As I indicated the syntax conversion process has already begun.  Please continually do "git pull" to keep your sources up to date.  As I go through the code I'm keeping a "blog" about the syntax needed to be cross-compatible between Python 2 & 3, and it is here:
https://docs.google.com/document/d/1ao8WbehWj5cyb03iTtJmpB4oJX3MqJFyGDAu2APn0XI/edit?usp=sharing

NKS


Nicholas K. Sauter, Ph. D.
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
(510) 486-5713

On Tue, Sep 4, 2018 at 12:07 PM, James Holton <jmholton@lbl.gov> wrote:
It has been brought to my attention that little attempt at humor could have been considered offensive. So clearly that that attempt failed. My sincere apologies to anyone who was offended.

 In all seriousness, I hope it is neither humorous nor offensive that I do appreciate all the hard work that goes into maintaining CCTBX, and we all know that 2.7->3.0 is coming. I am at best a minor contributor, but I think we can all identify with the crisis of time management between maintaining what you have and preparing for the future. None of us are lazy or bored. Quite the opposite. Graeme began this thread asking for "any thoughts", and my two thoughts are:
1) machine learning has in no way abandoned python 2.7
2) my limited sense of the community is one of reticence when it comes to python3.

I think that reticence comes from being already very busy maintaining one copy of your code, and knowing that maintaining two copies is going to be at least twice the work. Am I wrong in thinking there will be a period where CCTBX supports both python2.7 and python3 ? Once maintenance load is doubled, how much is left for new developments? These are not easy questions. My advise is one of caution, but one voice in the crowd does not speak for the whole. Graeme is right in thinking that discussion is in order, and I agree that face-to-face discussion is much less prone to offense than digital channels.

Back into lurk mode now...

-James


On 9/4/2018 10:04 AM, James Holton wrote:
It is most certainly not true that machine learning libraries require Python3.  Everything we're doing at SLAC is using 2.7.  I should admit this is mostly tensorflow-based stuff, but the install of the 2.7 version is quite painless.  On my CentOS 7 system it is:

yum install gcc gcc-c++ python-pip python-devel atlas atlas-devel gcc-gfortran openssl-devel libffi-devel
pip install --upgrade numpy scipy wheel cryptography
pip install --upgrade six scikit-learn protobuf
pip install --upgrade scikit-image
pip install --upgrade h5py
pip install --upgrade tensorflow-gpu
pip install --upgrade keras

  The 3.0 versions are available, and if you believe what you read on the internet they are all the rage and only loosers are still not using Python3.  And c'mon!  Use Python3 already!  But for all the developers I know who are actually doing real work the 2.7->3.0 transition is something they keep meaning to do and will get to someday soon. Like when things "calm down".

I'm still waiting for that to happen too...

-James Holton
MAD Scientist

On 9/3/2018 11:50 PM, Graeme.Winter@Diamond.ac.uk wrote:
Hi Billy

Sounds good - part of the reason I was asking is that we have students here at Diamond using CCTBX / DIALS as a library and also wanting to use machine learning libraries - however these all seem to be written in Python3 so at the moment we’re in the position of dumping out files in one Python and loading in another to work. We’d anticipated this being a temporary state of affairs as we thought the Python3 migration was more urgent on the LCLS side - turns out this was out-of-date information!

Anyhow, good to know, please shout if you’d like some help with the porting

Cheers Graeme


On 4 Sep 2018, at 06:47, Billy Poon <BKPoon@lbl.gov<mailto:BKPoon@lbl.gov>> wrote:

Hi Graeme,

I'll be starting some of the Python 3 work probably next week. In Cambridge, I'll be looking into building some dependencies as conda packages on Windows since it'll be easier to work with Rob in person.

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org<https://phenix-online.org/>


On Mon, Sep 3, 2018 at 11:03 AM Graeme.Winter@Diamond.ac.uk<mailto:Graeme.Winter@Diamond.ac.uk> <Graeme.Winter@diamond.ac.uk<mailto:Graeme.Winter@diamond.ac.uk>> wrote:
Nick,

Fair enough, no problem

I had a memory that there was a push from lcls via new psana? Anyhow, no worries

Cheers Graeme


________________________________
From: cctbxbb-bounces@phenix-online.org<mailto:cctbxbb-bounces@phenix-online.org> <cctbxbb-bounces@phenix-online.org<mailto:cctbxbb-bounces@phenix-online.org>> on behalf of Nicholas Sauter <nksauter@lbl.gov<mailto:nksauter@lbl.gov>>
Sent: 03 September 2018 18:57:03
To: cctbx mailing list
Subject: Re: [cctbxbb] Python 3 status

I've just begun syntax conversion (1% done).  I expect Billy and I will work on it over the next few months.  I don't believe it is a high priority discussion topic at present.
NKS

Nicholas K. Sauter, Ph. D.
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
(510) 486-5713

On Mon, Sep 3, 2018 at 12:35 AM, Graeme.Winter@Diamond.ac.uk<mailto:Graeme.Winter@Diamond.ac.uk><mailto:Graeme.Winter@Diamond.ac.uk<mailto:Graeme.Winter@Diamond.ac.uk>> <Graeme.Winter@diamond.ac.uk<mailto:Graeme.Winter@diamond.ac.uk><mailto:Graeme.Winter@diamond.ac.uk<mailto:Graeme.Winter@diamond.ac.uk>>> wrote:
Howdy,

OK, so I am guessing that the radio silence on this thread indicates that I’ve probably not missed much, and this is not really being actively pursued at this time in core CCTBX, so I will assume there is no interest in discussing progress in person later in the month - it’ll keep. Obviously getting the PHENIX and DIALS major releases out of the door as been / is the priority.

best wishes Graeme


On 29 Aug 2018, at 12:47, Graeme.Winter@Diamond.ac.uk<mailto:Graeme.Winter@Diamond.ac.uk><mailto:Graeme.Winter@Diamond.ac.uk<mailto:Graeme.Winter@Diamond.ac.uk>> <Graeme.Winter@diamond.ac.uk<mailto:Graeme.Winter@diamond.ac.uk><mailto:Graeme.Winter@diamond.ac.uk<mailto:Graeme.Winter@diamond.ac.uk>>> wrote:

Hi Folks,

Are there any updates on the progress to Python 3 compatibility? I know there is a project here

https://github.com/cctbx/cctbx_project/projects/2

but I have lost the thread of activities since I have been out of the office much of the summer. At the very least I know no progress has been made from this side of the pond as we’ve put this work down for now.

i would guess that a lot is on hold while the PHENIX release is done - however I thought I should check in case I have missed anything?

Part of why I ask is that there is a PHENIX meeting in Cambridge real soon now (mid September) and I wonder if it is worth folks from DIALS and PHENIX getting together at that time to discuss this?

Any thoughts?

Thanks & best wishes Graeme

--
This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

_______________________________________________
cctbxbb mailing list
cctbxbb@phenix-online.org<mailto:cctbxbb@phenix-online.org><mailto:cctbxbb@phenix-online.org<mailto:cctbxbb@phenix-online.org>>
http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________
cctbxbb mailing list
cctbxbb@phenix-online.org<mailto:cctbxbb@phenix-online.org><mailto:cctbxbb@phenix-online.org<mailto:cctbxbb@phenix-online.org>>
http://phenix-online.org/mailman/listinfo/cctbxbb


_______________________________________________
cctbxbb mailing list
cctbxbb@phenix-online.org<mailto:cctbxbb@phenix-online.org>
http://phenix-online.org/mailman/listinfo/cctbxbb
_______________________________________________
cctbxbb mailing list
cctbxbb@phenix-online.org<mailto:cctbxbb@phenix-online.org>
http://phenix-online.org/mailman/listinfo/cctbxbb


_______________________________________________
cctbxbb mailing list
cctbxbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/cctbxbb


_______________________________________________
cctbxbb mailing list
cctbxbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/cctbxbb