I've been experiencing the same error. I have made two changes to generate the docs:

• Replacing relative import statements like import .MyModule.X with absolute import statements like import MyPackage.MyModule.X.
• Tweaking the Sphinx-AutoAPI configuration in the file docs/conf.py: Instead of specifying the desired directories via the option autoapi_dirs = ["../source1", "../source2", "../source3"], pointing it to the packages root directory autoapi_dirs = [".."] and then specifying autoapi_ignore = ["*pattern1*", "*file2*", "*directory3*"] to exclude all problematic files/directories. _Note that the asterisks * where required to exclude the desired directories, like e.g. "directory3" to exclude all files in directory directory3/.

The second step I did because after changing the relative import statements I've been experiencing a further error described in this question.

Remark: I wanted to submit this as a comment, but I do not have enough "reputation". I hope this answer helps although I cannot explain the details.

Details

• I run sphinx-build -b html . _build in a docs directory located in the root folder of my project package.