In case anyone is encountering similar, further searching on stackexchange 
provided two solutions:

1. Modify the `__all__` attribute in `__init__.py`

https://stackoverflow.com/questions/15115514/how-do-i-document-classes-without-the-module-name/31594545#31594545

2. Modify the `__module__` attribute of the imported objects:
https://stackoverflow.com/questions/22096187/how-to-make-sphinx-respect-importing-classes-into-package-with-init-py

The latter is difficult when using `from mymodule import *`


On Wednesday, February 28, 2018 at 2:27:50 PM UTC+1, John wrote:
>
> Note, that I am able to document the module in this way:
>
> .. automodule:: shyft.api._api
>     :members:
>     :inherited-members:
>     :undoc-members:
>
> but this is not preferred as it results in all the index references being 
> to:
>
> shyft.api._api.SomeClass
>
> And for the API in practice, these should be referenced as 
> `shyft.api.SomeClass` due to the import in the `__init__.py` file.
>
>
>
> On Wednesday, February 28, 2018 at 2:12:23 PM UTC+1, John wrote:
>>
>> Hello,
>>
>> I just posted this before, but I don't see it appearing, apologies for a 
>> duplicate post.
>>
>> I am writing documentation for a boost:python project 
>> <https://github.com/statkraft/shyft-doc> with uses and underlying C++ 
>> .so file as a key module.
>>
>> It is read referenced within the `api.__init__.py` file in the following 
>> manner:
>>
>> from shyft.api._api import *
>>
>> I am trying every combination of :inherited-members:, :members:, 
>> :undoc-member:, etc.. but it seems only either functions/classes explicitly 
>> defined in the __init__.py file are exposed.
>>
>> How would I get the other modules/classes to be documented which exist 
>> within `_api.so`
>>
>> Thank you.
>>
>>
>>
>>

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