<html>
<head>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
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="moz-cite-prefix">Am 16.03.2016 um 05:41 schrieb mdehoon:<br>
</div>
<blockquote
cite="mid:biopython%2Fbiopython%2Fpull%2F782%2Fc197150898@github.com"
type="cite">
<p><a moz-do-not-send="true" href="https://github.com/peterjc"
class="user-mention">@peterjc</a> , <a moz-do-not-send="true"
href="https://github.com/MarkusPiotrowski"
class="user-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 moz-do-not-send="true"
href="https://github.com/MarkusPiotrowski"
class="user-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.</p>
<p>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
moz-do-not-send="true"
href="https://github.com/MarkusPiotrowski"
class="user-mention">@MarkusPiotrowski</a> if you'd like to
further revise this module, let's discuss on the mailing list.</p>
<p>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.</p>
<p
style="font-size:small;-webkit-text-size-adjust:none;color:#666;">—<br>
You are receiving this because you were mentioned.<br>
Reply to this email directly or <a moz-do-not-send="true"
href="https://github.com/biopython/biopython/pull/782#issuecomment-197150898">view
it on GitHub</a><img moz-do-not-send="true" alt=""
src="https://github.com/notifications/beacon/AES2UPhgGG3yZoahSl5kbn9-7nwMjOwYks5pt4oIgaJpZM4HutzA.gif"
height="1" width="1"></p>
<div itemscope="" itemtype="http://schema.org/EmailMessage">
<div itemprop="action" itemscope=""
itemtype="http://schema.org/ViewAction">
<link itemprop="url"
href="https://github.com/biopython/biopython/pull/782#issuecomment-197150898">
<meta itemprop="name" content="View Pull Request">
</div>
<meta itemprop="description" content="View this Pull Request on
GitHub">
</div>
</blockquote>
<br>
</body>
</html>