[cctbxbb] building sphinx documentation

James Stroud xtald00d at gmail.com
Fri Apr 19 13:37:06 PDT 2013 

On Apr 19, 2013, at 2:09 PM, Richard Gildea wrote:

> Hi Jan,
> 
> I think the cause of the incomplete documentation is down to the fact that when I run build_docs.sh I get a whole bunch of import errors for every compiled module that it tries to import. I am at a bit of a loss as to why this should be the case, as running the tests or importing modules at the command line works just fine. I have built cctbx using the system python (2.7.2) on mac os x (mountain lion).

It looks like sphinx-build is not using cctbx.python, so it has no idea from where to import the python modules. Try this

% your-favorite-editor `which sphinx-build`

And change the first line to something like

#! /path/to/cctbx.python

That line shouldn't point to the python that cctbx.python calls (i.e. the system python).

This assumes you did the following when you installed sphinx:

/path/to/cctbx.python setup.py build
/path/to/cctbx.python setup.py install

(or at least used the python called by cctbx.python in these two steps).

James



> Install sphinx:
>   http://sphinx-doc.org/latest/install.html#mac-os-x-install-sphinx-using-macports
>   sudo port install py27-sphinx
>   sudo port select --set python python27
> 
> This is the output I get on running ./build_docs.sh:
> 
> sphinx-build -b coverage -d _build/doctrees -D latex_paper_size=a4  . _build/coverage
> Running Sphinx v1.1.3
> loading pickled environment... not yet created
> building [coverage]: coverage overview
> updating environment: 129 added, 0 changed, 0 removed
> Traceback (most recent call last):                                                                                                                                                          
>   File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/sphinx/ext/autodoc.py", line 321, in import_object
>     __import__(self.modname)
>   File "/Users/rjgildea/cctbx/sources/cctbx_project/cctbx/adptbx.py", line 2, in <module>
>     from cctbx.array_family import flex # for tuple mappings
>   File "/Users/rjgildea/cctbx/sources/cctbx_project/cctbx/array_family/flex.py", line 2, in <module>
>     import scitbx.array_family.flex
>   File "/Users/rjgildea/cctbx/sources/cctbx_project/scitbx/array_family/flex.py", line 2, in <module>
>     import boost.optional # import dependency
>   File "/Users/rjgildea/cctbx/sources/cctbx_project/boost_adaptbx/boost/optional.py", line 2, in <module>
>     import boost.python
>   File "/Users/rjgildea/cctbx/sources/cctbx_project/boost_adaptbx/boost/python.py", line 57, in <module>
>     ext = import_ext("boost_python_meta_ext")
>   File "/Users/rjgildea/cctbx/sources/cctbx_project/boost_adaptbx/boost/python.py", line 36, in import_ext
>     + ["  "+p for p in sys.path]))
> ImportError: __import__("boost_python_meta_ext"): dlopen(/Users/rjgildea/cctbx/system_python_build/lib/boost_python_meta_ext.so, 2): Library not loaded: lib/libboost_python.dylib
>   Referenced from: /Users/rjgildea/cctbx/system_python_build/lib/boost_python_meta_ext.so
>   Reason: image not found
>   sys.path:
>     /Users/rjgildea/cctbx/sources/cctbx_project
>     /Users/rjgildea/cctbx/sources
>     /Users/rjgildea/cctbx/sources/cctbx_project/clipper_adaptbx
>     /Users/rjgildea/cctbx/sources/cctbx_project/boost_adaptbx
>     /Users/rjgildea/cctbx/sources/cctbx_project/libtbx/pythonpath
>     /Users/rjgildea/cctbx/system_python_build/lib
>     /Users/rjgildea/cctbx/system_python_build/bin
>     /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin
>     /Library/Python/2.7/site-packages/docutils-0.10-py2.7.egg
>     /Library/Python/2.7/site-packages/Jinja2-2.6-py2.7.egg
>     /Library/Python/2.7/site-packages/Pygments-1.6-py2.7.egg
>     /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip
>     /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
>     /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin
>     /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac
>     /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages
>     /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk
>     /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old
>     /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload
>     /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
>     /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info
>     /Library/Python/2.7/site-packages
> 
> etc.
> 
> Do you have any idea what I am might be doing wrong here?
> 
> Cheers,
> 
> Richard
> 
> 
> On 19 April 2013 05:10, Jan Marten Simons <marten at xtal.rwth-aachen.de> wrote:
> Am Donnerstag 18 April 2013 19:16:00 schrieben Sie:
> > Hi Jan,
> 
> Hi Richard,
> 
> > I have attempted to build the sphinx documentation using
> > dox.sphinx/build_docs.sh, and this appears to have run successfully and
> > produced some html which shows the table of contents etc. However, I can't
> > seem to find the documentation for any of the significant modules, e.g.
> > cctbx/xray/structure.py. When I navigate to the link for the structure
> > module within the xray package
> > (dox.sphinx/_build/html/cctbx/cctbx.xray.html#structure-module), I see
> > nothing other than a list of all the modules within the xray package. Am I
> > missing something here?
> 
> Have you followed the instructions given in the comments at the top of
> dox.sphinx/build_docs.sh?
> 
> Which version of Sphinx do you use? I'm using 1.1.3 regularly and get useful
> documentation (I've attached the "makescript" I use to build cctbx and the
> sphinx documentation. If you are interested in it I can also put the output of
> the sphinx run on my system with current svn on webserver over here.). Has
> your sphinx build completed successfully or did it abort (e.g. due to out of
> memory* or due to other problems)?
> Could you also check if build/dox.sphinx/cctbx/cctbx.xray.rst has all modules
> listed?
> 
> > As a novice to using sphinx, I don't like to add significant documentation
> > in sphinx style without being able to check via generating the
> > documentation that what I have written is correct sphinx-speak.
> I can totally understand this ;).
> 
> Cheers and hopefully we can get this working for you as well,
> Jan
> 
> *) For me running sphinx with all those modules selected needs about 3.3 GiB
> of virtual memory (RAM) and takes a few minutes to actually finish.
> 
> p.s.: Sorry didn't hit "reply all".
> 
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