pygr

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ID Status Summary
138 Done You documentation points to a porn site Type-Defect Priority-Medium
137 New building the docs fails with missing modules (seqfmt, cnestedlist, MySQLdb) Type-Defect Priority-Medium
136 New Is the UCLA metabase database down? Type-Defect Priority-Medium
135 New Can't build in Lion, because gcc-4.0 is gone after xcode 4 killed xcode 3 Type-Defect Priority-Medium OpSys-OSX
134 FixedNeedsReview UCSCEnsemblInterface fails with Genome doesn't exist error Type-Defect Priority-Critical
133 FixedNeedsReview libnclist: find_suboverlap_start doesn't check isub against nlists, can segfault Type-Defect Priority-Medium
132 New seqdb / blast tests should clean up index files Type-Enhancement Priority-Low
131 New SQLTable.new doesn't add new rows. Type-Defect Priority-High
130 New attrAlias not passed on when using sqlgraph.SQLGraph Type-Defect Priority-Medium Usability
129 Closed Link broken on pygr's google code site Type-Defect Priority-Medium
128 FixedNeedsReview Check Pyrex 0.9.9 support Type-Defect Priority-Medium
127 New no default annotationType for AnnotationDBs served by XMLRPC Type-Defect Priority-Medium
126 Invalid pygr requires 10.4 SDK on Mac OS X 10.6 Type-Defect Priority-Medium
125 Closed Problem with MetaBase server at UCLA . Type-Defect Priority-Medium
124 Invalid missing file (pygr/seqfmt.c: No such file or directory) from latest clone? Type-Defect Priority-Medium
123 New Add memory reporting for megatests Type-Defect Priority-Medium
122 New Add megatest for short-read mapping Type-Defect Priority-Medium
121 New formatdb fail tests litters file system with empty files Type-Defect Priority-Medium
120 New XMLRPC resource for Caenorhabditis brenneri Type-Task Priority-Medium Component-Persistence
119 FixedNeedsReview ShelveMetabase doesn't work with external bsddb3 Type-Defect Priority-Medium
118 New blockIterators mechanism does NOT require allocating new cursor Type-Enhancement Priority-Low
117 Closed run pep8.py on pygr source code Type-Enhancement Priority-Low
116 Invalid schema binding gives an integer key error Type-Defect Priority-Low
115 New Support NLMSA requerying with subintervals of original query sequence. Type-Defect Priority-Medium
114 New by default, unit tests should be gathered and run all together Type-Defect Priority-Medium
113 Accepted pass **kwargs for do_gunzip and run_gunzip (downloader.py) Type-Defect Priority-Low Milestone-Release0.8
112 Accepted Add download=True XML-RPC support for AnnotationDB Type-Enhancement Priority-Medium Milestone-Release0.8.2
111 New Refactor NLMSA methods to provide convenience functions with explicit names Type-Defect Priority-Medium
110 New Remove python2.3 support for pygr 0.9 Type-Other Priority-Medium Milestone-Release0.9
109 Invalid Graph(edgeDB=None) should switch to trivial edge packing mode Type-Enhancement Priority-Low
108 New Provide proper inverse classes for Mapping, Graph Type-Defect Priority-Medium
107 New deprecate multiValue mode for mapping.Mapping Type-Enhancement Priority-Low
106 New Add blast parameters to BlastMapping constructor Type-Enhancement Priority-Low
105 Accepted Provide convenience methods for adding new resources to running XML-RPC servers Type-Enhancement Priority-Medium Milestone-Release0.8.1
104 New Occasional garbage in megatest output with Python-2.4 Type-Defect Priority-Medium
103 Closed Excessive memory consumption in megatests Type-Defect Priority-Medium Milestone-Release0.8
102 Closed Possible memory leak in NLMSA code Type-Defect Priority-Medium ReviewBy-cjlee112 Milestone-Release0.8.1
101 New python2.3/setuptools bug: pyrexc not run Type-Defect Priority-Medium
100 Accepted Keep code-example Wiki pages in Git repository, synchronise them automatically Type-Enhancement Priority-Medium
99 Closed SQLTable.itervalues() can be interrupted by other queries Type-Defect Priority-Medium reviewby-kmdaily Milestone-Release0.8
98 New Install tests with pygr Type-Enhancement Priority-Low
97 Closed IOError: Iterator has no database Type-Defect Priority-Medium Milestone-Release0.8 reviewby-marecki
96 Closed Put license & copyright information in LICENSE.txt and/or at the top of README Type-Defect Priority-Medium
95 Closed Rename README to README.txt Type-Defect Priority-Medium
94 Closed add test for fixed blast parsing issue (negative orientation) Type-Defect Priority-Medium
93 Closed add test for fixed blast parsing issue (multirecord) Type-Defect Priority-Medium
92 Accepted Links to Web pages to replace verbose error messages Type-Enhancement Priority-Low
91 Accepted 0.7-0.8 compatibility (incl. testing) Type-Enhancement Priority-Medium Milestone-Release0.8
90 New support for http proxy? Type-Defect Priority-Medium Milestone-Release0.9
89 New Need for solexa seqdb with integer (64bit) ID which requires no hashing/indexing Type-Enhancement Priority-Medium Milestone-Release0.9
88 Closed Increase robustness of BLAST tests Type-Enhancement Priority-Critical Milestone-Release0.8 reviewby-cjlee112
87 Closed Commit 'runtest_single' to master. Type-Defect Priority-Medium ReviewBy-istvan.albert
86 Closed Commit 'cleanflag' branch to master Type-Defect Priority-Medium ReviewBy-the.good.doctor.is.in
85 Closed Commit 'nicer-error'' branch to master Type-Defect Priority-Medium ReviewBy-the.good.doctor.is.in
84 Closed Slicing on LPO produces Bus error Type-Defect Priority-High
83 Closed Track running time of megatests Type-Enhancement Priority-Medium Milestone-Release0.8 ReviewBy-marecki
82 Closed Update setup.cfg Type-Defect Priority-Medium Milestone-Release0.8
81 Closed Attribute error, ignored, in graph_test under python2.3 Type-Enhancement Priority-Medium Python-2.3 Milestone-Release0.8 ReviewBy-the.good.doctor.is.in
80 Closed pygr.downloader uses subprocess, which is not python2.3 compatible. Type-Defect Priority-Medium Python-2.3 Milestone-Release0.8 ReviewBy-the.good.doctor.is.in
79 Closed Multi-sequence blast support Type-Enhancement Priority-Medium Milestone-Release0.8 ReviewBy-alexander.alekseyenko
78 Closed Get rid of vague or imprecise error messages from tests Type-Enhancement Priority-Medium Milestone-Release0.8
77 New Maintain a dependency tree of tests Type-Enhancement Priority-Medium
76 Invalid ensembl.SeqRegion gives KeyError if missing coord system or bad seqID Type-Defect Priority-High ReviewBy-marecki Milestone-Release0.8
75 Accepted Implement a remote-management interface for XML-RPC servers Type-Enhancement Priority-Medium Milestone-Release1.0
74 Closed undefined 'al' in NLMSA.add_aligned_intervals Type-Defect Priority-Medium
73 Closed Incorporate metabase branch Type-Enhancement Priority-Medium ReviewBy-the.good.doctor.is.in
72 Closed Fix zombie dependence on pygr.poa Type-Defect Priority-Medium
71 Closed Support write operations to SQL databases Type-Enhancement Priority-Medium Milestone-Release0.8 reviewby-jqian.ubc
70 Closed Support for sqlite Type-Enhancement Priority-Medium Milestone-Release0.8 reviewby-the.good.doctor.is.in
69 Closed Make megatests more portable Type-Defect Priority-Medium Milestone-Release0.8 reviewby-the.good.doctor.is.in
68 Accepted Find, review, and post Rachel's summer docs Type-Task Priority-Medium
67 Closed Test Istvan's new setup.py on multiple platforms Type-Enhancement Priority-Medium Milestone-Release0.8 reviewby-cjlee112
66 FixedNeedsReview Code review: seqdb.py Type-Task Priority-Medium ReviewBy-cjlee112
65 Closed Code review: Istvan's test rewrite branch Type-Defect Priority-Medium
63 Duplicate Reduce complexity of setup.py Type-Other Priority-Medium Milestone-Release0.8
62 Accepted Shorter notifications, messages Type-Enhancement Priority-Medium Usability
61 Closed adding logging functionality Type-Enhancement Priority-Medium
60 Closed (patch) windows platform needs a 'b' flag to indicate binary formats Type-Defect Priority-Medium Milestone-Release0.8
59 Closed Move annotation classes to a separate module Type-Enhancement Priority-Low Milestone-Release0.8 reviewby-the.good.doctor.is.in
58 Closed Refactor top-level pygr.Data namespace access Type-Enhancement Priority-Low Milestone-Release0.8 ReviewBy-the.good.doctor.is.in
57 Closed Consider simplifying SeqPath start,stop attribute handling Type-Enhancement Priority-Low Milestone-Release0.8 reviewby-the.good.doctor.is.in
56 Invalid unable to access the sequence object via a saved bound schema attribute :( Type-Defect Priority-High
55 Invalid Types of acceptable sourceDB or targetDB for sqlgraph.GraphView Type-Enhancement Priority-High
54 Closed sqlgraph.GraphView unpickle-able error Type-Defect Priority-High Milestone-Release0.8 reviewby-jqian.ubc
53 Closed sqlgraph.GraphView ORDER-BY bug Type-Defect Priority-High Milestone-Release0.8 reviewby-jqian.ubc
52 Accepted Move from shelve to sqlite3 storage? Type-Enhancement Priority-High Milestone-Release0.8.1
51 WontFix sys.path problems in our test framework Type-Defect Priority-Low
50 Closed SQL "view" mapping and graph transformations Type-Enhancement Priority-Medium Milestone-Release0.8
49 Closed Initial delay for membership checking in seqdb.BlastDB Type-Enhancement Priority-Low Milestone-Release0.8
48 Closed megatest failure: cannot delete from dict Type-Defect Priority-Low Milestone-Release0.8
47 Closed KeyError on deleting pygr.Data resource Type-Defect Priority-Medium Milestone-Release0.8
46 Closed decorator syntax incompatible with Python 2.3 Type-Defect Priority-Medium Milestone-Release0.8
45 Closed BlastDB has gotten slow due to cache Type-Defect Priority-Critical Milestone-Release0.8
44 Closed tblastn and blastx support Type-Enhancement Priority-Low Milestone-Release0.8 reviewby-the.good.doctor.is.in
43 Closed add a test for SQLSequence class method problem Type-Enhancement Priority-Medium Milestone-Release0.8
42 Closed KeyError for BLAST results that return no hits Type-Defect Priority-Medium Milestone-Release0.8
41 Closed TBLASTN parsing error Type-Defect Priority-Medium Milestone-Release0.8
40 Closed add NLMSA convenience method for loading aligned intervals from any source Type-Enhancement Priority-Low Milestone-Release0.8 reviewby-the.good.doctor.is.in
39 New add schema grouping to pygr.Data Type-Enhancement Priority-Medium Milestone-Release1.0
38 Done write docs on running & managing a XMLRPC pygr.Data server Type-Task Priority-High Milestone-Release0.8