twine: README on PyPI rendered incorrectly if upload includes a wheel

Steps to reproduce the problem

I’ve reproduced this with the Resolwe project:

git clone https://github.com/genialis/resolwe.git
cd resolwe
mkvirtualenv resolwe
pip install --process-dependency-links -e .[docs,package,test]

For each of the variants, I’ve made the following common steps:

# bump version in resolwe/__about__.py
python setup.py clean -a
rm dist/*
rm -r *.egg-info

Then I’ve tested the following 4 variants:

Variant 1: Make sdist and whell and upload with twine

python setup.py sdist
python setup.py bdist_wheel
twine upload -r testpypi dist/*

Result is here -> README not rendered correctly.

Variant 2: Make sdist and whell and upload with setup.py upload

python setup.py sdist bdist_wheel upload -r testpypi

Result is here -> README rendered correctly.

Variant 3: Make sdist and upload with twine

python setup.py sdist
twine upload -r testpypi dist/*

Result is here -> README rendered correctly.

Variant 4: Make wheel and upload with twine

python setup.py bdist_wheel
twine upload -r testpypi dist/*

Result is here -> README not rendered correctly.

Summary

It appears that README is rendered incorrectly if twine upload includes a wheel.

Additional notes

The same problem also occurred when I uploaded the Resolwe 1.4.0 release to the real PyPI using Variant 1 described above. Note that the README is also incorrectly rendered on the new Warehouse-based PyPI frontend.

System information:

Fedora 24 with Python 3.5.2 and twine 1.8.1.

All contents of the virtualenv:

$ pip list --format=columns
Package                     Version    Location                    
--------------------------- ---------- ----------------------------
alabaster                   0.7.9      
appdirs                     1.4.0      
args                        0.1.0      
astroid                     1.4.9      
Babel                       2.3.4      
bleach                      1.5.0      
check-manifest              0.34       
clint                       0.5.1      
coverage                    4.3.4      
Django                      1.10.5     
django-autoslug             1.9.4.dev0 
django-filter               0.15.3     
django-guardian             1.4.6      
django-mathfilters          0.4.0      
django-versionfield2        0.5.0      
djangorestframework         3.5.3      
djangorestframework-filters 0.9.1      
docutils                    0.13.1     
elasticsearch               2.4.1      
elasticsearch-dsl           2.2.0      
html5lib                    0.9999999  
imagesize                   0.7.1      
isort                       4.2.5      
Jinja2                      2.9.4      
jsonschema                  2.5.1      
lazy-object-proxy           1.2.2      
MarkupSafe                  0.23       
mccabe                      0.6.0      
mock                        2.0.0      
packaging                   16.8       
pbr                         1.10.0     
pip                         9.0.1      
pkginfo                     1.4.1      
psycopg2                    2.6.2      
pycodestyle                 2.2.0      
pydocstyle                  1.1.1      
Pygments                    2.2.0      
pylint                      1.6.5      
pyparsing                   2.1.10     
python-dateutil             2.6.0      
pytz                        2016.10    
PyYAML                      3.12       
readme-renderer             16.0       
requests                    2.13.0     
requests-toolbelt           0.7.0      
resolwe                     1.4.0.4    /home/tadej/Genialis/resolwe
resolwe-runtime-utils       1.1.0      
setuptools                  34.0.2     
six                         1.10.0     
snowballstemmer             1.2.1      
Sphinx                      1.5.2      
sphinx-rtd-theme            0.1.9      
testfixtures                4.13.3     
twine                       1.8.1      
urllib3                     1.20       
wheel                       0.30.0a0   
wrapt                       1.10.8