The way my modules are structured, there is an __init__.py in both the 
python_modules_A and the python_modules_B directories. I declared two paths 
in my conf.py, one for python_modules_A and python_modules_B but when I run 
make.html, sphinx only recognizes the first path listed and ignores the 
second. 

For example, in my conf.py file, I used

sys.path.insert(0, os.path.abspath("../python_modules_A")) 
sys.path.insert(0, os.path.abspath("../python_modules_B"))

but get import errors for every python module in the python_modules_B 
directory. 

Another error that comes up when I list sys.path.insert(0, 
os.path.abspath("../python_modules_B")) first instead is that sphinx cannot 
recognize the path for functions/modules in python_modules_A that are 
imported into python_module_B modules. For example, in every module in 
python_module_B, I import a module/function defined in python_modules A 
called download parameters. Here is how it is listed below:

download_parameters.py is in python_modules_A directory
Below is the header and code in a2.py (which is in the python_modules_B 
directory):

import numpy as np
from python_modules_A.download_parameters import download_parameters
Class module_B
...
...

This error occurs: 

"from python_modules_A.download_parameters import download_parameters

ImportError: No module named python_modules_A.download_parameters"

Is there a way to fix this problem as well? Thanks. 

On Thursday, February 16, 2017 at 5:33:26 AM UTC-8, Peter Burdine wrote:
>
> Have you tried changing your sys.path to include both?  Eg:
> sys.path.insert(0, os.path.abspath(".."))
>
>
>
> Then for autodoc tried:
> .. automodule:: python_modules_A
>
> .. automodule:: python_modules_B
>
>
>
> How you include documentation for it may then depend on your module 
> structure (eg do you have an __init__.py? does it define __all__?)
>
> On Wednesday, February 15, 2017 at 3:05:18 PM UTC-8, nshea wrote:
>>
>> I am using sphinx autodoc to document python modules in multiple 
>> directories. I already have the rst files for each python module and can 
>> use autodoc when declaring a path to one directory with the python modules 
>> but I am trying to document python modules from two different directories. 
>> In the conf.py file, I used:
>>
>>
>> sys.path.insert(0, os.path.abspath("../python_modules_A"))
>>
>>
>> but would like to have paths to both python_modules_A and 
>> python_modules_B, since my modules are in both directories. Given the 
>> structure of my project team, I would like to avoid having to restructure 
>> the modules into one directory since they are separated by helper functions 
>> in python_module_A and classes/objects for the main module python_modules_B 
>> modules.
>>
>>
>> Below is how my directories are configured:
>>
>>
>> sphinx_doc_setup
>>
>>   conf.py
>>
>>   index.rst
>>
>>   a1.rst
>>
>>   b1.rst
>>
>>   a2.rst
>>
>>   b2.rst
>>
>> python_modules_A
>>
>>   a1.py
>>
>>   b1.py
>>
>> python_modules_B
>>
>>   a2.py
>>
>>   b2.py
>>
>>
>> Thanks for any help!
>>
>

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