On May 22, 2009, at 6:19 PM, Marek Szuba wrote:
> By the way, do you think we will still need > classutil.default_tmp_path() after this change? No, better to use Python's standard way of doing things. > in the "filepopen_cwd" branch attempts to make it possible for called > processes to use a different working directory than the current one > even if the subprocess module (whose Popen() method has got a > dedicated > keyword for this) is not present. This will be needed if, as Titus > suggested, we are to make formatdb run in the same directory as its > data files. I'm not convinced that we want to go this route. It seems klugey -- the user who tells Pygr to run formatdb or blastall is definitely not expecting Pygr to go changing the working directory as a side effect... Correct me if I'm wrong, but this temporary directory change would affect all threads running within our Python process, right? Istvan suggested we only release a Windows package for Python 2.5. In that case the standard library subprocess module takes care of the cwd keyword argument for us. Therefore the only possible concern is Python 2.3 on unix. If we really want to handle that case, we can do it trivially within the shell command we pass to system() -- this works on both unix and Windows/cygwin. Then the directory change happens in the child process, without affect the Python process at all. > 3. The "blast_test" branch has been extended with more parser-only > tests. Now every existing BLAST test which parses blastall output has > its canned-output counterpart. Great! We talked about adding a multiseq blast test to check that the multiseq results match the combined results of running all the sequences individually. Did you add that? -- Chris --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
