Question: When Should We Develop Biopython That Support Python 3.X?
11
gravatar for Young
8.9 years ago by
Young110
Young110 wrote:

As python 3.X becomming more and more popular,Can we developers take developing biopython that support python 3.X into consideration? I am a newer to biopython and find that biopython doesn't support python 3.X. It's really frustrated. Thank you !

python biopython • 3.0k views
ADD COMMENTlink modified 8.7 years ago by Dinesh Cyanam10 • written 8.9 years ago by Young110

Hopefully they'll pep8 the names too.

ADD REPLYlink written 8.7 years ago by Casbon3.2k

Note this question was asked back in 2010, and is out of date. After a period of beta-level support for Python 3, Biopython first officially supported Python 3 with Biopython 1.62 (August 2013) which was done using the 2to3 conversion script, and as of Biopython 1.63 (December 2013) supports Python 2 and 3 directly with the same code base.

ADD REPLYlink written 4.6 years ago by Peter5.8k
8
gravatar for Eric T.
8.9 years ago by
Eric T.2.4k
San Francisco, CA
Eric T.2.4k wrote:

There's a good chance NumPy will support Python 3 in a stable release sometime this year -- it's a stated goal of theirs, but getting there has been difficult. Once NumPy makes the switch, Biopython and probably a number of other scientific libraries for Python will start making sure 2to3 conversion works properly.

Biopython generally works with the development releases of Python 2.7, so there's a good chance converting to Python 3 with the 2to3 script will be mostly painless.

ADD COMMENTlink written 8.9 years ago by Eric T.2.4k
6
gravatar for Istvan Albert
8.9 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

Python 3 will only become widely used in sciences once numpy (the numerical library) gets ported from the version 2 of python. I would recommend staying with the 2.X line for the next year or two.

In fact, I have started to consider the possibility that the 3.X line will never get the sufficient traction to be popular in sciences.

ADD COMMENTlink written 8.9 years ago by Istvan Albert ♦♦ 80k
2

re numpy, it's pretty well converted:

$ py3 
Python 3.1.2 (r312:79147, May 17 2010, 21:50:36) [GCC 4.4.3] on linux2 Type "help", "copyright", "credits" or "license" for more information. 
>>> import numpy 
>>> numpy.test() 
Running unit tests for numpy NumPy version 2.0.0.dev8417 
[... lots of output ... ] 
Ran 2929 tests in 15.571s OK (KNOWNFAIL=5, SKIP=4) 
[?]

but yeah, there's not much motivation to switch now.

ADD REPLYlink modified 7 months ago by RamRS21k • written 8.9 years ago by brentp23k
1

@brentp: I did not know the porting of numpy was in this advanced stage, that's encouraging

ADD REPLYlink written 8.9 years ago by Istvan Albert ♦♦ 80k
1

numpy matters because how else would one operate on large vectors and matrices without it?

ADD REPLYlink written 8.9 years ago by Istvan Albert ♦♦ 80k

re numpy, it's pretty well converted:

$ py3
Python 3.1.2 (r312:79147, May 17 2010, 21:50:36) 
[GCC 4.4.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.test()
Running unit tests for numpy
NumPy version 2.0.0.dev8417
[... lots of output ... ]
Ran 2929 tests in 15.571s
OK (KNOWNFAIL=5, SKIP=4)
[?]

but yeah, there's not much motivation to switch now.

ADD REPLYlink modified 7 months ago by RamRS21k • written 8.9 years ago by brentp23k

Python 3 will see lots of speed improvements in the next years, e.g. by adding Unladen Swallow into the main line. So I do hope that the libraries finish their migration eventually.

ADD REPLYlink written 8.9 years ago by Michael Kuhn5.0k

The notion that what is hampering the usage of Python 3 in science is numpy is borderline ludicrous. After all, we, scientists, should be in the forefront of these type of developments, using things that people do not use still. Python 3 is not widely used in science, because Python 3 is still not used everywhere and not every third-party module is already ported to it. Every time I install a new module, I try to install it under Python 3.

ADD REPLYlink written 8.9 years ago by Paulo Nuin3.7k

Looks like NumPy and SciPy are pretty usable with Python 3 now: http://article.gmane.org/gmane.comp.python.numeric.general/39033

ADD REPLYlink written 8.7 years ago by Konrad690
2
gravatar for You
8.9 years ago by
You30
You30 wrote:

Although converting to python 3 is painful and tedious for many of the programmers who are familiar with python 2.However, if we are still hesitating we may lose the chance while other people or oragnisition may develop another biology analytical tool using python 3.

ADD COMMENTlink written 8.9 years ago by You30
1
gravatar for Dinesh Cyanam
8.6 years ago by
Ann Arbor, MI
Dinesh Cyanam10 wrote:

I am a newbie to programming and I recently got the O'Reilly "Bioinformatics Programming Using Python" book. This covers Python 3 and now I am in a fix - whether I should learn programming using Python 3 or should I get an older edition of the book which covers Python 2.x.

But from what I have read above I understand that by the development of the modules for Python 3.x is going on pretty well and also the Biopython github has this message posted - "Python 3 support is still incomplete, but the majority of modules are already functional." So I guess by the time I learn Python the numpy module and Biopython are ready for show time.

ADD COMMENTlink written 8.6 years ago by Dinesh Cyanam10
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