[cctbxbb] DIALS releases in PHENIX

Billy Poon BKPoon at lbl.gov
Thu Jul 15 06:01:46 PDT 2021


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 <rdo20 at cam.ac.uk> wrote:

> 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
>
>
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