[Bioperl-l] Seeking comments, Bio::Species memleak fix
cjfields at illinois.edu
Wed Jun 30 13:35:51 EDT 2010
I have a branch in github (topic/species_proxy) that converts
Bio::Species into a proxy class. This appears to fix a ton of problems
introduced during the Tree/Taxonomy refactoring a few years back.
1) No need for Scalar::Util::weaken within Bio::Species or
Bio::Tree::Node. Cleanup methods are handled during instance
2) This paves the way a bit more for eventual deprecation of
Bio::Species in 1.7.
3) Works with bioperl-db and BioSQL as is (passes on both my local
Ubuntu 9.10 and Mac OS X 10.6), perl 5.10 and 5.12, should work with
earlier perl versions.
1) For every Bio::Species, we have a Bio::Taxon, a Bio::Tree::Tree, and
a Bio::DB::Taxonomy (one instance more than the previous Bio::Species
implementation). We can probably reduce that down considerably by
creating the needed instances lazily.
bug 3017 use threads to get genbank file error
bug 2594 Bio::Species memory leak
and possibly others:
bug 2773 Bio::Tree::Node gets destroyed even though it is still live
If there are no comments, I'll merge this with the master branch in the
next few days.
(NOTE: skip the next two paragraphs if you don't want to read nasty
Bio::Species had previously inherited from Bio::Taxon, but also required
it to hold a Bio::Tree::Tree which contained a circular reference back
to the Bio::Species object, thus requiring Scalar::Util::weaken. This
has caused several hard-to-diagnose problems with premature garbage
collection, including some issues with threads (bug 3017).
The above proxy fix converts Bio::Species into a proxy class, which only
inherits the interface (Bio::Tree::NodeI), and delegates to an internal
Bio::Taxon and a Bio::Tree::Tree. Neither contained object has a
reference back to the Bio::Species instance, thus the class can perform
proper garbage collection.
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