Opened 11 years ago

Closed 10 years ago

#11953 closed enhancement (fixed)

Upgrade optional package biopython to version 1.60

Reported by: mhampton Owned by: tbd
Priority: major Milestone: sage-5.2
Component: packages: optional Keywords: biopython, sd40
Cc: Merged in: sage-5.2.rc0
Authors: Marshall Hampton, John Palmieri Reviewers: Marshall Hampton, John Palmieri
Report Upstream: N/A Work issues:
Branch: Commit:
Dependencies: Stopgaps:

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Description (last modified by John Palmieri)

Biopython 1.60 was released in June, 2012. There are numerous enhancements since 1.57.

New spkg: http://sage.math.washington.edu/home/palmieri/SPKG/biopython-1.60.spkg

Attachments (1)

trac_11953-biopython.patch (5.6 KB) - added by John Palmieri 10 years ago.
patch for biopython spkg, for review only

Download all attachments as: .zip

Change History (11)

comment:1 Changed 11 years ago by mhampton

Status: newneeds_review

This is a simple update, candidate spkg is at: http://sage.math.washington.edu/home/mhampton/biopython-1.58.spkg

comment:2 Changed 11 years ago by Jeroen Demeyer

Milestone: sage-4.7.3

Milestone sage-4.7.3 deleted

comment:3 Changed 11 years ago by mhampton

Description: modified (diff)
Milestone: sage-5.0
Summary: Upgrade optional package biopython to version 1.58Upgrade optional package biopython to version 1.59

comment:4 Changed 11 years ago by mhampton

I find it quite discouraging that no one ever reviewed the 1.58 spkg. The biopython project is very active, well maintained, and well tested. It would be nice if these upgrades could be reviewed more quickly.

New spkg is up at: http://sage.math.washington.edu/home/mhampton/biopython-1.59.spkg

Changed 10 years ago by John Palmieri

Attachment: trac_11953-biopython.patch added

patch for biopython spkg, for review only

comment:5 Changed 10 years ago by John Palmieri

Authors: Marshall HamptonMarshall Hampton, John Palmieri
Description: modified (diff)
Summary: Upgrade optional package biopython to version 1.59Upgrade optional package biopython to version 1.60

The new spkg builds and passes tests on several platforms. It's an easy update of an spkg: just drop in a new upstream source. The newest version has a few small cleanups to the spkg structure, as well.

comment:6 Changed 10 years ago by John Palmieri

Keywords: sd40 added

comment:7 Changed 10 years ago by mhampton

Milestone: sage-5.3sage-5.2
Reviewers: Marshall Hampton, John Palmieri
Status: needs_reviewpositive_review

comment:8 Changed 10 years ago by mhampton

Thanks very much John! The new spkg looks good.

comment:9 Changed 10 years ago by Harald Schilly

i just put the spkg on the server+mirrors.

comment:10 Changed 10 years ago by Jeroen Demeyer

Merged in: sage-5.2.rc0
Resolution: fixed
Status: positive_reviewclosed
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