- cctbxbb - phenix-online.org

Windows woes
by Luc Bourhis 09 Nov '18

09 Nov '18

Hi, Trying to install cctbx on Windows 10, 1. install latest python 2 from Python.org 2. python2 bootstrap.py —builder=cctbxlite —with-python=\path-to-python-from-step-1 It fails because of missing module “builtins”. So I installed pip, then used it to install “future”. Then I had to install “six” with pip. Am I being stupid or cctbx does not install out of the box anymore? Best wishes, Luc J Bourhis

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Python 3 and CCP4
by David Waterman 02 Nov '18

02 Nov '18

Hi folks, It's great to see the momentum building behind the project to migrate to Python 3. From the roadmap <https://github.com/cctbx/cctbx_project/wiki/Python-3-roadmap>, there is clearly still some way to go, but current activity makes me wonder if the proposed deadline of complete migration by 2020 might be beaten easily. What is not clear from the roadmap is whether there are any plans for a post-transition grace period, in which we have switched from writing forwards compatible Python 2 code to writing backwards compatible Python 3 code. Has this been thought about? Or will it be the case that the first commit of Py3-only code seals the deal? I ask because CCP4 has to support a large number of Python projects and these have not all considered the Python 3 switch nearly as seriously as cctbx yet. What I would like to request is a reasonable period of backwards compatibility is ensured to allow other CCP4 projects to catch up, and that this protected period is enshrined within the roadmap or developer guidelines. What do you think? Best wishes -- David

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construct hkl arrays from number of reflections and resolution
by Robert Oeffner 29 Oct '18

29 Oct '18

I would like a function that spits out an HKL array as a function of number of reflections, dmin and dmax. It's quite likely this has already been done somewhere in the CCTBX. Would anyone know if this is the case rather than me having to reinvent the wheel? Many thanks, Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234

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Bootstrap on macOS Mojave
by Graeme.Winter＠Diamond.ac.uk 17 Oct '18

17 Oct '18

Folks, For info: https://github.com/cctbx/cctbx_project/issues/240 wxPython appears to not build on macOS Mojave - possibly updated C++ standards or something who knows? But I guess because we are fixed on an old (4 years, just about [1]) version of wxPython this should not be a surprise. We should probably have some kind of answer for this though - thoughts? Many thanks Graeme ——— [1] https://wxpython.org/news/wxpython-3.0.2.0-release/index.html -- 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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Fwd: cctbx conventions
by Graeme.Winter＠Diamond.ac.uk 08 Oct '18

08 Oct '18

HI Folks, Question from a colleague - any ideas? Many thanks Graeme Begin forwarded message: From: "Bombardi, Alessandro (DLSLtd,RAL,SCI)" <alessandro.bombardi(a)diamond.ac.uk<mailto:[email protected]>> Subject: cctbx conventions Date: 8 October 2018 at 14:54:10 BST To: "Winter, Graeme (DLSLtd,RAL,LSCI)" <Graeme.Winter(a)Diamond.ac.uk<mailto:[email protected]>> Hi Graeme, I am trying to understand the convention used by cctbx, for the anomalous part of the atomic scattering factor. Do you know if it is written as f+f'+if'' with f'' >0 or with f+f'-if'' with f'' >0 can you help me? All the best, Alessandro -- 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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non-standard test naming in mmtbx
by Pearce, N.M. (Nick) 03 Oct '18

03 Oct '18

Hi, I’m trying to use the automatic pytest discovery in mmtbx and I notice that there are a few “libtbx-style” tests, namely "$D/conformation_dependent_library/test_cdl.py", "$D/conformation_dependent_library/test_cdl_esd.py", “$D/conformation_dependent_library/test_rdl.py", "$D/conformation_dependent_library/test_hpdl.py”, that follow the “pytest” naming convention, and are thus picked up by the pytest.discover() function. They then error because pytest cannot run them. There are — as far as I can tell — normal libtbx tests (they are registered in run_tests.py). Is there any reason they do not follow the typical naming convention? Changing their filenames and modifying run_tests.py accordingly seems to lead to the same behaviour when running tests. Is there any reason they should not be renamed from “test_*.py” to “tst_*.py”? Thanks, Nick

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Allocators
by Graeme.Winter＠Diamond.ac.uk 25 Sep '18

25 Sep '18

Hello All, In keeping with the spirit of https://github.com/cctbx/cctbx_project/wiki/cctbx-contributors-guide we would like to revisit the allocator work now Phenix 1.14 is out in the wild - however since we now know that this needs to be done we are interested in other points of view people have on ways to do this, and options people would like to have. It is important to note that we have no intention of changing the default behaviour, but we do want to be able to use customised allocators with flex arrays e.g. for handing out memory of well known and repeatedly used sizes (say, 16 M pixel double arrays) or allocate in specific areas for NUMA systems such as xeon phi. We prototyped this a while back and stepped the changes back out again to enable the phenix release to proceed smoothly, so we have a pretty good idea of the sorts of things we would expect to do however will welcome input if you would like additional features. As a baseline, we are talking as a parameter that PHENIX are no longer supporting CENTOS 5 32 bit (since ISTR this was a constraint before) Any thoughts? Appreciate a number of folks will be travelling back after the PHENIX workshop. Many 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

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Conda
by Graeme.Winter＠Diamond.ac.uk 24 Sep '18

24 Sep '18

Hello again, Trying to keep threads from getting warped :-) We’re interested in what the plans and timescales are for the move to Conda for a base to cctbx-related projects, and in particular - - what is planned? - when i.e. timescales (rough) - will bootstrap go away? I know from talking to Billy on Wednesday that this is back on the cards again now the PHENIX release is out, but I didn’t ask at the time fo the details… oops! Many 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

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Fwd: [git/cctbx] master: Python 3 syntax changes (790d9e315)
by Graeme.Winter＠Diamond.ac.uk 21 Sep '18

21 Sep '18

Folks, I expressed some surprise at this & friends however - - this is necessary to make the bootstrap process Python 3 compatible - the timetable for which said this should have been finished 9 months ago (https://github.com/cctbx/cctbx_project/wiki/Python-3-roadmap) - these changes were discussed and agreed (https://github.com/cctbx/cctbx_project/pull/199) The only part of this which was not approved was reverted before the request was merged (I felt that this annotation was helpful as the changes themselves go back ~6 months so people have possibly forgotten the context) Best wishes Graeme Begin forwarded message: From: CCTBX commit <diamondlightsource.jenkins(a)GMAIL.COM<mailto:[email protected]>> Subject: [git/cctbx] master: Python 3 syntax changes (790d9e315) Date: 21 September 2018 at 14:25:29 BST To: <CCTBX-COMMIT(a)JISCMAIL.AC.UK<mailto:[email protected]>> Reply-To: <cctbxbb(a)PHENIX-ONLINE.ORG<mailto:[email protected]>> Repository : ssh://ws133.diamond.ac.uk/cctbx On branch : master ________________________________ commit 790d9e315a2a6ae5a875ba86b461ed570c77280d Author: Markus Gerstel <markus.gerstel(a)diamond.ac.uk<mailto:[email protected]>> Date: Thu May 24 12:16:38 2018 +0100 Python 3 syntax changes Replace the reduce(add, ...) function by sum(). reduce() is no longer in the global namespace in python 3. ________________________________ 790d9e315a2a6ae5a875ba86b461ed570c77280d scitbx/math/__init__.py | 34 ++++++++++++++++------------------ 1 file changed, 16 insertions(+), 18 deletions(-) diff --git a/scitbx/math/__init__.py b/scitbx/math/__init__.py index a13405f92..49e295eb0 100644 --- a/scitbx/math/__init__.py +++ b/scitbx/math/__init__.py @@ -1,11 +1,13 @@ -from __future__ import division, absolute_import +from __future__ import absolute_import, division, print_function + +import math + from scitbx.math.ext import * import scitbx.linalg.eigensystem import scitbx.math.gaussian # implicit import from scitbx import matrix from scitbx.array_family import flex from boost import rational # implicit import -import math gaussian_fit_1d_analytical.__doc__ = """ Fits a gaussian function to a list of points. @@ -88,16 +90,14 @@ def r3_rotation_average_rotation_matrix_from_matrices(*matrices): """ if not matrices: - raise TypeError, "Average of empty sequence" + raise TypeError("Average of empty sequence") - import operator import scitbx.matrix - average = reduce( - operator.add, - [ scitbx.matrix.col( r3_rotation_matrix_as_unit_quaternion( e ) ) - for e in matrices ] - ) + average = sum( + scitbx.matrix.col( r3_rotation_matrix_as_unit_quaternion( e ) ) + for e in matrices + ) return r3_rotation_unit_quaternion_as_matrix( average.normalize() ) @@ -111,13 +111,12 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver """ if not matrices: - raise TypeError, "Average of empty sequence" + raise TypeError("Average of empty sequence") if maxiter < 0 or convergence <= 0: - raise ValueError, "Invalid iteration parameters" + raise ValueError("Invalid iteration parameters") from scitbx.math import so3_lie_algebra - import operator conv_sq = convergence * convergence norm = 1.0 / len( matrices ) @@ -125,10 +124,9 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver for i in range( maxiter ): inverse = current.inverse() - log_diff = norm * reduce( - operator.add, - [ so3_lie_algebra.element.from_rotation_matrix( matrix = inverse * m ) - for m in matrices ] + log_diff = norm * sum( + so3_lie_algebra.element.from_rotation_matrix( matrix = inverse * m ) + for m in matrices ) if log_diff.norm_sq() < conv_sq: @@ -136,7 +134,7 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver current *= log_diff.exponential() - raise RuntimeError, "Iteration limit exceeded" + raise RuntimeError("Iteration limit exceeded") def euler_angles_as_matrix(angles, deg=False): if (deg): @@ -174,7 +172,7 @@ class erf_verification(object): if (self.max_delta < delta): self.max_delta = delta if (delta > self.tolerance): - print x, expected_result, result, delta + print(x, expected_result, result, delta) class minimum_covering_sphere_nd(object): ________________________________ To unsubscribe from the CCTBX-COMMIT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1 -- 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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Re: [cctbxbb] [git/cctbx] master: Python 3 syntax changes (790d9e315)
by Graeme Winter 21 Sep '18

21 Sep '18

Folks, I expressed some surprise at this & friends however - - this is necessary to make the bootstrap process Python 3 compatible - the timetable for which said this should have been finished 9 months ago (https://github.com/cctbx/cctbx_project/wiki/Python-3-roadmap <https://github.com/cctbx/cctbx_project/wiki/Python-3-roadmap>) - these changes were discussed and agreed (https://github.com/cctbx/cctbx_project/pull/199 <https://github.com/cctbx/cctbx_project/pull/199>) The only part of this which was not approved was reverted before the request was merged (I felt that this annotation was helpful as the changes themselves go back ~6 months so people have possibly forgotten the context) Best wishes Graeme > On 21 Sep 2018, at 14:25, CCTBX commit <diamondlightsource.jenkins(a)GMAIL.COM> wrote: > > Repository : ssh://ws133.diamond.ac.uk/cctbx > On branch : master > > > > commit 790d9e315a2a6ae5a875ba86b461ed570c77280d > Author: Markus Gerstel <markus.gerstel(a)diamond.ac.uk> > Date: Thu May 24 12:16:38 2018 +0100 > > Python 3 syntax changes > > Replace the reduce(add, ...) function by sum(). > reduce() is no longer in the global namespace in python 3. > > > > > 790d9e315a2a6ae5a875ba86b461ed570c77280d > scitbx/math/__init__.py | 34 ++++++++++++++++------------------ > 1 file changed, 16 insertions(+), 18 deletions(-) > > diff --git a/scitbx/math/__init__.py b/scitbx/math/__init__.py > index a13405f92..49e295eb0 100644 > --- a/scitbx/math/__init__.py > +++ b/scitbx/math/__init__.py > @@ -1,11 +1,13 @@ > -from __future__ import division, absolute_import > +from __future__ import absolute_import, division, print_function > + > +import math > + > from scitbx.math.ext import * > import scitbx.linalg.eigensystem > import scitbx.math.gaussian # implicit import > from scitbx import matrix > from scitbx.array_family import flex > from boost import rational # implicit import > -import math > > gaussian_fit_1d_analytical.__doc__ = """ > Fits a gaussian function to a list of points. > @@ -88,16 +90,14 @@ def r3_rotation_average_rotation_matrix_from_matrices(*matrices): > """ > > if not matrices: > - raise TypeError, "Average of empty sequence" > + raise TypeError("Average of empty sequence") > > - import operator > import scitbx.matrix > > - average = reduce( > - operator.add, > - [ scitbx.matrix.col( r3_rotation_matrix_as_unit_quaternion( e ) ) > - for e in matrices ] > - ) > + average = sum( > + scitbx.matrix.col( r3_rotation_matrix_as_unit_quaternion( e ) ) > + for e in matrices > + ) > > return r3_rotation_unit_quaternion_as_matrix( average.normalize() ) > > @@ -111,13 +111,12 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver > """ > > if not matrices: > - raise TypeError, "Average of empty sequence" > + raise TypeError("Average of empty sequence") > > if maxiter < 0 or convergence <= 0: > - raise ValueError, "Invalid iteration parameters" > + raise ValueError("Invalid iteration parameters") > > from scitbx.math import so3_lie_algebra > - import operator > > conv_sq = convergence * convergence > norm = 1.0 / len( matrices ) > @@ -125,10 +124,9 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver > > for i in range( maxiter ): > inverse = current.inverse() > - log_diff = norm * reduce( > - operator.add, > - [ so3_lie_algebra.element.from_rotation_matrix( matrix = inverse * m ) > - for m in matrices ] > + log_diff = norm * sum( > + so3_lie_algebra.element.from_rotation_matrix( matrix = inverse * m ) > + for m in matrices > ) > > if log_diff.norm_sq() < conv_sq: > @@ -136,7 +134,7 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver > > current *= log_diff.exponential() > > - raise RuntimeError, "Iteration limit exceeded" > + raise RuntimeError("Iteration limit exceeded") > > def euler_angles_as_matrix(angles, deg=False): > if (deg): > @@ -174,7 +172,7 @@ class erf_verification(object): > if (self.max_delta < delta): > self.max_delta = delta > if (delta > self.tolerance): > - print x, expected_result, result, delta > + print(x, expected_result, result, delta) > > class minimum_covering_sphere_nd(object): > > > To unsubscribe from the CCTBX-COMMIT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1>

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