Re: [cctbxbb] building sphinx documentation

With Nat's help I have managed to get it working by modifying build_docs.sh by replacing LD_LIBRARY_PATH with DYLD_LIBRARY_PATH (needed for mac os x), and added the line export LIBTBX_BUILD=/path/to/cctbx/build/. Is there a way to tell sphinx-build to use the cctbx.python without editing the sphinx-build file? A couple of comments based on a successful run of documentation build: 1) It seems that sphinx tries to import absolutely every import command it finds in the files - in the cctbx there are a lot of conditional imports that depend on certain external packages being present. Therefore it seems that unless I have absolutely every package installed and build every module, then I will end up with a huge number of tracebacks in the output from sphinx. I am not sure if there is anything that can be done about this. 2) Is there a way to tell sphinx not to look at certain files? I don't claim to understand how the libtbx_refresh.py modules work, but sphinx tries to import them, and unsurprisingly fails. Cheers, Richard On 19 April 2013 13:37, James Stroud wrote:

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-macp... 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 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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