If you save a PEP8-uncompliant bot script in ./scripts/userscripts and run pycodestyles on it, you will not get any warnings back. But if you copy that file elsewhere and run pycodestyle there, you will get warnings.
Save this file both in /tmp and in ./scripts/userscripts:
Note that last line in the file contains white-spaces, which is a violation of PEP8.
Here is the output of pycodestyles, first in the ./scripts/userscripts/ directory and next in /tmp:
➜ userscripts git:(master) pycodestyle T.py ➜ userscripts git:(master) ➜ userscripts git:(master) cd /tmp ➜ /tmp pycodestyle T.py T.py:3:1: W293 blank line contains whitespace T.py:3:1: W391 blank line at end of file ➜ /tmp