[cctbxbb] Backwards compatibility; Python 2.3?

Mon Jun 12 00:43:39 PDT 2017

Colleagues

In related news, it looks like you are gearing up for a Phenix release 1.12

For this, if you are including DIALS I would recommend pulling from the 1.6 branch rather than the trunk - we are likely to put out a 1.6.1 on there sometime soon, and 1.6 is there at the moment, and this is stable and tested (i.e. better than a random pull from master)

How does this sound?

Thanks Graeme

From: cctbxbb-bounces at phenix-online.org [mailto:cctbxbb-bounces at phenix-online.org] On Behalf Of Billy Poon
Sent: 10 June 2017 19:34
To: cctbx mailing list
Subject: Re: [cctbxbb] Backwards compatibility; Python 2.3?

Hi all,

I agree that we should just target Python 2.7 for running cctbx programs and support Python >= 2.5 for the installation process since we provide our own copy of Python in our installers.

We can work on removing checks and cleaning up code paths for specific versions of Python 2 when we migrate to Python 3.

On Fri, Jun 9, 2017 at 4:08 PM Paul Adams <pdadams at lbl.gov<mailto:pdadams at lbl.gov>> wrote:
Hi Graeme,

  good points. I hope others in the group can weigh in, but I’m okay with limiting Python 2.5 to bootstrap and have everything else Python 2.7 compliant. I’m not sure what the implications, if any, for rest of the code base are, but given that we distribute with Python 2.7 then I guess things should be okay. We do make Phenix builds and run tests on several platforms with a system python 2.5.  Thoughts anyone else?

  Cheers,
        Paul

> On Jun 9, 2017, at 1:54 PM, graeme.winter at diamond.ac.uk<mailto:graeme.winter at diamond.ac.uk> wrote:
>
> Dear Paul,
>
> For bootstrap I completely appreciate the need for e.g. Python 2.5 or 2.6 compatibility - however does this then necessarily apply to the whole of cctbx and therefore by extension to dials etc. when the very first thing bootstrap does is install Python 2.7?
>
> The root of my question is trying to explain things to our new starter Nick (who initiated this thread) then coming to a halt as I realised I did not understand why some of these peculiarities were present - beyond "historical reasons"
>
> If we were to limit bootstrap.py to Python 2.5 compatibility and subsequently assume everything else is "allowed" 2.7 language level would that cause any problems? It may allow cleanup / removal of things which were from the future when added but are now part of the standard library. Do we even test on a python 2.5 machine?
>
> I'd also like to acknowledge that I appreciate how important these choices are to Phenix, hence trying to understand fully
>
> Hope this makes sense, best wishes 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 Paul Adams [pdadams at lbl.gov<mailto:pdadams at lbl.gov>]
> Sent: 09 June 2017 16:58
> To: cctbx mailing list
> Subject: Re: [cctbxbb] Backwards compatibility; Python 2.3?
>
> Others can correct me, but I believe that we use Python < 2.7 for building Phenix on several platforms because this is what the system Python is (needed to start the bootstrap). We have to support older platforms for compatibility reasons. Unfortunately, end users aren’t as likely to keep their os as up to date as developers would like.
>
>> On Jun 9, 2017, at 5:43 AM, graeme.winter at diamond.ac.uk<mailto:graeme.winter at diamond.ac.uk> wrote:
>>
>> Folks,
>>
>> Does *anyone* actually use Python < 2.7 with CCTBX for anything other than kicking off bootstrap?
>>
>> If not, then we could relax this back to using Python 2.7+ (which is a spritely 7 years old already)
>>
>> Thanks Graeme
>>
>> -----Original Message-----
>> From: cctbxbb-bounces at phenix-online.org<mailto:cctbxbb-bounces at phenix-online.org> [mailto:cctbxbb-bounces at phenix-online.org<mailto:cctbxbb-bounces at phenix-online.org>] On Behalf Of Nicholas Devenish
>> Sent: 08 June 2017 09:00
>> To: cctbx mailing list
>> Subject: Re: [cctbxbb] Backwards compatibility; Python 2.3?
>>
>> On Wed, Jun 7, 2017 at 12:26 PM, Marcin Wojdyr <wojdyr at gmail.com<mailto:wojdyr at gmail.com>> wrote:
>>> It makes sense to repeat this kind of question from time to time. At
>>> some point Python 2.5 won't be needed anymore.
>>
>> So, the whole codebase supports 2.5, or just the bootstrapping part?
>> As far as I know, bootstrapping (and thus via 2.7) is the only documented way of installing? Are there any opportunities to switch over to bootstrapped python earlier in the process?
>>
>> If it is the whole package, are there any automated tests with 2.5?
>> (If not, do we know that it's all still 2.5 compatible?)
>>
>> Nick
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> Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
> Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
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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 80, Room 247
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
Berkeley, CA 94720, USA.

Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov<mailto:LBenvenue at lbl.gov> ][ 1-510-495-2506 ]
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Billy K. Poon
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Lawrence Berkeley National Laboratory
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