DIALS releases in PHENIX
Hi Folks Following from - # select dials-3.5 branch + # select dials-3.2 branch def _add_git(self, module, parameters, destination=None): super(PhenixBuilder, self)._add_git(module, parameters, destination) if (module == 'dials' or module == 'dxtbx' or module == 'xia2') and self.python3: @@ -2339,9 +2339,9 @@ class PhenixBuilder(CCIBuilder): if module == 'dxtbx': self.add_step(self.shell(command=['git', 'remote', 'set-url', 'origin', 'https://github.com/dials/dxtbx.git'], workdir=workdir)) self.add_step(self.shell(command=['git', 'fetch', 'origin'], workdir=workdir)) - self.add_step(self.shell(command=['git', 'checkout', 'dials-2.2'], workdir=workdir)) + self.add_step(self.shell(command=['git', 'checkout', 'dials-3.2'], workdir=workdir)) self.add_step(self.shell( - command=['git', 'branch', '--set-upstream-to=origin/dials-2.2', 'dials-2.2'], + command=['git', 'branch', '--set-upstream-to=origin/dials-3.2', 'dials-3.2'], workdir=workdir)) I was wondering - what are the constraints in PHENIX builds which mean bouncing around between extremely different DIALS releases is necessary? I note the shift from 2.2 to 3.2 would give a significant change in behaviour to the end user (who ultimately we may end up having to help with debugging) If we knew better why these changes were coming through, maybe we could help to keep PHENIX up to date? I would draw comparisons with CCP4 however they have been stuck in 2.2-series forever now as they’re still not able to support Python3 - will be in CCP4 8.x which will be ready any time now. I only mention this as it would be really good to start eliminating obsolete versions from distribution as “please go to dials.github.io and install a non-ancient version” is annoying advice to an end user with a fresh install of PHENIX or CCP4. Thanks 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
Hi Graeme, We are trying to build Phenix on Windows with python3. The problem we have is that when bootstrap.y reaches the libtbx.scons stage Xia2 is then trying to pip install something into the conda python but fails and the build breaks. Using an older Dials version is a fall back that at least enables us to build Phenix with python3 on Windows. Would you be able to point us to a newer Dials version that builds using conda with bootstrap on Windows for python3? Rob On 15/07/2021 08:18, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:
Hi Folks
Following from
- # select dials-3.5 branch + # select dials-3.2 branch def _add_git(self, module, parameters, destination=None): super(PhenixBuilder, self)._add_git(module, parameters, destination) if (module == 'dials' or module == 'dxtbx' or module == 'xia2') and self.python3: @@ -2339,9 +2339,9 @@ class PhenixBuilder(CCIBuilder): if module == 'dxtbx': self.add_step(self.shell(command=['git', 'remote', 'set-url', 'origin', 'https://github.com/dials/dxtbx.git'], workdir=workdir)) self.add_step(self.shell(command=['git', 'fetch', 'origin'], workdir=workdir)) - self.add_step(self.shell(command=['git', 'checkout', 'dials-2.2'], workdir=workdir)) + self.add_step(self.shell(command=['git', 'checkout', 'dials-3.2'], workdir=workdir)) self.add_step(self.shell( - command=['git', 'branch', '--set-upstream-to=origin/dials-2.2', 'dials-2.2'], + command=['git', 'branch', '--set-upstream-to=origin/dials-3.2', 'dials-3.2'], workdir=workdir))
I was wondering - what are the constraints in PHENIX builds which mean bouncing around between extremely different DIALS releases is necessary? I note the shift from 2.2 to 3.2 would give a significant change in behaviour to the end user (who ultimately we may end up having to help with debugging)
If we knew better why these changes were coming through, maybe we could help to keep PHENIX up to date?
I would draw comparisons with CCP4 however they have been stuck in 2.2-series forever now as they’re still not able to support Python3 - will be in CCP4 8.x which will be ready any time now.
I only mention this as it would be really good to start eliminating obsolete versions from distribution as “please go to dials.github.io and install a non-ancient version” is annoying advice to an end user with a fresh install of PHENIX or CCP4.
Thanks Graeme
-- - Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus The Keith Peters Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234 -- This email has been checked for viruses by AVG. https://www.avg.com
Hi Graeme,
Those changes are just for developer builds. The Python 3 installer for
Phenix will have DIALS 3.5.
--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Fax: (510) 486-5909
Web: https://phenix-online.org
On Thu, Jul 15, 2021 at 3:33 AM Robert Oeffner
Hi Graeme,
We are trying to build Phenix on Windows with python3. The problem we have is that when bootstrap.y reaches the libtbx.scons stage Xia2 is then trying to pip install something into the conda python but fails and the build breaks. Using an older Dials version is a fall back that at least enables us to build Phenix with python3 on Windows.
Would you be able to point us to a newer Dials version that builds using conda with bootstrap on Windows for python3?
Rob
On 15/07/2021 08:18, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:
Hi Folks
Following from
- # select dials-3.5 branch + # select dials-3.2 branch def _add_git(self, module, parameters, destination=None): super(PhenixBuilder, self)._add_git(module, parameters, destination) if (module == 'dials' or module == 'dxtbx' or module == 'xia2') and self.python3: @@ -2339,9 +2339,9 @@ class PhenixBuilder(CCIBuilder): if module == 'dxtbx': self.add_step(self.shell(command=['git', 'remote', 'set-url', 'origin', 'https://github.com/dials/dxtbx.git'], workdir=workdir)) self.add_step(self.shell(command=['git', 'fetch', 'origin'], workdir=workdir)) - self.add_step(self.shell(command=['git', 'checkout', 'dials-2.2'], workdir=workdir)) + self.add_step(self.shell(command=['git', 'checkout', 'dials-3.2'], workdir=workdir)) self.add_step(self.shell( - command=['git', 'branch', '--set-upstream-to=origin/dials-2.2', 'dials-2.2'], + command=['git', 'branch', '--set-upstream-to=origin/dials-3.2', 'dials-3.2'], workdir=workdir))
I was wondering - what are the constraints in PHENIX builds which mean bouncing around between extremely different DIALS releases is necessary? I note the shift from 2.2 to 3.2 would give a significant change in behaviour to the end user (who ultimately we may end up having to help with debugging)
If we knew better why these changes were coming through, maybe we could help to keep PHENIX up to date?
I would draw comparisons with CCP4 however they have been stuck in 2.2-series forever now as they’re still not able to support Python3 - will be in CCP4 8.x which will be ready any time now.
I only mention this as it would be really good to start eliminating obsolete versions from distribution as “please go to dials.github.io and install a non-ancient version” is annoying advice to an end user with a fresh install of PHENIX or CCP4.
Thanks Graeme
-- - Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus The Keith Peters Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234
-- This email has been checked for viruses by AVG. https://www.avg.com
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participants (3)
-
Billy Poon -
Robert Oeffner -
Winter, Graeme (DLSLtd,RAL,LSCI)