19/08/2020 6:00:06.51 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 98629 100 98629 0 0 98629 0 0:00:01 --:--:-- 0:00:01 342k 19/08/2020 6:00:13.59 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 ******************************************************************************* 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 a22751ef4..d4b384e7f master -> origin/master + a2264f30a...053e026cf delta_cc_half_sigma -> origin/delta_cc_half_sigma (forced update) * [new branch] dials-3.1 -> origin/dials-3.1 + 03456a473...8ecf59f9b dials-next -> origin/dials-next (forced update) a3a419810..00a84c273 dials-next-2.2 -> origin/dials-next-2.2 0e7c6f144..891d386e1 dont-copy-input -> origin/dont-copy-input * [new branch] import_select_reference -> origin/import_select_reference * [new branch] mypy -> origin/mypy 3e1c5fddd..e99b22424 not-params -> origin/not-params * [new branch] python38default -> origin/python38default a5a8f06d0..794bff46b reindex-cb-op-test -> origin/reindex-cb-op-test * [new branch] resolution_none -> origin/resolution_none * [new branch] rewrite_news -> origin/rewrite_news * [new branch] scaled_flag -> origin/scaled_flag * [new tag] v3.1.0 -> v3.1.0 Updating a22751ef4..d4b384e7f Fast-forward .codecov.yml | 5 + .conda-envs/linux.txt | 2 +- .conda-envs/macos.txt | 2 +- .conda-envs/windows.txt | 2 +- AUTHORS | 1 + CHANGELOG.rst | 66 +++ README.md | 1 + algorithms/indexing/assign_indices.py | 8 +- algorithms/indexing/indexer.py | 14 +- algorithms/indexing/model_evaluation.py | 16 +- algorithms/indexing/test_index.py | 26 + algorithms/refinement/gaussian_smoother.h | 1 + algorithms/refinement/gaussian_smoother_2D.h | 2 + algorithms/refinement/gaussian_smoother_3D.h | 3 + .../parameterisation/model_parameters.py | 9 +- .../scan_varying_model_parameters.py | 6 +- algorithms/refinement/target.py | 5 - algorithms/scaling/algorithm.py | 13 +- .../model/components/smooth_scale_components.py | 12 +- algorithms/scaling/model/model.py | 45 +- algorithms/scaling/observers.py | 46 +- algorithms/scaling/scaling_library.py | 102 +--- algorithms/scaling/test_scaling_library.py | 18 +- command_line/background.py | 16 +- command_line/combine_experiments.py | 30 +- command_line/generate_tutorial_text.py | 74 +++ command_line/integrate.py | 19 +- command_line/plot_reflections.py | 41 +- command_line/rl_csv.py | 2 - command_line/search_beam_position.py | 2 - command_line/shadow_plot.py | 16 +- command_line/stereographic_projection.py | 2 +- doc/sphinx/documentation/tutorials/index.rst | 1 + doc/sphinx/documentation/tutorials/mpro_x0692.rst | 622 +++++++++++++++++++++ .../processing_in_detail_betalactamase.rst | 4 +- doc/sphinx/index.rst | 1 + newsfragments/1184.misc | 1 - newsfragments/1216.misc | 1 - newsfragments/1235.feature | 7 - newsfragments/1235.removal | 2 - newsfragments/1236.feature | 1 - newsfragments/1275.bugfix | 1 - newsfragments/1285.feature | 1 - newsfragments/1288.misc | 2 - newsfragments/1300.bugfix | 1 - newsfragments/1302.feature | 6 - newsfragments/1306.removal | 1 - newsfragments/1312.misc | 1 - newsfragments/1313.removal | 1 - newsfragments/1316.bugfix | 2 - newsfragments/1319.feature | 1 - newsfragments/1320.misc | 7 - newsfragments/1322.misc | 1 - newsfragments/1325.misc | 1 - newsfragments/1328.misc | 1 - newsfragments/1330.feature | 1 - newsfragments/1332.feature | 1 - report/plots.py | 4 +- test/command_line/test_anvil_correction.py | 6 +- test/command_line/test_combine_experiments.py | 32 ++ test/command_line/test_integrate.py | 39 +- test/command_line/test_show.py | 4 +- .../command_line/test_stereographic_projections.py | 19 +- test/test_plot_reflections.py | 26 +- test/util/test_masking.py | 44 +- util/image_viewer/spotfinder_frame.py | 14 +- util/masking.py | 6 + util/test_resolution_analysis.py | 2 +- 68 files changed, 1152 insertions(+), 320 deletions(-) create mode 100644 doc/sphinx/documentation/tutorials/mpro_x0692.rst delete mode 100644 newsfragments/1184.misc delete mode 100644 newsfragments/1216.misc delete mode 100644 newsfragments/1235.feature delete mode 100644 newsfragments/1235.removal delete mode 100644 newsfragments/1236.feature delete mode 100644 newsfragments/1275.bugfix delete mode 100644 newsfragments/1285.feature delete mode 100644 newsfragments/1288.misc delete mode 100644 newsfragments/1300.bugfix delete mode 100644 newsfragments/1302.feature delete mode 100644 newsfragments/1306.removal delete mode 100644 newsfragments/1312.misc delete mode 100644 newsfragments/1313.removal delete mode 100644 newsfragments/1316.bugfix delete mode 100644 newsfragments/1319.feature delete mode 100644 newsfragments/1320.misc delete mode 100644 newsfragments/1322.misc delete mode 100644 newsfragments/1325.misc delete mode 100644 newsfragments/1328.misc delete mode 100644 newsfragments/1330.feature delete mode 100644 newsfragments/1332.feature Current branch master is up to date. Updating 'probe': At revision 103. Updating 'reduce': At revision 317. From https://github.com/cctbx/dxtbx 00d9702..979ede8 master -> origin/master * [new branch] factor_ev_angstrom -> origin/factor_ev_angstrom * [new branch] more-nexus-than-nexus -> origin/more-nexus-than-nexus * [new branch] mpi_average_fixes -> origin/mpi_average_fixes * [new branch] multiimage_use_indices -> origin/multiimage_use_indices * [new branch] nexus-py-fixes -> origin/nexus-py-fixes * [new branch] py3_imagepickle -> origin/py3_imagepickle Updating 00d9702..979ede8 Fast-forward CHANGELOG.rst | 22 ++++ SConscript | 1 + boost_python/imageset_ext.cc | 6 +- command_line/radial_average.py | 5 +- command_line/show_mask_info.py | 19 ++++ format/Format.py | 14 ++- format/FormatHDF5EigerNearlyNexus.py | 4 +- format/FormatHDF5PAL.py | 2 +- format/FormatMultiImage.py | 3 + format/FormatNexus.py | 8 +- format/FormatNexusJungfrauHack.py | 6 +- format/nexus.py | 102 ++++++++++++++---- imageset.py | 13 +++ model/__init__.py | 2 + model/boost_python/detector.cc | 1 - model/boost_python/model_ext.cc | 2 + model/boost_python/spectrum.cc | 83 +++++++++++++++ model/spectrum.h | 132 ++++++++++++++++++++++++ newsfragments/177.feature | 1 - tests/command_line/test_show_mask_info.py | 13 +++ tests/format/test_FormatHDF5EigerNearlyNexus.py | 2 +- tests/model/test_spectrum.py | 90 ++++++++++++++++ tests/serialize/test_xds.py | 10 +- util/__init__.py | 18 +++- 24 files changed, 513 insertions(+), 46 deletions(-) create mode 100644 command_line/show_mask_info.py create mode 100644 model/boost_python/spectrum.cc create mode 100644 model/spectrum.h delete mode 100644 newsfragments/177.feature create mode 100644 tests/command_line/test_show_mask_info.py create mode 100644 tests/model/test_spectrum.py 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\dxtbx: 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