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...@stsci.edu> 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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