- cctbxbb - phenix-online.org

Re: [cctbxbb] [git/cctbx] master: Generate libtbx.* wrappers from correct directory (ad736e2c8)
by Billy Poon 01 Jun '18

01 Jun '18

I don't think this is working on macOS. The configuration step is generating error messages like, Ignored: [Errno 2] No such file or directory: <command path> In lines 1640-1643, self.write_dispatcher( source_file=libtbx.env.under_base(os.path.join('bin', ep.name)), target_file=os.path.join('bin', 'libtbx.' + ep.name), ) the source_file argument is always being constructed as <base>/bin/<command> instead of using the directory from self.get_setuptools_script_dir(). Should it be the bin_directory variable instead (e.g. source_file=os.path.join(bin_directory, ep.name))? As a side note, conda will put everything in bin because there is no framework. For access to the window manager, you would call pythonw, which points to a python inside a .app bundle. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Fri, Jun 1, 2018 at 3:15 AM CCTBX commit < diamondlightsource.jenkins(a)gmail.com> wrote: > Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx > On branch : master > > ------------------------------ > > > commit ad736e2c8e65407615a7e6604b0544687ed8058c > Author: Markus Gerstel <markus.gerstel(a)diamond.ac.uk> > Date: Thu May 31 08:27:09 2018 +0100 > > Generate libtbx.* wrappers from correct directory > > Python console scripts don't necessarily land in base/bin, specifically > on MacOS this is not the case. Use setuptools etc. to find the actual > Python console script location and use that directory instead. Fixes > #177 > > Add a function to regenerate all Python console scripts which can be > called from an installer to relocate paths. > > > ------------------------------ > > > ad736e2c8e65407615a7e6604b0544687ed8058c > libtbx/env_config.py | 74 +++++++++++++++++++++++++----- > libtbx/fastentrypoints.py | 112 > ++++++++++++++++++++++++++++++++++++++++++++++ > 2 files changed, 176 insertions(+), 10 deletions(-) > > diff --git a/libtbx/env_config.py b/libtbx/env_config.py > index de5fc72dd..25daa2cb3 100644 > --- a/libtbx/env_config.py > +++ b/libtbx/env_config.py > @@ -1562,23 +1562,77 @@ selfx: > source_file=source_file, > target_file=module_name+"."+command) > > + def get_setuptools_script_dir(): > + ''' > + Find the location of python entry point console_scripts, ie. things > like > + 'pip', 'pytest', ... > + This is different from simple /base/bin, eg. on MacOS. > + > + > https://stackoverflow.com/questions/25066084/get-entry-point-script-file-lo… > + ''' > + from setuptools import Distribution > + from setuptools.command.install import install > + class OnlyGetScriptPath(install): > + def run(self): > + # does not call install.run() by design > + self.distribution.install_scripts = self.install_scripts > + dist = Distribution({'cmdclass': {'install': OnlyGetScriptPath}}) > + dist.dry_run = True # not sure if necessary, but to be safe > + dist.parse_config_files() > + command = dist.get_command_obj('install') > + command.ensure_finalized() > + command.run() > + return dist.install_scripts > + > + def regenerate_entry_point_console_scripts(self, verbose=True): > + ''' > + Creates all console_scripts entry point scripts from scratch and > overwrites existing ones. > + This is intended to be used by installers to relocate the entry point > script paths. > + ''' > + try: > + import distutils.dist > + import libtbx.fastentrypoints # monkeypatches setuptools > + import pkg_resources > + import setuptools.command.easy_install > + except ImportError: > + return > + > + # Prepare generic script generator > + distribution = distutils.dist.Distribution({'name': 'setuptools'}) > + command = setuptools.command.easy_install.easy_install(distribution) > + command.args = ['wheel'] # dummy argument > + command.finalize_options() > + > + # Force regeneration of all known console_scripts > + for pkg_resources_dist in pkg_resources.working_set: > + console_scripts = > pkg_resources_dist.get_entry_map().get('console_scripts') > + if console_scripts: > + if verbose: > + print("Regenerating commands for %s: %s" % ( > + pkg_resources_dist, > + list(console_scripts), > + )) > + command.install_wrapper_scripts(pkg_resources_dist) > + > def generate_entry_point_dispatchers(self): > - # Write indirect dispatcher scripts for all console_scripts entry > points > - # that have existing dispatcher scripts in the base/bin directory, but > - # add a 'libtbx.' prefix. > - base_bin_directory = libtbx.env.under_base('bin') > - if not os.path.isdir(base_bin_directory): > + ''' > + Write indirect dispatcher scripts for all console_scripts entry points > + that have existing dispatcher scripts in the base/bin directory, but > + add a 'libtbx.' prefix. > + ''' > + try: > + import pkg_resources > + bin_directory = get_setuptools_script_dir() > + except ImportError: > + return > + if not os.path.isdir(bin_directory): > return # do not create console_scripts dispatchers, only point to > them > > - base_bin_dispatchers = set(os.listdir(base_bin_directory)) > + base_bin_dispatchers = set(os.listdir(bin_directory)) > existing_dispatchers = filter(lambda f: f.startswith('libtbx.'), > self.bin_path.listdir()) > existing_dispatchers = set(map(lambda f: f[7:], existing_dispatchers)) > entry_point_candidates = base_bin_dispatchers - existing_dispatchers > > - try: > - import pkg_resources > - except ImportError: > - return > entry_points = pkg_resources.iter_entry_points('console_scripts') > entry_points = filter(lambda ep: ep.name in entry_point_candidates, > entry_points) > for ep in entry_points: > diff --git a/libtbx/fastentrypoints.py b/libtbx/fastentrypoints.py > new file mode 100644 > index 000000000..9707f74a3 > --- /dev/null > +++ b/libtbx/fastentrypoints.py > @@ -0,0 +1,112 @@ > +# noqa: D300,D400 > +# Copyright (c) 2016, Aaron Christianson > +# All rights reserved. > +# > +# Redistribution and use in source and binary forms, with or without > +# modification, are permitted provided that the following conditions are > +# met: > +# > +# 1. Redistributions of source code must retain the above copyright > +# notice, this list of conditions and the following disclaimer. > +# > +# 2. Redistributions in binary form must reproduce the above copyright > +# notice, this list of conditions and the following disclaimer in the > +# documentation and/or other materials provided with the distribution. > +# > +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS > +# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED > +# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A > +# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT > +# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, > +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED > +# TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR > +# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF > +# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING > +# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS > +# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. > +''' > +Monkey patch setuptools to write faster console_scripts with this format: > + > + import sys > + from mymodule import entry_function > + sys.exit(entry_function()) > + > +This is better. > + > +(c) 2016, Aaron Christianson > +http://github.com/ninjaaron/fast-entry_points > +''' > +from setuptools.command import easy_install > +import re > +TEMPLATE = '''\ > +# -*- coding: utf-8 -*- > +# EASY-INSTALL-ENTRY-SCRIPT: '{3}','{4}','{5}' > +__requires__ = '{3}' > +import re > +import sys > + > +from {0} import {1} > + > +if __name__ == '__main__': > + sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) > + sys.exit({2}())''' > + > + > +@classmethod > +def get_args(cls, dist, header=None): # noqa: D205,D400 > + """ > + Yield write_script() argument tuples for a distribution's > + console_scripts and gui_scripts entry points. > + """ > + if header is None: > + # pylint: disable=E1101 > + header = cls.get_header() > + spec = str(dist.as_requirement()) > + for type_ in 'console', 'gui': > + group = type_ + '_scripts' > + for name, ep in dist.get_entry_map(group).items(): > + # ensure_safe_name > + if re.search(r'[\\/]', name): > + raise ValueError("Path separators not allowed in script > names") > + script_text = TEMPLATE.format( > + ep.module_name, ep.attrs[0], '.'.join(ep.attrs), > + spec, group, name) > + # pylint: disable=E1101 > + args = cls._get_script_args(type_, name, header, script_text) > + for res in args: > + yield res > + > + > +# pylint: disable=E1101 > +easy_install.ScriptWriter.get_args = get_args > + > + > +def main(): > + import os > + import re > + import shutil > + import sys > + dests = sys.argv[1:] or ['.'] > + filename = re.sub('\.pyc$', '.py', __file__) > + > + for dst in dests: > + shutil.copy(filename, dst) > + manifest_path = os.path.join(dst, 'MANIFEST.in') > + setup_path = os.path.join(dst, 'setup.py') > + > + # Insert the include statement to MANIFEST.in if not present > + with open(manifest_path, 'a+') as manifest: > + manifest.seek(0) > + manifest_content = manifest.read() > + if 'include fastentrypoints.py' not in manifest_content: > + manifest.write(('\n' if manifest_content else '') + > + 'include fastentrypoints.py') > + > + # Insert the import statement to setup.py if not present > + with open(setup_path, 'a+') as setup: > + setup.seek(0) > + setup_content = setup.read() > + if 'import fastentrypoints' not in setup_content: > + setup.seek(0) > + setup.truncate() > + setup.write('import fastentrypoints\n' + setup_content) > > ------------------------------ > > To unsubscribe from the CCTBX-COMMIT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1 >

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show() not __str__ - why?
by Graeme.Winter＠Diamond.ac.uk 01 Jun '18

01 Jun '18

Folks, Came up in conversation - how come the motif for printing / providing object info is to call show() and pass a file handle rather than the more pythonic __str__? See e.g. https://github.com/dials/dials/blob/b499c6191caa18e04ddaf190321a3da6c14af55… I know in dials we could do it differently however we inherited the motif from cctbx & I am not sure why things work that way - figured there must be a reason... This is also under discussion under https://github.com/dials/dials/pull/567 but I thought it was worth making sure we knew the reasons why cctbx uses it's own way of doing something... (also it's quite annoying that printing things will give you say space_group object i.e. much like printing type(object), when you want to see it's contents - like printing j and being told it is an int!) 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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Berkeley Server Downtown (5/29 - 5/31)
by Billy Poon 30 May '18

30 May '18

Dear all, On Tuesday, May 29, our servers will be shut down starting at 5:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available by 10:00 am Pacific on Thursday (5/31) at the latest. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Automated Travis CI for phenix
by Elliot Nelson 25 May '18

25 May '18

Hi I'm looking to run automated integration tests for software, which currently runs from CCTBX, but also calls phenix scripts. These are phenix.fmodel and phenix.maps. Currently I have a docker image which sources CCP4 to get access to CCTBX, but this will not allow me to test stuff reliant on the phenix scripts. As Phenix is not downloadable on command line (CCP4 build can be got through wget command), it is not obvious as the best way to setup up such a docker build on travis CI. I wouldn't want to source a local download of the software as i am unsure of the licesining implications of hosting a copy of the software. Any suggestions would be greatly appreciated? Software (with dockerfile): https://github.com/nelse003/exhaustive_search <https://github.com/nelse003/exhaustive_search>Current docker image: https://hub.docker.com/r/nelse003/ccp4_phenix_docker/ Thanks Elliot DPhil Student, Systems Approaches to Biomedical Science<http://www.sabsidc.ox.ac.uk/> Protein Crystallography<http://www.thesgc.org/groupprofile/9489>, Structural Genomics Consortium, NDM, University of Oxford Oxford Protein Informatics Group<http://opig.stats.ox.ac.uk/>, Department of Statistics, University of Oxford

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mmtbx.f_model.manager.deep_copy() does not work correctly when twinned?
by Keitaro Yamashita 15 May '18

15 May '18

Dear CCTBX developers, I found phenix.maps did not recognize twinning. Clearly, "fmodel" in the following code should be "fmodel_". (underscore missing) https://github.com/cctbx/cctbx_project/blob/41df8498857c186a3f83351090683b3… However, this did not solve the problem. This is due to fmodel_.deep_copy() in line 1530. For example, fmodel_.info().show_rfactors_targets_scales_overall() fmodel_.deep_copy().info().show_rfactors_targets_scales_overall() These two lines show different stats in case of twinning (fmodel_ is mmtbx.twinning.twin_f_model.twin_model_manager object). So deep_copy() is not working correctly. I found that something was wrong with fmodel_ts1.deep_copy() here. https://github.com/cctbx/cctbx_project/blob/master/mmtbx/twinning/twin_f_mo… Does anybody know how to solve this copying issue? Best regards, Keitaro

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mmtbx/examples/simulate_experimental_data.py
by Elliot Nelson 10 May '18

10 May '18

Hi All, I'm trying to generate some simulated mtz files. My main aim is to test a script which looks to determine ligand occupancy (https://github.com/nelse003/exhaustive_search/blob/master/exhaustive_search…) by looking at |Fo-Fc| over the ligand/ ground-state the ligand replaces. To test this I would like to generate mtz files from pdb models with a ligand occupancy that has varied between 0-1, which the above script would hopefully recover the occupancy. I have tried to use mmtbx/examples/simulate_experimental_data.py (https://github.com/cctbx/cctbx-playground/blob/8f23c190a9f8d2ed2b5845385f56… ) to generate an mtz file. So far I have been able to generate mtz files using the simulate_experimental_data.py, these have the columns: H K L FOBS(+) SIGFOBS(+) FOBS(-) SIGFOBS(-) I can use this outputted mtz for running tests of my scripts ,However as this has no PHI columns, I cannot display this in coot. I have tried to add the phi column from the refined mtz of the orignal data using CAD, but have not yet managed to do this succesfully. I feel that this may be an overcomplicated, and potentially superseded way of generating simulated mtz data. Any advice on alternatives would be really useful? Apologies if this is not very clear. Thanks Elliot Nelson

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Jenkins testing on cctbx branches other than master
by markus.gerstel＠diamond.ac.uk 09 May '18

09 May '18

Hello everyone, As requested we now also run Jenkins tests on all branches that are not master. The current settings are as follows: (this is currently exactly the same we do for testing on the master branch) We test the following modules: libtbx, scitbx, cctbx, iotbx, rstbx, fable and dxtbx The following other modules are present and configured: dials_regression, phenix_regression The following modules are not configured: dials, xia2, xfel, iota, prime, simtbx Let me know if you want any changes here. Results will look like this: https://github.com/cctbx/cctbx_project/commits/testbranch If you hover over the green tick mark (or the red cross) of the top 3 commits you see that these are results from cctbx-branch testing. We do generate emails for failed tests and failed builds as usual, but there will be no 'this build is now fixed'/'back to normal' emails. -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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Re: [cctbxbb] [Dials-support] Issue with hierarchy.as_pdb_string
by Graeme.Winter＠Diamond.ac.uk 28 Apr '18

28 Apr '18

Morning all, Mike came to the DIALS list with some pdb-reading related issues - however in DIALS land we usually don’t mess with this kind of stuff - is there someone who can help him out here please? Many thanks Graeme On 27 Apr 2018, at 18:14, Wall, Michael E <mewall(a)lanl.gov<mailto:[email protected]>> wrote: Hi, I'm seeing the following issue with a fresh build of dials development source, downloaded within the last hour. There's no error using dials v1-9-1. Is this a bug? Something that's being revised right now? Thanks, Mike Traceback (most recent call last): File "../../src/xenm_new.py", line 609, in <module> ftmp.write(pdb_in.hierarchy.as_pdb_string(crystal_symmetry=pdb_in.input.crystal_symmetry())) File "/home/mewall/packages/dials_devel/modules/cctbx_project/iotbx/pdb/__init__.py", line 1191, in crystal_symmetry self_symmetry = self.crystal_symmetry_from_cryst1() File "/home/mewall/packages/dials_devel/modules/cctbx_project/iotbx/pdb/__init__.py", line 1168, in crystal_symmetry_from_cryst1 return cryst1_interpretation.crystal_symmetry(cryst1_record=line) File "/home/mewall/packages/dials_devel/modules/cctbx_project/iotbx/pdb/cryst1_interpretation.py", line 138, in crystal_symmetry unit_cell=u) File "/home/mewall/packages/dials_devel/modules/cctbx_project/iotbx/pdb/cryst1_interpretation.py", line 87, in space_group_info try: return sgtbx.space_group_info(self.symbol) File "/home/mewall/packages/dials_devel/modules/cctbx_project/cctbx/sgtbx/__init__.py", line 97, in __init__ symbols = space_group_symbols(symbol) Boost.Python.ArgumentError: Python argument types in space_group_symbols.__init__(space_group_symbols, str) did not match C++ signature: __init__(_object*, int space_group_number) __init__(_object*, int space_group_number, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > extension='') __init__(_object*, int space_group_number, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > extension='', std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > table_id='') __init__(_object*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > symbol) __init__(_object*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > symbol, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > table_id='') ------------------------------------------------------------------------------ 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 -- 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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scitbx without numpy - still supported?
by Nicholas Devenish 24 Apr '18

24 Apr '18

Hi All, I've been tweaking the code to allow versions of boost higher than 1.63, which has involved poking at the scitbx-numpy bridge code. There seems to be some level of branching in the code for supporting building without numpy - but on the other hand numpy seems to be used exclusively for all flex.type.__init__ functions that I can find? Is building without numpy still supported? Thanks, Nick

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Misuse of libtbx/configure.py
by Robert Oeffner 09 Apr '18

09 Apr '18

Hi, I'm not sure when this has been put into configure.py as I have had taken my eyes of the ball lately regarding Windows builds. But it seems that during bootstrap build the configure.py step is now doing more than just configuring modules. On my PC the excerpt below from stdout shows an error during the configure.py step Processing: "c:\busers\oeffner\nightlybuild\x32\current\modules\dials\libtbx_refresh.py" requires mock>=2.0, has 2.0.0 requirement orderedset is not currently met, package not installed attempting install of orderedset... Collecting orderedset Using cached orderedset-2.0.1.tar.gz Installing collected packages: orderedset Running setup.py install for orderedset: started Running setup.py install for orderedset: finished with status 'error' Complete output from command C:\Busers\oeffner\NightlyBuild\x32\Current\base\bin\python\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\oeffner\\appdata\\local\\temp\\pip-build-smhifw\\orderedset\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record c:\users\oeffner\appdata\local\temp\pip-0seb8q-record\install-record.txt --single-version-externally-managed --compile: running install running build running build_py creating build creating build\lib.win32-2.7 creating build\lib.win32-2.7\orderedset copying lib\orderedset\__init__.py -> build\lib.win32-2.7\orderedset running build_ext building 'orderedset._orderedset' extension error: Microsoft Visual C++ 9.0 is required (Unable to find vcvarsall.bat). Get it from http://aka.ms/vcpython27 ---------------------------------------- Command "C:\Busers\oeffner\NightlyBuild\x32\Current\base\bin\python\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\oeffner\\appdata\\local\\temp\\pip-build-smhifw\\orderedset\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record c:\users\oeffner\appdata\local\temp\pip-0seb8q-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in c:\users\oeffner\appdata\local\temp\pip-build-smhifw\orderedset\ You are using pip version 9.0.1, however version 9.0.3 is available. You should consider upgrading via the 'python -m pip install --upgrade pip' command. install failed. please check manually My first concern with this approach is that the bootstrap process doesn't stop. It carries on and eventually builds the Phenix software suite. This may or may not be a broken build as it is not clear whether the above failure to build orderedset was a showstopper for something. Secondly, I thought that modules would not be installed anywhere else than when building base components or when downloading sources. For a small project it is a nice and sneaky solution to have certain build steps second guessing what dependencies are missing and then installing them "on the fly", if not covertly. But for a large project such as CCTBX with several teams using that as a common framework this becomes messy I would argue. A quick and dirty fix for the above error might be just to put vcvarsall.bat in the PATH environment. But that is not a solution since bootstrap.py has been fashioned to use different versions of Visual C++, some of which are not invoked through a vcvarsall.bat file. I appreciate the need to install additional component modules for python. But would it not be more tidy to install these during the base step of the bootstrap process? Is there any reason why this cannot happen? Regards, 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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simtbx - Pilatus example available
by James Holton 08 Apr '18

08 Apr '18

Took most of last week, but I finally got it to work. tst_nanoBragg_pilatus.py will create a Pilatus-like image, complete with bad pixels, window panes, thickness effects, module-to-module misalignment and 0.1 deg of phi rotation. It takes one optional argument, which is the image number in a sequence of 3600. I've processed this simulated data set with xia2 and XDS and found the anomalous signal has the right sign. This required some edits and additions to the simTBX code as well as FormatCBFMini.as_file() that I think fixed a beam center consistency bug. Now if you dxtbx.load() and FormatCBFMiniPilatus.as_file() you get the same beam center in both input and output headers. I also enhanced the header to make it look more like the ones in DIALS regression. A new "SIM.F000" value is now available for marking the "direct beam" on the image itself. I spent most of Friday and all of this morning trying to follow the check-in procedure we laid out during the DIALS workshop. Not sure how, but it suddenly started working just now. I believe I have checked in this code into the simtbx_sandbox branch of cctbx_project. Is Jenkins looking at this yet? Is anyone looking at this yet? -James Holton MAD Scientist

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print dxtbx.model.Scan()
by James Holton 05 Apr '18

05 Apr '18

The following sequence of commands: % source build/setpaths.csh % libtbx.python >>> import dxtbx >>> from dxtbx import model >>> print dxtbx.model.Scan() seems to cause Python itself to core dump. Is this expected? show_stack(1): <stdin>(1) <module> libc backtrace (25 frames, most recent call last): /home/jamesh/projects/cctbx-dev/build/../base/bin/python2.7() [0x400659] /lib64/libc.so.6(__libc_start_main+0xfd) [0x34e961ed1d] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(Py_Main+0xc74) [0x7f93eb5c2b74] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(PyRun_AnyFileExFlags+0x4c) [0x7f93eb5ad78c] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(PyRun_InteractiveLoopFlags+0x4e) [0x7f93eb5ad04e] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(PyRun_InteractiveOneFlags+0x195) [0x7f93eb5ace35] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32) [0x7f93eb58d4e2] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x88e) [0x7f93eb58d3ce] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3ef0) [0x7f93eb589de0] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(PyFile_WriteObject+0x78) [0x7f93eb503b58] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(+0x958f2) [0x7f93eb5288f2] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(PyObject_Str+0xa) [0x7f93eb52879a] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(_PyObject_Str+0x7b) [0x7f93eb5286ab] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(+0xb5a1e) [0x7f93eb548a1e] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x43) [0x7f93eb584fd3] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7f93eb4dc093] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(+0x5b6cf) [0x7f93eb4ee6cf] /home/jamesh/projects/cctbx-dev/base/bin/../lib/libpython2.7.so.1.0(PyObject_Call+0x53) [0x7f93eb4dc093] /home/jamesh/projects/cctbx-dev/build/lib/libboost_python.so(+0x2d088) [0x7f93e3f23088] /home/jamesh/projects/cctbx-dev/build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x43) [0x7f93e3f34013] /home/jamesh/projects/cctbx-dev/build/lib/libboost_python.so(+0x2fe08) [0x7f93e3f25e08] /home/jamesh/projects/cctbx-dev/build/lib/libboost_python.so(boost::python::objects::function::call(_object*, _object*) const+0xef) [0x7f93e3f251ff] /home/jamesh/projects/cctbx-dev/build/lib/dxtbx_model_ext.so(boost::python::objects::caller_py_function_impl<boost::python::detail::caller<std::string (*)(dxtbx::model::Scan const&), boost::python::default_call_policies, boost::mpl::vector2<std::string, dxtbx::model::Scan const&> > >::operator()(_object*, _object*)+0x83) [0x7f93db88a7a3] /home/jamesh/projects/cctbx-dev/build/lib/dxtbx_model_ext.so(dxtbx::model::boost_python::scan_to_string(dxtbx::model::Scan const&)+0x319) [0x7f93db871929] /lib64/libc.so.6() [0x34e9632510] Segmentation fault (Python and libc call stacks above)

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Exceptions squashed by easy_mp (revenge of)
by Graeme.Winter＠Diamond.ac.uk 03 Apr '18

03 Apr '18

Folks, Following up on user reports again of errors within easy_mp - all that gets logged is “something went wrong” i.e. Using multiprocessing with 10 parallel job(s) Traceback (most recent call last): File "/home/user/bin/dials-installer/build/../modules/dials/command_line/integrate.py", line 613, in <module> halraiser(e) File "/home/user/bin/dials-installer/build/../modules/dials/command_line/integrate.py", line 611, in <module> script.run() File "/home/user/bin/dials-installer/build/../modules/dials/command_line/integrate.py", line 341, in run reflections = integrator.integrate() File "/home/user/bin/dials-installer/modules/dials/algorithms/integration/integrator.py", line 1214, in integrate self.reflections, _, time_info = processor.process() File "/home/user/bin/dials-installer/modules/dials/algorithms/integration/processor.py", line 271, in process preserve_exception_message = True) File "/home/user/bin/dials-installer/modules/dials/util/mp.py", line 171, in multi_node_parallel_map preserve_exception_message = preserve_exception_message) File "/home/user/bin/dials-installer/modules/dials/util/mp.py", line 53, in parallel_map preserve_exception_message = preserve_exception_message) File "/home/user/bin/dials-installer/modules/cctbx_project/libtbx/easy_mp.py", line 627, in parallel_map result = res() File "/home/user/bin/dials-installer/modules/cctbx_project/libtbx/scheduling/result.py", line 119, in __call__ self.traceback( exception = self.exception() ) File "/home/user/bin/dials-installer/modules/cctbx_project/libtbx/scheduling/stacktrace.py", line 115, in __call__ self.raise_handler( exception = exception ) File "/home/user/bin/dials-installer/modules/cctbx_project/libtbx/scheduling/mainthread.py", line 100, in poll value = target( *args, **kwargs ) File "/home/user/bin/dials-installer/modules/dials/util/mp.py", line 91, in __call__ preserve_exception_message = self.preserve_exception_message) File "/home/user/bin/dials-installer/modules/cctbx_project/libtbx/easy_mp.py", line 627, in parallel_map result = res() File "/home/user/bin/dials-installer/modules/cctbx_project/libtbx/scheduling/result.py", line 119, in __call__ self.traceback( exception = self.exception() ) File "/home/user/bin/dials-installer/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: exit code = -9 I forget why it was decided that keeping the proper stack trace was a bad thing, but could this be revisited? It would greatly help to see it in the output of the program (if as is the case here I do not have the user data) My email-fu is not strong enough to dig out the previous conversation 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

3 6

Re: [cctbxbb] [git/cctbx] master: New command: libtbx.install (914c74bf1)
by Pavel Afonine 13 Mar '18

13 Mar '18

Just out of curiosity: what's your definition of "real world"? Pavel On 3/13/18 03:49, CCTBX commit wrote: > Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx > On branch : master > > ------------------------------------------------------------------------ > > > commit 914c74bf195b5e5d4fa2c4145da3e5f89c7e5872 > Author: Markus Gerstel <markus.gerstel(a)diamond.ac.uk> > Date: Tue Mar 13 10:43:22 2018 +0000 > > New command: libtbx.install > > This downloads and configures from a select list of cctbx/libtbxish > modules in a similar manner to pip in the real world. This will not > update or install any libraries in the base build, but assuming > those libraries are present libtbx.install should work. > > > ------------------------------------------------------------------------ > > > 914c74bf195b5e5d4fa2c4145da3e5f89c7e5872 > libtbx/command_line/install.py | 118 > +++++++++++++++++++++++++++++++++++++++++ > 1 file changed, 118 insertions(+) > > diff --git a/libtbx/command_line/install.py > b/libtbx/command_line/install.py > new file mode 100644 > index 000000000..47ad94eb5 > --- /dev/null > +++ b/libtbx/command_line/install.py > @@ -0,0 +1,118 @@ > +from __future__ import absolute_import, division, print_function > + > +import collections > +import os > +import sys > +from optparse import SUPPRESS_HELP, OptionParser > + > +import procrunner > + > +import libtbx.load_env > +from libtbx.auto_build.bootstrap import Toolbox > + > +# Basically 'pip' for selected libtbx/cctbx modules. > + > + > +def is_source_repository(path): > + return (path / '.git').isdir() or (path / '.svn').isdir() > + > +def run(args): > + parser = OptionParser(usage="libtbx.install [package]", > + description="Installs an additional cctbx > package") > + parser.add_option("-?", action="help", help=SUPPRESS_HELP) > + options, args = parser.parse_args(args) > + > + modules_directory = list(filter(lambda dir: not > is_source_repository(dir), libtbx.env.repository_paths)) > + if not modules_directory: > + sys.exit("No repository path candidate found. Can't install > modules without an installation root.") > + if len(modules_directory) > 1: > + print("More than one repository path candidate found.") > + installation_root = modules_directory[0] > + print("Using %s as installation root" % abs(installation_root)) > + > + packages_to_configure = set() > + > + errors = False > + for package in args: > + if (installation_root / package).isdir(): > + print("Skipping package %s: Directory already exists in > installation root" % package) > + errors = True > + continue > + if package not in warehouse: > + print("Skipping package %s: Never heard of this before" % package) > + errors = True > + continue > + > + downloaded = False > + for mech, call in mechanisms.items(): > + if mech in warehouse[package]: > + print("Attempting to obtain %s using %s..." % (package, > mech), end='') > + sys.stdout.flush() > + if call(abs(installation_root / package), > warehouse[package][mech]): > + assert (installation_root / package).isdir(), "Installation > failed" > + downloaded = True > + print("success") > + break > + else: > + assert not (installation_root / package).isdir(), "Install > mechanism %s did not fail cleanly" % mech > + print("failed") > + if not downloaded: > + print("Skipping package %s: Could not install" % package) > + errors = True > + continue > + > + packages_to_configure.add(package) > + > + if packages_to_configure: > + packages_to_configure = sorted(packages_to_configure) > + print("Configuring packages %s" % ", ".join(packages_to_configure)) > + os.chdir(abs(libtbx.env.build_path)) > + result = procrunner.run_process(['libtbx.configure'] + > packages_to_configure) > + if result['exitcode']: errors = True > + > + if errors: > + sys.exit(1) > + > +def install_git(location, source): > + try: > + result = procrunner.run_process(['git', 'clone', '--recursive', > source, location], print_stdout=False, print_stderr=False) > + if result['exitcode']: > + return False > + Toolbox.set_git_repository_config_to_rebase(os.path.join(location, > '.git', 'config')) > + return True > + except OSError: > + return False # git may not be installed > + > +def install_zip(location, source): > + os.mkdir(location) > + tempfile = os.path.join(location, '.tmp.zip') > + etagfile = os.path.join(location, '..tmp.zip.etag') > + def cleanup(): > + try: os.remove(tempfile) > + except OSError: pass > + try: os.remove(etagfile) > + except OSError: pass > + if Toolbox.download_to_file(source['url'], tempfile) <= 0: > + cleanup() > + os.rmdir(location) > + return False > + Toolbox.unzip(tempfile, location, trim_directory=source.get('trim', 0)) > + cleanup() > + return True > + > +mechanisms = collections.OrderedDict(( > + ('git-auth', install_git), > + ('git-anon', install_git), > + ('http-zip', install_zip), > +)) > + > +warehouse = { > + 'i19': { > + 'git-auth': '[email protected]:/xia2/i19', > + 'git-anon': 'https://github.com/xia2/i19.git', > + 'http-zip': { 'url': > 'https://github.com/xia2/i19/archive/master.zip', 'trim': 1 }, > + }, > +} > + > +if __name__ == '__main__': > + run(sys.argv[1:])

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Re: [cctbxbb] [git/cctbx] master: rename test files, remove them from run_tests (23a4a6fe4)
by Pavel Afonine 05 Mar '18

05 Mar '18

Just to make sure: you are converting to use pytest this particular codes (fable), correct? Pavel P.S.: I'm allergic to pytest. On 3/3/18 07:46, CCTBX commit wrote: > This in preparation for pytestification.

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Revisiting cctbx/iotbx/dxtbx dependencies
by Aaron Brewster 20 Feb '18

20 Feb '18

Hey folks, especially Rob and Luc. So after a quick change to iotbx/libtbx_config, it turns out there's a way to get a super minimum version of cctbx, without configuring dxtbx, and it takes advantage of existing mechanisms: - python bootstrap.py --builder=cctbx hot update - python modules/cctbx_project/libtbx/auto_build/install_base_packages.py openssl python python_compatibility certifi numpy cython png libsvm pytest pythonextra jinja2 junitxml biopython docutils sphinx pyopengl misc freetype matplotlib pillow gettext glib expat fontconfig render pixman tiff cairo gtk fonts wxpython - mkdir build; cd build - ../base/bin/python ../modules/cctbx_project/libtbx/configure.py cctbx iotbx - make Now, some details as to why this works. First, the cctbx builder in boostrap.py doesn't download cbflib so cbflib is never configured. Next, the base step of bootstrap.py is simply a call to install_base_packages.py with a list of required packages. You can just run it standalone and get the packages you need. Here, I ran "python bootstrap.py --builder=cctbx base", killed it after I saw the list of packages it was going to install, then ran install_base_packages manually after removing hdf5 and lz4 (which depends on hdf5) from the list. One could imagine removing other packages depending on your use case. With that, I could run configure.py directly. I can't use cctbx by itself as the cctbx/maptbx/SConscript file has a dependency on iotbx, but configuring cctbx and iotbx together seems to work. The key trick was to make iotbx only depend on dxtbx if dxtbx is explicitly configured. I used a keyword in libtbx_configure added by Luc a bit ago: optional_modules_only_if_explicit_request. I committed that change just now. Outstanding questions: 1. Is there interest in making this a builder? It would be straightforward to add a builder named cctbx_minimal which would just do the above steps 2. Is there further need for making cbflib and hdf5 optional in dxtbx? I purport there is not as the above procedure seems to satisfy the use case, but I can be persuaded otherwise. Thanks, -Aaron

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Re: [cctbxbb] [git/cctbx] master: use larger tolerance (0b81ca799)
by Graeme.Winter＠diamond.ac.uk 12 Feb '18

12 Feb '18

Pavel, This commit did not fix test on OS X High Sierra libtbx.python "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/maptbx/tst_interpolation.py" [FAIL] 1.4s Time: 1.39 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/maptbx/tst_interpolation.py", line 128, in <module> exercise(f = f, gx = gx, gy = gy, gz = gz, function_type=function_type) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/maptbx/tst_interpolation.py", line 99, in exercise assert approx_equal(it, 0.0, 1.e-4) AssertionError cheers Graeme On 11 Feb 2018, at 00:14, CCTBX commit <diamondlightsource.jenkins(a)GMAIL.COM<mailto:[email protected]>> wrote: Repository : ssh://g18-sc-serv-03.diamond.ac.uk/cctbx On branch : master ________________________________ commit 0b81ca7992f9cf7730eb007aff6e8c30bd2ba71b Author: Pavel <pafonine(a)lbl.gov<mailto:[email protected]>> Date: Sat Feb 10 16:14:51 2018 -0800 use larger tolerance ________________________________ 0b81ca7992f9cf7730eb007aff6e8c30bd2ba71b cctbx/maptbx/tst_interpolation.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cctbx/maptbx/tst_interpolation.py b/cctbx/maptbx/tst_interpolation.py index 918ba68fd..90dec8a46 100644 --- a/cctbx/maptbx/tst_interpolation.py +++ b/cctbx/maptbx/tst_interpolation.py @@ -96,15 +96,15 @@ def exercise(f,gx,gy,gz,function_type, eps = 1.e-6): if(function_type=="L"): cntr+=1 for it in [tl,gxl,gyl,gzl, tq,gxq,gyq,gzq, tt,gxt,gyt,gzt]: - assert approx_equal(it, 0.0) + assert approx_equal(it, 0.0, 1.e-4) if(function_type=="Q"): cntr+=1 for it in [tq,gxq,gyq,gzq, tt,gxt,gyt,gzt]: - assert approx_equal(it, 0.0) + assert approx_equal(it, 0.0, 1.e-4) if(function_type=="C"): cntr+=1 for it in [tt,gxt,gyt,gzt]: - assert approx_equal(it, 0.0) + assert approx_equal(it, 0.0, 1.e-4) if(abs(tl)>eps and abs(tq)>eps): assert tl >=tq if(function_type=="F"): cntr+=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] [Dials-support] indexing success rates
by Aaron Brewster 05 Feb '18

05 Feb '18

Right, typically if I don't know the cell, I'll index a bunch of images with no target, then use cluster.unit_cell on the results to get a consensus cell, then re-index with that cell. For dials.stills_process, the default of fft1d works pretty well generally, but to get the best results, indexing.method_list=fft1d,fft3d might be better. There, if the first method fails the second is tried. real_space_grid_search can also be used. Getting a specific image in a composite file (such as hdf5) isn't a use case I've hit often, so I don't have an easy solution there. It's possible an image range parameter to dials.import would be useful? -Aaron On Sat, Feb 3, 2018 at 1:02 AM, Graeme Winter <graeme.winter(a)gmail.com> wrote: > Hi Aaron > > (and DIALS) > > For stills / single images - should dials.index switch by magic to default > fft1d? > > Of is that the responsibility of e.g. xia2 / cctbx.xfel to worry about? > > It has to be said, more often than not, particularly for screening, we do > not know cell / symmetry a priori (at diamond anyways) > > A related question > > If I have a data block / strong pickle from 1000 stills, how can I index > e.g. image 672? Do I have to split this into 1000 separate things? > > @JH - thanks for this - I think some rigorous testing will be useful here. > > Cheers Graeme > > On 3 Feb 2018, at 08:37, Aaron Brewster <asbrewster(a)lbl.gov> wrote: > > Hi James, thanks. I looked at random image 15 and after trying a bunch of > stuff it indexes fine if I use indexing.method=fft3d. The default for > stills processing is fft1d, so I find this super interesting. > > For what it's worth, I pretty much never process stills without a target > cell. I generated ~30 random images using your script and indexed them, > then I got the unit cells with "dials.show *refined*.json | grep cell". > They were all about the same. So I re-indexed random image 15 using fft1d > but I also specified known_symmetry.cell=50,60,70,90,90,90 and it indexed > fine. > > So, either indexing.method=fft3d or known_symmetry.cell=50,60,70,90,90,90 > is sufficient to index random image 15. Certainly for experimental data I > would recommend using known_symmetry as the results are always better. > However, I'd like to look deeper at fft1d vs fft3d at some point. > > Cc'ing dials-support. > > Thanks! > -Aaron > > > > On Fri, Feb 2, 2018 at 1:35 PM, James Holton <jmholton(a)lbl.gov> wrote: > >> While testing the new simTBX diffraction image simulator Aaron and I >> found that some rather beautiful-looking images still won't index. >> Subsequently, I followed up with mosflm, which does succeed in these cases, >> even without prior knowledge of the cell or space group. >> >> I have now run this 1000 times, varying only the crystal orientation, and >> found 171 cases of dials.stills_process failing to index the simulated >> image whereas mosflm had no trouble, and 5 cases where mosflm failed and >> dials.stills_process succeeded. There were no overlapping cases where both >> programs failed. >> >> I have tarballed up the relevant files here: >> http://bl831.als.lbl.gov/~jamesh/bugreports/dials_index_020218.tgz >> >> The tarball contains a "runme.com" shell script for reproducing these >> results, and also the tst_nanoBragg_forindex.py jiffy for making a test >> image given a provided random-number seed. For example: >> >> libtbx.python ./tst_nanoBragg_forindex.py random 15 >> >> will create a file called noiseimage_001.cbf that dials.stills_process >> cannot index (at least in my hands). For those of you who don't have >> mosflm installed, the tarball incluses a copy, and the "autoindex.com" >> script should run on any linux system. >> >> Any ideas as to why there is this discrepancy? Feels like an opportunity >> for a non-trivial improvement. >> >> Something to ponder over the weekend, I suppose. Note that I recently >> checked in a few bug fixes to simTBX, but this analysis is unaffected by >> them, so you shouldn't have to update your build to reproduce this. >> >> Cheers, >> >> -James Holton >> MAD Scientist >> >> >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______ > _________________________________________ > DIALS-support mailing list > DIALS-support(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/dials-support > > >

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indexing success rates
by James Holton 03 Feb '18

03 Feb '18

While testing the new simTBX diffraction image simulator Aaron and I found that some rather beautiful-looking images still won't index. Subsequently, I followed up with mosflm, which does succeed in these cases, even without prior knowledge of the cell or space group. I have now run this 1000 times, varying only the crystal orientation, and found 171 cases of dials.stills_process failing to index the simulated image whereas mosflm had no trouble, and 5 cases where mosflm failed and dials.stills_process succeeded. There were no overlapping cases where both programs failed. I have tarballed up the relevant files here: http://bl831.als.lbl.gov/~jamesh/bugreports/dials_index_020218.tgz The tarball contains a "runme.com" shell script for reproducing these results, and also the tst_nanoBragg_forindex.py jiffy for making a test image given a provided random-number seed. For example: libtbx.python ./tst_nanoBragg_forindex.py random 15 will create a file called noiseimage_001.cbf that dials.stills_process cannot index (at least in my hands). For those of you who don't have mosflm installed, the tarball incluses a copy, and the "autoindex.com" script should run on any linux system. Any ideas as to why there is this discrepancy? Feels like an opportunity for a non-trivial improvement. Something to ponder over the weekend, I suppose. Note that I recently checked in a few bug fixes to simTBX, but this analysis is unaffected by them, so you shouldn't have to update your build to reproduce this. Cheers, -James Holton MAD Scientist

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Fwd: [git/cctbx] master: Allow compiling standalone statically linked executable of Phaser on Windows and MinGW platforms requires: static linking of some boost libraries, additional preprocessor defines for Windows build, additional library specified ...
by Graeme.Winter＠diamond.ac.uk 02 Feb '18

02 Feb '18

Tried sending before got rejected ... Begin forwarded message: From: Graeme Winter <graeme.winter(a)gmail.com<mailto:[email protected]>> Date: 1 February 2018 at 18:51:58 GMT To: cctbxbb(a)PHENIX-ONLINE.ORG<mailto:[email protected]> Cc: CCTBX-COMMIT(a)JISCMAIL.AC.UK<mailto:[email protected]> Subject: Re: [git/cctbx] master: Allow compiling standalone statically linked executable of Phaser on Windows and MinGW platforms requires: static linking of some boost libraries, additional preprocessor defines for Windows build, additional library specified for rstbx build (29fc06f71) Just after this commit all our builds died at diamond Is build bot happy? Curious if local issue Cheers Graeme On 1 Feb 2018, at 18:07, CCTBX commit <diamondlightsource.jenkins(a)GMAIL.COM<mailto:[email protected]>> wrote: Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx On branch : master ________________________________ commit 29fc06f714e1059cb9f4eaac35cc2024178237dc Author: Robert Oeffner <rdo20(a)cam.ac.uk<mailto:[email protected]>> Date: Thu Feb 1 18:07:49 2018 +0000 Allow compiling standalone statically linked executable of Phaser on Windows and MinGW platforms requires: static linking of some boost libraries, additional preprocessor defines for Windows build, additional library specified for rstbx build ________________________________ 29fc06f714e1059cb9f4eaac35cc2024178237dc boost_adaptbx/SConscript | 13 +++++++------ libtbx/SConscript | 4 +++- rstbx/SConscript | 2 +- 3 files changed, 11 insertions(+), 8 deletions(-) diff --git a/boost_adaptbx/SConscript b/boost_adaptbx/SConscript index 8696c1510..b8b58ce2d 100644 --- a/boost_adaptbx/SConscript +++ b/boost_adaptbx/SConscript @@ -32,8 +32,9 @@ print("BOOST_VERSION: %i" %env_etc.boost_version) # any issue. if (libtbx.env.build_options.enable_boost_threads and env_etc.boost_thread_support): - boost_thread_uses_winthreads = (sys.platform == 'win32' and - not env_etc.compiler.endswith('mingw')) + boost_thread_uses_winthreads = (sys.platform == 'win32') + # MinGW compiler 5.3.0 appears to compile boost_threads + # with the same condition as win32. # This environment is to be used latter to build Boost libraries # So we need a clean one without extra library linking. env_boost_shlibs_base = env_base.Copy() @@ -264,7 +265,7 @@ e.g. with "yum install python-dev" or "apt-get install python-dev". libs.append('rt') if boost_thread_uses_winthreads: libs.append('boost_chrono') - env_boost_threads.SharedLibrary( + env_boost_threads.StaticLibrary( target='#lib/boost_thread', source=boost_thread_src, LIBS=libs) @@ -280,7 +281,7 @@ e.g. with "yum install python-dev" or "apt-get install python-dev". # For Windows (c.f. point 2 above) env_boost_system.Append( CPPDEFINES={'BOOST_SYSTEM_DYN_LINK':1}) - env_boost_system.SharedLibrary( + env_boost_system.StaticLibrary( target='#lib/boost_system', source=boost_system_src) @@ -294,7 +295,7 @@ e.g. with "yum install python-dev" or "apt-get install python-dev". os.path.join(env_etc.boost_dist, 'libs', 'chrono', 'src', '*.cpp'))] # For Windows (c.f. point 2 above) env_boost_chrono.Append(CPPDEFINES={'BOOST_CHRONO_DYN_LINK':1}) - env_boost_chrono.SharedLibrary( + env_boost_chrono.StaticLibrary( target='#lib/boost_chrono', source=boost_chrono_src, LIBS=['boost_system']) @@ -308,7 +309,7 @@ e.g. with "yum install python-dev" or "apt-get install python-dev". env_etc.include_registry.append( env=env_boost_threads_test, paths=[env_etc.boost_adaptbx_include]) - env_boost_threads_test.SharedLibrary( + env_boost_threads_test.StaticLibrary( target="#lib/boost_adaptbx_boost_thread_test_ext", source="tests/boost_thread_test.cpp") diff --git a/libtbx/SConscript b/libtbx/SConscript index b4fcc5df9..b956956f2 100644 --- a/libtbx/SConscript +++ b/libtbx/SConscript @@ -364,7 +364,9 @@ For newer versions, please adjust this SConscript. "/D_SECURE_SCL=0", "/D_CRT_SECURE_NO_DEPRECATE", "/DNOMINMAX", - #"/DWIN32", + "/DWIN32", + "/DDLL_EXPORTS", + "/D_WIN32_WINNT=_WIN32_WINNT_WIN7", "/bigobj", # for heavy use of template libraries "/wd4996", # warning C4996: ... was declared deprecated "/wd4068", # warning C4068: unknown pragma diff --git a/rstbx/SConscript b/rstbx/SConscript index 422a9864c..76ba4d1c5 100644 --- a/rstbx/SConscript +++ b/rstbx/SConscript @@ -40,7 +40,7 @@ if (not env_etc.no_boost_python): Import("env_boost_python_ext") env_rstbx_boost_python_ext = env_boost_python_ext.Clone() env_rstbx_boost_python_ext.Prepend( - LIBS=["rstbx", "cctbx", "scitbx_boost_python"]) + LIBS=["rstbx", "ann", "cctbx", "scitbx_boost_python"]) env_rstbx_boost_python_ext.SharedLibrary( target="#lib/rstbx_ext", source="ext.cpp") env_rstbx_boost_python_ext.SharedLibrary( -- 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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Tidy up CCTBX
by Dr. Robert Oeffner 27 Jan '18

27 Jan '18

Hi all, I'm wondering if we could make efforts to refactor code modules in the cctbx_project so as making it have the minimum number of dependencies. This would be helpful to other users of the CCTBX that wishes to develop code on top of it. In the longer term it would also make it easier for us to deploy CCTBX as a Python wheel installer and by implication, spread the gospel of the wonders of the CCTBX. What is currently complicating this is the inclusion of the dxtbx module within the cctbx_project. It is being used by Dials. So my question is if it would be possible to move this project into the Dials code? If the dxtbx was just another small module it wouldn't be much of a problem. But the dxtbx depends on the cbflib and HDF5 components. If you want to build CCTBX from sources that's cumbersome. Why? Because CCTBX as deployed from CCI on http://cci.lbl.gov/cctbx_build/ is only built for a few select platforms. Building CCTBX on a different platform from those with bootstrap compels us to also build cbflib and HDF5 from scratch. Although this is not impossible it does increase the entry barrier for other potential users of the CCTBX who wish to incorporate the CCTBX in their programs: If all a user wants is to calculate allowed origins and symmetry sites for a given space group then an alternative to CCTBX might be preferable rather than having to massively expand their project with the seemingly unrelated HDF5 component. In other words, as it stands now the CCTBX is not straightforward for others to adopt. What do other people think? Regards, 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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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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