On Jul 27, 2009, at 4:39 PM, Christopher Lee wrote:
> > Hi Titus, > I have one question about your silencio commit in blast.py, which > always blocks display of stderr output from formatdb. This is the > only change in the silencio branch that modifies behavior of Pygr > itself rather than just of the test suite. Given that formatdb is > prone to failure, I'm not sure Pygr should suppress formatdb's error > messages so completely as this commit would impose. If I understood > right, you made this change mainly to hide error messages during the > test_formatdb_fail() test. I propose the following compromise: > > - add a new option showFormatdbMessages to BlastMapping(). By default > this would be True. Setting it to False would activate your > redirection code that hides the stdout / stderr output from formatdb. > > - test_formatdb_fail() would invoke this option to prevent formatdb > error messages from being displayed during the test. I don't think users should care about formatdb output unless it fails. How about just having formatdb output sent to notice or debug iff all of the formatdbs fail? BlastMapping already has too many kwargs, and I think people will only care about formatdb when they can't get it to work. Ultimately, however, I will be happy as long as those error messages don't clutter up the output of the tests ;) --titus --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
