[cctbxbb] Python 3 status

James Holton jmholton at lbl.gov
Tue Sep 4 12:07:16 PDT 2018 

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 at 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 at lbl.gov<mailto:BKPoon at 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 at Diamond.ac.uk<mailto:Graeme.Winter at Diamond.ac.uk> 
>> <Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at 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 at phenix-online.org<mailto:cctbxbb-bounces at phenix-online.org> 
>> <cctbxbb-bounces at phenix-online.org<mailto:cctbxbb-bounces at phenix-online.org>> 
>> on behalf of Nicholas Sauter <nksauter at lbl.gov<mailto:nksauter at 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 at Diamond.ac.uk<mailto:Graeme.Winter at Diamond.ac.uk><mailto:Graeme.Winter at Diamond.ac.uk<mailto:Graeme.Winter at Diamond.ac.uk>> 
>> <Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk><mailto:Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at 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 at Diamond.ac.uk<mailto:Graeme.Winter at Diamond.ac.uk><mailto:Graeme.Winter at Diamond.ac.uk<mailto:Graeme.Winter at Diamond.ac.uk>> 
>>> <Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk><mailto:Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at 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
>>>
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