<div dir="ltr">I'm in Prague for the pre-BOSC 2017 CodeFest, where quite a few<div>Biopython contributors are present, and finally wrote this pull request:</div><div><br></div><div><a href="https://github.com/biopython/biopython/pull/1333">https://github.com/biopython/biopython/pull/1333</a></div><div><br></div><div>Peter<br></div><div><br><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jun 26, 2017 at 9:47 AM, Peter Cock <span dir="ltr"><<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Thanks Andrew,<div><br></div><div>I think we are agreed about dropping Python 2.7 support by 2020, although</div><div>please do comment on the Biopython 2 thread as well.</div><div><br></div><div>I will prepare a pull request adding the 2020 language to the README.rst</div><div>and NEWS.rst files, and once that's merged we can ask to be added to</div><div><a href="http://www.python3statement.org/" target="_blank">http://www.python3statement.<wbr>org/</a> </div><span class="gmail-HOEnZb"><font color="#888888"><div><br></div><div>Peter</div></font></span></div><div class="gmail-HOEnZb"><div class="gmail-h5"><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jun 26, 2017 at 5:46 AM, Andrew Guy <span dir="ltr"><<a href="mailto:andrew.guy@burnet.edu.au" target="_blank">andrew.guy@burnet.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi all,<div><br></div><div>Just wanted to add my thoughts as someone who is a relatively new user of Biopython (last ~3 years) and Python in general.</div><div><br></div><div>I thankfully started with Python 3.x when I was first learning, and have never needed to use Python 2.7 (that I can recall) other than to check backwards compatibility for code I've written - the bulk of the big Python scientific modules (e.g. Numpy, Scipy, scikit-learn) are all Python 3 compatible. To add to this, using a virtual environment (e.g. pip virtualenv) to manage dependencies is something that everyone should be doing, and I don't think it's asking too much to require this if anyone wants to use an older compute cluster and a new version of Biopython.</div><div><br></div><div>To add to sentiments that have been expressed a few times already, I also think it would be wonderful to be able to use some of the newer Python features in the code base going forward, especially if there is talk of moving to a new Biopython 2.x version.</div><div><br></div><div>I'll add my vote to<b> a)</b> moving to Python 3.x for Biopython 2.x and<b> b)</b> keep a Biopython 1.x version that supports <i>critical</i> bug fixes but is otherwise considered to be unsupported. I think the move to Biopython 2.x would mark an excellent point from which to drop Python 2.x. Old scripts/programs will still use the final 1.x release, whereas code that uses the new API will be written with Python 3.x in mind.</div><div><br></div><div>Regards,</div><div><br></div><div>Andrew</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="gmail-m_-7956034893111808259h5">On 26 June 2017 at 11:51, João Rodrigues <span dir="ltr"><<a href="mailto:j.p.g.l.m.rodrigues@gmail.com" target="_blank">j.p.g.l.m.rodrigues@gmail.com</a><wbr>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div class="gmail-m_-7956034893111808259h5"><div dir="ltr"><div><div>As we say in Portuguese, 'this discussion grew a beard'. Tiago, you are absolutely right.<br><br></div>I'll say it again. My opinion is that we should move to Python 3.x for Biopython 2.x *but* keep a version of Biopython 1.x that we support for critical bug fixes for those users stuck with Python 2.x (for whatever reason).<br><br></div>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. <br><br>(<a href="https://en.wikipedia.org/wiki/The_Old_Man_of_Restelo" target="_blank">I have the impression I'm of the youngest here and already this guy</a>)<br></div>
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