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).
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.