[cctbxbb] Python 3 status

Tue Sep 4 12:57:36 PDT 2018

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 at 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 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@
>>> 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 phe
>>> nix-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
>>> discu <https://maps.google.com/?q=priority+discu&entry=gmail&source=g>ssion
>>> 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
>>>>
>>>> --
>>>> 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 at phenix-online.org<mailto:cctbxbb at phenix-online.org><mailto:
>>>> cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>>
>>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>>
>>>
>>> _______________________________________________
>>> cctbxbb mailing list
>>> cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org><mailto:
>>> cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>>
>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>
>>>
>>> _______________________________________________
>>> cctbxbb mailing list
>>> cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>
>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>> _______________________________________________
>>> cctbxbb mailing list
>>> cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>
>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>
>>>
>>> _______________________________________________
>>> cctbxbb mailing list
>>> cctbxbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>
>>
>>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20180904/3626fd7f/attachment-0001.htm>