January 2013 - cctbxbb - phenix-online.org

Using cctbx::uctbx::unit_cell in c++ code / boosted to Python
by Graeme.Winter＠diamond.ac.uk 25 Jan '13

25 Jan '13

Hi Folks, Been working on some c++ coding using boost etc (which I have to say is great) however I found one bit of weirdness. If I want to generate a cctbx::uctbx::unit_cell in c++ code then access this from Python I get Traceback (most recent call last): File "tst_x2tbx.py", line 67, in <module> tst_x2tbx(sys.argv[1]) File "tst_x2tbx.py", line 6, in tst_x2tbx import x2tbx File "/Users/graeme/svn/cctbx/sources/x2tbx/__init__.py", line 7, in <module> ext = boost.python.import_ext("x2tbx_ext", optional = False) File "/Users/graeme/svn/cctbx/sources/cctbx_project/boost_adaptbx/boost/python.py", line 36, in import_ext + [" "+p for p in sys.path])) ImportError: __import__("x2tbx_ext"): dlopen(/Users/graeme/svn/cctbx/prebuild/lib/x2tbx_ext.so, 2): Symbol not found: cctbx::uctbx::unit_cell::unit_cell(scitbx::af::tiny<double, 6ul> const&) Referenced from: /Users/graeme/svn/cctbx/prebuild/lib/x2tbx_ext.so Expected in: flat namespace in /Users/graeme/svn/cctbx/prebuild/lib/x2tbx_ext.so sys.path: …. unless I have import cctbx.uctbx # explicit import at the top of the Python code - have I done something wrong with the SConscript? I found something similar with import scitbx.array_family.flex # explicit import which libtbx.clean_clutter complains about as I don't reference it (hence the additional comment) Equally I could just leave the additional clutter there but it feels like I should not need it... 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

4 8

Sphinx documentation
by Graeme.Winter＠diamond.ac.uk 21 Jan '13

21 Jan '13

Hi Folks, I installed sphinx and tried building the documentation but I got an error: File ./xfel/xfel.cxi.gfx.rst already exists, skipping. File ./xfel/xfel.cxi.merging.rst already exists, skipping. File ./xfel/xfel.cxi.rst already exists, skipping. File ./xfel/xfel.metrology.rst already exists, skipping. File ./xfel/xfel.rst already exists, skipping. File ./xfel/modules.rst already exists, skipping. sphinx-build -b coverage -d _build/doctrees -D latex_paper_size=a4 . _build/coverage Making output directory... Running Sphinx v1.2pre loading pickled environment... not yet created building [coverage]: coverage overview updating environment: 206 added, 0 changed, 0 removed reading sources... [ 0%] cctbx/cctbx Exception occurred: File "/Users/graeme/svn/cctbx/phenix/phenix-dev-1241/build/mac-intel-osx-x86_64/base/Python.framework/Versions/Current/lib/python2.7/site-packages/Sphinx-1.2predev_20130121-py2.7.egg/sphinx/ext/autodoc.py", line 595, in filter_members membername in self.options.special_members: TypeError: argument of type 'object' is not iterable The full traceback has been saved in /var/folders/j1/cgsqy8fs1lxdyjggcsb3twsw0000gn/T/sphinx-err-jjM5C8.log, if you want to report the issue to the developers. Please also report this if it was a user error, so that a better error message can be provided next time. Either send bugs to the mailing list at <http://groups.google.com/group/sphinx-users/>, or report them in the tracker at <http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks! make: *** [coverage] Error 1 cp: ./_build/coverage/python.txt: No such file or directory cp: ./_build/coverage/c.txt: No such file or directory sphinx-build -b html -d _build/doctrees -D latex_paper_size=a4 . _build/html Making output directory... Running Sphinx v1.2pre loading pickled environment... not yet created building [html]: targets for 206 source files that are out of date updating environment: 206 added, 0 changed, 0 removed reading sources... [ 0%] cctbx/cctbx Exception occurred: File "/Users/graeme/svn/cctbx/phenix/phenix-dev-1241/build/mac-intel-osx-x86_64/base/Python.framework/Versions/Current/lib/python2.7/site-packages/Sphinx-1.2predev_20130121-py2.7.egg/sphinx/ext/autodoc.py", line 595, in filter_members membername in self.options.special_members: TypeError: argument of type 'object' is not iterable The full traceback has been saved in /var/folders/j1/cgsqy8fs1lxdyjggcsb3twsw0000gn/T/sphinx-err-lONSky.log, if you want to report the issue to the developers. Please also report this if it was a user error, so that a better error message can be provided next time. Either send bugs to the mailing list at <http://groups.google.com/group/sphinx-users/>, or report them in the tracker at <http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks! make: *** [html] Error 1 Did I do something wrong? I just grabbed sphinx from the internet. Should I have got it from someplace else? OS X Lion / svn cctbx. 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

2 1

Phil (dumb) question
by Graeme.Winter＠diamond.ac.uk 14 Jan '13

14 Jan '13

Hi Folks, I have a toy example where I should be overriding Phil defaults: phil_defaults = ''' resolutionizer { rmerge = 0.0 .type = float completeness = 0.0 .type = float isigma = 1.0 .type = float misigma = 2.0 .type = float bins = 100 .type = int } ''' more = ''' resolutionizer { isigma = 2.0 misigma = 4.0 } ''' from libtbx.phil import parse working_phil = parse(phil_defaults) working_phil.fetch(parse(more)) working_phil.show() but it seems I am not: Graemes-MacBook-Pro:scale graeme$ cctbx.python toy.py resolutionizer { rmerge = 0.0 completeness = 0.0 isigma = 1.0 misigma = 2.0 bins = 100 } Am I doing something dumb? I hope so as I really cannot find my error. 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

2 2

Simple cctbx / boost c++ extension example
by Graeme.Winter＠diamond.ac.uk 11 Jan '13

11 Jan '13

Hi Folks, Just say I wanted to write a new from the ground up module for cctbx which wanted to include some C++ code, and a SConscript etc. so I can run libtbx.configure toytbx (say) And then find from toytbx import cplusplus_functions would work.... Is there an example I could follow? (I have not looked through the newsletters, I suppose I should have... but I could not seen anything obvious in the documents) Thanks, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- 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

2 6