[Biopython-dev] Pull Request for Codon Alignment GSoC project

Zheng Ruan zruan1991 at gmail.com
Thu Jan 23 21:50:07 UTC 2014

Sorry for the late update. But I fixed the compatibility issues of my code
and it's now able to run under different python environment.
It seems I messed up my commit in the summer, so I manually rebased all the
code. The individual commit message may not be informative now.

The Travis CI result can be found at
Failure in python3.3 is in the Consensus test and I assume it's not my
problem hopefully.

My pull request: https://github.com/biopython/biopython/pull/259


On Fri, Nov 15, 2013 at 6:16 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Fri, Nov 15, 2013 at 2:57 AM, Zheng Ruan <zruan1991 at gmail.com> wrote:
> > Hi all,
> >
> > Since a beta version of biopython has been released, it might be safe to
> > merge my GSoC work.
> We'll normally only do minor bug fixes and documentation improvements
> between a beta and final release, but this is perfect timing for getting
> your
> work merged immediately after Biopython 1.63 is out.
> (So far there have been no problems reported with the beta, and
> we've fixed some newline issues when testing under Windows)
> > I just made a pull request and there seems to be some
> > problems when running the code in different platforms. In
> > python2.7 and python3.3, the error message complains they
> > cannot find CodonAlign module. I'm not sure why this happens.
> Some discussion is on the pull request itself:
> https://github.com/biopython/biopython/pull/259
> > The dependency of Scipy and Numpy might also
> > introduce some problems for the testing. Thanks!
> We've got a mechanism for skipping tests when a dependency
> is missing - the MissingExternalDependencyError and
> MissingPythonDependencyError exceptions. You need
> to use this in test_CodonAlign.py, see test_PDB.py etc.
> Related to this we would need to install new dependencies
> on some of the buildbot slaves and perhaps TravisCI.
> Regards,
> Peter

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