sphinx-build fail - autodoc can't import/find module

Question

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building [html]: targets for 1 source files that are out of date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.

Solution 1

Autodoc can't find your modules, because they are not in sys.path.

You have to include the path to your modules in in the sys.path in your conf.py. Look at the top of your conf.py (just after the import of sys), there is a sys.path.insert() statement, which you can adapt.

By the way: you can use the Makefile created by Sphinx to create your documentation. Just call

make

to see the options.

If something went wrong before try:

make clean

before running make html.

Solution 2

solution

It sounds like os.path.append() is working OK for folks, but if you follow the conf.py template, you would insert the module path to the front of sys.path using os.path.insert(0, ...), and just add an extra .

import os
import sys
sys.path.insert(0, os.path.abspath('..'))

If you have setup your sphinx project to use separate build and source directories, that call should instead be:

sys.path.insert(0, os.path.abspath('../..'))

about sys.path ...

To run python code, the python interpreter needs to know where it is. With the sphinx config being a python script, it's location needs to be made known, which is done by adding it the the sys.path variable using the insert method (see the docs on module search path).

The path added to sys.path in this case is a "relative" path, which is specified using dots. This is a general way of specifying the path, which allows the code to be moved and still point correctly to the correct path in your codebase.

. - current path of the conf.py

.. - parent path of the conf.py

../.. - parent of the parent path, etc.

I use linux, so directories are specified with a forward slash, but a cross-platform method for specifying parent directories can be acheived with pathlib.

from pathlib import Path

parent = Path(__file__).parent
parents_parent = Path(__file__).parents[1]

Solution 3

in conf.py

just add the path to your project folder.

sys.path.append('/home/workspace/myproj/myproj')

Solution 4

If

1. module root path is correctly set in conf.py
2. __init__.py is placed correctly
3. rst syntax is correct

and your autodoc still cannot find the modules...

It may be because the dependencies of those modules are not satisfied under your python environment. You will want to check if all the import statements are working within the modules.

Solution 5

I don't know why (maybe in my case autodoc couldn't install my package), but I always got module-not-found errors until I explicitly included all directories containing modules to the path.

For the following example folder structure

project_dir
|- setup.py
|- src
|  |- __init__.py
|  |- source1.py
|  |- sub_project
|     |- __init__.py
|     |- source2.py 
|- docs
    |- conf.py
    |- source
    |  |- index.rst
    |- _build       

I included

for x in os.walk('../../src'):
  sys.path.insert(0, x[0])

to the beginning of conf.py such that all involved directories would be added.

View more solutions

Comments

[Rico]

Where would this go? I have index.rst in /docs/source and /ys_utils. I'm guessing this should be in the docs version? I'm just using the default index.rst file that was created with sphinx-quickstart.

[bmu]

-1 as from the traceback it seems clear that the modules are not in sys.path, so autodoc cn't find them. The .rst files are found.

[firegurafiku]

Path hard-coding isn't the best thing you can do with your conf.py.

[fnkr]

If you have a project structure like /app, /docs, ... you might to use sys.path.append(os.path.join(os.path.dirname(__name__), '..')) and then use .. automodule:: app in your .rst-file.

[cglacet]

I don't get why sphinx needs dependencies, is it because of the possibility of having tests within docstrings? Can this be avoided (I don't need any package, I just want sphinx to parse docstring to html).

[filip stepniak]

If you don't want to import these dependencies use autodoc_mock_imports in your conf.py file: sphinx-doc.org/en/master/usage/extensions/…

[Felix B.]

for some weird reason os.path.abspath(os.path.split(__file__)[0] + '../../') does not work while os.path.abspath('../..')) does work. I have no idea why.

[JimB]

In conf.py, add print(sys.executable) My sphinx-build was invoking py-3.8 but my venv was py-3.7.

[CGFoX]

Could you explain what sys.path.insert(0, os.path.abspath('..')) really does? Does it point to local dependencies/code so not stuff installed via pip?

[CGFoX]

Hm, I have an external dependency installed via pip which I can import without problems when running Python in the command line. But sphinx does not pick it up and throws and error "no module..". sys.executable points to the correct Python installation. What could be the problem?

[ryanjdillon]

@FelixB. perhaps it is the trailing forward slash.

[ryanjdillon]

@CGFoX I've added some commentary on sys.path.