<html><head></head><body><div style="color:#000; background-color:#fff; font-family:Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10px"><div dir="ltr" id="yui_3_16_0_1_1498696593980_5194"><div>> It can see plenty of
issues where it could help. In my specific case all the PopGen code is
stopped for 10 years because I would need to write very fast code (say
in</div><div id="yui_3_16_0_1_1498696593980_5937">> Cython). This would be an extension module, not a core module because
it would impart a very big dependency on the system.</div><div id="yui_3_16_0_1_1498696593980_5195"><div id="yui_3_16_0_1_1498696593980_5310"><br id="yui_3_16_0_1_1498696593980_5196" clear="none"></div><div id="yui_3_16_0_1_1498696593980_5250" dir="ltr">I would suggest to first check how far numpy can help to speed up the code. If there are still some parts that need very fast code, you could write it as a C extension. That avoids the dependency on Cython. I'd be happy to help you with the C code.<br></div><div id="yui_3_16_0_1_1498696593980_5251"><br id="yui_3_16_0_1_1498696593980_5196" clear="none"></div></div><div id="yui_3_16_0_1_1498696593980_5197"><div>> Modules would allow a core with very strict policies and dependencies _but_ extensions that could be way more relaxed.</div><div id="yui_3_16_0_1_1498696593980_6535">> It
would also lower the barrier of entry for new content. Everyone could
publish an extension. If the extension would survive time (which most do
not - creating a <br></div><div>> maintenance burden in the core) then it could
eventually be made a core extension. Now the policy in practice is to
add very little innovation out of the fear that it will <br></div><div>> become stagnant
and not-supported by the main author (say after publication). An
extension system would accommodate both innovation whereas preserving
the core <br></div><div>> quality. <br></div><div><br></div><div dir="ltr" id="yui_3_16_0_1_1498696593980_6206">But do you need Biopython for that? A module that may not be supported after publication could exist outside of Biopython.<br id="yui_3_16_0_1_1498696593980_5201" clear="none"></div></div><div id="yui_3_16_0_1_1498696593980_5202"><br id="yui_3_16_0_1_1498696593980_5203" clear="none"></div><div id="yui_3_16_0_1_1498696593980_5204"><div id="yui_3_16_0_1_1498696593980_5980">> Currently
we have a gigantic monolith that in practice imposes very conservative
technologies and changes. I suspect that is why we do not see anything
really exciting</div><div id="yui_3_16_0_1_1498696593980_5981">> with Biopython for the better part of the last decade,</div><div id="yui_3_16_0_1_1498696593980_6216"><br></div><div id="yui_3_16_0_1_1498696593980_6577">I agree that we have been way too conservative in improving Biopython. This is just as much (or even more so) a problem with core parts of Biopython, e.g. with Seq objects and alphabets. But this is just a matter of choice: We can just decide to be less conservative.</div><div><br></div><div id="yui_3_16_0_1_1498696593980_6587">Best,</div><div id="yui_3_16_0_1_1498696593980_6588">-Michiel.</div><div id="yui_3_16_0_1_1498696593980_6589"><br></div></div></div><div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted" style="display: block;"> <div style="font-family: 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 size="2" face="Arial"> On Thursday, June 29, 2017 12:06 AM, Tiago Antão <tiagoantao@gmail.com> wrote:<br></font></div> <br><br> <div class="y_msg_container"><div id="yiv9337490036"><div><div dir="ltr">It can see plenty of issues where it could help. In my specific case all the PopGen code is stopped for 10 years because I would need to write very fast code (say in Cython). This would be an extension module, not a core module because it would impart a very big dependency on the system.<div><br clear="none"></div><div>Modules would allow a core with very strict policies and dependencies _but_ extensions that could be way more relaxed.</div><div><br clear="none"></div><div>It would also lower the barrier of entry for new content. Everyone could publish an extension. If the extension would survive time (which most do not - creating a maintenance burden in the core) then it could eventually be made a core extension. Now the policy in practice is to add very little innovation out of the fear that it will become stagnant and not-supported by the main author (say after publication). An extension system would accommodate both innovation whereas preserving the core quality. <br clear="none"></div><div><br clear="none"></div><div>Currently we have a gigantic monolith that in practice imposes very conservative technologies and changes. I suspect that is why we do not see anything really exciting with Biopython for the better part of the last decade,</div></div><div class="yiv9337490036gmail_extra"><br clear="none"><div class="yiv9337490036yqt5381872743" id="yiv9337490036yqt31631"><div class="yiv9337490036gmail_quote">On 28 June 2017 at 04:25, Michiel de Hoon <span dir="ltr"><<a rel="nofollow" shape="rect" ymailto="mailto:mjldehoon@yahoo.com" target="_blank" href="mailto:mjldehoon@yahoo.com">mjldehoon@yahoo.com</a>></span> wrote:<br clear="none"><blockquote class="yiv9337490036gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div style="color:#000;background-color:#fff;font-family:Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10px;"><div dir="ltr" id="yiv9337490036m_4366980446051291029yui_3_16_0_1_1498644225839_45791"><span id="yiv9337490036m_4366980446051291029yui_3_16_0_1_1498644225839_45863">I agree with Joao here. I don't see an immediate and overriding problem that modularity would solve, and I can see many drawbacks.</span></div><div dir="ltr"><span id="yiv9337490036m_4366980446051291029yui_3_16_0_1_1498644225839_45863"><br clear="none"></span></div><div dir="ltr"><span id="yiv9337490036m_4366980446051291029yui_3_16_0_1_1498644225839_45863">Best,</span></div><div dir="ltr"><span id="yiv9337490036m_4366980446051291029yui_3_16_0_1_1498644225839_45863">-Michiel</span></div> <div class="yiv9337490036m_4366980446051291029qtdSeparateBR"><br clear="none"><br clear="none"></div><div class="yiv9337490036m_4366980446051291029yahoo_quoted" style="display:block;"> <div style="font-family: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;"><span class="yiv9337490036"> </span><div dir="ltr"><font size="2" face="Arial"> On Monday, June 26, 2017 11:03 AM, João Rodrigues <<a rel="nofollow" shape="rect" ymailto="mailto:j.p.g.l.m.rodrigues@gmail.com" target="_blank" href="mailto:j.p.g.l.m.rodrigues@gmail.com">j.p.g.l.m.rodrigues@gmail.com</a> > wrote:<br clear="none"></font></div> <br clear="none"><br clear="none"> <div class="yiv9337490036m_4366980446051291029y_msg_container"><span class="yiv9337490036"></span><div id="yiv9337490036m_4366980446051291029yiv5820356184"><div><div dir="ltr">Copied from the other thread where I mistakenly posted:<br clear="none"><br clear="none">I think we should focus on other topics such as
modularity. What do the proponents of the said modularity say about it?
What are its advantages? I personally think a big disadvantage is that
with one package install you get a wide array of tools for a variety of
subjects. With a constellation of modules you might end up with an
up-to-date core and an out-of-date lone module somewhere, which makes
things much much harder not only to maintain but also to debug in case
of issues. <div class="yiv9337490036m_4366980446051291029yiv5820356184yqt2693074091" id="yiv9337490036m_4366980446051291029yiv5820356184yqtfd23041"><br clear="none"><br clear="none"></div></div><div class="yiv9337490036m_4366980446051291029yiv5820356184yqt2693074091" id="yiv9337490036m_4366980446051291029yiv5820356184yqtfd49977">
</div></div></div><span class="yiv9337490036"></span><div class="yiv9337490036m_4366980446051291029yqt2693074091" id="yiv9337490036m_4366980446051291029yqtfd49057">______________________________ _________________<br clear="none">Biopython-dev mailing list<br clear="none"><a rel="nofollow" shape="rect" ymailto="mailto:Biopython-dev@mailman.open-bio.org" target="_blank" href="mailto:Biopython-dev@mailman.open-bio.org">Biopython-dev@mailman.open- bio.org</a><br clear="none"><a rel="nofollow" shape="rect" target="_blank" href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev">http://mailman.open-bio.org/ mailman/listinfo/biopython-dev</a></div><br clear="none"><br clear="none"></div> </div> </div> </div></div></div></blockquote></div></div><br clear="none"><br clear="all"><div><br clear="none"></div>-- <br clear="none"><div class="yiv9337490036gmail_signature"><div dir="ltr">Tiago Antao<div>Scientific and HPC programmer</div><div><a rel="nofollow" shape="rect" target="_blank" href="http://tiago.org/">http://tiago.org</a></div><div><a rel="nofollow" shape="rect" target="_blank" href="https://github.com/tiagoantao/">https://github.com/tiagoantao/</a><br clear="none"></div></div></div>
</div></div></div><br><br></div> </div> </div> </div></div></body></html>