Hi Graeme and Markus, Yes, we have a release ready and we're just waiting a week to see if any major bugs arise before we officially announce it. Barring any major issues, we will follow up with you next week about the migration to git. As for upgrades, I'm fine with going to 2.7.12, but we'd have to test everything before committing the change. Also, I was going to update numpy and migrate PIL to Pillow. There are some API changes going from PIL to Pillow and I think I had some issues with numpy, which is why they were not upgraded with the other packages. And since I have virtual machines already set up, testing should be faster. Also, I'm looking into revamping the Phenix GUI in preparation for a migration to Python 3 in 2020 (Python 2 support ends in 2020). Since there is a lot of basic code that need to be rewritten for the GUI, I'm starting to prepare now. Are there any issues with moving to Python 3 in a few years? I think Boost should support Python 3, but I have not personally tested it. -- 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 On Wed, Oct 12, 2016 at 5:59 AM, wrote:

Hi,

Looking at https://www.phenix-online.org/download/nightly_builds.cgi there is now a 1.11 build without 'rc' suffix available. Are we now in the one week cooling off period? Will revive the move-to-git-schedule once we know more on this...

As one of the first post-phenix-release changes I would like to upgrade bootstrap from installing python 2.7.8 to python >=2.7.9. For obvious reasons I would suggest going directly to the current stable 2.7.12. Are there any concerns regarding this?

-Markus

________________________________ From: [email protected] [[email protected]] on behalf of [email protected] [[email protected]] Sent: Friday, October 07, 2016 14:07 To: [email protected] Subject: [cctbxbb] Monthly "how far are we from moving to git" message

Good afternoon / morning / evening (depending on your locale)

I’m just running a bootstrap build and having to check out the whole of cctbx one … file … at … a … time from svn & it reminded me we were going to move over to git at some point – ISTR was determined by the PHENIX release.

Just wondering how this is going & how long it is likely to be until we can get this ball rolling :)

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

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Hi Graeme, For dials, buildbot downloads the latest source from github and uses that. So for the currently available Phenix build, we are using the source from last night (10/12). Should we use the latest stable release for the official Phenix release? -- 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 On Thu, Oct 13, 2016 at 2:03 AM, wrote:

HI Billy

All sounds good and I certainly approve of the forward looking to 2020 J

I wonder, could you tell me what revision of dials you have in phenix 1.11? For our debugging purposes it is useful to know

Thanks Graeme

*From:* [email protected] [mailto:cctbxbb-bounces@ phenix-online.org] *On Behalf Of *Billy Poon *Sent:* 12 October 2016 21:46 *To:* cctbx mailing list *Subject:* Re: [cctbxbb] Monthly "how far are we from moving to git" message

Hi Graeme and Markus,

Yes, we have a release ready and we're just waiting a week to see if any major bugs arise before we officially announce it. Barring any major issues, we will follow up with you next week about the migration to git.

As for upgrades, I'm fine with going to 2.7.12, but we'd have to test everything before committing the change. Also, I was going to update numpy and migrate PIL to Pillow. There are some API changes going from PIL to Pillow and I think I had some issues with numpy, which is why they were not upgraded with the other packages. And since I have virtual machines already set up, testing should be faster.

Also, I'm looking into revamping the Phenix GUI in preparation for a migration to Python 3 in 2020 (Python 2 support ends in 2020). Since there is a lot of basic code that need to be rewritten for the GUI, I'm starting to prepare now. Are there any issues with moving to Python 3 in a few years? I think Boost should support Python 3, but I have not personally tested it.

--

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

On Wed, Oct 12, 2016 at 5:59 AM, wrote:

Hi,

Looking at https://www.phenix-online.org/download/nightly_builds.cgi there is now a 1.11 build without 'rc' suffix available. Are we now in the one week cooling off period? Will revive the move-to-git-schedule once we know more on this...

As one of the first post-phenix-release changes I would like to upgrade bootstrap from installing python 2.7.8 to python >=2.7.9. For obvious reasons I would suggest going directly to the current stable 2.7.12. Are there any concerns regarding this?

-Markus

________________________________ From: [email protected] [[email protected]] on behalf of [email protected] [[email protected]] Sent: Friday, October 07, 2016 14:07 To: [email protected] Subject: [cctbxbb] Monthly "how far are we from moving to git" message

Good afternoon / morning / evening (depending on your locale)

I’m just running a bootstrap build and having to check out the whole of cctbx one … file … at … a … time from svn & it reminded me we were going to move over to git at some point – ISTR was determined by the PHENIX release.

Just wondering how this is going & how long it is likely to be until we can get this ball rolling :)

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 [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

--

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 [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Hi Graeme and Markus, We're still testing the release, so the announcement will come out probably next week. Also, github.com is currently down due to the DDOS attack on our East Coast. -- 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 On Fri, Oct 14, 2016 at 11:56 PM, wrote:

Hi Billy

Thinking about it, it may be worth making a proper release to coincide with this (and also for CCP4, who asked recently too…)

Will follow up internally

Best wishes Graeme

On 13 Oct 2016, at 18:07, Billy Poon mailto:[email protected]> wrote:

Hi Graeme,

For dials, buildbot downloads the latest source from github and uses that. So for the currently available Phenix build, we are using the source from last night (10/12). Should we use the latest stable release for the official Phenix release?

-- 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 Thu, Oct 13, 2016 at 2:03 AM, > wrote: HI Billy

All sounds good and I certainly approve of the forward looking to 2020 ☺

I wonder, could you tell me what revision of dials you have in phenix 1.11? For our debugging purposes it is useful to know

Thanks Graeme

From: [email protected] [mailto:[email protected]] On Behalf Of Billy Poon Sent: 12 October 2016 21:46 To: cctbx mailing list Subject: Re: [cctbxbb] Monthly "how far are we from moving to git" message

Hi Graeme and Markus,

Yes, we have a release ready and we're just waiting a week to see if any major bugs arise before we officially announce it. Barring any major issues, we will follow up with you next week about the migration to git.

As for upgrades, I'm fine with going to 2.7.12, but we'd have to test everything before committing the change. Also, I was going to update numpy and migrate PIL to Pillow. There are some API changes going from PIL to Pillow and I think I had some issues with numpy, which is why they were not upgraded with the other packages. And since I have virtual machines already set up, testing should be faster.

Also, I'm looking into revamping the Phenix GUI in preparation for a migration to Python 3 in 2020 (Python 2 support ends in 2020). Since there is a lot of basic code that need to be rewritten for the GUI, I'm starting to prepare now. Are there any issues with moving to Python 3 in a few years? I think Boost should support Python 3, but I have not personally tested it.

-- 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) 486-5709tel:%28510%29%20486-5709 Fax: (510) 486-5909tel:%28510%29%20486-5909 Web: https://phenix-online.orghttps://phenix-online.org/

On Wed, Oct 12, 2016 at 5:59 AM, > wrote: Hi,

Looking at https://www.phenix-online.org/download/nightly_builds.cgi there is now a 1.11 build without 'rc' suffix available. Are we now in the one week cooling off period? Will revive the move-to-git-schedule once we know more on this...

As one of the first post-phenix-release changes I would like to upgrade bootstrap from installing python 2.7.8 to python >=2.7.9. For obvious reasons I would suggest going directly to the current stable 2.7.12. Are there any concerns regarding this?

-Markus

________________________________ From: [email protected] [[email protected]] on behalf of [email protected]< mailto:[email protected]> [[email protected]] Sent: Friday, October 07, 2016 14:07 To: [email protected]mailto:[email protected] Subject: [cctbxbb] Monthly "how far are we from moving to git" message

Good afternoon / morning / evening (depending on your locale)

I’m just running a bootstrap build and having to check out the whole of cctbx one … file … at … a … time from svn & it reminded me we were going to move over to git at some point – ISTR was determined by the PHENIX release.

Just wondering how this is going & how long it is likely to be until we can get this ball rolling :)

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 [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

--

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 [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb