The following file contents will produce an empty coverage report (create directory "testsub" first):
print "statement 1"
print "statement 2"
Issue tested and exists in both 3.01 and 2.80-2 (current for Ubuntu 9.04 repository).
Workaround: specify an absolute file location via COVERAGE_FILE. This provides correct output in 3.01, but not in 2.80-2.
Adjusting the .coverage filename to include an absolute path via something like filename = os.path.join( os.path.abspath( os.path.split(filename)), os.path.split(filename)) would probably resolve.