Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-11-12

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All times shown according to UTC.

Time Nick Message
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02:04 CIA-113 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * r439c4c6 / Bio/DB/Tree/Node.pm : Minor doc cleanup. - http://bit.ly/a9sfQa
02:04 CIA-113 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * rddca0cd / (3 files in 2 dirs): Adding methods for populating trees, and for a tree object to load its state from the database. - http://bit.ly/caGfJJ
02:04 CIA-113 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * re4fe4db / (4 files in 2 dirs): Added tag/value method stubs to db trees (no-ops at this point). Added populate_tree. Various fixes to SQLite. Changed _load_from_db to deal with recursion. - http://bit.ly/9QsgMP
02:04 CIA-113 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * r4fedfee / t/Tree/DB/TreeDB.t : Tests for db-aware tree object. - http://bit.ly/a93fzz
02:04 CIA-113 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * ra267634 / t/Tree/TreeIO.t : Small typo fix. - http://bit.ly/9ZzeyN
04:47 CIA-113 bioperl-live: Chris Fields topic/phyloxml_output_refac * r4e8e24c / Bio/TreeIO/phyloxml.pm : (somewhere over Ohio) <sequence> now working - http://bit.ly/deISf3
04:47 CIA-113 bioperl-live: Chris Fields topic/phyloxml_output_refac * ra1dbfa3 / Bio/TreeIO/phyloxml.pm : (somewhere over Indiana) back out some sequence stuff to work out sequence_relation stuff - http://bit.ly/aYEDEa
04:47 CIA-113 bioperl-live: Chris Fields topic/phyloxml_output_refac * r606617a / Bio/TreeIO/phyloxml.pm : (somewhere between Chicago and Champaign) get clade_relation, sequence_relation working - http://bit.ly/dim3No
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06:50 kblin hehe
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15:01 CIA-113 bioperl-live: Greg Jordan topic/tree_api_refresh * r4514fbd / (17 files in 4 dirs): Completely gutted, refactored, rehashed, and revamped the Tree API. Removed all documentation for now; will spend today adding new POD and use cases. - http://bit.ly/9tYyr8
15:13 CIA-113 bioperl-live: Chris Fields topic/phyloxml_output_refac * ra0a4994 / Bio/TreeIO/phyloxml.pm : more relation fixes - http://bit.ly/dpRqrE
16:05 CIA-113 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * r4dfe14f / (3 files in 3 dirs): Changed root_node to root in Tree to match TreeI signature. Added score property for trees (prescribed by TreeI). - http://bit.ly/a937rt
16:45 CIA-113 bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * rb328142 / Bio/Tree/Node.pm : document sorting option - http://bit.ly/bltS6S
16:45 CIA-113 bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * r53d3220 / Bio/DB/Tree/Node.pm : document sorting option - http://bit.ly/c6RLKL
16:47 CIA-113 bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * r6c51ddc / Bio/Tree/Tree.pm : either/or for ordering - http://bit.ly/cLOQqx
16:50 CIA-113 bioperl-live: Greg Jordan topic/tree_api_refresh * rfa7a680 / (5 files in 2 dirs): Make NodeFunctionsI not inherit from NodeI -- Node.pm now inherits both NodeI and NodeFunctionsI. - http://bit.ly/bCwNha
17:07 CIA-113 bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * r062113b / Bio/Tree/Tree.pm : some formatting - http://bit.ly/b9MMuA
17:07 CIA-113 bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * raa71c20 / t/Tree/DB/Tree.t : potentially temporary, tree testing - http://bit.ly/945u3w
17:48 CIA-113 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * r3e4f5a6 / t/Tree/DB/TreeIO-DB.t : Test script for parsing trees into a database. - http://bit.ly/bWQHa2
17:48 CIA-113 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * r02a2697 / (4 files in 4 dirs): Various fixes to make the database loading work. - http://bit.ly/aOp4Fx
18:02 CIA-113 bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * rd54ece6 / t/Tree/DB/Tree.t : do sub-tree analysis - http://bit.ly/aMJH8x
18:02 CIA-113 bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * rdc5b5b7 / (5 files in 5 dirs): Merge branch 'topic/tree_dbsqlite_memoryfix' of github.com:bioperl/bioperl-live into topic/tree_dbsqlite_memoryfix - http://bit.ly/cfQQLg
18:17 deafferret wow... commit fest!
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21:44 CIA-64 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * ref1d89a / Bio/TreeIO/TreeEventDBBuilder.pm : Fix uninitialized value error if called from outside (which apparently some parsers do). - http://bit.ly/b60hQN
21:44 CIA-64 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * r4514ce3 / Bio/DB/Tree/Node.pm : Some cleanup, added bootstrap. Implemented children(). - http://bit.ly/9CmgEu
21:44 CIA-64 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * r91f2251 / (3 files in 3 dirs): Implemented fetching nodes by parent, added tests whether trees are correctly inserted. - http://bit.ly/9CHVGh
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