- cctbxbb - phenix-online.org

Build error, bootstrap.py
by Allan Lyckegaard 21 Mar '17

21 Mar '17

Hi all, I am trying to install cctbx on my Mac (Sierra) using bootstrap.py with my Anaconda python. When executing 'python bootstrap.py --with-python=/Users/myuser/miniconda2/envs/python2/bin/python --builder=cctbx’ I get the following error: /usr/bin/c++ -o dxtbx/format/boost_python/nexus_ext.o -c -DBOOST_HAS_INT128=1 -DBOOST_ALL_NO_LIB -DBOOST_PYTHON_MAX_BASES=2 -Wmost -Wno-unknown-pragmas -Wno-logical-op-parentheses -Wno-unused-local-typedefs -I/Users/myuser/Development/cctbx/modules/boost -fPIC -fno-strict-aliasing -Wno-c++0x-extensions -Wno-array-bounds -DNDEBUG -O3 -ffast-math -I/Users/myuser/miniconda2/envs/python2/include -I/Users/myuser/Development/cctbx/base/include -I/Users/myuser/Development/cctbx/build/include -I/Users/myuser/Development/cctbx/modules/cctbx_project -I/Users/myuser/miniconda2/envs/python2/include/python2.7 /Users/myuser/Development/cctbx/modules/cctbx_project/dxtbx/format/boost_python/nexus_ext.cc warning: unknown warning option '-Wno-unused-local-typedefs' [-Wunknown-warning-option] 1 warning generated. /usr/bin/c++ -o lib/dxtbx_format_nexus_ext.so -w -bundle -undefined dynamic_lookup dxtbx/format/boost_python/nexus_ext.o -L/Users/myuser/Development/cctbx/base/lib -lm -lhdf5 ld: library not found for -lhdf5 clang: error: linker command failed with exit code 1 (use -v to see invocation) scons: *** [lib/dxtbx_format_nexus_ext.so] Error 1 scons: building terminated because of errors. usr+sys time: 8.69 seconds wall clock time: 21.70 seconds Process failed with return code 2 Any suggestions to how I solve this? I have not seen anywhere in the documentation that an hdf5 installation is a prerequisite. Cheers, /Allan

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hkl and F
by James Holton 05 Mar '17

05 Mar '17

Hello all, Is there any standard way to get the "C++ signature" of a python object? I'm trying to get my _ext.cpp working, and its' maddening trying to figure out how to declare objects that need to be exposed via boost. -James

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Quick Boost python question
by Nicholas Sauter 22 Feb '17

22 Feb '17

<http://phenix-online.org/mailman/listinfo/cctbxbb>Quick question from James Holton and myself. We want to use a boost python *.add_property() to add a make_getter and make_setter to our wrapper, so we can expose a class variable to the Python layer. However, we want to execute a change of measurement units, i.e., the Python value will always be given in millimetres, and the C++ value always in metres. How can this be done within a simple add_property() paradigm? Nick

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Berkeley Server Downtime (1/13 - 1/14)
by Billy Poon 16 Jan '17

16 Jan '17

Dear all, On Friday, January 13, 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 the next day (1/14) by 6:00 pm Pacific 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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Re: [cctbxbb] iotbx.merging_statistics test failing: data file removed from phenix_regression
by richard.gildea＠diamond.ac.uk 07 Jan '17

07 Jan '17

Hi Tom, Thanks for the quick response! To run this specific test: $ libtbx.python $(libtbx.find_in_repositories iotbx/regression/tst_merging_statistics.py) The test also uses the file phenix_regression/wizards/unmerged.mtz which I guess was also removed with the same commit? $ grep phenix_regression $(libtbx.find_in_repositories iotbx/regression/tst_merging_statistics.py) if (not libtbx.env.has_module("phenix_regression")) : print "phenix_regression not configured, skipping." relative_path="phenix_regression/wizards/p9_se_w2.sca", relative_path="phenix_regression/harvesting/unmerged.sca", relative_path="phenix_regression/harvesting/refine.mtz", relative_path="phenix_regression/reflection_files/i_anomalous.mtz", relative_path="phenix_regression/wizards/unmerged.mtz", relative_path="phenix_regression/reflection_files/AUTOMATIC_DEFAULT_scaled_unmerged_WAVE1.mtz", $ libtbx.find_in_repositories phenix_regression/wizards/unmerged.mtz Sorry: libtbx.find_in_repositories: cannot locate "phenix_regression/wizards/unmerged.mtz" The other files still seem to be present in phenix_regression. Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________________ From: Terwilliger, Thomas Charles [terwilliger(a)lanl.gov] Sent: 06 January 2017 15:57 To: Gildea, Richard (DLSLtd,RAL,LSCI); cctbxbb(a)phenix-online.org Cc: Terwilliger, Thomas Charles Subject: Re: iotbx.merging_statistics test failing: data file removed from phenix_regression Hi Richard, Thanks for pointing that out! I'll fix it. Yes, I deleted that file when I moved all the small files in phenix_regression/wizards/ into sub-directories. I made the mistake of assuming that only wizards/ regression tests used files in the wizards/ directory (I should have run all the cctbx regression tests to make sure). All the best, Tom T ________________________________________ From: richard.gildea(a)diamond.ac.uk <richard.gildea(a)diamond.ac.uk> Sent: Friday, January 6, 2017 8:51 AM To: cctbxbb(a)phenix-online.org; Terwilliger, Thomas Charles Subject: iotbx.merging_statistics test failing: data file removed from phenix_regression Hi all, The test for iotbx.merging_statistics has recently started failing as a result of one of the files it uses for testing being deleted, phenix_regression/wizards/p9_se_w2.sca: https://github.com/cctbx/cctbx_project/blob/master/iotbx/regression/tst_mer… Would it be possible to restore this file to phenix_regression so that the test will pass? $ svn log -r r3879 -v ------------------------------------------------------------------------ r3879 | terwill | 2016-12-29 02:48:15 +0000 (Thu, 29 Dec 2016) | 1 line Changed paths: D /trunk/wizards/000README D /trunk/wizards/4c5q.pdb D /trunk/wizards/ATP.pdb D /trunk/wizards/MM-all.tgz D /trunk/wizards/NAD.pdb D /trunk/wizards/PARAMS_1.eff D /trunk/wizards/a2u-data.mtz D /trunk/wizards/a2u-sigmaa.mtz D /trunk/wizards/a2u.sca D /trunk/wizards/a2u_short.pdb D /trunk/wizards/anb.pdb D /trunk/wizards/autosol_unmerged_False.std D /trunk/wizards/autosol_unmerged_True.std D /trunk/wizards/autosol_unmerged_p9.std D /trunk/wizards/bad_model.pdb D /trunk/wizards/check.xyz D /trunk/wizards/check_multiple_input_files_042908.tgz D /trunk/wizards/check_multiple_input_files_062608.tgz D /trunk/wizards/check_multiple_input_files_070508.tgz D /trunk/wizards/check_multiple_input_files_2011-03-03.tgz D /trunk/wizards/check_multiple_input_files_2011-06-29.tgz D /trunk/wizards/check_multiple_input_files_2011-11-04.tgz D /trunk/wizards/clean.com D /trunk/wizards/cocn.cif D /trunk/wizards/coords.pdb D /trunk/wizards/coords1.ali D /trunk/wizards/coords1.mtz D /trunk/wizards/coords1.pdb D /trunk/wizards/coords_A001.pdb D /trunk/wizards/coords_rna.pdb D /trunk/wizards/coords_rna_gap.pdb D /trunk/wizards/data_for_commands_in_doc.tgz D /trunk/wizards/find_all_ligands.eff D /trunk/wizards/find_all_ligands.standard D /trunk/wizards/find_ncs_ncs.standard D /trunk/wizards/find_ncs_resolve.standard D /trunk/wizards/fobs.mtz D /trunk/wizards/fobs_std.mtz D /trunk/wizards/fobs_std_edit.mtz D /trunk/wizards/gene-5.pdb D /trunk/wizards/generate.com D /trunk/wizards/get_cc_mtz_mtz.standard D /trunk/wizards/get_cc_mtz_pdb.standard D /trunk/wizards/ha.pdb D /trunk/wizards/ha_lig.pdb D /trunk/wizards/ha_perfect.pdb D /trunk/wizards/ha_perfect_2.pdb D /trunk/wizards/hipip.pdb D /trunk/wizards/hipip_2.sca D /trunk/wizards/hipip_shortseq.dat D /trunk/wizards/ignore.dat D /trunk/wizards/inf.sca D /trunk/wizards/ki.sca D /trunk/wizards/ligand.pdb D /trunk/wizards/mad.eff D /trunk/wizards/mad.mtz D /trunk/wizards/map_coeffs.mtz D /trunk/wizards/map_coeffs_1.mtz D /trunk/wizards/map_coeffs_2.mtz D /trunk/wizards/map_to_object.standard D /trunk/wizards/maps_only.standard D /trunk/wizards/mir.eff D /trunk/wizards/mlt.mtz D /trunk/wizards/mlt_gap.pdb D /trunk/wizards/mlt_regression.tgz D /trunk/wizards/mol1.pdb D /trunk/wizards/mol2.pdb D /trunk/wizards/mr_rosetta.eff D /trunk/wizards/mult_regr.tgz D /trunk/wizards/multi.pdb D /trunk/wizards/multi.pdb.mtz D /trunk/wizards/my_autobuild.eff D /trunk/wizards/my_automr.eff D /trunk/wizards/my_autosol.eff D /trunk/wizards/my_ligand.pdb D /trunk/wizards/my_ligandfit.eff D /trunk/wizards/my_target.pdb D /trunk/wizards/native.sca D /trunk/wizards/noligand.mtz D /trunk/wizards/omit_lig_results.list D /trunk/wizards/omit_regr.tgz D /trunk/wizards/p.pdb D /trunk/wizards/p21.sym D /trunk/wizards/p9-seq.dat D /trunk/wizards/p9-sites.xyz D /trunk/wizards/p9_ha.pdb D /trunk/wizards/p9_se_w2.sca D /trunk/wizards/part_mlt.pdb D /trunk/wizards/partial.pdb D /trunk/wizards/partial_refine_001.pdb D /trunk/wizards/partial_refine_001_map_coeffs.mtz D /trunk/wizards/peak.sca D /trunk/wizards/perfect.mtz D /trunk/wizards/perfect_rna.mtz D /trunk/wizards/phaser_1_offset.mtz D /trunk/wizards/pt.sca D /trunk/wizards/quick_clashlist.standard D /trunk/wizards/random.pdb D /trunk/wizards/random_0.7_mlt.mtz D /trunk/wizards/resolve_1_offset.mtz D /trunk/wizards/rna.seq D /trunk/wizards/run_multi.eff D /trunk/wizards/run_multi_new.eff D /trunk/wizards/seq.dat D /trunk/wizards/seq1.dat D /trunk/wizards/seq2.dat D /trunk/wizards/seq_mlt.dat D /trunk/wizards/short_seq.standard D /trunk/wizards/side.pdb D /trunk/wizards/sir_sad.eff D /trunk/wizards/sites_mlt.pdb D /trunk/wizards/smiles.dat D /trunk/wizards/solve.setup D /trunk/wizards/start.pdb D /trunk/wizards/starting_map.mtz D /trunk/wizards/test3.gz D /trunk/wizards/test9.gz D /trunk/wizards/test_ampl_int_autobuild.tgz D /trunk/wizards/test_labels_1.std D /trunk/wizards/test_labels_2.std D /trunk/wizards/test_labels_3.std D /trunk/wizards/test_missing.std D /trunk/wizards/test_multi.tgz D /trunk/wizards/test_ncs.standard D /trunk/wizards/test_ncs_find_ncs.standard D /trunk/wizards/test_ncs_lc.pdb D /trunk/wizards/test_resno.std D /trunk/wizards/test_resno.tgz D /trunk/wizards/unmerged.mtz D /trunk/wizards/w1.sca D /trunk/wizards/w1_rna.sca D /trunk/wizards/w2.sca remove unneeded files ------------------------------------------------------------------------ Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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iotbx.merging_statistics test failing: data file removed from phenix_regression
by richard.gildea＠diamond.ac.uk 07 Jan '17

07 Jan '17

Hi all, The test for iotbx.merging_statistics has recently started failing as a result of one of the files it uses for testing being deleted, phenix_regression/wizards/p9_se_w2.sca: https://github.com/cctbx/cctbx_project/blob/master/iotbx/regression/tst_mer… Would it be possible to restore this file to phenix_regression so that the test will pass? $ svn log -r r3879 -v ------------------------------------------------------------------------ r3879 | terwill | 2016-12-29 02:48:15 +0000 (Thu, 29 Dec 2016) | 1 line Changed paths: D /trunk/wizards/000README D /trunk/wizards/4c5q.pdb D /trunk/wizards/ATP.pdb D /trunk/wizards/MM-all.tgz D /trunk/wizards/NAD.pdb D /trunk/wizards/PARAMS_1.eff D /trunk/wizards/a2u-data.mtz D /trunk/wizards/a2u-sigmaa.mtz D /trunk/wizards/a2u.sca D /trunk/wizards/a2u_short.pdb D /trunk/wizards/anb.pdb D /trunk/wizards/autosol_unmerged_False.std D /trunk/wizards/autosol_unmerged_True.std D /trunk/wizards/autosol_unmerged_p9.std D /trunk/wizards/bad_model.pdb D /trunk/wizards/check.xyz D /trunk/wizards/check_multiple_input_files_042908.tgz D /trunk/wizards/check_multiple_input_files_062608.tgz D /trunk/wizards/check_multiple_input_files_070508.tgz D /trunk/wizards/check_multiple_input_files_2011-03-03.tgz D /trunk/wizards/check_multiple_input_files_2011-06-29.tgz D /trunk/wizards/check_multiple_input_files_2011-11-04.tgz D /trunk/wizards/clean.com D /trunk/wizards/cocn.cif D /trunk/wizards/coords.pdb D /trunk/wizards/coords1.ali D /trunk/wizards/coords1.mtz D /trunk/wizards/coords1.pdb D /trunk/wizards/coords_A001.pdb D /trunk/wizards/coords_rna.pdb D /trunk/wizards/coords_rna_gap.pdb D /trunk/wizards/data_for_commands_in_doc.tgz D /trunk/wizards/find_all_ligands.eff D /trunk/wizards/find_all_ligands.standard D /trunk/wizards/find_ncs_ncs.standard D /trunk/wizards/find_ncs_resolve.standard D /trunk/wizards/fobs.mtz D /trunk/wizards/fobs_std.mtz D /trunk/wizards/fobs_std_edit.mtz D /trunk/wizards/gene-5.pdb D /trunk/wizards/generate.com D /trunk/wizards/get_cc_mtz_mtz.standard D /trunk/wizards/get_cc_mtz_pdb.standard D /trunk/wizards/ha.pdb D /trunk/wizards/ha_lig.pdb D /trunk/wizards/ha_perfect.pdb D /trunk/wizards/ha_perfect_2.pdb D /trunk/wizards/hipip.pdb D /trunk/wizards/hipip_2.sca D /trunk/wizards/hipip_shortseq.dat D /trunk/wizards/ignore.dat D /trunk/wizards/inf.sca D /trunk/wizards/ki.sca D /trunk/wizards/ligand.pdb D /trunk/wizards/mad.eff D /trunk/wizards/mad.mtz D /trunk/wizards/map_coeffs.mtz D /trunk/wizards/map_coeffs_1.mtz D /trunk/wizards/map_coeffs_2.mtz D /trunk/wizards/map_to_object.standard D /trunk/wizards/maps_only.standard D /trunk/wizards/mir.eff D /trunk/wizards/mlt.mtz D /trunk/wizards/mlt_gap.pdb D /trunk/wizards/mlt_regression.tgz D /trunk/wizards/mol1.pdb D /trunk/wizards/mol2.pdb D /trunk/wizards/mr_rosetta.eff D /trunk/wizards/mult_regr.tgz D /trunk/wizards/multi.pdb D /trunk/wizards/multi.pdb.mtz D /trunk/wizards/my_autobuild.eff D /trunk/wizards/my_automr.eff D /trunk/wizards/my_autosol.eff D /trunk/wizards/my_ligand.pdb D /trunk/wizards/my_ligandfit.eff D /trunk/wizards/my_target.pdb D /trunk/wizards/native.sca D /trunk/wizards/noligand.mtz D /trunk/wizards/omit_lig_results.list D /trunk/wizards/omit_regr.tgz D /trunk/wizards/p.pdb D /trunk/wizards/p21.sym D /trunk/wizards/p9-seq.dat D /trunk/wizards/p9-sites.xyz D /trunk/wizards/p9_ha.pdb D /trunk/wizards/p9_se_w2.sca D /trunk/wizards/part_mlt.pdb D /trunk/wizards/partial.pdb D /trunk/wizards/partial_refine_001.pdb D /trunk/wizards/partial_refine_001_map_coeffs.mtz D /trunk/wizards/peak.sca D /trunk/wizards/perfect.mtz D /trunk/wizards/perfect_rna.mtz D /trunk/wizards/phaser_1_offset.mtz D /trunk/wizards/pt.sca D /trunk/wizards/quick_clashlist.standard D /trunk/wizards/random.pdb D /trunk/wizards/random_0.7_mlt.mtz D /trunk/wizards/resolve_1_offset.mtz D /trunk/wizards/rna.seq D /trunk/wizards/run_multi.eff D /trunk/wizards/run_multi_new.eff D /trunk/wizards/seq.dat D /trunk/wizards/seq1.dat D /trunk/wizards/seq2.dat D /trunk/wizards/seq_mlt.dat D /trunk/wizards/short_seq.standard D /trunk/wizards/side.pdb D /trunk/wizards/sir_sad.eff D /trunk/wizards/sites_mlt.pdb D /trunk/wizards/smiles.dat D /trunk/wizards/solve.setup D /trunk/wizards/start.pdb D /trunk/wizards/starting_map.mtz D /trunk/wizards/test3.gz D /trunk/wizards/test9.gz D /trunk/wizards/test_ampl_int_autobuild.tgz D /trunk/wizards/test_labels_1.std D /trunk/wizards/test_labels_2.std D /trunk/wizards/test_labels_3.std D /trunk/wizards/test_missing.std D /trunk/wizards/test_multi.tgz D /trunk/wizards/test_ncs.standard D /trunk/wizards/test_ncs_find_ncs.standard D /trunk/wizards/test_ncs_lc.pdb D /trunk/wizards/test_resno.std D /trunk/wizards/test_resno.tgz D /trunk/wizards/unmerged.mtz D /trunk/wizards/w1.sca D /trunk/wizards/w1_rna.sca D /trunk/wizards/w2.sca remove unneeded files ------------------------------------------------------------------------ Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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easy_mp.multi_core_run function
by R.D. Oeffner 20 Dec '16

20 Dec '16

Hi, I needed a way to do multiprocessing job runs in a simple fashion on a multicore PC. Gabor provided much of the underlying machinery in libtbx for that. But I have often found I'm wasting too much time setting it all up. So I crafted a small function, easy_mp.multi_core_run(), out of his example in Computational Crystallography Newsletter (2013). 4, p21 which does exactly that. Unlike easy_mp.parallel_map() this function continues if one of the jobs crashes catastrophically. It takes as arguments name of function to be parallelised, a list of argument tuples and number of processors to run on. As the jobs completes it returns an iterator of tuples of arguments with corresponding results. Example: def RunMyJob(args1, args2): pass def GatherResults(parmres): pass from libtbx import easy_mp argstuples = [(args1a, args2a), (args1b, args2b), (args1c, args2c) ] for i, parmres in enumerate(easy_mp.multi_core_run( RunMyJob, argstuples, nproc)): GatherResults( parmres ) I'm interested in comments or if this kind of simple function is already available elsewhere. 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 mobile: +44(0)7712 887162

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Making branches by accident
by Graeme.Winter＠diamond.ac.uk 19 Dec '16

19 Dec '16

Morning all I am seeing a certain amount of "Merge branch 'master' of github.com:cctbx/cctbx_project" coming through on the commits - this usually means you did not do a git pull -rebase before the git push. This can be set to the default by using the spell Markus sent out git config --global pull.rebase true This will need to be done on each machine you push from, else getting the habit of doing a git pull -rebase before push is a good one. We have had this on and off with DIALS but it tends to pass easily enough. What bad happens? Nothing really but the history becomes confusing... So: may be worth checking that you have the pull.rebase thing set? Cheerio Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Re: [cctbxbb] issue tracker on https://github.com/cctbx/cctbx_project
by markus.gerstel＠diamond.ac.uk 11 Dec '16

11 Dec '16

Hi, Yes, we can do that with the tools we have. (Jenkins + Python + Github API) -Markus On 9 Dec 2016 16:13, Graeme.Winter(a)diamond.ac.uk wrote: Hi Nigel, all That could be harder but not beyond our capabilities I expect However the response seems to be a resounding go for it, so I’m sure the issue tracker will be activated RSN Best wishes Graeme From: cctbxbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Nigel Moriarty Sent: 09 December 2016 15:43 To: cctbx mailing list Subject: Re: [cctbxbb] issue tracker on https://github.com/cctbx/cctbx_project One feature that would be cool is to set a (say) weekly email to remind developers of the issues assigned to them. In my other collabs, there is a complaints that the issues are not being noticed... Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov<mailto:[email protected]> Fax : 510-486-5909 Web : CCI.LBL.gov<http://CCI.LBL.gov> On Fri, Dec 9, 2016 at 7:40 AM, Aaron Brewster <asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: Also +1. I like how it's possible to reference issues in commits by using #, which then show up as links in the commit emails and website history. One can cite issue numbers, or even interact with them. For example, if your commit includes the phrase "closes #42" or "fixes #42", then issue 42 will be closed when you push your commit. It's Nifty. -Aaron On Fri, Dec 9, 2016 at 7:29 AM, Nigel Moriarty <nwmoriarty(a)lbl.gov<mailto:[email protected]>> wrote: We at Phenix would like to see how the issue/bug tracker works as it's an important feature we'd like to use when we migrate our other repos to GitHub. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709<tel:%28510%29%20486-5709> Email : NWMoriarty(a)LBL.gov<mailto:[email protected]> Fax : 510-486-5909<tel:%28510%29%20486-5909> Web : CCI.LBL.gov<http://CCI.LBL.gov> On Fri, Dec 9, 2016 at 6:23 AM, Luc Bourhis <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: Hi Graeme, Does anyone have an objection to opening up the issue tracker on […] Your thoughts? +1 Best wishes, Luc _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org<mailto:[email protected]> 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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issue tracker on https://github.com/cctbx/cctbx_project
by Graeme.Winter＠diamond.ac.uk 10 Dec '16

10 Dec '16

Good afternoon all Does anyone have an objection to opening up the issue tracker on https://github.com/cctbx/cctbx_project at the moment we make a lot of use of issue trackers for dials and xia2, and for cctbx this would be helpful - so we could for example host issues in a more appropriate place like https://github.com/dials/dials/issues/265 which would be more "at home" in cctbx Your thoughts? Thanks & best wishes Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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