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:
  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 <[email protected]> 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".

_______________________________________________
cctbxbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/cctbxbb


_______________________________________________
cctbxbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/cctbxbb