"Source file found twice" error with mypy>=0.780 in python for vscode

Question

In my python project, after upgrading mypy from 0.770 to 0.782 an error is received in files where there were previously no type errors:

my_pkg_name\__init__.py: error: Source file found twice under different module names: 'top_pkg.my_pkg_name' and 'my_pkg_name'
Found 1 error in 1 file (checked 1 source file)

I'm pretty sure this is related to Issue #8944 on mypy and the way which vscode-python executes mypy on the open files. I've tried adding various mypy flags (e.g. --namespace-packages, --no-namespace-packages) but this did not resolve the issue.

my_pkg_name does contain an __init__.py and so does top_pkg. With mypy==0.770 this was not a problem.

Looking at the extension's output this is how mypy is invoked:

> ~\.virtualenvs\OfflineSystem.38\Scripts\python.exe `
   c:\Users\***\.vscode\extensions\ms-python.python-2020.8.108011\pythonFiles\pyvsc-run-isolated.py mypy `
   --ignore-missing-imports --follow-imports=silent --show-column-numbers `
   d:\***\top_pkg\my_pkg_name\sub_pkg\my_file.py

Should change something in the mypy-related vscode settings for this to work?

Answer 1

I had a similar issue, but not via VSCode. The fix in my case was to remove an __init__.py file from a directory that was being included by adding it to the MYPYPATH, and so wasn't actually being treated as a module (so it shouldn't really have had the __init__.py file).

You said you tried adding the --namespace-packages flag, but I think you would need --no-namespace-packages to disable the new checker which might be causing your problem.

Answer 2

In my case adding an __init__.py helped as it was missing from the particular module.

Answer 3

For me --explicit-package-bases worked.

From mypy documentation

This flag tells mypy that top-level packages will be based in either the current directory, or a member of the MYPYPATH environment variable or mypy_path config option. This option is only useful in in the absence of init.py. See Mapping file paths to modules for details