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libtbx.configure crashes RE: new requirements for libtbx_refresh.py
by markus.gerstel＠diamond.ac.uk 23 Jan '18

23 Jan '18

Hi everyone, You may find that with the latest cctbx_project updates your libtbx.configure / make reconf crashes with (...) File "(..)/modules/annlib_adaptbx/libtbx_refresh.py", line 6 print message ^ SyntaxError: invalid syntax make: *** [reconf] Error 1 Solution: Changes are required in annlib_adaptbx, and you do not have the latest version on your system. Please run cd $(libtbx.find_in_repositories annlib_adaptbx)/.. rm -rf annlib_adaptbx git clone https://github.com/cctbx/annlib_adaptbx.git Background: This is related to my earlier email attached below. I couldn't figure out how to update the static tarball of annlib_adaptbx myself, and found it easier to just convert the repository including history. Said repository now lives at https://github.com/cctbx/annlib_adaptbx. Bootstrap has been updated to pull from this location. To avoid duplication the old repository copy we kept at https://github.com/dials/annlib_adaptbx for DIALS release control now points there, too. I note there is another copy at https://github.com/cctbx-xfel/annlib_adaptbx/network where you may also want to change the existing labels to the correct commit tree. Whoever maintains this - let me know if you want any help. Builds are still running but it looks like this is the only bit which may require intervention on your end. -Markus From: cctbxbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of markus.gerstel(a)diamond.ac.uk Sent: 16 January 2018 09:29 To: cctbxbb(a)phenix-online.org Subject: [cctbxbb] new requirements for libtbx_refresh.py Hello everyone, There will soon be a requirement for all libtbx_refresh.py and run_tests.py of cctbx modules to contain the line from __future__ import absolute_import, division, print_function I have modified those that I have write access to (everything in cctbx_project, all default modules, dials*, labelit*, phenix*, xia2*), but there may be others that I am not aware of/do not use/do not have access to. (While you are at it ideally you would want to make sure these files are valid Python2 and 3 code, but that is not strictly required at this time.) For more information on the patch that requires this change see https://github.com/cctbx/cctbx_project/commit/ecd7192930961fde31c4ba29a049b… -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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GRC / cctbx catch up
by Graeme.Winter＠diamond.ac.uk 16 Jan '18

16 Jan '18

Folks, Who’s going to GRC on diffraction methods this summer? Would it be good to have a cctbx developer’s meeting on the Wednesday afternoon which is “free” - seems like a good opportunity? Cheers 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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new requirements for libtbx_refresh.py
by markus.gerstel＠diamond.ac.uk 16 Jan '18

16 Jan '18

Hello everyone, There will soon be a requirement for all libtbx_refresh.py and run_tests.py of cctbx modules to contain the line from __future__ import absolute_import, division, print_function I have modified those that I have write access to (everything in cctbx_project, all default modules, dials*, labelit*, phenix*, xia2*), but there may be others that I am not aware of/do not use/do not have access to. (While you are at it ideally you would want to make sure these files are valid Python2 and 3 code, but that is not strictly required at this time.) For more information on the patch that requires this change see https://github.com/cctbx/cctbx_project/commit/ecd7192930961fde31c4ba29a049b… -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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How to hack at the autobuild?
by Luc Bourhis 15 Dec '17

15 Dec '17

Hi, I have found a few issues with auto build on recent versions of Fedora. I need to edit files in libtbx/autobuild to fix them but then I want to test that running bootstrap works. But then bootstrap.py always pull from github. I don’t want to push my changes to github until it’s solid though. How do you guys approach that? Best wishes, Luc

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What does get numpy to be install during bootstrap?
by Luc Bourhis 14 Dec '17

14 Dec '17

Hi, I noticed that bootstrap.py does indirectly result in the installation of numpy but a quick swipe of the code did not reveal to me what does get it installed. Since I am sure somebody knows… Best wishes, Luc

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Fwd: [Dials-support] dials.stills_process crash report
by Graeme.Winter＠diamond.ac.uk 13 Dec '17

13 Dec '17

Folks Once again, lack of stack traces in easy_mp is a big annoyance I forget the reasons why printing the actual error was a bad thing, but I do remember a discussion some 18 mo past Not wishing to replay the entire transaction, but could we revisit this? Thanks Graeme Begin forwarded message: From: <Danny.Axford(a)Diamond.ac.uk<mailto:[email protected]>> Subject: [Dials-support] dials.stills_process crash report Date: 12 December 2017 at 17:43:41 GMT To: <dials-support(a)lists.sourceforge.net<mailto:[email protected]>> Cc: martin.appleby(a)diamond.ac.uk<mailto:[email protected]> Perhaps this means something to someone. This is the SACLA data again, it seems to run happily and then hit a problematic frame? Martin and I see the error at pretty much the same point in the dataset, we were both running on local machines rather than the cluster. Cheers, Danny Detector 1 RMSDs by panel: ---------------------------------------------------- | Panel | Nref | RMSD_X | RMSD_Y | RMSD_DeltaPsi | | id | | (px) | (px) | (deg) | ---------------------------------------------------- | 1 | 89 | 0.37442 | 0.48949 | 0.2192 | | 2 | 69 | 0.49627 | 0.4847 | 0.21385 | | 5 | 90 | 0.48267 | 0.59909 | 0.22839 | | 6 | 70 | 0.6094 | 0.55592 | 0.20944 | ---------------------------------------------------- Traceback (most recent call last): File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20171212/build/../modules/dials/command_line/stills_process.py", line 870, in <module> halraiser(e) File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20171212/build/../modules/dials/command_line/stills_process.py", line 868, in <module> script.run() File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20171212/build/../modules/dials/command_line/stills_process.py", line 383, in run preserve_exception_message=True) File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20171212/modules/cctbx_project/libtbx/easy_mp.py", line 623, in parallel_map result = res() File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20171212/modules/cctbx_project/libtbx/scheduling/result.py", line 119, in __call__ self.traceback( exception = self.exception() ) File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20171212/modules/cctbx_project/libtbx/scheduling/stacktrace.py", line 86, in __call__ raise exception RuntimeError: Please report this error to dials-support(a)lists.sourceforge.net<mailto:[email protected]>: exit code = -9 -- 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 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://slashdot.org/>! http://sdm.link/slashdot _______________________________________________ DIALS-support mailing list DIALS-support(a)lists.sourceforge.net<mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/dials-support

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Re: [cctbxbb] cctbxbb Digest, Vol 105, Issue 3
by Mooers, Blaine H.M. (HSC) 08 Dec '17

08 Dec '17

Hi Gianluca , You might try getting the sources for 2.7 from here: https://gist.github.com/0x414A/8b64178e69d9f8331938 Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine University of Oklahoma Health Sciences Center 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Faculty webpage X-ray lab (LBSF) COBRE in Structural Biology SSRL UEC Facebook Page SSRL UEC SSRL SAC LCLS UEC EasyPyMOL Molecular Graphics Small Angle Scattering office: (405) 271-8300 lab: (405) 271-8313 e-mail: blaine-mooers(a)ouhsc.edu ________________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of cctbxbb-request(a)phenix-online.org [cctbxbb-request(a)phenix-online.org] Sent: Friday, December 08, 2017 2:00 PM To: cctbxbb(a)phenix-online.org Subject: cctbxbb Digest, Vol 105, Issue 3 Send cctbxbb mailing list submissions to cctbxbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… or, via email, send a message with subject or body 'help' to cctbxbb-request(a)phenix-online.org You can reach the person managing the list at cctbxbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of cctbxbb digest..." Today's Topics: 1. Importing PyQt4 in litbx.python (Gianluca SANTONI) 2. Re: Importing PyQt4 in litbx.python (markus.gerstel(a)diamond.ac.uk) 3. Re: Importing PyQt4 in litbx.python (Gianluca SANTONI) ---------------------------------------------------------------------- Message: 1 Date: Fri, 8 Dec 2017 13:18:13 +0100 From: Gianluca SANTONI <gianluca.santoni(a)esrf.fr> To: cctbx mailing list <cctbxbb(a)phenix-online.org> Subject: [cctbxbb] Importing PyQt4 in litbx.python Message-ID: <09889a85-3126-af38-05f3-8af190cdfd07(a)esrf.fr> Content-Type: text/plain; charset=utf-8; format=flowed Dear all, I'm having some troubles recently in importing pyqt4 in libtbx.python under Debian8. It used to work with a previous build compiled from the sources, but I don't find a reasonable way to make it work from the bootstrap installation. More details: 1) If I do in libtbx.python sys.path.append('/usr/lib/python2.7/dist-packages/') and "from PyQt4 import QtCore", I get an unidentified symbol: PyUnicodeUCS4_AsLatin1String 2) If I try to compile cctbx as I did in the past "python ../libtbx/configure.py cctbx" no make file is produced. Maybe I'm missing something Thanks everybody for your help. Gian -- Gianluca Santoni, PhD ESRF structural biology group 71 avenue des Martyrs 38027 Grenoble cedex (France) ------------------------------ Message: 2 Date: Fri, 8 Dec 2017 12:40:13 +0000 From: <markus.gerstel(a)diamond.ac.uk> To: <cctbxbb(a)phenix-online.org> Subject: Re: [cctbxbb] Importing PyQt4 in litbx.python Message-ID: <f8d53c3e-c8d8-4941-9540-c9b80f95441d(a)email.android.com> Content-Type: text/plain; charset=utf-8 Hi, There is an issue open on UCS4 which is somewhat related: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cctbx_cctbx… We currently don't use UCS4, and your system pyqt4 does. You would have to install (and potentially, compile) it for the cctbx python directly. A 3 minute research from my mobile phone suggests that you might be able to download the sources as tar.gz files and then do something along the lines of cctbx.python -m pip install SIP cctbx.python -m pip install pyqt-source.tar.gz but this is untested, and I haven't used pyqt before. -Markus On 8 Dec 2017 12:19, Gianluca SANTONI <gianluca.santoni(a)esrf.fr> wrote: Dear all, I'm having some troubles recently in importing pyqt4 in libtbx.python under Debian8. It used to work with a previous build compiled from the sources, but I don't find a reasonable way to make it work from the bootstrap installation. More details: 1) If I do in libtbx.python sys.path.append('/usr/lib/python2.7/dist-packages/') and "from PyQt4 import QtCore", I get an unidentified symbol: PyUnicodeUCS4_AsLatin1String 2) If I try to compile cctbx as I did in the past "python ../libtbx/configure.py cctbx" no make file is produced. Maybe I'm missing something Thanks everybody for your help. Gian -- Gianluca Santoni, PhD ESRF structural biology group 71 avenue des Martyrs 38027 Grenoble cedex (France) _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… -- 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 ------------------------------ Message: 3 Date: Fri, 8 Dec 2017 14:20:26 +0100 From: Gianluca SANTONI <gianluca.santoni(a)esrf.fr> To: cctbxbb(a)phenix-online.org Subject: Re: [cctbxbb] Importing PyQt4 in litbx.python Message-ID: <820c8b08-d380-dd46-e25a-e9ee9e4b076b(a)esrf.fr> Content-Type: text/plain; charset=utf-8; format=flowed Hi Markus, I could fix everyting by compiling both libraries from source with cctbx.python. Hope this helps others with similar problem too. cctbx.python -m pip install SIP cctbx.python -m pip install pyqt-source.tar.gz did not work. There is actually no PyPi package for sip in python2.7 Cheers Gian Gianluca Santoni, PhD ESRF structural biology group 71 avenue des Martyrs 38027 Grenoble cedex (France) On 08/12/2017 13:40, markus.gerstel(a)diamond.ac.uk wrote: > Hi, > > There is an issue open on UCS4 which is somewhat related: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cctbx_cctbx… > > We currently don't use UCS4, and your system pyqt4 does. You would have to install (and potentially, compile) it for the cctbx python directly. > > A 3 minute research from my mobile phone suggests that you might be able to download the sources as tar.gz files and then do something along the lines of > > cctbx.python -m pip install SIP > cctbx.python -m pip install pyqt-source.tar.gz > > but this is untested, and I haven't used pyqt before. > > -Markus > > On 8 Dec 2017 12:19, Gianluca SANTONI <gianluca.santoni(a)esrf.fr> wrote: > Dear all, > I'm having some troubles recently in importing pyqt4 in libtbx.python > under Debian8. > It used to work with a previous build compiled from the sources, but I > don't find a reasonable way to make it work from the bootstrap installation. > > More details: > > 1) If I do in libtbx.python > sys.path.append('/usr/lib/python2.7/dist-packages/') and "from PyQt4 > import QtCore", I get an > > unidentified symbol: PyUnicodeUCS4_AsLatin1String > > 2) If I try to compile cctbx as I did in the past "python > ../libtbx/configure.py cctbx" no make file is produced. Maybe I'm > missing something > > Thanks everybody for your help. > Gian > > -- > Gianluca Santoni, PhD > ESRF structural biology group > 71 avenue des Martyrs > 38027 Grenoble cedex (France) > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > ------------------------------ _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… End of cctbxbb Digest, Vol 105, Issue 3 ***************************************

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Re: [cctbxbb] Importing PyQt4 in litbx.python
by markus.gerstel＠diamond.ac.uk 08 Dec '17

08 Dec '17

Hi, There is an issue open on UCS4 which is somewhat related: https://github.com/cctbx/cctbx_project/issues/60 We currently don't use UCS4, and your system pyqt4 does. You would have to install (and potentially, compile) it for the cctbx python directly. A 3 minute research from my mobile phone suggests that you might be able to download the sources as tar.gz files and then do something along the lines of cctbx.python -m pip install SIP cctbx.python -m pip install pyqt-source.tar.gz but this is untested, and I haven't used pyqt before. -Markus On 8 Dec 2017 12:19, Gianluca SANTONI <gianluca.santoni(a)esrf.fr> wrote: Dear all, I'm having some troubles recently in importing pyqt4 in libtbx.python under Debian8. It used to work with a previous build compiled from the sources, but I don't find a reasonable way to make it work from the bootstrap installation. More details: 1) If I do in libtbx.python sys.path.append('/usr/lib/python2.7/dist-packages/') and "from PyQt4 import QtCore", I get an unidentified symbol: PyUnicodeUCS4_AsLatin1String 2) If I try to compile cctbx as I did in the past "python ../libtbx/configure.py cctbx" no make file is produced. Maybe I'm missing something Thanks everybody for your help. Gian -- Gianluca Santoni, PhD ESRF structural biology group 71 avenue des Martyrs 38027 Grenoble cedex (France) _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org 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

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Importing PyQt4 in litbx.python
by Gianluca SANTONI 08 Dec '17

08 Dec '17

Dear all, I'm having some troubles recently in importing pyqt4 in libtbx.python under Debian8. It used to work with a previous build compiled from the sources, but I don't find a reasonable way to make it work from the bootstrap installation. More details: 1) If I do in libtbx.python sys.path.append('/usr/lib/python2.7/dist-packages/') and "from PyQt4 import QtCore", I get an unidentified symbol: PyUnicodeUCS4_AsLatin1String 2) If I try to compile cctbx as I did in the past "python ../libtbx/configure.py cctbx" no make file is produced. Maybe I'm missing something Thanks everybody for your help. Gian -- Gianluca Santoni, PhD ESRF structural biology group 71 avenue des Martyrs 38027 Grenoble cedex (France)

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cctbx.miller problem
by 李选选 06 Dec '17

06 Dec '17

> > Dear cctbx developers, > > I’m Xuanxuan, and I’m using cctbx to develop a crystallography-related algorithm. Recently, I found there is something wrong when I use miller package to generate miller indices for given space group and unit cell parameters. Maybe it’s my mistake, or it’s a bug. > > Here are some details. I just use the following code to generate a list of miller indices for a Fd-3m crystal. > > ms = miller.build_set( > crystal_symmetry=crystal.symmetry( > space_group_symbol='Fd-3m', > unit_cell=(5.4307,5.4307,5.4307,90.00,90.0,90.00)), > anomalous_flag=False, > d_min=0.4) > > And I found some reflections are missing, like 220, 311, which should exist according to the reflection conditions listed in this page http://img.chem.ucl.ac.uk/sgp/large/227az2.htm <http://img.chem.ucl.ac.uk/sgp/large/227az2.htm>. > > Looking forward to your response. > > Thanks, > Xuanxuan

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