Mayavi support #42

agramfort · 2015-07-13T15:55:26Z

patch to add mayavi support on top of #36

agramfort · 2015-07-14T07:49:44Z

@Titan-C we're making progress here.

Can you have a look?

So far for us the images are moved to the bottom which is weird but besides this it works great.

Titan-C · 2015-07-14T09:13:10Z

Can you have a look?

It looks ok. I would add a short example to show a plot in mayavi.
Also to make the test in travis pass one has to put mayavi in the requirements.txt file to install it.

So far for us the images are moved to the bottom which is weird but besides this it works great.

Do you mean bottom miss aligned? or bottom shown after the code? Because as part of adopting the notebook layout I put the images after the code.

Are you doing the sprint during the holiday? I can go today.

GaelVaroquaux · 2015-07-14T09:16:31Z

Are you doing the sprint during the holiday? I can go today.

We are at 'La paillasse' today: https://github.com/mne-tools/mne-python/wiki/NeuroCoding-2015

agramfort · 2015-07-14T11:09:03Z

done. Let's see if travis is happy

larsoner · 2015-07-17T16:59:41Z

Travis is happy now

larsoner · 2015-07-17T17:00:19Z

FYI I added the raise_gallery option, which makes it possible to have it raise errors as it encounters them in doc building, which we have found useful

agramfort · 2015-07-17T17:06:21Z

let's wait for the PR to be merged.

larsoner · 2015-07-17T17:06:58Z

I did it as part of the commit that made Travis happy. Do you want me to undo the commit and split it up?

larsoner · 2015-07-17T17:08:33Z

Just a reminder at some point we also need to add support for plot_gallery=fast command-line option, which will make it skip examples marked as slow

agramfort · 2015-07-17T17:39:48Z

yep !

lesteve · 2015-07-31T07:37:30Z

#36 has been merged now and you need to rebase it seems like.

agramfort · 2015-07-31T07:44:39Z

Yeah will do today

On 31 juil. 2015, at 09:37, Loïc Estève notifications@github.com wrote:

#36 has been merged now and you need to rebase it seems like.

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agramfort · 2015-07-31T12:19:41Z

rebased and travis is happy. Ready for review

lesteve · 2015-07-31T14:26:34Z

doc/conf.py

+try:
+    from mayavi import mlab
+    use_mayavi = True
+except ImportError, e:


This is not python 3 compatible and is old way of doing things in python 2. Slightly annoying that the tests pass, but oh well this is part of the doc generation and not really the sphinxgallery package ...

Since you are not using the exception you might as well just do:

except ImportError:

agramfort · 2015-07-31T20:40:14Z

comments addressed.

agramfort · 2015-08-01T21:14:16Z

any more comment?

…gures

agramfort · 2015-08-03T17:28:42Z

done

agramfort · 2015-08-03T17:29:24Z

doc/index.rst

@@ -22,6 +22,7 @@ Contents:
   reference
   auto_examples/index
   tutorials/index
+   auto_mayavi_examples/index


but now this link will not exist unless mayavi is present... maybe it's just a sphinx warning so no big deal...

lesteve · 2015-08-04T07:35:31Z

sphinxgallery/docs_resolv.py

@@ -409,6 +409,8 @@ def embed_code_links(app, exception):
    """Embed hyperlinks to documentation into example code"""
    if exception is not None:
        return
+    if not app.builder.config.plot_gallery:
+        return  # no need to embed


I missed that in my previous reviews. Why don't you want to put hyperlinks inside the example in case plot_gallery is False? Is it because it can fail if there is a parsing error of the script ?

Yes

On 4 août 2015, at 09:35, Loïc Estève notifications@github.com wrote:

In sphinxgallery/docs_resolv.py:

@@ -409,6 +409,8 @@ def embed_code_links(app, exception):
"""Embed hyperlinks to documentation into example code"""
if exception is not None:
return

if not app.builder.config.plot_gallery:

return # no need to embed
I missed that in my previous reviews. Why don't you want to put hyperlinks inside the example in case plot_gallery is False? Is it because it can fail if there is a parsing error of the script ?

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Then could you improve the comment?

And also because when writing narrative doc you don't want to plot and wait for all the embedding

On 4 août 2015, at 09:35, Loïc Estève notifications@github.com wrote:

In sphinxgallery/docs_resolv.py:

@@ -409,6 +409,8 @@ def embed_code_links(app, exception):
"""Embed hyperlinks to documentation into example code"""
if exception is not None:
return

if not app.builder.config.plot_gallery:

return # no need to embed
I missed that in my previous reviews. Why don't you want to put hyperlinks inside the example in case plot_gallery is False? Is it because it can fail if there is a parsing error of the script ?

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Reply to this email directly or view it on GitHub.

@lesteve please take over. I am mostly on my phone these days. It will be faster if you do a cosmit on your side. Je te donne carte blanche :)

lesteve · 2015-08-04T07:49:34Z

Just curious, is there a way to do the equivalent of matplotlib.use('Agg') so that the mayavi figures don't pop up while generating the doc?

GaelVaroquaux · 2015-08-04T08:04:00Z

Just curious, is there a way to do the equivalent of matplotlib.use('Agg') so
that the mayavi figures don't pop up while generating the doc?

You want to set the mlab enfine as the offscreenengine.

http://docs.enthought.com/mayavi/mayavi/auto/example_offscreen.html

This should be easily done by the following:

from mayavi import mlab
mlab.options.offscreen = True

lesteve · 2015-08-04T08:48:12Z

OK I just tried to generate the doc with the mayavi example and I got an error that the MNE-Python people know about ... mne-tools/mne-python#2062.

The last comment on the issue seems to indicate that it works with pyface master, but is there any better option?

For completeness I installed mayavi through Anaconda.

For reference, here is the log from sphinx:

# Sphinx version: 1.3.1
# Python version: 2.7.10 (CPython)
# Docutils version: 0.12 release
# Jinja2 version: 2.8
# Last messages:
#   pickling environment...
#   done
#   checking consistency...
#   done
#   preparing documents...
#   done
#   writing output... [  5%] advanced_configuration
#   writing output... [ 11%] auto_examples/index
#   writing output... [ 17%] auto_examples/just_code
#   writing output... [ 23%] auto_examples/plot_gallery_version
# Loaded extensions:
#   sphinx.ext.autodoc (1.3.1) from /volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphin
#   sphinx.ext.intersphinx (1.3.1) from /volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/s
#   sphinx.ext.doctest (1.3.1) from /volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphin
#   sphinx.ext.mathjax (1.3.1) from /volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphin
#   sphinx.ext.coverage (1.3.1) from /volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphi
#   sphinx.ext.todo (1.3.1) from /volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/e
#   alabaster (0.7.3) from /volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/alabaster/__init__.pyc
#   sphinxgallery.gen_gallery (unknown version) from /home/le243287/dev/sphinx-gallery/sphinxgallery/gen_gallery.pyc
Traceback (most recent call last):
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/cmdline.py", line 245, in 
    app.build(opts.force_all, filenames)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/application.py", line 264,
    self.builder.build_update()
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/builders/__init__.py", lin
    'out of date' % len(to_build))
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/builders/__init__.py", lin
    self.write(docnames, list(updated_docnames), method)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/builders/__init__.py", lin
    self._write_serial(sorted(docnames), warnings)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/builders/__init__.py", lin
    self.write_doc(docname, doctree)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/builders/html.py", line 43
    self.docwriter.write(doctree, destination)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/docutils/writers/__init__.py", line 80, in write
    self.translate()
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/writers/html.py", line 53,
    self.document.walkabout(visitor)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/docutils/nodes.py", line 174, in walkabout
    if child.walkabout(visitor):
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/docutils/nodes.py", line 174, in walkabout
    if child.walkabout(visitor):
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/docutils/nodes.py", line 166, in walkabout
    visitor.dispatch_visit(self)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/docutils/nodes.py", line 1882, in dispatch_visit
    return method(node)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/writers/html.py", line 720
    HTMLTranslator.visit_literal_block(self, node)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/writers/html.py", line 331
    **highlight_args)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/Sphinx-1.3.1-py2.7.egg/sphinx/highlighting.py", line 185
    hlsource = highlight(source, lexer, formatter)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/pygments/__init__.py", line 87, in highlight
    return format(lex(code, lexer), formatter, outfile)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/pygments/__init__.py", line 66, in format
    formatter.format(tokens, realoutfile)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/pygments/formatter.py", line 95, in format
    return self.format_unencoded(tokensource, outfile)
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/pygments/formatters/html.py", line 838, in format_unenco
    for t, piece in source:
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/pygments/formatters/html.py", line 684, in _wrap_div
    for tup in inner:
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/pygments/formatters/html.py", line 697, in _wrap_pre
    for tup in inner:
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/pygments/formatters/html.py", line 716, in _format_lines
    for ttype, value in tokensource:
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/pygments/filter.py", line 20, in _apply
    for token in filter_.filter(lexer, stream):
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/pygments/filters/__init__.py", line 194, in filter
    for ttype, value in stream:
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/pygments/lexer.py", line 192, in streamer
    for i, t, v in self.get_tokens_unprocessed(text):
  File "/volatile/le243287/miniconda3/envs/mayavi/lib/python2.7/site-packages/pyface/ui/qt4/code_editor/pygments_highlighter.py", line
    for item in action(self, m):
TypeError: 'NoneType' object is not callable

agramfort · 2015-08-04T08:49:54Z

yeah I had to install pyface master ...

GaelVaroquaux · 2015-08-04T08:50:46Z

yeah I had to install pyface master ...

WTF

lesteve · 2015-08-04T09:10:13Z

For completeness, pyface original issue (fixed in master) enthought/pyface#113.

lesteve · 2015-08-04T09:16:13Z

You don't actually need pyface master, pip install pyface fixed it for me.

It's just that the version provided by conda is 4.4 which is from Dec 4, 2013 for some reason.

agramfort · 2015-08-04T09:42:06Z

Cool

On 4 août 2015, at 11:16, Loïc Estève notifications@github.com wrote:

You don't actually need pyface master, pip install pyface fixed it for me.

It's just that the version provided by conda is 4.4 which is from Dec 4, 2013 for some reason.

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lesteve · 2015-08-04T11:16:19Z

@lesteve please take over. I am mostly on my phone these days. It will be faster if you do a cosmit on your side. Je te donne carte blanche :)

OK I'll merge that as is and patch it up myself.

Mayavi support

agramfort · 2015-08-04T11:21:38Z

thanks

agramfort mentioned this pull request Jul 13, 2015

WIP: refactoring of doc (switch to sphinx gallery) mne-tools/mne-python#2279

Closed

agramfort force-pushed the mayavi_support branch 4 times, most recently from e2b1f0d to 2a2f0d7 Compare July 15, 2015 08:18

agramfort force-pushed the mayavi_support branch 2 times, most recently from 6c1b335 to 73f1512 Compare July 31, 2015 12:08

ENH : add mayavi support

4607f77

agramfort force-pushed the mayavi_support branch from 73f1512 to 4607f77 Compare July 31, 2015 12:15

lesteve reviewed Jul 31, 2015
View reviewed changes

address comments

532f64c

move figure_list = []

91408d8

move mayavi examples in dedicated folder and rename to find_mayavi_fi…

46d0d18

…gures

agramfort reviewed Aug 3, 2015
View reviewed changes

lesteve mentioned this pull request Aug 4, 2015

add mayavi support #17

Closed

lesteve reviewed Aug 4, 2015
View reviewed changes

lesteve added a commit that referenced this pull request Aug 4, 2015

Merge pull request #42 from agramfort/mayavi_support

9bbbc49

Mayavi support

lesteve merged commit 9bbbc49 into sphinx-gallery:master Aug 4, 2015

florian-wagner mentioned this pull request Aug 11, 2015

Basic pg.viewer support for 3D visualizations gimli-org/gimli#15

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4 tasks

lesteve mentioned this pull request Aug 17, 2015

Prevent mayavi figures from popping up when generating the doc #56

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Mayavi support #42

Mayavi support #42

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Mayavi support #42

Mayavi support #42

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