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-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
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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