Python – sphinx-build fail – autodoc can’t import/find module

I'm trying to get started with Sphinx and seem to have relentless problems.

Command: docs/sphinx-quickstart

I answer all the questions and everything works fine.

Command: docs/ls

Everything looks normal. Result: build Makefile source

Command: sphinx-build -d build/doctrees source build/html

It seems to work. I was able to open the index.html file and see a "shell" of what I'm wanting.

When I try and put my actual source code as the source folder I run into problems.

Command: sphinx-build -d build/doctrees ../ys_utils build/html

Result:

Making output directory...
Running Sphinx v1.1.3
loading pickled environment... not yet created
No builder selected, using default: html
loading intersphinx inventory from http://docs.python.org/objects.inv...
building [html]: targets for 1 source files that are out of date
updating environment: 1 added, 0 changed, 0 removed
Traceback (most recent call last):                                                                                               
  File "/usr/local/lib/python2.6/dist-packages/Sphinx-1.1.3-py2.6.egg/sphinx/ext/autodoc.py", line 321, in import_object
    __import__(self.modname)
ImportError: No module named ys_utils
Traceback (most recent call last):
  File "/usr/local/lib/python2.6/dist-packages/Sphinx-1.1.3-py2.6.egg/sphinx/ext/autodoc.py", line 321, in import_object
    __import__(self.modname)
ImportError: No module named ys_utils.test_validate_ut
Traceback (most recent call last):
  File "/usr/local/lib/python2.6/dist-packages/Sphinx-1.1.3-py2.6.egg/sphinx/ext/autodoc.py", line 321, in import_object
    __import__(self.modname)
ImportError: No module named ys_utils.git_utils
Traceback (most recent call last):
  File "/usr/local/lib/python2.6/dist-packages/Sphinx-1.1.3-py2.6.egg/sphinx/ext/autodoc.py", line 321, in import_object
    __import__(self.modname)
ImportError: No module named setup.setup

/home/ricomoss/workspace/nextgen/ys_utils/ys_utils.rst:4: WARNING: autodoc can't import/find module 'ys_utils', it reported error: "No module named ys_utils", please check your spelling and sys.path
/home/ricomoss/workspace/nextgen/ys_utils/ys_utils.rst:10: WARNING: autodoc can't import/find module 'ys_utils.test_validate_ut', it reported error: "No module named ys_utils.test_validate_ut", please check your spelling and sys.path
/home/ricomoss/workspace/nextgen/ys_utils/ys_utils.rst:12: WARNING: don't know which module to import for autodocumenting u'UnitTests' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
/home/ricomoss/workspace/nextgen/ys_utils/ys_utils.rst:18: WARNING: autodoc can't import/find module 'ys_utils.git_utils', it reported error: "No module named ys_utils.git_utils", please check your spelling and sys.path
/home/ricomoss/workspace/nextgen/ys_utils/ys_utils.rst:24: WARNING: autodoc can't import/find module 'setup.setup', it reported error: "No module named setup.setup", please check your spelling and sys.path
WARNING: master file /home/ricomoss/workspace/nextgen/ys_utils/index.rst not found
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/ricomoss/workspace/nextgen/ys_utils/ys_utils.rst:: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [ 50%] index                                                                                                   
Exception occurred:
  File "/usr/local/lib/python2.6/dist-packages/Sphinx-1.1.3-py2.6.egg/sphinx/environment.py", line 1213, in get_doctree
    f = open(doctree_filename, 'rb')
IOError: [Errno 2] No such file or directory: '/home/ricomoss/workspace/nextgen/docs/build/doctrees/index.doctree'
The full traceback has been saved in /tmp/sphinx-err-jjJ7gM.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
Either send bugs to the mailing list at <http://groups.google.com/group/sphinx-dev/>,
or report them in the tracker at <http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks!

I am a complete newbie to Sphinx and relatively new to this kind of documentation. Can anyone offer some suggestions?

Edit:

I'd like to be able to use a Makefile to handle this. As of now I have two folders in my project.

nextgen/ls

docs ys_utils

I need nextgen/docs/Makefile to generate the HTML for ys_utils and all other modules I'm going to have.