Did anyone have a solution to this problem?  I have exactly the same 
scenario, where I import classes into a top level namespace, and Sphinx v4 
cannot disambiguate between the top-level version and the lower-level 
module version.  E.g.
```

WARNING: more than one target found for 'any' cross-reference 'Catalog': 
could be :py:class:`treecorr.Catalog` or 
:py:class:`treecorr.catalog.Catalog`

```
My current workaround it to downgrade to Sphinx 3.5.4, which works as I 
expect.  Is this an intended "feature" of Sphinx 4.x?  Can I add something 
to the config file to get back to the old resolution behavior?

Thanks,
Mike

On Wednesday, June 9, 2021 at 5:40:29 AM UTC-4 [email protected] wrote:

>
> Hello,
>
> We use Sphinx and AutoAPI to generate the API documentation for our Python 
> project.
> Our project consists of several sub-modules, each of which is defined with 
> an `__init__.py` file containing an `__all__` list. In order to get AutoAPI 
> to produce detailed documentation
> for each individual class, we also have an `__all__` list at the end of 
> each source file which
> lists the classes to document.
>
> Unfortunately, when generating the documentation for this project we get a 
> lot of warnings such as:
>
> Projects/PSyclone/src/psyclone/transformations.py:docstring of 
> psyclone.transformations.KernelGlobalsToArguments.validate:: WARNING: more 
> than one target found for cross-reference 'TransformationError': 
> psyclone.psyir.transformations.TransformationError, 
> psyclone.psyir.transformations.transformation_error.TransformationError
>
> where the `TransformationError` class is implemented in 
> psyclone/psyir/transformations/transformation_error.py but is made 
> available as part of the `psyclone.psyir.transformations` module.
>
> I would have thought this was a fairly common use case. Are we doing 
> something unexpected or is there some way of getting AutoAPI to do the 
> 'right thing'?
>
> I'm using Sphinx 4.0.2 and autoapi 2.0.1 under Ubuntu 20.04 and python 
> 3.8.5.
>
> BTW, you can see the config file at: 
> https://github.com/stfc/PSyclone/blob/master/doc/reference_guide/source/conf.py
>
> Many thanks,
>
> Andy.
>

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