Originally reported in pypi/warehouse#4341.
It looks like long_description is full of Windows-style carriage-return characters (^M) which seem to have confused twine/pkginfo about what is and what isn't part of long_description.
My project at PyPI is at: https://pypi.org/project/gff3tool/1.4.2.
Libraries used:
wheel==0.31.1
setuptools==39.1.0
twine==1.11.0