Re: [cctbxbb] Python 3 status

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, [email protected] 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a temporary state of affairs as we thought the Python3 migration was more urgent on the LCLS side - turns out this was out-of-date information!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 mailto:[email protected]> 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.orghttps://phenix-online.org/

On Mon, Sep 3, 2018 at 11:03 AM [email protected]mailto:[email protected] mailto:[email protected]> 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: [email protected]mailto:[email protected] mailto:[email protected]> on behalf of Nicholas Sauter mailto:[email protected]> 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, [email protected]mailto:[email protected]mailto:[email protected]> mailto:[email protected]mailto:[email protected]>> 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, [email protected]mailto:[email protected]mailto:[email protected]> mailto:[email protected]mailto:[email protected]>> 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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