11/09/2020 6:00:06.31 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 12 98898 12 12339 0 0 12339 0 0:00:08 --:--:-- 0:00:08 25493 100 98898 100 98898 0 0 98898 0 0:00:01 --:--:-- 0:00:01 193k 11/09/2020 6:00:14.43 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. 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Performing actions: cleanup hot update base build ******************************************************************************* An environment containing git-lfs and/or svn will be installed during the "base" step. Pleaser re-run the "update" step after "base" completes, so that git-lfs files for phenix_regression will be downloaded. ******************************************************************************* ******************************************************************************* An environment containing git-lfs and/or svn will be installed during the "base" step. Pleaser re-run the "update" step after "base" completes, so that git-lfs files for phenix_examples will be downloaded. ******************************************************************************* Installing base packages using: python modules\cctbx_project\libtbx\auto_build\install_conda.py --builder=phenix --install_conda --python=27 ===== Running in .: deleting dist, tests, doc, tmp, base, base_tmp, build, conda_base Existing non-git directory -- don't know what to do. skipping: annlib Existing non-git directory -- don't know what to do. skipping: scons Existing non-git directory -- don't know what to do. skipping: ccp4io Existing non-git directory -- don't know what to do. skipping: 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 57c0213bf..87929e297 master -> origin/master * [new branch] match-reflections -> origin/match-reflections * [new branch] reindex-cache -> origin/reindex-cache * [new branch] sigma_calculation_optimisation -> origin/sigma_calculation_optimisation Updating 57c0213bf..87929e297 Fast-forward .pre-commit-config.yaml | 6 ++ algorithms/background/glm/algorithm.py | 2 +- algorithms/background/modeller.py | 5 +- algorithms/background/simple/algorithm.py | 42 +++++++------ algorithms/clustering/observers.py | 4 +- algorithms/clustering/plots.py | 1 + algorithms/clustering/test_observers.py | 9 ++- algorithms/clustering/test_plots.py | 4 +- algorithms/clustering/test_unit_cell.py | 3 + algorithms/clustering/unit_cell.py | 9 +-- .../image/centroid/generate_bias_lookup_table.py | 2 +- .../centroid/test_generate_bias_lookup_table.py | 1 + algorithms/indexing/assign_indices.py | 4 +- .../indexing/basis_vector_search/__init__.py | 3 +- .../indexing/basis_vector_search/combinations.py | 6 +- .../indexing/basis_vector_search/conftest.py | 5 +- algorithms/indexing/basis_vector_search/fft1d.py | 7 +-- algorithms/indexing/basis_vector_search/fft3d.py | 17 ++---- .../indexing/basis_vector_search/optimise.py | 2 +- .../basis_vector_search/real_space_grid_search.py | 6 +- .../basis_vector_search/test_combinations.py | 7 ++- .../indexing/basis_vector_search/test_optimise.py | 3 +- .../basis_vector_search/test_strategies.py | 4 +- .../indexing/basis_vector_search/test_utils.py | 3 +- algorithms/indexing/bravais_settings.py | 5 +- algorithms/indexing/indexer.py | 20 ++++--- algorithms/indexing/known_orientation.py | 3 +- algorithms/indexing/lattice_search/__init__.py | 6 +- .../indexing/lattice_search/low_res_spot_match.py | 5 +- .../indexing/lattice_search/test_lattice_search.py | 10 ++-- algorithms/indexing/max_cell.py | 5 +- algorithms/indexing/model_evaluation.py | 6 +- algorithms/indexing/nave_parameters.py | 3 +- algorithms/indexing/non_primitive_basis.py | 9 ++- algorithms/indexing/refinement.py | 1 - algorithms/indexing/stills_indexer.py | 11 ++-- algorithms/indexing/symmetry.py | 4 +- algorithms/indexing/test_assign_indices.py | 13 ++-- .../indexing/test_compare_orientation_matrices.py | 4 +- algorithms/indexing/test_index.py | 16 +++-- algorithms/indexing/test_max_cell.py | 7 ++- algorithms/indexing/test_model_evaluation.py | 4 +- algorithms/indexing/test_non_primitive_basis.py | 6 +- algorithms/indexing/test_phi_scan.py | 6 +- algorithms/indexing/test_symmetry.py | 3 +- algorithms/integration/__init__.py | 2 +- algorithms/integration/filtering.py | 1 - algorithms/integration/image_integrator.py | 6 +- algorithms/integration/integrator_stills.py | 8 ++- algorithms/integration/kapton_2019_correction.py | 5 +- algorithms/integration/kapton_correction.py | 5 +- algorithms/integration/overlaps_filter.py | 3 +- algorithms/integration/parallel_integrator.py | 13 ++-- algorithms/integration/report.py | 14 +++-- .../integration/stills_significance_filter.py | 5 +- algorithms/integration/sum/__init__.py | 2 +- algorithms/integration/test_processor.py | 12 ++-- algorithms/merging/merge.py | 28 ++++----- algorithms/profile_model/gaussian_rs/__init__.py | 2 +- algorithms/profile_model/gaussian_rs/algorithm.py | 14 ++--- algorithms/profile_model/gaussian_rs/calculator.py | 5 +- algorithms/profile_model/gaussian_rs/model.py | 9 +-- .../refinement/analysis/centroid_analysis.py | 3 +- algorithms/refinement/constraints.py | 5 +- algorithms/refinement/corrgram.py | 4 +- algorithms/refinement/engine.py | 5 +- .../refinement/outlier_detection/__init__.py | 4 +- algorithms/refinement/outlier_detection/mcd.py | 2 +- .../refinement/outlier_detection/outlier_base.py | 5 +- .../refinement/outlier_detection/sauter_poon.py | 2 +- algorithms/refinement/parameterisation/__init__.py | 3 +- .../refinement/parameterisation/autoreduce.py | 6 +- .../refinement/parameterisation/beam_parameters.py | 6 +- .../refinement/parameterisation/configure.py | 70 +++++++++++----------- .../parameterisation/crystal_parameters.py | 8 ++- .../parameterisation/detector_parameters.py | 12 ++-- .../parameterisation/goniometer_parameters.py | 6 +- .../parameterisation/prediction_parameters.py | 7 ++- .../prediction_parameters_stills.py | 3 +- .../scan_varying_beam_parameters.py | 8 ++- .../scan_varying_crystal_parameters.py | 12 ++-- .../scan_varying_detector_parameters.py | 13 ++-- .../scan_varying_goniometer_parameters.py | 12 ++-- .../scan_varying_model_parameters.py | 6 +- .../scan_varying_prediction_parameters.py | 5 +- .../refinement/prediction/managed_predictors.py | 2 + algorithms/refinement/refinement_helpers.py | 5 +- algorithms/refinement/refiner.py | 42 +++++++------ algorithms/refinement/reflection_manager.py | 12 ++-- algorithms/refinement/restraints/restraints.py | 9 ++- .../restraints/restraints_parameterisation.py | 14 +++-- algorithms/refinement/rotation_decomposition.py | 2 + algorithms/refinement/sparse_engine.py | 21 +++---- algorithms/refinement/target.py | 7 +-- algorithms/refinement/target_stills.py | 5 +- algorithms/refinement/two_theta_refiner.py | 16 ++--- algorithms/refinement/weighting_strategies.py | 2 +- algorithms/scaling/Ih_table.py | 6 +- algorithms/scaling/active_parameter_managers.py | 6 +- algorithms/scaling/algorithm.py | 67 +++++++++++++-------- algorithms/scaling/basis_functions.py | 3 +- algorithms/scaling/combine_intensities.py | 5 +- .../scaling/cross_validation/cross_validate.py | 5 +- .../scaling/cross_validation/crossvalidator.py | 5 +- .../cross_validation/test_crossvalidation.py | 8 ++- algorithms/scaling/error_model/engine.py | 12 ++-- algorithms/scaling/error_model/error_model.py | 12 ++-- .../scaling/error_model/error_model_target.py | 1 + .../scaling/model/components/scale_components.py | 4 +- .../model/components/smooth_scale_components.py | 11 ++-- algorithms/scaling/model/model.py | 25 ++++---- algorithms/scaling/observers.py | 52 ++++++++-------- algorithms/scaling/outlier_rejection.py | 3 +- algorithms/scaling/parameter_handler.py | 3 +- algorithms/scaling/plots.py | 4 +- algorithms/scaling/reflection_selection.py | 7 ++- algorithms/scaling/scale_and_filter.py | 3 +- algorithms/scaling/scaler.py | 54 +++++++++-------- algorithms/scaling/scaler_factory.py | 15 +++-- algorithms/scaling/scaling_library.py | 20 ++++--- algorithms/scaling/scaling_options.py | 1 + algorithms/scaling/scaling_refiner.py | 9 +-- algorithms/scaling/scaling_restraints.py | 2 + algorithms/scaling/scaling_utilities.py | 11 ++-- algorithms/scaling/target_function.py | 5 +- algorithms/scaling/test_Ih_table.py | 6 +- algorithms/scaling/test_basis_function.py | 8 +-- algorithms/scaling/test_combine_intensities.py | 11 ++-- algorithms/scaling/test_error_model.py | 18 +++--- algorithms/scaling/test_gaussian_smoother.py | 5 +- algorithms/scaling/test_model.py | 18 +++--- algorithms/scaling/test_observers.py | 17 +++--- algorithms/scaling/test_outlier_rejection.py | 9 ++- algorithms/scaling/test_param_manager.py | 11 ++-- algorithms/scaling/test_plots.py | 4 +- algorithms/scaling/test_reflection_selection.py | 16 +++-- algorithms/scaling/test_scale.py | 32 +++++++--- algorithms/scaling/test_scale_and_filter.py | 15 +++-- algorithms/scaling/test_scale_components.py | 12 ++-- algorithms/scaling/test_scaler.py | 29 +++++---- algorithms/scaling/test_scaler_factory.py | 25 ++++---- algorithms/scaling/test_scaling_library.py | 18 +++--- algorithms/scaling/test_scaling_restaints.py | 8 ++- algorithms/scaling/test_scaling_utilities.py | 20 ++++--- algorithms/scaling/test_target_function.py | 20 ++++--- algorithms/scaling/test_targetscaler.py | 11 ++-- algorithms/scaling/test_weighting.py | 12 ++-- algorithms/scaling/weighting.py | 1 + algorithms/shoebox/__init__.py | 2 +- algorithms/simulation/generate_test_reflections.py | 7 ++- algorithms/simulation/reciprocal_space.py | 8 +-- algorithms/spot_finding/factory.py | 9 ++- algorithms/spot_finding/finder.py | 7 ++- algorithms/spot_finding/per_image_analysis.py | 6 +- algorithms/spot_finding/test_per_image_analysis.py | 1 + algorithms/spot_prediction/__init__.py | 2 +- algorithms/spot_prediction/reflection_predictor.py | 11 +++- algorithms/statistics/cc_half_algorithm.py | 36 +++++------ algorithms/statistics/delta_cchalf.py | 9 +-- algorithms/statistics/fast_mcd.py | 3 +- algorithms/symmetry/__init__.py | 9 +-- algorithms/symmetry/absences/laue_groups_info.py | 3 +- algorithms/symmetry/absences/plots.py | 1 + .../symmetry/absences/run_absences_checks.py | 2 +- algorithms/symmetry/absences/screw_axes.py | 9 ++- .../symmetry/absences/test_laue_group_info.py | 6 +- algorithms/symmetry/absences/test_plots.py | 3 +- algorithms/symmetry/absences/test_screw_axes.py | 6 +- algorithms/symmetry/cosym/__init__.py | 15 ++--- algorithms/symmetry/cosym/_generate_test_data.py | 6 +- algorithms/symmetry/cosym/observers.py | 7 ++- algorithms/symmetry/cosym/plots.py | 1 + algorithms/symmetry/cosym/seed_clustering.py | 4 +- algorithms/symmetry/cosym/target.py | 6 +- .../symmetry/cosym/test_cosym_analyse_datasets.py | 6 +- .../symmetry/cosym/test_cosym_symmetry_analysis.py | 5 +- algorithms/symmetry/cosym/test_cosym_target.py | 3 +- algorithms/symmetry/cosym/test_observers.py | 4 +- algorithms/symmetry/cosym/test_plots.py | 3 +- algorithms/symmetry/laue_group.py | 8 ++- algorithms/symmetry/origin.py | 8 ++- algorithms/symmetry/reindex_to_reference.py | 5 +- .../test_correlation_coefficient_accumulator.py | 1 + algorithms/symmetry/test_laue_group.py | 1 + algorithms/symmetry/test_reindex_to_reference.py | 3 +- .../test_score_symmetry_element_subgroup.py | 3 +- array_family/boost_python/flex_reflection_table.cc | 1 + array_family/flex.py | 9 ++- array_family/flex_ext.py | 18 +++--- array_family/reflection_table.h | 3 + command_line/align_crystal.py | 10 ++-- command_line/anvil_correction.py | 9 +-- command_line/apply_mask.py | 8 ++- command_line/assign_experiment_identifiers.py | 5 +- command_line/augment_spots.py | 3 +- command_line/background.py | 9 +-- command_line/check_indexing_symmetry.py | 7 ++- command_line/cluster_exec.py | 3 +- command_line/cluster_unit_cell.py | 5 +- command_line/combine_experiments.py | 24 ++++---- command_line/compare_orientation_matrices.py | 3 +- command_line/complete_full_sphere.py | 12 ++-- command_line/compute_delta_cchalf.py | 4 +- command_line/convert_to_cbf.py | 3 +- command_line/cosym.py | 22 ++++--- command_line/create_profile_model.py | 8 +-- command_line/damage_analysis.py | 21 ++++--- command_line/detect_blanks.py | 2 +- command_line/dials_import.py | 36 ++++++----- command_line/estimate_gain.py | 3 +- command_line/estimate_resolution.py | 8 +-- command_line/export.py | 5 +- command_line/export_best.py | 3 +- command_line/export_bitmaps.py | 7 ++- command_line/filter_reflections.py | 13 ++-- command_line/find_bad_pixels.py | 4 +- command_line/find_hot_pixels.py | 5 +- command_line/find_shared_models.py | 9 +-- command_line/find_spots.py | 10 ++-- command_line/find_spots_client.py | 3 +- command_line/find_spots_server.py | 5 +- command_line/frame_orientations.py | 10 ++-- command_line/generate_distortion_maps.py | 12 ++-- command_line/generate_mask.py | 9 +-- command_line/generate_tutorial_text.py | 3 +- command_line/geometry_viewer.py | 15 +++-- command_line/goniometer_calibration.py | 3 +- command_line/image_viewer.py | 3 +- command_line/import_xds.py | 8 +-- command_line/index.py | 15 +++-- command_line/integrate.py | 19 +++--- command_line/make_sphinx_html.py | 5 +- command_line/merge.py | 15 ++--- command_line/merge_cbf.py | 3 +- command_line/merge_reflection_lists.py | 1 + command_line/missing_reflections.py | 4 +- command_line/model_background.py | 10 ++-- command_line/modify_geometry.py | 3 +- command_line/plot_Fo_vs_Fc.py | 15 +++-- command_line/plot_reflections.py | 6 +- command_line/plot_scan_varying_model.py | 14 +++-- command_line/plugins.py | 3 +- command_line/predict.py | 3 +- command_line/reciprocal_lattice_viewer.py | 4 +- command_line/refine.py | 21 ++++--- command_line/refine_bravais_settings.py | 3 +- command_line/refine_error_model.py | 32 +++++----- command_line/reflection_viewer.py | 4 +- command_line/reindex.py | 13 ++-- command_line/report.py | 26 ++++---- command_line/rl_csv.py | 6 +- command_line/rl_png.py | 2 +- command_line/rs_mapper.py | 7 ++- command_line/scale.py | 10 +++- command_line/search_beam_position.py | 13 ++-- command_line/sequence_to_stills.py | 5 +- command_line/shadow_plot.py | 6 +- command_line/show.py | 8 ++- command_line/show_extensions.py | 3 +- command_line/slice_sequence.py | 6 +- command_line/sort_reflections.py | 3 +- command_line/split_experiments.py | 7 ++- command_line/spot_counts_per_image.py | 3 +- command_line/stereographic_projection.py | 9 ++- command_line/stills_process.py | 49 +++++++++------ command_line/symmetry.py | 35 ++++++----- command_line/two_theta_offset.py | 3 +- command_line/two_theta_refine.py | 20 +++---- command_line/unit_cell_histogram.py | 4 +- command_line/version.py | 5 +- data/lookup.py | 1 + data/multiprocessing.py | 1 + doc/examples/boilerplate.py | 14 ++--- .../read_experiment_and_data/experiment_data.py | 3 +- doc/sphinx/conf.py | 6 +- doc/sphinx/update_release_list.py | 4 +- extensions/auto_background_ext.py | 3 +- ...dispersion_extended_spotfinder_threshold_ext.py | 4 +- extensions/dispersion_spotfinder_threshold_ext.py | 2 +- extensions/glm_background_ext.py | 1 + extensions/gmodel_background_ext.py | 1 + extensions/simple_background_ext.py | 1 + installer/bootstrap.py | 4 +- installer/dials_installer.py | 3 +- libtbx_refresh.py | 9 ++- newsfragments/1377.api | 2 + newsfragments/README.MD | 7 ++- nexus/__init__.py | 2 + precommitbx/_precommitbx/main.py | 2 + precommitbx/installer.py | 8 ++- precommitbx/setup.py | 1 + pychef/__init__.py | 3 +- pychef/test_pychef.py | 6 +- pyproject.toml | 12 ++-- report/analysis.py | 6 +- report/html_report.py | 1 + report/plots.py | 13 ++-- report/test_analysis.py | 20 ++++--- report/test_plots.py | 12 ++-- setup.py | 3 +- test/algorithms/background/test_gmodel.py | 5 +- test/algorithms/background/test_modeller.py | 4 +- .../background/test_mosflm_outlier_rejector.py | 8 ++- .../algorithms/background/test_outlier_rejector.py | 10 ++-- .../test_generate_test_refl.py | 4 +- .../image/fill_holes/test_simple_fill.py | 3 +- test/algorithms/image/filter/test_distance.py | 9 ++- .../image/filter/test_index_of_dispersion.py | 3 +- .../image/filter/test_mean_and_variance.py | 12 ++-- test/algorithms/image/filter/test_median.py | 2 + test/algorithms/image/filter/test_summed_area.py | 3 +- test/algorithms/image/test_centroid.py | 32 ++++++---- test/algorithms/image/threshold/test_local.py | 39 ++++++++---- .../integration/profile/test_circle_sampler.py | 9 ++- .../integration/profile/test_empirical_modeller.py | 10 ++-- .../integration/profile/test_grid_sampler.py | 6 +- .../profile/test_multi_experiment_modeller.py | 6 +- .../integration/profile/test_profile_fitting.py | 1 + .../integration/profile/test_single_sampler.py | 6 +- test/algorithms/integration/test_corrections.py | 6 +- .../algorithms/integration/test_filter_overlaps.py | 1 + test/algorithms/integration/test_filtering.py | 1 + test/algorithms/integration/test_interface.py | 30 ++++++---- test/algorithms/integration/test_kapton.py | 6 +- .../integration/test_parallel_integrator.py | 32 +++++----- test/algorithms/polygon/clip/test_clipping.py | 3 +- .../polygon/test_spatial_interpolation.py | 22 ++++--- test/algorithms/refinement/setup_geometry.py | 12 +--- test/algorithms/refinement/setup_minimiser.py | 9 ++- test/algorithms/refinement/test_beam_parameters.py | 4 +- .../algorithms/refinement/test_centroid_outlier.py | 2 + test/algorithms/refinement/test_constraints.py | 17 ++++-- .../refinement/test_crystal_parameters.py | 17 +++--- .../algorithms/refinement/test_cspad_refinement.py | 3 +- .../refinement/test_detector_parameters.py | 20 +++---- test/algorithms/refinement/test_dials-423.py | 7 ++- test/algorithms/refinement/test_finite_diffs.py | 40 +++++++------ .../refinement/test_goniometer_parameters.py | 10 ++-- .../test_hierarchical_detector_refinement.py | 20 +++---- .../refinement/test_multi_experiment_refinement.py | 40 ++++++------- .../test_multi_panel_detector_parameterisation.py | 57 +++++++----------- .../refinement/test_orientation_refinement.py | 48 +++++++-------- .../refinement/test_parameter_auto_reduction.py | 24 ++++---- .../refinement/test_prediction_parameters.py | 40 ++++++------- .../refinement/test_ref_passage_categorisation.py | 22 +++---- .../refinement/test_refine_multi_stills.py | 6 +- .../refinement/test_refine_multi_wedges.py | 4 +- .../refinement/test_refinement_regression.py | 45 +++++++------- test/algorithms/refinement/test_refiner_config.py | 11 ++-- test/algorithms/refinement/test_refiner_units.py | 1 + .../refinement/test_restraints_gradients.py | 9 ++- .../refinement/test_restraints_parameterisation.py | 51 ++++++++-------- .../refinement/test_rotation_decomposition.py | 3 +- .../test_scan_varying_beam_refinement.py | 1 + .../test_scan_varying_block_calculation.py | 17 +++--- .../test_scan_varying_model_parameters.py | 26 ++++---- .../test_scan_varying_prediction_parameters.py | 28 +++++---- .../test_stills_prediction_parameters.py | 47 ++++++--------- .../refinement/test_stills_refinement.py | 34 +++++------ .../test_stills_spherical_relp_derivatives.py | 26 ++++---- .../refinement/test_sv_multi_panel_refinement.py | 2 + .../refinement/test_two_theta_refinement.py | 22 +++---- test/algorithms/refinement/test_xfel_metrology.py | 14 +++-- .../reflection_basis/test_beam_vector_map.py | 4 +- .../reflection_basis/test_coordinate_system.py | 4 +- .../reflection_basis/test_grid_index_generator.py | 4 +- .../algorithms/reflection_basis/test_map_frames.py | 16 +++-- test/algorithms/reflection_basis/test_transform.py | 11 ++-- test/algorithms/shoebox/test_bbox_calculator.py | 9 ++- test/algorithms/shoebox/test_mask_foreground.py | 13 ++-- test/algorithms/shoebox/test_mask_overlapping.py | 8 ++- .../shoebox/test_partiality_calculator.py | 3 +- .../spot_prediction/test_index_generator.py | 8 ++- .../spot_prediction/test_pixel_to_miller_index.py | 3 +- .../spot_prediction/test_ray_predictor.py | 25 ++++---- .../spot_prediction/test_reeke_index_generator.py | 8 +-- .../spot_prediction/test_rotation_angles.py | 6 +- .../test_scan_static_reflection_predictor.py | 1 + .../spot_prediction/test_scan_varying_predictor.py | 20 +++---- .../test_scan_varying_reflection_predictor.py | 12 ++-- .../spot_prediction/test_spot_prediction.py | 16 +++-- .../test_stills_reflection_predictor.py | 5 +- .../statistics/test_delta_cchalf_algorithm.py | 6 +- test/algorithms/statistics/test_fast_mcd.py | 17 +++--- test/array_family/test_flex_shoebox.py | 8 +-- test/array_family/test_identifiers_handling.py | 3 +- test/array_family/test_reflection_table.py | 8 ++- test/command_line/test_anvil_correction.py | 4 +- .../test_assign_experiment_identifiers.py | 4 +- test/command_line/test_check_indexing_symmetry.py | 1 + test/command_line/test_cluster_unit_cell.py | 3 +- test/command_line/test_combine_experiments.py | 7 ++- test/command_line/test_compute_delta_cchalf.py | 4 +- test/command_line/test_cosym.py | 6 +- test/command_line/test_create_profile_model.py | 1 + test/command_line/test_damage_analysis.py | 5 +- test/command_line/test_detect_blanks.py | 1 + test/command_line/test_estimate_resolution.py | 2 + test/command_line/test_export.py | 10 ++-- test/command_line/test_export_bitmaps.py | 1 + test/command_line/test_filter_reflections.py | 1 + test/command_line/test_find_spots.py | 2 +- test/command_line/test_find_spots_server_client.py | 5 +- test/command_line/test_frame_orientations.py | 6 +- test/command_line/test_generate_distortion_maps.py | 16 ++--- test/command_line/test_generate_mask.py | 9 +-- test/command_line/test_import.py | 1 + test/command_line/test_import_xds.py | 1 + test/command_line/test_integrate.py | 6 +- test/command_line/test_merge.py | 4 +- test/command_line/test_modify_geometry.py | 1 + test/command_line/test_plot_scan_varying_model.py | 1 + test/command_line/test_predict.py | 1 + .../test_preservation_of_experiment_identifiers.py | 2 + test/command_line/test_refine.py | 5 +- test/command_line/test_refine_bravais_settings.py | 2 + test/command_line/test_reindex.py | 6 +- test/command_line/test_search_beam_position.py | 11 ++-- test/command_line/test_sequence_to_stills.py | 1 + test/command_line/test_show.py | 3 +- test/command_line/test_show_extensions.py | 1 + test/command_line/test_slice_sequence.py | 4 +- test/command_line/test_split_experiments.py | 4 +- .../command_line/test_stereographic_projections.py | 3 +- test/command_line/test_stills_process.py | 6 +- test/command_line/test_symmetry.py | 16 ++--- test/command_line/test_two_theta_refine.py | 1 + test/framework/test_interface.py | 8 +-- test/model/data/test_pixel_list.py | 15 +++-- test/model/data/test_shoebox.py | 6 +- test/test_phil.py | 5 +- test/test_scan_varying_integration_bug.py | 5 +- test/util/__init__.py | 1 + test/util/test_batch_handling.py | 9 +-- test/util/test_exception_handler.py | 4 +- test/util/test_exclude_images.py | 12 ++-- test/util/test_filter_reflections_export.py | 28 +++++---- test/util/test_masking.py | 6 +- test/util/test_multi_dataset_handling.py | 8 ++- test/util/test_nexus.py | 6 +- test/util/test_nexus_multi_experiment.py | 10 +++- test/util/test_observer.py | 3 +- test/util/test_options.py | 8 ++- util/__init__.py | 7 ++- util/ascii_art.py | 1 + util/batch_handling.py | 2 + util/best.py | 4 +- util/cluster_map.py | 3 +- util/command_line.py | 3 +- util/detect_blanks.py | 1 - util/exclude_images.py | 6 +- util/export_mmcif.py | 9 +-- util/export_mtz.py | 15 ++--- util/export_sadabs.py | 3 +- util/export_xds_ascii.py | 2 +- util/filter_reflections.py | 15 ++--- util/image_viewer/mask_frame.py | 11 ++-- util/image_viewer/rstbx_frame.py | 14 +++-- util/image_viewer/slip_viewer/calibration_frame.py | 1 + util/image_viewer/slip_viewer/frame.py | 14 +++-- util/image_viewer/slip_viewer/pyslip.py | 18 +++--- util/image_viewer/slip_viewer/rotate_detector.py | 2 + util/image_viewer/slip_viewer/score_frame.py | 6 +- util/image_viewer/slip_viewer/tile_generation.py | 5 +- util/image_viewer/slip_viewer/uc_frame.py | 5 +- util/image_viewer/spotfinder_frame.py | 32 +++++----- util/image_viewer/spotfinder_wrap.py | 10 ++-- util/image_viewer/viewer_tools.py | 3 +- util/intensity_explorer.py | 3 +- util/log.py | 3 +- util/masking.py | 12 ++-- util/missing_reflections.py | 2 +- util/mp.py | 1 + util/multi_dataset_handling.py | 1 + util/nexus/__init__.py | 6 +- util/nexus/nx_mx.py | 6 +- util/nexus/nx_reflections.py | 1 + util/options.py | 16 +++-- util/phil.py | 4 +- util/pprint.py | 3 +- util/pycbf_extra.py | 5 +- util/reciprocal_lattice/conftest.py | 1 + util/reciprocal_lattice/test_render_3d.py | 1 + util/reciprocal_lattice/viewer.py | 6 +- util/resolution_analysis.py | 12 ++-- util/scale_down_image.py | 5 +- util/test_detect_blanks.py | 1 + util/test_missing_reflections.py | 1 + util/test_python_streambuf.py | 6 +- util/test_resolution_analysis.py | 2 +- util/test_slice.py | 3 +- util/wx_viewer.py | 12 ++-- util/xds.py | 3 +- viewer/bitmap_from_array.py | 1 + viewer/flex_3d_array_viewer_tests.py | 2 +- viewer/slice_viewer.py | 4 +- viewer/viewer_low_level_util.py | 10 ++-- 497 files changed, 2509 insertions(+), 1983 deletions(-) create mode 100644 newsfragments/1377.api Current branch master is up to date. Updating 'probe': At revision 103. Updating 'reduce': At revision 318. Already up to date. Current branch master is up to date. Already up to date. Current branch master is up to date. There is no tracking information for the current branch. Please specify which branch you want to rebase against. See git-pull(1) for details. git pull If you wish to set tracking information for this branch you can do so with: git branch --set-upstream-to=origin/ master ===== 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\phenix_dev_doc: git pull --rebase ===== Running in modules\amber_library: git pull --rebase Existing non-git directory -- don't know what to do. skipping: ccp4io_adaptbx ===== Running in modules\solve_resolve: git pull --rebase Process failed with return code 1