08/06/2019 6:00:01.55 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 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 90300 100 90300 0 0 90300 0 0:00:01 --:--:-- 0:00:01 235k 08/06/2019 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:4ipsm__annlib.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:4ipsm__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:e41nma_scons.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:e41nma_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:3m6o39_ccp4io.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:3m6o39_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:xmdc4__eigen.tar.gz ===== Running in modules: getting remote file rdo20@cci.lbl.gov:xmdc4__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 8718ebd81..526fc43cb master -> origin/master + e38f3dd55...a9a0e9bc5 index-refactor -> origin/index-refactor (forced update) * [new branch] remove-batch-analysis -> origin/remove-batch-analysis 1c2f3842e..c13a64b37 stills_imgview -> origin/stills_imgview Updating 8718ebd81..526fc43cb Fast-forward CHANGELOG.rst | 0 algorithms/clustering/plots.py | 1 - algorithms/image/fill_holes/simple.h | 3 +- algorithms/image/filter/boost_python/distance.cc | 25 +- .../image/filter/boost_python/mean_and_variance.cc | 3 +- algorithms/image/filter/distance.h | 99 +- algorithms/image/filter/mean_and_variance.h | 5 +- algorithms/image/threshold/boost_python/local.cc | 45 + algorithms/image/threshold/local.h | 688 ++++++++ algorithms/indexing/__init__.py | 142 +- algorithms/indexing/assign_indices.py | 159 ++ .../indexing/basis_vector_search/__init__.py | 0 .../indexing/basis_vector_search/combinations.py | 208 +++ .../indexing/basis_vector_search/conftest.py | 37 + .../indexing/basis_vector_search/optimise.py | 67 + .../indexing/basis_vector_search/strategies.py | 590 +++++++ .../basis_vector_search/test_combinations.py | 101 ++ .../indexing/basis_vector_search/test_optimise.py | 40 + .../basis_vector_search/test_strategies.py | 36 + .../indexing/compare_orientation_matrices.py | 20 - algorithms/indexing/fft1d.py | 103 -- algorithms/indexing/fft3d.py | 764 --------- algorithms/indexing/indexer.py | 1801 ++------------------ algorithms/indexing/known_orientation.py | 8 +- algorithms/indexing/lattice_search.py | 406 +++++ algorithms/indexing/max_cell.py | 30 +- algorithms/indexing/model_evaluation.py | 360 ++++ algorithms/indexing/nave_parameters.py | 55 +- algorithms/indexing/nearest_neighbor.py | 24 +- algorithms/indexing/non_primitive_basis.py | 67 + algorithms/indexing/real_space_grid_search.py | 171 -- algorithms/indexing/refinement.py | 98 +- algorithms/indexing/stills_indexer.py | 421 ++--- algorithms/indexing/symmetry.py | 225 ++- .../indexing/test_assign_indices.py | 50 +- .../indexing/test_compare_orientation_matrices.py | 76 +- .../indexing/test_index.py | 209 ++- algorithms/indexing/test_lattice_search.py | 101 ++ algorithms/indexing/test_max_cell.py | 15 +- algorithms/indexing/test_model_evaluation.py | 291 ++++ algorithms/indexing/test_non_primitive_basis.py | 53 + .../indexing/test_phi_scan.py | 22 +- algorithms/indexing/test_symmetry.py | 137 ++ algorithms/integration/parallel_integrator.py | 36 - algorithms/refinement/outlier_detection/mcd.py | 3 - .../refinement/parameterisation/configure.py | 5 +- algorithms/refinement/refiner.py | 20 +- algorithms/refinement/reflection_manager.py | 57 +- algorithms/refinement/target.py | 9 +- algorithms/spot_finding/factory.py | 24 +- algorithms/spot_finding/per_image_analysis.py | 1 - algorithms/spot_finding/threshold.py | 72 + algorithms/symmetry/cosym/__init__.py | 9 +- algorithms/symmetry/cosym/seed_clustering.py | 3 +- algorithms/symmetry/determine_space_group.py | 9 - array_family/flex.py | 44 +- command_line/analyse_output.py | 181 +- command_line/calc_rmsds.py | 103 -- command_line/compute_delta_cchalf.py | 2 - command_line/cosym.py | 71 +- command_line/estimate_gain.py | 14 +- command_line/find_spots_server.py | 13 +- command_line/generate_tutorial_text.py | 8 +- command_line/import_stream.py | 6 +- command_line/index.py | 257 ++- command_line/integrate.py | 6 +- command_line/plot_detector_shifts.py | 1 - command_line/plot_find_spots_client.py | 46 +- command_line/plot_reflections.py | 15 +- command_line/plugins.py | 4 + command_line/refine.py | 771 +++++---- command_line/search_beam_position.py | 79 +- command_line/simple_strategy.py | 23 +- command_line/split_experiments.py | 2 - command_line/stills_process.py | 34 +- .../algorithms/dials.algorithms.indexing.rst | 64 +- .../documentation/tutorials/dials_for_ed.rst | 3 +- .../tutorials/multi_crystal_analysis.rst | 11 +- .../tutorials/small_molecule_tutorial.rst | 2 +- extensions/__init__.py | 4 + ...dispersion_extended_spotfinder_threshold_ext.py | 138 ++ extensions/dispersion_spotfinder_threshold_ext.py | 4 +- libtbx_config | 35 +- libtbx_refresh.py | 7 +- newsfragments/.gitignore | 1 + newsfragments/758.feature | 1 + precommitbx/installer.py | 241 ++- pyproject.toml | 7 +- test/algorithms/image/filter/test_distance.py | 52 +- test/algorithms/image/threshold/test_local.py | 75 +- test/algorithms/indexing/test_symmetry.py | 69 - test/algorithms/refinement/test_constraints.py | 6 +- .../refinement/test_refine_multi_wedges.py | 5 +- test/array_family/test_reflection_table.py | 32 +- test/command_line/test_cosym.py | 41 + test/command_line/test_find_hot_pixels.py | 5 +- test/command_line/test_refine.py | 13 +- test/command_line/test_search_beam_position.py | 42 +- test/command_line/test_spotfinder.py | 17 +- test/command_line/test_stills_process.py | 2 +- util/image_viewer/slip_viewer/calibration_frame.py | 62 - util/image_viewer/slip_viewer/slip_display.py | 4 +- util/image_viewer/spotfinder_frame.py | 16 +- 103 files changed, 5931 insertions(+), 4712 deletions(-) create mode 100644 CHANGELOG.rst create mode 100644 algorithms/indexing/assign_indices.py create mode 100644 algorithms/indexing/basis_vector_search/__init__.py create mode 100644 algorithms/indexing/basis_vector_search/combinations.py create mode 100644 algorithms/indexing/basis_vector_search/conftest.py create mode 100644 algorithms/indexing/basis_vector_search/optimise.py create mode 100644 algorithms/indexing/basis_vector_search/strategies.py create mode 100644 algorithms/indexing/basis_vector_search/test_combinations.py create mode 100644 algorithms/indexing/basis_vector_search/test_optimise.py create mode 100644 algorithms/indexing/basis_vector_search/test_strategies.py delete mode 100644 algorithms/indexing/fft1d.py delete mode 100644 algorithms/indexing/fft3d.py create mode 100644 algorithms/indexing/lattice_search.py create mode 100644 algorithms/indexing/model_evaluation.py create mode 100644 algorithms/indexing/non_primitive_basis.py delete mode 100644 algorithms/indexing/real_space_grid_search.py rename {test/algorithms => algorithms}/indexing/test_assign_indices.py (77%) rename {test/algorithms => algorithms}/indexing/test_compare_orientation_matrices.py (52%) rename {test/algorithms => algorithms}/indexing/test_index.py (81%) create mode 100644 algorithms/indexing/test_lattice_search.py create mode 100644 algorithms/indexing/test_model_evaluation.py create mode 100644 algorithms/indexing/test_non_primitive_basis.py rename {test/algorithms => algorithms}/indexing/test_phi_scan.py (92%) create mode 100644 algorithms/indexing/test_symmetry.py delete mode 100644 command_line/calc_rmsds.py create mode 100644 extensions/dispersion_extended_spotfinder_threshold_ext.py create mode 100644 newsfragments/.gitignore create mode 100644 newsfragments/758.feature delete mode 100644 test/algorithms/indexing/test_symmetry.py Current branch master is up to date. Updating 'probe': At revision 96. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx ed81e0f..70ee2c5 master -> origin/master 495bef7..ae3482f format-registration -> origin/format-registration + 381aae7...5538404 py3_testbed2 -> origin/py3_testbed2 (forced update) Updating ed81e0f..70ee2c5 Fast-forward .python3-test-failures | 484 ++++++++++++++++++++++++++++++++++++++ CHANGELOG.rst | 0 libtbx_config | 7 +- newsfragments/.gitignore | 1 + pyproject.toml | 7 +- tests/model/test_crystal_model.py | 6 +- tests/python3_test_filter.py | 36 +++ 7 files changed, 531 insertions(+), 10 deletions(-) create mode 100644 .python3-test-failures create mode 100644 CHANGELOG.rst create mode 100644 newsfragments/.gitignore create mode 100644 tests/python3_test_filter.py 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 4630. Updating 'opt_resources': At revision 6. Updating 'phenix': A phenix\conda_envs A phenix\conda_envs\phenix_py27_linux-64.txt A phenix\conda_envs\phenix_py36_linux-64.txt A phenix\conda_envs\phenix_py27_osx-64.txt A phenix\conda_envs\phenix_py36_osx-64.txt A phenix\conda_envs\phenix_py27_win-64.txt A phenix\conda_envs\phenix_py36_win-64.txt U phenix\CHANGES U phenix\phenix\command_line\amber_run_tests.py U phenix\phenix\pdb_tools\rama_z_score\rama_z_score.py U phenix\phenix\refinement\runtime.py U phenix\phenix\programs\get_pdb_validation_report.py Updated to revision 12945. 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 202. 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\tutorials\cryo_fit_cmdline.txt U phenix_html\rst_files\reference\cryo_fit2.txt Updated to revision 1329. Updating 'king': At revision 28. Already up to date. Current branch master is up to date. Updating 'amber_adaptbx': U amber_adaptbx\command_line\AmberPrepClass.py Updated to revision 366. Updating 'labelit': At revision 2072. Updating 'elbow': At revision 3773. 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