Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-11-11

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All times shown according to UTC.

Time Nick Message
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01:58 CIA-57 bioperl-live: Chris Fields topic/phyloxml_output_refac * r7213f86 / (Bio/TreeIO/phyloxml.pm Bio/TreeIO/Writer/PhyloXMLHelper.pm): add a simple class to generate XML nodes, which may or many not be merged into the main parser - http://bit.ly/aaDLZ9
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11:11 CIA-57 bioperl-live: DaveMessina master * r67fedbf / (Bio/SeqIO/seqxml.pm t/SeqIO/seqxml.t): added schemaLocation method and constants for XML header info - http://bit.ly/9Xnibq
12:46 kai pyrimidine: when you wake up, what's the deal with the 1-6-2 branch?
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15:52 CIA-57 bioperl-live: Greg Jordan topic/tree_api_refresh * r1bec491 / (Bio/Tree/Tree.pm Bio/Tree/TreeI.pm Bio/TreeIO/newick.pm): Add is_rooted method to TreeI and a rooted() getter / setter to Tree. Auto-set the rooted flag according to convention in newick.pm. - http://bit.ly/ahxWGW
17:03 CIA-57 bioperl-live: Chris Fields master * r47b1feb / t/Ontology/OntologyEngine.t : fix test that relied on the highly optional Error.pm - http://bit.ly/bd4Nse
17:16 CIA-57 bioperl-live: Chris Fields master * rf0e3bed / Build.PL : add Error as a recommends, but indicate it as very optional - http://bit.ly/b7Fe7B
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18:09 CIA-57 bioperl-live: Chris Fields topic/phyloxml_output_refac * r318f921 / (Bio/TreeIO/Writer/PhyloXMLHelper.pm Bio/TreeIO/phyloxml.pm): check in latest phyloxml commits, may move code from helper back into the parser at some point - http://bit.ly/9zM8cN
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18:14 pyrimidine_ kai: I ran into problems with merging everything over from master to the 1.6 branch, largely b/c that branch was created prior to the git migration
18:15 pyrimidine_ 1.6.1 happened to be released prior to the git migration (release in sept 2009, migration in may 2010) but 1.6.2 has stalled due to these problems.
18:16 pyrimidine_ however, since nothing has changed in master API-wise, it didn't make sense to let that stall us, so we are just arbitrarily setting up a new 1.6.2 off master
18:18 kblin ah, I see
18:18 kblin does it make sense to get my build scripts to start packaging that version?
18:27 pyrimidine_ kai: possibly
18:27 pyrimidine_ but I would hold off maybe until we have an alpha out
18:28 kblin ok
18:28 pyrimidine_ 1.6.2 will also likely be the last 1.6.x release, except maybe critical bug fixes.  We need to move on and fix some of the more significant problems (modularizing the monolith, etc)
18:30 kblin sure, I just got software out there that depends on git master right now, and I'd like to have this covered first. the code's bad enough without having to grab the deps from git :)
18:31 kblin I can cope for now, but I've got a bugfix release scheduled for the day after bioperl 1.6.2 happens :)
18:32 kblin currently making use of my time by writing tests and refactoring a lot of cruft
18:43 pyrimidine_ kblin: it's easy enough to merge those over if we need to; we'll probably have some alphas prior to a final release
18:45 kblin pyrimidine_: if the 1-6-2 branch is what will turn into the release, I think all the patches I need are in there
18:50 pyrimidine_ kblin: ok
20:49 CIA-57 bioperl-live: Chris Fields topic/phyloxml_output_refac * ra953a2f / (Bio/TreeIO/Writer/PhyloXMLHelper.pm Bio/TreeIO/phyloxml.pm): write_xml now catching more nested data, a few more to go (sequence, etc) - http://bit.ly/aa1HKU
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21:13 CIA-57 bioperl-live: Chris Fields topic/phyloxml_output_refac * r20ebaa1 / Bio/TreeIO/phyloxml.pm : beginnings of sequence information - http://bit.ly/aazbPV
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21:49 CIA-57 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * r5d69c4f / t/Tree/DB/NodeDB.t : Revamped test script for db-aware nodes. This is working now. (+7 more commits...) - http://bit.ly/b42Gpx
22:03 deafferret gak!   & commute
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23:37 CIA-113 bioperl-live: Scott Cain master * r2d4422b / Bio/DB/GFF.pm : fixing glob behavior on MacOS X when there are spaces in paths (presumably fixes it on other OSes as well). - http://bit.ly/9SU91W
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