diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 39e35ce..991ec6f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -57,6 +57,7 @@ jobs:
         uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
+          flags: ${{ matrix.setup_config_enabled == 'yes' && 'setupconfig' || 'base' }}
 
   publish:
     name: Publish package to PyPI