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Subject:

Re: Python3 and MTZ

From:

Paul Adams <[log in to unmask]>

Reply-To:

Paul Adams <[log in to unmask]>

Date:

Wed, 6 Jun 2018 16:31:07 -0400

Content-Type:

text/plain

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Parts/Attachments

text/plain (125 lines)

Dear Kay,

  I’m even more biased that Graeme of course, but I agree completely with what he says. You can write code that is compatible with both 2.7 and 3 and easily make use of the libraries available. Cctbx, and Phenix, are moving to python 3 compatibility in the not so distant future.

  Cheers,
	Paul 

> On Jun 6, 2018, at 4:22 PM, [log in to unmask] <[log in to unmask]> wrote:
> 
> Dear Kay,
> 
> 
> While I am obviously biased, I have to say that using cctbx (even if it is "old" Python) has a lot to be said for it - there are a lot of tools in there which are useful once you have read the reflection data & want to do crystallography.
> 
> 
> Re: Python 3: within xia2, DIALS and other cctbx-derived projects we have moved to writing Python which is compatible with 2.7.x and 3.x language standards - by and large it is not a hardship and means you can write code today which will continue to be useful. There is a wider push to migrate cctbx to 2.7.x and 3.x compatibility however it is a large code base and it's a fair amount of work. There's more to it than just adding brackets after print though :-)
> 
> 
> Best wishes Graeme
> 
> ________________________________
> From: CCP4 bulletin board <[log in to unmask]> on behalf of Kay Diederichs <[log in to unmask]>
> Sent: 06 June 2018 19:47:07
> To: ccp4bb
> Subject: Re: [ccp4bb] Python3 and MTZ
> 
> Dear Nicolas,
> 
> my (our) motivation is purely that when learning Python today, and developing something from scratch, Python3 appears like the better choice (compared to version 2) - provided that basic crystallographic libraries can be used.
> 
> Just a note (for those whose operating system provides only one of the two Python flavours): RHEL7 has Python2 as system library, but Python3 can be installed in parallel (using "Software Collections"). The user makes a choice by setting the PATH variable.
> 
> best,
> 
> Kay
> 
> On Wed, 6 Jun 2018 15:43:16 +0200, Nicolas FOOS <[log in to unmask]> wrote:
> 
>> Dear Kay,
>> 
>> depending of the motivation to develop in python3 (could be due to an OS
>> using python3 by default or you really prefer to work with python3). If
>> it's due to the OS, a possible strategy is to use virtualenv
>> (https://virtualenv.pypa.io/en/stable/) which let you use python2 even
>> if python3 is the default version for the OS. It exist probably other
>> method to have a contain installation of python2 with all the library needs.
>> 
>> I used this strategy (virtualenv) to install ccp4 (with the installer
>> which needed python2) on a manjaro linux (Arch based) running python3
>> and that works very well.
>> 
>> Nicolas
>> 
>> Nicolas Foos
>> PhD
>> Structural Biology Group
>> European Synchrotron Radiation Facility (E.S.R.F)
>> 71, avenue des Martyrs
>> CS 40220
>> 38043 GRENOBLE Cedex 9
>> +33 (0)6 76 88 14 87
>> +33 (0)4 76 88 45 19
>> 
>> On 06/06/2018 14:25, Kay Diederichs wrote:
>>> Dear all,
>>> 
>>> I haven't tried to read MTZ files from Python until now, but for a new
>>> project in my lab I'd like to do that - and with Python3.
>>> 
>>> Googling around, it seems that iotbx from cctbx is not (yet)
>>> Python3-compatible.
>>> 
>>> So, what are my options?
>>> 
>>> thanks,
>>> 
>>> Kay
>> 
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-- 
Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

Building 33, Room 347
Building 978, Room 4126
Tel: 1-510-486-4225, Fax: 1-510-486-5909
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345
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Executive Assistant: Louise Benvenue [ [log in to unmask] ][ 1-510-495-2506 ]
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