How to remove trailing whitespace in code, using another script?

fileinput seems to be for multiple input streams. This is what I would do:

with open("test.txt") as file:
    for line in file:
        line = line.rstrip()
        if line:
            print(line)

You don't see any output from the print statements because FileInput redirects stdout to the input file when the keyword argument inplace=1 is given. This causes the input file to effectively be rewritten and if you look at it afterwards the lines in it will indeed have no trailing or leading whitespace in them (except for the newline at the end of each which the print statement adds back).

If you only want to remove trailing whitespace, you should use rstrip() instead of strip(). Also note that the if lines == '': continue is causing blank lines to be completely removed (regardless of whether strip or rstrip gets used).

Unless your intent is to rewrite the input file, you should probably just use for line in open(filename):. Otherwise you can see what's being written to the file by simultaneously echoing the output to sys.stderr using something like the following (which will work in both Python 2 and 3):

from __future__ import print_function
import fileinput
import sys

for line in (line.rstrip() for line in
                fileinput.FileInput("test.txt", inplace=1)):
    if line:
        print(line)
        print(line, file=sys.stderr)