Opened 14 years ago

Closed 13 years ago

#6634 closed defect (fixed)

[with spkg, positive review] biopython 1.49b broken with python-2.6; biopython upgrade

Reported by: mhampton Owned by: tbd
Priority: major Milestone: sage-4.1.2
Component: packages: optional Keywords: biopython, bioinformatics
Cc: Merged in: Sage 4.1.2.alpha2
Authors: Marshall Hampton Reviewers: Alex Ghitza
Report Upstream: N/A Work issues:
Branch: Commit:
Dependencies: Stopgaps:

Status badges

Description

Biopython 1.49b doesn't install with python-2.6, so we should update the package. Currently biopython is at 1.51-beta, for which a spkg is provided, but we should switch to 1.51 as soon as it comes out since it will have significant improvements.

Change History (7)

comment:1 Changed 14 years ago by mhampton

Summary: biopython 1.49b broken with python-2.6[with spkg, needs review] biopython 1.49b broken with python-2.6

Temporary spkg to fix this, until 1.51 comes out, is at: http://www.d.umn.edu/~mhampton/biopython-1.51b.spkg

comment:2 Changed 14 years ago by tkeller

1.51b spkg installs cleanly and works fine with sage 4.1 on my linux kubuntu 9.04

comment:3 Changed 13 years ago by mhampton

Summary: [with spkg, needs review] biopython 1.49b broken with python-2.6[with spkg, needs review] biopython 1.49b broken with python-2.6; biopython upgrade

I have made a spkg for biopython-1.51, which was released today:

http://sage.math.washington.edu/home/mhampton/biopython-1.51.spkg

Running the test suite gives some errors, but some of these are due to missing optional components. I am inquiring about these on the biopython development list, but I don't think any of them are important enough to block this as an optional spkg.

comment:4 Changed 13 years ago by mhampton

Reviewers: tkeller

tkeller,

Can you review this new package? Besides testing installation, if you check that the spkg-install and SPKG.txt make sense then you can change the heading to [with spkg, positive review] and this can go into the optional packages.

In case you don't know, spkgs are just .tar.bz files with the extension renamed. I usually unpack a temporary copy somewhere other than my sage folder in order to take a look when reviewing.

-Marshall

comment:5 Changed 13 years ago by AlexGhitza

Authors: Marshall Hampton
Milestone: sage-4.1.2
Reviewers: tkellerAlex Ghitza
Summary: [with spkg, needs review] biopython 1.49b broken with python-2.6; biopython upgrade[with spkg, positive review] biopython 1.49b broken with python-2.6; biopython upgrade

Marshall,

I had started looking at this yesterday, so I just finished it now. It builds successfully on sage.math, 32-bit Linux and 32-bit OSX 10.5. Let's get it in!

One comment: if you happen to have some toy (or serious) Sage code using biopython, I strongly encourage you to get it into Sage so that we have at least some examples.

comment:6 Changed 13 years ago by mvngu

Is there a reason why biopython-1.51.spkg is not under revision control?

[mvngu@mod mvngu]$ tar -jxf biopython-1.51.spkg 
[mvngu@mod mvngu]$ cd biopython-1.51/
[mvngu@mod biopython-1.51]$ hg st
abort: There is no Mercurial repository here (.hg not found)!

comment:7 Changed 13 years ago by mvngu

Merged in: Sage 4.1.2.alpha2
Resolution: fixed
Status: newclosed

Merged in the optional packages repository at

http://www.sagemath.org/packages/optional/

The updated spkg is available at

http://www.sagemath.org/packages/optional/biopython-1.51.spkg

Note: See TracTickets for help on using tickets.