On Wed, Jan 07, 2009 at 11:14:26AM -0800, Christopher Lee wrote: -> in the interest of making pygr easier to understand and work with, -> I've tried to subdivide large modules (such as seqdb) into smaller, -> more coherent pieces. For example, I recently moved all the BLAST -> support out of seqdb.py into a new module blast.py. -> -> Perhaps we should also move annotation functionality out of seqdb into -> a new module (annotate.py or annotation.py?). AnnotationDB doesn't -> depend on seqdb; I don't think the prospective annotation.py would -> even need to import seqdb... Their association is purely conceptual. -> -> One consideration: backwards compatibility for unpickling and thus -> pygr.Data. Unpickling looks for classes based on the module location -> saved when the object was originally pickled, so to maintain the -> ability to unpickle (e.g. retrieve from pygr.Data) existing annotation -> resources, we'd have seqdb import a few key classes (AnnotationDB and -> kin) from annotation.py, so that those names continue to be accessible -> from the seqdb namespace as before. -> -> What do you think? Does this seem worthwhile, and should we include -> this in the 0.8 release?
Yes, that makes sense! I'm agnostic about the release timing. How about adding __all__ attributes to modules, too? Then we can know what's supposed to be exported. cheers, --titus -- C. Titus Brown, [email protected] --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
