[cctbxbb] building sphinx documentation

Richard Gildea rgildea at gmail.com
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:

  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  .
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):

line 321, in import_object
  File "/Users/rjgildea/cctbx/sources/cctbx_project/cctbx/adptbx.py", line
2, in <module>
    from cctbx.array_family import flex # for tuple mappings
line 2, in <module>
    import scitbx.array_family.flex
line 2, in <module>
    import boost.optional # import dependency
line 2, in <module>
    import boost.python
line 57, in <module>
    ext = import_ext("boost_python_meta_ext")
line 36, in import_ext
    + ["  "+p for p in sys.path]))
ImportError: __import__("boost_python_meta_ext"):
2): Library not loaded: lib/libboost_python.dylib
  Referenced from:
  Reason: image not found












Do you have any idea what I am might be doing wrong here?



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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> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
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