manage.py makemessages only looks for directories in the current directory. Therefore, you need to create a symbolic link from a third-party application to your project directory:
ln -s ~/.virtualenvs/myvenv/local/lib/python2.7/site-packages/app app mkdir locale python manage.py makemessages -l cz -s
Note the -s . It forces makemessages follow symbolic links.
Another caveat is that if app already localized, then .po will create the app/locale/cz file instead of locale .
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