13/06/2019 6:00:01.59 Get bootstrap.py % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 90300 100 90300 0 0 90300 0 0:00:01 --:--:-- 0:00:01 312k 13/06/2019 6:00:02.30 C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty dist /MIR /COPYALL 1>nul ) & rmdir /S /Q dist\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty tests /MIR /COPYALL 1>nul ) & rmdir /S /Q tests\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty doc /MIR /COPYALL 1>nul ) & rmdir /S /Q doc\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty tmp /MIR /COPYALL 1>nul ) & rmdir /S /Q tmp\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty base /MIR /COPYALL 1>nul ) & rmdir /S /Q base\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty base_tmp /MIR /COPYALL 1>nul ) & rmdir /S /Q base_tmp\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty build /MIR /COPYALL 1>nul ) & rmdir /S /Q build\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty conda_base /MIR /COPYALL 1>nul ) & rmdir /S /Q conda_base\ & ) The system cannot find the file specified. Performing actions: cleanup hot update base build Installing base packages using: python modules\cctbx_project\libtbx\auto_build\install_base_packages.py --python-shared --all --phenix --labelit --dials --xia2 --nproc=20 --skip-if-exists ===== Running in .: deleting dist, tests, doc, tmp, base, base_tmp, build, conda_base ===== Running in modules: create remote temporary archive rdo20@cci.lbl.gov:pbvpz7_annlib.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:pbvpz7_annlib.tar.gz ===== Running in modules: delete remote temporary archive of annlib ===== Running in modules: extracting archive files to annlib ===== Running in modules: delete local temporary archive of annlib ===== Running in modules: create remote temporary archive rdo20@cci.lbl.gov:kedpmf_scons.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:kedpmf_scons.tar.gz ===== Running in modules: delete remote temporary archive of scons ===== Running in modules: extracting archive files to scons ===== Running in modules: delete local temporary archive of scons ===== Running in modules: create remote temporary archive rdo20@cci.lbl.gov:49icak_ccp4io.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:49icak_ccp4io.tar.gz ===== Running in modules: delete remote temporary archive of ccp4io ===== Running in modules: extracting archive files to ccp4io ===== Running in modules: delete local temporary archive of ccp4io ===== Running in modules: create remote temporary archive rdo20@cci.lbl.gov:euyxar_eigen.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:euyxar_eigen.tar.gz ===== Running in modules: delete remote temporary archive of eigen ===== Running in modules: extracting archive files to eigen ===== Running in modules: delete local temporary archive of eigen ===== Downloading https://gitcdn.xyz/repo/dials/dependencies/dials-1.13/msgpack-3.1.1.tar.gz: 484 kB From https://github.com/dials/dials 6cb2ce750..4f54dc3d7 master -> origin/master Updating 6cb2ce750..4f54dc3d7 Fast-forward algorithms/indexing/indexer.py | 3 +- algorithms/indexing/model_evaluation.py | 3 +- algorithms/refinement/__init__.py | 10 + algorithms/refinement/constraints.py | 4 +- algorithms/refinement/engine.py | 7 +- .../refinement/parameterisation/autoreduce.py | 25 +- .../refinement/parameterisation/configure.py | 54 +- .../parameterisation/crystal_parameters.py | 3 +- .../parameterisation/prediction_parameters.py | 4 +- algorithms/refinement/refiner.py | 12 +- algorithms/refinement/reflection_manager.py | 16 +- .../restraints/restraints_parameterisation.py | 8 +- algorithms/refinement/sparse_engine.py | 4 +- algorithms/refinement/weighting_strategies.py | 4 +- command_line/refine.py | 15 +- command_line/stills_detector_hybrid_refine.py | 594 --------------------- ...dispersion_extended_spotfinder_threshold_ext.py | 2 - extensions/dispersion_spotfinder_threshold_ext.py | 2 + .../refinement/test_parameter_auto_reduction.py | 4 +- test/algorithms/refinement/test_refiner_config.py | 46 ++ test/command_line/test_refine.py | 48 +- .../test_stills_detector_hybrid_refine.py | 88 --- 22 files changed, 168 insertions(+), 788 deletions(-) delete mode 100644 command_line/stills_detector_hybrid_refine.py create mode 100644 test/algorithms/refinement/test_refiner_config.py delete mode 100644 test/command_line/test_stills_detector_hybrid_refine.py Current branch master is up to date. Updating 'probe': At revision 96. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx f3daa9c..3bd0ecd master -> origin/master * [new branch] XTC_timestamp_identifier -> origin/XTC_timestamp_identifier + a98c09d...7a80ffd py3_testbed2 -> origin/py3_testbed2 (forced update) Updating f3daa9c..3bd0ecd Fast-forward command_line/install_format.py | 208 ++++++++++++++++++++++--------- command_line/show_matching_formats.py | 20 +-- command_line/show_registry.py | 25 ++-- datablock.py | 69 +++-------- format/Format.py | 64 +++------- format/FormatHDF5SaclaMPCCD.py | 27 ++-- format/FormatMultiImage.py | 40 +++--- format/Registry.py | 227 ++++++++++++++++++---------------- format/RegistryHelpers.py | 72 ----------- libtbx_config | 2 +- libtbx_refresh.py | 8 +- model/experiment_list.py | 70 +++++++---- newsfragments/34.feature | 21 ++++ pytest.ini | 4 + tests/test_datablock.py | 10 +- tests/test_regression_images.py | 69 +++++------ 16 files changed, 482 insertions(+), 454 deletions(-) delete mode 100644 format/RegistryHelpers.py create mode 100644 newsfragments/34.feature Current branch master is up to date. Updating 'ccp4io_adaptbx': At revision 143. Updating 'solve_resolve': At revision 1726. Updating 'clipper': At revision 19. Updating 'ksdssp': At revision 14. Updating 'phenix_regression': At revision 4633. Updating 'opt_resources': At revision 6. Updating 'phenix': U phenix\wxGUI2\Programs\StructureSearch.py U phenix\wxGUI2\Programs\PDBValidationReport.py U phenix\wxGUI2\program_template\get_pdb_validation_report.py U phenix\phenix\command_line\structure_search.py U phenix\phenix\programs\get_pdb_validation_report.py Updated to revision 12960. Updating 'Plex': At revision 8. Updating 'tntbx': At revision 50. Updating 'pulchra': At revision 8. Updating 'PyQuante': At revision 25. Already up to date. Current branch master is up to date. Already up to date. Current branch master is up to date. Updating 'suitename': At revision 11. Already up to date. Current branch master is up to date. Updating 'chem_data': Fetching external item into 'chem_data\geostd': External at revision 203. At revision 317. X chem_data\geostd Performing status on external item at 'chem_data\geostd': Already up to date. Current branch master is up to date. warning: redirecting to https://git.uis.cam.ac.uk/cimr-phaser/phaser_regression.git/ Already up to date. Current branch master is up to date. Updating 'phenix_examples': At revision 96. Updating 'reel': At revision 265. Updating 'phenix_html': U phenix_html\rst_files\faqs\cryo_fit2_FAQ.txt Updated to revision 1330. Updating 'king': At revision 28. Already up to date. Current branch master is up to date. Updating 'amber_adaptbx': D amber_adaptbx\deprecated U amber_adaptbx\command_line\AmberPrepClass.py D amber_adaptbx\tests\files\1dy5\test_phenix.refine.1 A amber_adaptbx\tests\files\1dy5\test_phenix.refine U amber_adaptbx\tests\files\1dy5\non-les\4phenix_1dy5.pdb U amber_adaptbx\tests\files\1dy5\non-les\amber1.log U amber_adaptbx\tests\files\1dy5\non-les\tail.log U amber_adaptbx\tests\files\1dy5\non-les\1dy5.min.out U amber_adaptbx\tests\files\1dy5\non-les\4amber_1dy5.rst7 U amber_adaptbx\tests\files\1dy5\non-les\non-les.log U amber_adaptbx\tests\files\1dy5\non-les\4amber_1dy5.prmtop U amber_adaptbx\tests\files\1dy5\test_AmberPrep Updated to revision 383. Updating 'labelit': At revision 2072. Updating 'elbow': D elbow\elbow\utilities\environment.py Updated to revision 3777. Updating 'muscle': At revision 10. Updating 'gui_resources': At revision 58. python: can't open file 'modules\cctbx_project\libtbx\auto_build\install_base_packages.py': [Errno 2] No such file or directory ===== Running in modules: extracting files from msgpack-3.1.1.tar.gz ===== Running in modules\dials: git pull --rebase ===== Running in modules: svn update probe --non-interactive --trust-server-cert ===== Running in modules: svn update reduce --non-interactive --trust-server-cert ===== Running in modules\dxtbx: git pull --rebase ===== Running in modules: svn update ccp4io_adaptbx --non-interactive --trust-server-cert ===== Running in modules: svn update solve_resolve --non-interactive --trust-server-cert ===== Running in modules: svn update clipper --non-interactive --trust-server-cert ===== Running in modules: svn update ksdssp --non-interactive --trust-server-cert ===== Running in modules: svn update phenix_regression --non-interactive --trust-server-cert ===== Running in modules: svn update opt_resources --non-interactive --trust-server-cert ===== Running in modules: svn update phenix --non-interactive --trust-server-cert ===== Running in modules: svn update Plex --non-interactive --trust-server-cert ===== Running in modules: svn update tntbx --non-interactive --trust-server-cert ===== Running in modules: svn update pulchra --non-interactive --trust-server-cert ===== Running in modules: svn update PyQuante --non-interactive --trust-server-cert ===== Running in modules\boost: git pull --rebase Existing non-git directory -- don't know what to do. skipping: cctbx_project ================================================================================ CCTBX moved to git on November 22, 2016. To update cctbx_project to the last available subversion revision please run "svn update" while in the cctbx_project directory. ******************************************************************************** ===== Running in modules\annlib_adaptbx: git pull --rebase ===== Running in modules: svn update suitename --non-interactive --trust-server-cert ===== Running in modules\xia2: git pull --rebase ===== Running in modules: svn update chem_data --non-interactive --trust-server-cert ===== Running in modules\phaser: git pull --rebase ===== Running in modules\phaser_regression: git pull --rebase ===== Running in modules: svn update phenix_examples --non-interactive --trust-server-cert ===== Running in modules: svn update reel --non-interactive --trust-server-cert ===== Running in modules: svn update phenix_html --non-interactive --trust-server-cert ===== Running in modules: svn update king --non-interactive --trust-server-cert ===== Running in modules\cbflib: git pull --rebase ===== Running in modules: svn update amber_adaptbx --non-interactive --trust-server-cert ===== Running in modules: svn update labelit --non-interactive --trust-server-cert ===== Running in modules: svn update elbow --non-interactive --trust-server-cert ===== Running in modules: svn update muscle --non-interactive --trust-server-cert ===== Running in modules: svn update gui_resources --non-interactive --trust-server-cert removing .pyc files in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules, walk? True removed 0 files ===== Running in .: base Process failed with return code 2