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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