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

[Zheng Ruan]

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
https://travis-ci.org/biopython/biopython/builds/17506590.
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

Thanks,
Ruan


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
>