- cctbxbb - phenix-online.org

who else has troubles to commit to cctbx now?
by Pavel Afonine 16 Nov '16

16 Nov '16

Can't commit anything since yesterday: pva_mbp:/Users/pafonine/phenix_dev/modules/cctbx_project/mmtbx % svn commit -m "test" maps/correlation.py Sending maps/correlation.py Transmitting file data .svn: E000013: Commit failed (details follow): svn: E000013: Can't create directory '/svn/p/cctbx/code/db/transactions/25717-1.txn': Permission denied pva_mbp:/Users/pafonine/phenix_dev/modules/cctbx_project/mmtbx % Nigel has the same issue. I don't see any warnings on sourceforge. Pavel

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command line syntax for multiple scope PHIL
by R.D. Oeffner 09 Nov '16

09 Nov '16

Say a program, myprog, has a master PHIL definition like: minimization.input .multiple = True { file_name = None .type = str nval = None .type = int } and a PHIL input file like: minimization.input { file_name = experiment1.dat nval = 42 } minimization.input { file_name = experiment2.dat nval = 13 } so that the user on the command line can type "myprog phil_input.txt" What would be the equivalent command line syntax of the PHIL input above? 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 mobile: +44(0)7712 887162

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Failing shelxl test
by Graeme.Winter＠diamond.ac.uk 09 Nov '16

09 Nov '16

Folks, I keep getting this error: libtbx.python "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py" P31 [FAIL] Time: 1.38 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py", line 253, in <module> run(args=sys.argv[1:]) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py", line 250, in run debug_utils.parse_options_loop_space_groups(args, run_call_back) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/debug_utils.py", line 120, in parse_options_loop_space_groups show_cpu_times, **kwds) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/debug_utils.py", line 83, in loop_space_groups call_back_result = call_back(flags, space_group_info, **kwds) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py", line 244, in run_call_back verbose=flags.Verbose) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py", line 234, in exercise run_shelx(shelx_titl, structure_factors, verbose=verbose) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py", line 210, in run_shelx check_anisou(shelx_titl, xray_structure, shelx_pdb, verbose) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/development/run_shelx.py", line 163, in check_anisou assert TotalMismatches == 0 AssertionError Please verify these tests manually. it is annoying as I understand it is to do with a change in shelxl - would it be OK to comment the test out to allow builds to pass? I am not sure it is useful at the moment Thank you 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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Re: [cctbxbb] Git status update
by markus.gerstel＠diamond.ac.uk 04 Nov '16

04 Nov '16

Hello everyone, since I have received no complaints and heard nothing to the contrary, so I thought I would let you know on the current state of the git migration: Until *Thursday, 1 September 2016*, 07:59 BST/08:59 CEST/11:59 pm PDT Cctbx development happens on Sourceforge. Note that cctbx development is "frozen" in preparation for the phenix release. If you are actively developing cctbx you should *now* sign up for a GitHub account. If you are not among the 27 people that have already joined the cctbx project at https://github.com/cctbx then please send me a mail with your github account name so I can invite you. In preparation for the move to github you should also install git on your machines. Set up your local installation of git on each machine you are using by running > git config --global pull.rebase true > git config --global user.name "John Doe" > git config --global user.email "your_email(a)example.com" Use an email address you have set up in your GitHub account at https://github.com/settings/emails. Note that this address will be forever publically readable! If you do not want your mail address to be public, you need to verify any (private) mail address with GitHub and then check the /Keep my email address private/ box at the link above. You can then use the dummy address <yourgithubname>@users.noreply.github.com instead. Other useful settings may be > git config --global alias.up "pull --rebase" To enable a *git up* command working much like svn up does. > git config --global alias.unstage "reset HEAD" *git unstage* to easily undo *git add*/*git rm*. > git config --global alias.mkremotebranch "push origin -u" *git mkremotebranch* will copy your current local branch to GitHub. > git config --global alias.rmremotebranch "push origin --delete" *git rmremotebranch <name>* will delete said branch from GitHub. > git config --global color.ui auto This adds color to the git output, which some may find useful for eg. *git status*. On the 1st of September the transitional period starts, and we will begin changing scripts to point to the new code locations. The transition may be delayed somewhat if the phenix release encounters any delays. I will send you further updates closer to the day. You can find and comment on the transition plan at https://docs.google.com/document/d/1bTiGbnvw8lNUrBLbRmhEdnd22McDqBbiKxcpyga… Best wishes -Markus -- 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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use_internal_variance in iotbx.merging_statistics
by Keitaro Yamashita 02 Nov '16

02 Nov '16

Dear Phenix/CCTBX developers, iotbx/merging_statistics.py is used by phenix.merging_statistics, phenix.table_one, and so on. By upgrading phenix from 1.10.1 to 1.11, merging statistics-related codes were significantly changed. Previously, miller.array.merge_equivalents() was always called with argument use_internal_variance=False, which is consistent with XDS, Aimless and so on. Currently, use_internal_variance=True is default, and cannot be changed by users (see below). These changes were made by @afonine and @rjgildea in rev. 22973 (Sep 26, 2015) and 23961 (Mar 8, 2016). Could anyone explain why these changes were introduced? https://sourceforge.net/p/cctbx/code/22973 https://sourceforge.net/p/cctbx/code/23961 My points are: - We actually cannot control use_internal_variance= parameter because it is not passed to merge_equivalents() in class filter_intensities_by_sigma. - In previous versions, if I gave XDS output to phenix.merging_statistics, <I/sigma> values calculated in the same way (as XDS does) were shown; but not in the current version. - For (for example) phenix.table_one users who expect this behavior, it can give inconsistency. The statistics would not be consistent with the data used in refinement. cf. the related discussion in cctbxbb: http://phenix-online.org/pipermail/cctbxbb/2012-October/000611.html Best regards, Keitaro

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Monthly "how far are we from moving to git" message
by Graeme.Winter＠diamond.ac.uk 21 Oct '16

21 Oct '16

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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sginfo and sgtbx
by Pascal 21 Oct '16

21 Oct '16

Hi, Just out of curiosity, sginfo website mentions that it has been superseeded by sgtbx. Is that a brand new implementation? I don't recognize sginfo code at all. Also, anyone can confirm that sgtbx is tightly embedded is cctbx and cannot be used standalone? Regards, Pascal

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flex.int.as_double() performance
by richard.gildea＠diamond.ac.uk 11 Oct '16

11 Oct '16

Hi, Whilst looking into performance of various DIALS routines recently, I noticed that the flex.int.as_double() conversion takes roughly 3x as long as the equivalent functionality in numpy: (the choice of a 2527x2463 array is simply because this is the size of the raw data array for a Pilatus 6M detector) import time from dials.array_family import flex n = 100 a = flex.int(flex.grid(2527, 2463)) t0 = time.time() for i in range(n): b = a.as_double() t1 = time.time() t = t1-t0 print "flex.int.as_double(): %.2fs (%.3fs/call)" %(t, t/n) import numpy as np a = np.random.randint(100, size=a.all()) t0 = time.time() for i in range(n): b = a.astype(np.float64) t1 = time.time() t = t1-t0 print "numpy.astype(np.float64): %.2fs (%.3fs/call)" %(t, t/n) $ libtbx.python time_as_double.py flex.int.as_double(): 5.76s (0.058s/call) numpy.astype(np.float64): 1.86s (0.019s/call) This is the current version of the as_double function: static flex_double as_double(f_t const& a) { shared_plain<double> result(a.size(), init_functor_null<double>()); for(std::size_t i=0;i<a.size();i++) result[i] = a[i]; return flex_double(result, a.accessor()); } Replacing the above code with the following, I see a significant runtime improvement, now flex.int.as_double() is marginally quicker than the equivalent numpy routine: static flex_double as_double(f_t const& a) { shared_plain<double> result(a.begin(), a.end()); return flex_double(result, a.accessor()); } $ libtbx.python time_as_double.py flex.int.as_double(): 1.64s (0.016s/call) numpy.astype(np.float64): 1.82s (0.018s/call) Is there any obvious reason why making this change would be A Bad Thing? In the context of dials spot-finding, this change results in a 22s saving (out of a total 172s with the original code) when running dials.find_spots on a 540 image Pilatus 6M dataset using a single processor, so it is definitely a noticeable speed-up. All timings done on a macbook pro. Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE -- 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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"import pickle"
by markus.gerstel＠diamond.ac.uk 23 Sep '16

23 Sep '16

Hi everyone, I note that we are using "import pickle" on some 57 occasions. Is there a particular reason we don't import cPickle? For example: --- libtbx/env_config.py (revision 25451) +++ libtbx/env_config.py (working copy) @@ -7,7 +7,10 @@ from libtbx import adopt_init_args import platform import shutil -import pickle +try: + import cPickle as pickle +except: + import pickle from cStringIO import StringIO import re import sys, os This should still work on all systems without issue. According to python docs the only difference is that cPickle can't be subclassed. If it's alright with you I would go through those imports and update them to use cPickle where possible. -Markus -- 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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bootstrap / svn method / say reason not anonymous && http
by Graeme.Winter＠diamond.ac.uk 21 Sep '16

21 Sep '16

Hello folks, In bootstrap.py is there any logical reason why we can’t use %sfmethod for anonymous as well as authenticated access to the cctbx_project sources i.e. in # Core CCTBX repositories # These must all provide anonymous access. class cctbx_module(SourceModule): module = 'cctbx_project' anonymous = ['svn','svn://svn.code.sf.net/p/cctbx/code/trunk'] authenticated = ['svn', '%(sfmethod)s://%(sfuser)[email protected]/p/cctbx/code/trunk'] also respect %(sfmethod) in place of svn as transport layer. Will help people behind firewalls. Appreciate that this will also need changing when we move to git anyhow… but meantimes there are people out there this would help. Not keen to make this change myself without checking first…! 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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