[cctbxbb] building sphinx documentation

Fri Apr 19 13:09:44 PDT 2013

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).

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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>
>
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