<div dir="ltr"><div>Hello everyone,</div><div><br></div>> <span style="color:rgb(33,33,33)">So, in theory, you can end up with dozens of extensions that are out of sync with the core in terms of 'core' dependencies and it's up to the maintainers of those extensions to keep them up-to-date. That's my main concern. We have a monolith that works. It is conservative and that's exactly why it works. Otherwise, for example, I would install the core and your Cython-based lightining fast PopGen code and then you grow bored of it, a new version of Cython comes along that has some incompatibilities with your code, and now it doesn't work. Worse even, I release a blinding fast PDBParser using a new feature in Cython and now you have two incompatible extensions.<br><br>Yes, that is one concern that the modular setup can introduce. It is a trouble when you want to use two non-core extensions which depend on an incompatible versions of the core module. This applies if your application wants to make use of both non-core modules.<br><br>However, I would argue that in that case, it would be easier for you push for a change in the PopGen module (taking on your example). You would have less code to look at (since you only want to change PopGen) and less person to convince that your changes are worth a new release (which in this case is Tiago, the PopGen maintainer). It would also be easier for you to fork PopGen and maintain further, if you wish to do so. All of this boils down to PopGen being smaller and, to a larger degree than it is now, independent from the rest of Biopython.<br><br>Contrast this with what happens in the monolith setup: PDBParser is stuck using a suboptimal parser because another module is not updated. Yes, there is consistency in a sense that everything works together. But this is consistency by the lowest common denominator: all modules need to adhere to the oldest (and probably least maintained) module. Not to mention the increased burden to the core developers when a maintainer for a module decides to spend less time maintaining.<br><br>If you are interested in using non-compatible core modules inside a pipeline (so both modules are used at different steps in the pipeline), there are various pipeline frameworks and/or containers today that provide more granular level of isolation. In other words, you can run incompatible biopython versions in the same pipeline.<br><br>> </span><span style="color:rgb(33,33,33)">I agree that we should 'refresh' our dependencies to be able to do cool things. And modularity is incredibly attractive. But the main advantage of modularity - lowering the standards of biopython code - is also, in my opinion, it's main disadvantage.<br><br>I would say it actually encourages people to contribute more :). And yes, this may come at a cost of some biopython non-core modules having 'lower quality' than other modules. But I think that is not necessarily bad. Useful modules with good documentation and good code quality are more likely to be used.<br><br>> </span><font color="#212121">Question: How is scikit handling their different modules?</font><br><br><font color="#212121">They have different teams for the core package and the toolkits (modules), as far as I know [<a href="https://www.scipy.org/scikits.html">https://www.scipy.org/scikits.html</a>]. It seems that anyone can register a module with the scikit namespace (at least I could not find any specific mention of the toolkit development requiring permission from the core team). Even the license of the toolkit can be different. (slightly unrelated, but there is also a scikit-bio package: <a href="http://scikit-bio.org/">http://scikit-bio.org/</a>).<br><br>(P.S. just so that everyone is on the same page, we actually do have a GitHub ticket on this modularization proposal here: <a href="https://github.com/biopython/biopython/issues/349">https://github.com/biopython/biopython/issues/349</a> ~ there were already some discussion as you can see).<br><br>Best regards,<br>Bow</font></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Jun 28, 2017 at 7:10 PM João Rodrigues <<a href="mailto:j.p.g.l.m.rodrigues@gmail.com">j.p.g.l.m.rodrigues@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">So, in theory, you can end up with dozens of extensions that are out of sync with the core in terms of 'core' dependencies and it's up to the maintainers of those extensions to keep them up-to-date. That's my main concern. We have a monolith that works. It is conservative and that's exactly why it works. Otherwise, for example, I would install the core and your Cython-based lightining fast PopGen code and then you grow bored of it, a new version of Cython comes along that has some incompatibilities with your code, and now it doesn't work. Worse even, I release a blinding fast PDBParser using a new feature in Cython and now you have two incompatible extensions. <div><br></div><div>Being very honest, there is no barrier to anyone developing anything new here. If you want to use Cython, go ahead and do it and then worst case scenario, we have a dependency warning and check that can simply skip compilation of that code. It's what happens with Numpy at the moment IIRC. You can also bundle the c code, instead of compiling the pyx on install, and compile it regularly using GCC, skipping Cython altogether. </div><div><br></div><div>I agree that we should 'refresh' our dependencies to be able to do cool things. And modularity is incredibly attractive. But the main advantage of modularity - lowering the standards of biopython code - is also, in my opinion, it's main disadvantage. </div><div><br></div><div>Question: How is scikit handling their different modules?</div></div><div class="gmail_extra"><br><div class="gmail_quote">2017-06-28 8:05 GMT-07:00 Tiago Antão <span dir="ltr"><<a href="mailto:tiagoantao@gmail.com" target="_blank">tiagoantao@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><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></div><div>Modules would allow a core with very strict policies and dependencies _but_ extensions that could be way more relaxed.</div><div><br></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></div><div><br></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="gmail_extra"><div><div class="m_6630240820384689508h5"><br><div class="gmail_quote">On 28 June 2017 at 04:25, Michiel de Hoon <span dir="ltr"><<a href="mailto:mjldehoon@yahoo.com" target="_blank">mjldehoon@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_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 id="m_6630240820384689508m_-5291783102745619670m_4366980446051291029yui_3_16_0_1_1498644225839_45791" dir="ltr"><span id="m_6630240820384689508m_-5291783102745619670m_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="m_6630240820384689508m_-5291783102745619670m_4366980446051291029yui_3_16_0_1_1498644225839_45863"><br></span></div><div dir="ltr"><span id="m_6630240820384689508m_-5291783102745619670m_4366980446051291029yui_3_16_0_1_1498644225839_45863">Best,</span></div><div dir="ltr"><span id="m_6630240820384689508m_-5291783102745619670m_4366980446051291029yui_3_16_0_1_1498644225839_45863">-Michiel</span></div> <div class="m_6630240820384689508m_-5291783102745619670m_4366980446051291029qtdSeparateBR"><br><br></div><div class="m_6630240820384689508m_-5291783102745619670m_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> <div dir="ltr"><font size="2" face="Arial"> On Monday, June 26, 2017 11:03 AM, João Rodrigues <<a href="mailto:j.p.g.l.m.rodrigues@gmail.com" target="_blank">j.p.g.l.m.rodrigues@gmail.com</a>> wrote:<br></font></div> <br><br> </span><div class="m_6630240820384689508m_-5291783102745619670m_4366980446051291029y_msg_container"><span><div id="m_6630240820384689508m_-5291783102745619670m_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="m_6630240820384689508m_-5291783102745619670m_4366980446051291029yiv5820356184yqt2693074091" id="m_6630240820384689508m_-5291783102745619670m_4366980446051291029yiv5820356184yqtfd23041"><br clear="none"><br clear="none"></div></div><div class="m_6630240820384689508m_-5291783102745619670m_4366980446051291029yiv5820356184yqt2693074091" id="m_6630240820384689508m_-5291783102745619670m_4366980446051291029yiv5820356184yqtfd49977">
</div></div></div></span><span><div class="m_6630240820384689508m_-5291783102745619670m_4366980446051291029yqt2693074091" id="m_6630240820384689508m_-5291783102745619670m_4366980446051291029yqtfd49057">_______________________________________________<br clear="none">Biopython-dev mailing list<br clear="none"><a shape="rect" href="mailto:Biopython-dev@mailman.open-bio.org" target="_blank">Biopython-dev@mailman.open-bio.org</a><br clear="none"><a shape="rect" href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a></div><br><br></span></div> </div> </div> </div></div></div></blockquote></div><br><br clear="all"><div><br></div></div></div><span>-- <br><div class="m_6630240820384689508m_-5291783102745619670gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Tiago Antao<div>Scientific and HPC programmer</div><div><a href="http://tiago.org" target="_blank">http://tiago.org</a></div><div><a href="https://github.com/tiagoantao/" target="_blank">https://github.com/tiagoantao/</a><br></div></div></div>
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</blockquote></div><br></div>
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