self.section(title, source, style, lineno - 1, 
messages)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
line 308, in section
 self.new_subsection(title, lineno, messages)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
line 376, in new_subsection
 node=section_node, match_titles=1)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
line 266, in nested_parse
 node=node, match_titles=match_titles)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
line 195, in run
 results = StateMachineWS.run(self, input_lines, 
input_offset)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/statemachine.py", 
line 232, in run
 context, state, transitions)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/statemachine.py", 
line 420, in check_line
 return method(match, context, next_state)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
line 2239, in explicit_markup
 nodelist, blank_finish = 
self.explicit_construct(match)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
line 2251, in explicit_construct
 return method(self, expmatch)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
line 1994, in directive
 directive_class, match, type_name, option_presets)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/states.py", 
line 2043, in run_directive
 result = directive_instance.run()
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/docutils-0.5-py2.6.egg/docutils/parsers/rst/__init__.py", 
line 364, in run
 self.state, self.state_machine)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
line 414, in plot_directive
 options, state_machine)
 File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", 
line 337, in _plot_directive
 shutil.copyfile(plot_path, os.path.join(destdir, 
fname))
 File "/usr/lib64/python2.6/shutil.py", line 52, in 
copyfile
 fsrc = open(src, 'rb')
IOError: [Errno 2] No such file or directory: 
u'/home/nwagner/svn/matplotlib/doc/mpl_examples/axes_grid/demo_fixed_size_axes.py'
> /usr/lib64/python2.6/shutil.py(52)copyfile()
-> fsrc = open(src, 'rb')

On Tue, Dec 22, 2009 at 7:17 AM, Ghose, Kaushik <
Kau...@hm...> wrote:
> Hi,
>
> Regarding Greg ́s post about how to organize plotting code for data. This is
> a common issue encountered regardless of who collected the data or how the
> data was generated. I ́m an experimental neuroscientist in that I collect the
> data that I then analyze to test hypotheses and models. After some thrashing
> about I ́ve kind of settled with the following design (parts in common with
> Greg)
>
> 1. Analysis and plotting are separate. Analysis often takes a lot of CPU
> time, whereas plotting doesn ́t. A given analysis can be plotted in many
> different ways and often I want to tweak plots. I don ́t want to recompute
> the data each time. So a pragmatic way is to save the analysed data as a
> pickle file and have the plotting code load it.
>
> 2. Analysis code is written to be run non-interactively using the command
> line options package to pass parameters/instructions. Useful when I want to
> run the code on remote machines, or parallelize the code.
>
I don't do very heavy computations that always require multiple cores to
perform the analysis. Most of the time a fast-single computer is enough for
my analysis-plotting needs. This said I want to comment on the last two
points of your e-mail.
>
> 3. No GUIs. This has saved me so much time. I just write plotting code that
> pops up (or saves as pdf) one figure according to command line options. If I
> need a new type of figure I just copy the code into a new script/module and
> save it separately. This is much easier to debug than interactive GUIs that
> do a gazillion things.
>
Sometimes GUIs simplify things a lot especially when I am doing quick-looks
to the data. You can take a look at Traits [
http://code.enthought.com/projects/traits/] Your opinions might change after
seeing how easy to design a GUI for your needs.
>
> 4. Source control. Don ́t delete any code, save it under different folders
> organized by idea or by date. I've always found myself asking, months later,
> I made a plot like this, where is it, I want to see what I did there.
>
There is even a better approach for this. You can use web-based source-code
management systems (e.g. code.google.com or www.sourceforge.net) Either way
they provide great amount of flexibility for solo or multiple developer
projects.
>
> That's the current credo that has helped me waste a little less time when I
> want to test an idea with my data.
>
> Best
> -Kaushik
>
> ------------------------------
>
> Message: 7
> Date: 2009年12月21日 17:42:40 -0500
> From: Greg Novak <no...@uc...>
> Subject: [Matplotlib-users] Best practices for organizing plotting
> code?
> To: mat...@li...
> Message-ID:
> <ad0...@ma...>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello,
> I do computational science and I think I'm typical in that I've
> accumulated a huge pile of code to post-process simulations and draw
> plots. I think the number of lines of plotting code is now greater
> than the number of lines in the actual simulation code... The problem
> with plotting code is that so much of it has such a short
> lifetime---you have an idea, spend some time writing code to draw the
> relevant plot, then the plot isn't interesting and you delete the
> code. Therefore there's little incentive to spend any time making
> sure that plotting code is at all well-designed. Nevertheless, _some_
> of it tends to live a long time and get ever more complicated---then
> the lack of design becomes ever more painful as time goes on. You
> simply don't know at the beginning which code will be thrown away and
> which will live a long time.
>
> Over the years I've developed my favorite way to organize my plotting
> code but it's far from perfect and I'd love to gather ideas from the
> MPL community. So, my current "design principles" are basically
> these:
>
> 1) Don't over-design. A simple system that's used consistently is
> better than a half-implemented complicated system. Furthermore, most
> plotting code gets thrown away, so keeping overhead down is one of the
> primary considerations.
>
> 2) Keep computation separate from plotting wherever possible.
> Therefore I have functions like "def compute_optical_depth(...)" that
> compute the physical quantities to be plotted and "def
> plot_optical_depth(...)" that handle everything about the visual
> appearance of the plot. Then when I want to draw some other plot
> involving optical depth, the calculation is neatly packaged into a
> function.
>
> 3) Keep annotation, axis labels, legends, etc, separate from the code
> that actually draws the lines on the axes. This allows you to compose
> plots to a certain extent. I often find myself saying "I want plot B
> to look just like plot A but with this extra information, extra lines,
> extra annotation, or whatever" If the function that draws plot A just
> puts the data on the axes without axis labels, etc, then the function
> that draws plot B can easily use it directly. If the function that
> draws plot A _also_ draws a bunch of annotations and labels, then the
> function that draws plot B must either get rid of them or hope they
> still make sense in the new context.
>
> 4) Don't put clf() and cla() all over the place. When working
> interactively, it's very tempting to put clf()'s into every function
> that draws a plot in order to save a few keystrokes. However, plots
> don't know the context into which they're being drawn, therefore they
> have no authority to clear the screen. They may "own" the whole
> plotting window, or they may be incorporated into a larger context.
> The function that worries about axis labels, annotations, and titles
> is allowed to call cla(). The function that worries about subplots is
> allowed to call clf(). If you might use the code over a slow link
> (e.g. connecting to a supercomputing site via residential DSL) then no
> function should call draw() -- that's the user's job.
>
> The upshot of these is that I end up with four layers of functions:
>
> 1) compute_physical_quantity(...): just handles numbers
> 2) draw_physical_quantity(...): has calls to pylab.plot() handling
> colors, linestyles, etc, but not annotations
> 3) some_plot(...): has calls to draw_physical_quantity(),
> some_related_physical_quantity(), along with axis labels, annotations,
> legends, and pylab.cla()
> 4) some_figure(...): has multiple panels with calls to
> pylab.subplot(), pylab.clf(), some_plot_a(), some_plot_b(), etc.
>
> Sometimes layers 2 and 3 are combined because I'm lazy if layer 2
> would really be just a single call to pylab.plot.
>
> Please remember that I'm not writing these down because I think
> they're so great that everyone needs to know about them. I'm hoping
> that people will respond with much better ideas that I can adopt for
> myself.
>
> Thanks,
> Greg
>
> ------------------------------------------------------------------------------
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>
-- 
Gökhan

A couple more thoughts on this:
> 4) Don't put clf() and cla() all over the place. 
absolutely --
my addition to this is to use the OO API more than the pylab one. Put 
all your plotting code into functions that take an axes object as a 
parameter, then go from there. That way you have separated the 
generation of figures (collections os axes) from the plotting itself.
you can do the same at a higher level too -- put your code that creates 
the figures in a function that take a figure as an argument -- then you 
can use the same code to generate PDFs, embed in a GUI, etc.
HTH,
-Chris
-- 
Christopher Barker, Ph.D.
Oceanographer
Emergency Response Division
NOAA/NOS/OR&R (206) 526-6959 voice
7600 Sand Point Way NE (206) 526-6329 fax
Seattle, WA 98115 (206) 526-6317 main reception
Chr...@no...

Hi,
Regarding Greg ́s post about how to organize plotting code for data. This is a common issue encountered regardless of who collected the data or how the data was generated. I ́m an experimental neuroscientist in that I collect the data that I then analyze to test hypotheses and models. After some thrashing about I ́ve kind of settled with the following design (parts in common with Greg)
1. Analysis and plotting are separate. Analysis often takes a lot of CPU time, whereas plotting doesn ́t. A given analysis can be plotted in many different ways and often I want to tweak plots. I don ́t want to recompute the data each time. So a pragmatic way is to save the analysed data as a pickle file and have the plotting code load it.
2. Analysis code is written to be run non-interactively using the command line options package to pass parameters/instructions. Useful when I want to run the code on remote machines, or parallelize the code.
3. No GUIs. This has saved me so much time. I just write plotting code that pops up (or saves as pdf) one figure according to command line options. If I need a new type of figure I just copy the code into a new script/module and save it separately. This is much easier to debug than interactive GUIs that do a gazillion things.
4. Source control. Don ́t delete any code, save it under different folders organized by idea or by date. I've always found myself asking, months later, I made a plot like this, where is it, I want to see what I did there.
That's the current credo that has helped me waste a little less time when I want to test an idea with my data.
Best
-Kaushik
------------------------------
Message: 7
Date: 2009年12月21日 17:42:40 -0500
From: Greg Novak <no...@uc...>
Subject: [Matplotlib-users] Best practices for organizing plotting
 code?
To: mat...@li...
Message-ID:
 <ad0...@ma...>
Content-Type: text/plain; charset=ISO-8859-1
Hello,
I do computational science and I think I'm typical in that I've
accumulated a huge pile of code to post-process simulations and draw
plots. I think the number of lines of plotting code is now greater
than the number of lines in the actual simulation code... The problem
with plotting code is that so much of it has such a short
lifetime---you have an idea, spend some time writing code to draw the
relevant plot, then the plot isn't interesting and you delete the
code. Therefore there's little incentive to spend any time making
sure that plotting code is at all well-designed. Nevertheless, _some_
of it tends to live a long time and get ever more complicated---then
the lack of design becomes ever more painful as time goes on. You
simply don't know at the beginning which code will be thrown away and
which will live a long time.
Over the years I've developed my favorite way to organize my plotting
code but it's far from perfect and I'd love to gather ideas from the
MPL community. So, my current "design principles" are basically
these:
1) Don't over-design. A simple system that's used consistently is
better than a half-implemented complicated system. Furthermore, most
plotting code gets thrown away, so keeping overhead down is one of the
primary considerations.
2) Keep computation separate from plotting wherever possible.
Therefore I have functions like "def compute_optical_depth(...)" that
compute the physical quantities to be plotted and "def
plot_optical_depth(...)" that handle everything about the visual
appearance of the plot. Then when I want to draw some other plot
involving optical depth, the calculation is neatly packaged into a
function.
3) Keep annotation, axis labels, legends, etc, separate from the code
that actually draws the lines on the axes. This allows you to compose
plots to a certain extent. I often find myself saying "I want plot B
to look just like plot A but with this extra information, extra lines,
extra annotation, or whatever" If the function that draws plot A just
puts the data on the axes without axis labels, etc, then the function
that draws plot B can easily use it directly. If the function that
draws plot A _also_ draws a bunch of annotations and labels, then the
function that draws plot B must either get rid of them or hope they
still make sense in the new context.
4) Don't put clf() and cla() all over the place. When working
interactively, it's very tempting to put clf()'s into every function
that draws a plot in order to save a few keystrokes. However, plots
don't know the context into which they're being drawn, therefore they
have no authority to clear the screen. They may "own" the whole
plotting window, or they may be incorporated into a larger context.
The function that worries about axis labels, annotations, and titles
is allowed to call cla(). The function that worries about subplots is
allowed to call clf(). If you might use the code over a slow link
(e.g. connecting to a supercomputing site via residential DSL) then no
function should call draw() -- that's the user's job.
The upshot of these is that I end up with four layers of functions:
1) compute_physical_quantity(...): just handles numbers
2) draw_physical_quantity(...): has calls to pylab.plot() handling
colors, linestyles, etc, but not annotations
3) some_plot(...): has calls to draw_physical_quantity(),
some_related_physical_quantity(), along with axis labels, annotations,
legends, and pylab.cla()
4) some_figure(...): has multiple panels with calls to
pylab.subplot(), pylab.clf(), some_plot_a(), some_plot_b(), etc.
Sometimes layers 2 and 3 are combined because I'm lazy if layer 2
would really be just a single call to pylab.plot.
Please remember that I'm not writing these down because I think
they're so great that everyone needs to know about them. I'm hoping
that people will respond with much better ideas that I can adopt for
myself.
Thanks,
Greg