Ticket #11953 (closed enhancement: fixed)

Opened 19 months ago

Last modified 10 months ago

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: Work issues:
Report Upstream: N/A Reviewers: Marshall Hampton, John Palmieri
Authors: Marshall Hampton, John Palmieri Merged in: sage-5.2.rc0
Dependencies: Stopgaps:

Description (last modified by jhpalmieri) (diff)

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

trac_11953-biopython.patch Download (5.6 KB) - added by jhpalmieri 10 months ago.
patch for biopython spkg, for review only

Change History

comment:1 Changed 19 months ago by mhampton

  • Status changed from new to needs_review

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

comment:2 Changed 19 months ago by jdemeyer

  • Milestone sage-4.7.3 deleted

Milestone sage-4.7.3 deleted

comment:3 Changed 14 months ago by mhampton

  • Summary changed from Upgrade optional package biopython to version 1.58 to Upgrade optional package biopython to version 1.59
  • Description modified (diff)
  • Milestone set to sage-5.0

comment:4 Changed 14 months 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 months ago by jhpalmieri

patch for biopython spkg, for review only

comment:5 Changed 10 months ago by jhpalmieri

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

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 months ago by jhpalmieri

  • Keywords biopython, sd40 added; biopython removed

comment:7 Changed 10 months ago by mhampton

  • Status changed from needs_review to positive_review
  • Reviewers set to Marshall Hampton, John Palmieri
  • Milestone changed from sage-5.3 to sage-5.2

comment:8 Changed 10 months ago by mhampton

Thanks very much John! The new spkg looks good.

comment:9 Changed 10 months ago by schilly

i just put the spkg on the server+mirrors.

comment:10 Changed 10 months ago by jdemeyer

  • Status changed from positive_review to closed
  • Resolution set to fixed
  • Merged in set to sage-5.2.rc0
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