| |
ID |
Type |
Status |
Priority |
Milestone |
Owner |
ReviewBy |
|
Summary + Labels |
... |
| |
12 |
Enhancement
|
New
|
Medium
|
----
|
deepreds
|
----
|
|
Disallow overwriting seqdb.BlastDB in pygr.Data or Print out error message on overwriting attempt
|
|
| |
33 |
Enhancement
|
Assigned
|
High
|
Release0.8
|
cjlee112
|
----
|
|
Standardize ensembl components
|
|
| |
36 |
Enhancement
|
Accepted
|
Medium
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
add SSL XMLRPC client and server support
|
|
| |
39 |
Enhancement
|
New
|
Medium
|
Release1.0
|
cjlee112
|
----
|
|
add schema grouping to pygr.Data
|
|
| |
52 |
Enhancement
|
Accepted
|
High
|
Release0.8.1
|
cjlee112
|
----
|
|
Move from shelve to sqlite3 storage?
|
|
| |
62 |
Enhancement
|
Accepted
|
Medium
|
----
|
istvan.albert
|
----
|
|
Shorter notifications, messages
Usability
|
|
| |
66 |
Task
|
FixedNeedsReview
|
Medium
|
----
|
the.good.doctor.is.in
|
cjlee112
|
|
Code review: seqdb.py
|
|
| |
68 |
Task
|
Accepted
|
Medium
|
----
|
the.good.doctor.is.in
|
----
|
|
Find, review, and post Rachel's summer docs
|
|
| |
75 |
Enhancement
|
Accepted
|
Medium
|
Release1.0
|
pygr-bug...@googlegroups.com
|
----
|
|
Implement a remote-management interface for XML-RPC servers
|
|
| |
77 |
Enhancement
|
New
|
Medium
|
----
|
the.good.doctor.is.in
|
----
|
|
Maintain a dependency tree of tests
|
|
| |
89 |
Enhancement
|
New
|
Medium
|
Release0.9
|
deepreds
|
----
|
|
Need for solexa seqdb with integer (64bit) ID which requires no hashing/indexing
|
|
| |
90 |
Defect
|
New
|
Medium
|
Release0.9
|
pygr-bug...@googlegroups.com
|
----
|
|
support for http proxy?
|
|
| |
91 |
Enhancement
|
Accepted
|
Medium
|
Release0.8
|
pygr-bug...@googlegroups.com
|
----
|
|
0.7-0.8 compatibility (incl. testing)
|
|
| |
92 |
Enhancement
|
Accepted
|
Low
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
Links to Web pages to replace verbose error messages
|
|
| |
98 |
Enhancement
|
New
|
Low
|
----
|
the.good.doctor.is.in
|
----
|
|
Install tests with pygr
|
|
| |
99 |
Defect
|
FixedNeedsReview
|
Medium
|
Release0.8
|
pygr-bug...@googlegroups.com
|
kmdaily
|
|
SQLTable.itervalues() can be interrupted by other queries
|
|
| |
100 |
Enhancement
|
Accepted
|
Medium
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
Keep code-example Wiki pages in Git repository, synchronise them automatically
|
|
| |
101 |
Defect
|
New
|
Medium
|
----
|
the.good.doctor.is.in
|
----
|
|
python2.3/setuptools bug: pyrexc not run
|
|
| |
103 |
Defect
|
FixedNeedsReview
|
Medium
|
Release0.8
|
cjlee112
|
----
|
|
Excessive memory consumption in megatests
|
|
| |
104 |
Defect
|
New
|
Medium
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
Occasional garbage in megatest output with Python-2.4
|
|
| |
105 |
Enhancement
|
Accepted
|
Medium
|
Release0.8.1
|
pygr-bug...@googlegroups.com
|
----
|
|
Provide convenience methods for adding new resources to running XML-RPC servers
|
|
| |
106 |
Enhancement
|
New
|
Low
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
Add blast parameters to BlastMapping constructor
|
|
| |
107 |
Enhancement
|
New
|
Low
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
deprecate multiValue mode for mapping.Mapping
|
|
| |
108 |
Defect
|
New
|
Medium
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
Provide proper inverse classes for Mapping, Graph
|
|
| |
110 |
Other
|
New
|
Medium
|
Release0.9
|
pygr-bug...@googlegroups.com
|
----
|
|
Remove python2.3 support for pygr 0.9
|
|
| |
111 |
Defect
|
New
|
Medium
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
Refactor NLMSA methods to provide convenience functions with explicit names
|
|
| |
112 |
Enhancement
|
Accepted
|
Medium
|
Release0.8.2
|
pygr-bug...@googlegroups.com
|
----
|
|
Add download=True XML-RPC support for AnnotationDB
|
|
| |
113 |
Defect
|
Accepted
|
Low
|
Release0.8
|
cjlee112
|
----
|
|
pass **kwargs for do_gunzip and run_gunzip (downloader.py)
|
|
| |
114 |
Defect
|
New
|
Medium
|
----
|
the.good.doctor.is.in
|
----
|
|
by default, unit tests should be gathered and run all together
|
|
| |
115 |
Defect
|
New
|
Medium
|
----
|
alexander.alekseyenko
|
----
|
|
Support NLMSA requerying with subintervals of original query sequence.
|
|
| |
118 |
Enhancement
|
New
|
Low
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
blockIterators mechanism does NOT require allocating new cursor
|
|
| |
119 |
Defect
|
FixedNeedsReview
|
Medium
|
----
|
marecki
|
----
|
|
ShelveMetabase doesn't work with external bsddb3
|
|
| |
120 |
Task
|
New
|
Medium
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
XMLRPC resource for Caenorhabditis brenneri
|
|
| |
121 |
Defect
|
New
|
Medium
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
formatdb fail tests litters file system with empty files
|
|
| |
122 |
Defect
|
New
|
Medium
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
Add megatest for short-read mapping
|
|
| |
123 |
Defect
|
New
|
Medium
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
Add memory reporting for megatests
|
|
| |
125 |
Defect
|
New
|
Medium
|
----
|
pygr-bug...@googlegroups.com
|
----
|
|
Problem with MetaBase server at UCLA .
|
|