[Biopython-dev] Changed in C API

[Dragoslav Zaric]

Dear Peter,

You write this:

"What I suggest you do first, is make sure you can get
the latest Biopython source code from git, compile it
under Python 2, and run the unit tests. Then try 2to3
and running the tests under Python 3 (see the README
file)."

Can you tell me how do I run unit tests in any python version ??

Are there unit tests for C modules or these tests cover everything ??

Kind regards

On Tue, Oct 26, 2010 at 2:01 PM, Dragoslav Zaric
<zaricdragoslav at gmail.com> wrote:
> Do not worry Peter,
>
> I am writing from work, that is why I am using windows. At home I have
> two lap tops
> and both are Linux :) I do not have windows on any partition :)
>
> I use and developo only on Linux outside of main job.
>
> Ok, when I get home I will read
>
> http://wiki.python.org/moin/PortingExtensionModulesToPy3k
>
> and start to work on
>
> Bio/Motif/_pwm.c
>
> Kind regards
>
>
> On Tue, Oct 26, 2010 at 1:47 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> On Tue, Oct 26, 2010 at 10:11 AM, Dragoslav Zaric
>> <zaricdragoslav at gmail.com> wrote:
>>> Ok Peter,
>>>
>>> First it is my mistake that I was talking about python code upgrade.
>>> I understand that you want me to do C code upgrade, but at the
>>> end all should work together so this is why I looked at overall upgrade
>>> process.
>>>
>>> I have downloaded latest python source code and I have searched
>>> for .c files and .h files and this is what I have found:
>>>
>>> Bio\Cluster\cluster.c
>>> Bio\Cluster\clustermodule.c
>>> Bio\cMarkovModelmodule.c
>>> Bio\cpairwise2module.c
>>> Bio\csupport.c
>>> Bio\KDTree\KDTree.c
>>> Bio\KDTree\KDTreemodule.c
>>> Bio\Motif\_pwm.c
>>> Bio\Nexus\cnexus.c
>>> Bio\PDB\mmCIF\lex.yy.c
>>> Bio\PDB\mmCIF\mmcif_test.c
>>> Bio\PDB\mmCIF\MMCIFlexmodule.c
>>> Bio\trie.c
>>> Bio\triemodule.c
>>>
>>> Bio\Cluster\cluster.h
>>> Bio\csupport.h
>>> Bio\KDTree\KDTree.h
>>> Bio\KDTree\Neighbor.h
>>> Bio\trie.h
>>
>> What OS are you using? From the slashes I'd guess
>> Windows (which may complicate things - getting the
>> compilers all setup is more work).
>>
>>>
>>> Are these all files you want me to upgrade to python 3.1 ?
>>>
>>
>> Yes - but not all of them are equally important, and some
>> will be more complicated to port.
>>
>> For example, the Nexus, MarkovModelmodule and
>> cMarkovModelmodule C code have a Python fallback
>> (i.e. the C code is not essential, just faster).
>>
>> Some of those (e.g. Bio.Cluster and Bio.KDTree) depend
>> on NumPy, which may make things more complicated.
>> You will need to install NumPy (for both Python 2 and 3).
>>
>> Some may have string encoding issues (bytes vs unicode),
>> e.g. Nexus, Motif
>>
>> The mmCIF module is not urgent. This is a file parser for
>> the Bio.PDB code, and we have discussed replacing this
>> in C. One reason for this is it currently depends on the
>> 3rd party library flex.
>>
>> I think Bio/Motif/_pwm.c would be a good module to start
>> with. It is a short simple module exposing a single
>> function to Python.
>>
>> You should read this:
>> http://wiki.python.org/moin/PortingExtensionModulesToPy3k
>>
>> Peter
>>
>
>
>
> --
> Dragoslav Zaric
>
> Professional Programmer
> MSc Astrophysics
>



-- 
Dragoslav Zaric

Professional Programmer
MSc Astrophysics