<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10px"><div id="yui_3_16_0_ym18_1_1458349739686_29258">Hi Markus,</div><div id="yui_3_16_0_ym18_1_1458349739686_29257"><br></div><div id="yui_3_16_0_ym18_1_1458349739686_29425">Great to hear you are willing to work further on this module.<br></div><div id="yui_3_16_0_ym18_1_1458349739686_29353">I would suggest to write the documentation first, not for Bio.pairwise2 as it currently is, but for Bio.pairwise2 as you would like it to be. Then we can discuss on the mailing list, and once we agree on the design of the module we can make further changes to the code. This will make it easier for Biopython users and developers to try and test the code while it's under development.</div><div id="yui_3_16_0_ym18_1_1458349739686_29871">You may consider also that a module for pairwise alignment may fit better under Bio.Align rather than as a standalone module. That would also allow us to develop a pairwise alignment module under Bio.Align while keeping Bio.pairwise2 untouched. Bio.pairwise2 can then be deprecated over time.</div><div id="yui_3_16_0_ym18_1_1458349739686_30073"><br></div><div id="yui_3_16_0_ym18_1_1458349739686_30061">-Michiel<br></div><div id="yui_3_16_0_ym18_1_1458349739686_29194"><span></span></div> <div class="qtdSeparateBR"><br><br></div><div style="display: block;" class="yahoo_quoted"> <div style="font-family: HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 10px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"><font face="Arial" size="2"> On Wednesday, March 16, 2016 7:53 PM, PD Dr. Markus Piotrowski <Markus.Piotrowski@ruhr-uni-bochum.de> wrote:<br></font></div> <br><br> <div class="y_msg_container"><div id="yiv5853756221">
<div>
Dear Michiel,<br>
<br>
I'm happy to work further on the module in the future. E.g. I think
there are still some performance gains possible when using
*score_only* (and I wonder if I will be able to implement Miller and
Myers algorithm which works in linear space).<br>
Also, some of the interesting parameters like *penalize_end_gaps*
and *score_only* should really be mentioned in the doctest part.<br>
I also agree that the user interface is quite unpythonic (I'm still
not sure if I have understood how the decoding is going on...).<br>
Regarding the cpairwise2module.c I have to say that this is the
first time I coded in C (it took me 2 days to until I was able to
compile it under Windows, with at least one day
installing/de-installing/re-installing Microsofts Visual Studio),
thus I tried to introduce as few changes as possible. Suggestions
are very welcome.<br>
<br>
Markus<br>
<br>
<div class="yiv5853756221moz-cite-prefix">Am 16.03.2016 um 05:41 schrieb mdehoon:<br>
</div>
<blockquote type="cite">
<div><a rel="nofollow" target="_blank" href="https://github.com/peterjc" class="yiv5853756221user-mention">@peterjc</a> , <a rel="nofollow" target="_blank" href="https://github.com/MarkusPiotrowski" class="yiv5853756221user-mention">@MarkusPiotrowski</a> : Thanks for your
contribution.<br>
I think that the pairwise2 code has not had a dedicated
maintainer since 2005, and while we have done some maintenance
on it in the past, I don't think we currently have a real expert
for this code among the Biopython developers. So I would suggest
to accept the changes by <a rel="nofollow" target="_blank" href="https://github.com/MarkusPiotrowski" class="yiv5853756221user-mention">@MarkusPiotrowski</a> as is, as he has
looked at the code in much detail and is likely the most
familiar with the code now.</div>
<div>I also think that the user interface to pairwise2 is rather
unpythonic, with arguments encoded in the function names, and it
currently lacks documentation. I would be in favor of a further
revision of this module (after accepting the current changes) to
make it more intuitive and pythonic to users. <a rel="nofollow" target="_blank" href="https://github.com/MarkusPiotrowski" class="yiv5853756221user-mention">@MarkusPiotrowski</a> if you'd like to
further revise this module, let's discuss on the mailing list.</div>
<div>The only comment on the submitted code is that some functions
in cpairwise2module.c (for example calc_affine_penalty) could be
declared static if they are not used outside of this file.</div>
<div style="font-size:small;color:#666;">—<br>
You are receiving this because you were mentioned.<br>
Reply to this email directly or <a rel="nofollow" target="_blank" href="https://github.com/biopython/biopython/pull/782#issuecomment-197150898">view
it on GitHub</a><img alt="" src="https://github.com/notifications/beacon/AES2UPhgGG3yZoahSl5kbn9-7nwMjOwYks5pt4oIgaJpZM4HutzA.gif" height="1" width="1"></div>
<div>
<div>
</div>
</div>
</blockquote>
<br>
</div>
</div><br>_______________________________________________<br>Biopython-dev mailing list<br><a ymailto="mailto:Biopython-dev@mailman.open-bio.org" href="mailto:Biopython-dev@mailman.open-bio.org">Biopython-dev@mailman.open-bio.org</a><br><a href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a><br><br></div> </div> </div> </div></div></body></html>