15/09/2020 6:00:04.59 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 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 98898 100 98898 0 0 98898 0 0:00:01 --:--:-- 0:00:01 363k 15/09/2020 6:00:10.34 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 83fbc7986..ab0842ac5 master -> origin/master 88c187e2d..c563cd297 dials-3.1 -> origin/dials-3.1 33d17537a..7f1e1de13 dials-next -> origin/dials-next ae6b31461..fe384dc31 image-viewer-fixes -> origin/image-viewer-fixes * [new branch] procrunner -> origin/procrunner Updating 83fbc7986..ab0842ac5 Fast-forward CHANGELOG.rst | 18 +++++++++ algorithms/integration/integrator.py | 3 +- .../refinement/parameterisation/configure.py | 8 ++++ algorithms/refinement/refiner.py | 7 ++-- algorithms/refinement/reflection_manager.py | 31 ++++++++++----- newsfragments/1374.feature | 2 + newsfragments/1374.removal | 2 + newsfragments/1399.misc | 1 - .../refinement/test_reflection_manager.py | 46 ++++++++++++++++++++++ 9 files changed, 104 insertions(+), 14 deletions(-) create mode 100644 newsfragments/1374.feature create mode 100644 newsfragments/1374.removal delete mode 100644 newsfragments/1399.misc create mode 100644 test/algorithms/refinement/test_reflection_manager.py Current branch master is up to date. Updating 'probe': At revision 103. Updating 'reduce': At revision 318. From https://github.com/phenix-project/phenix_dev_doc 2a620f7..65f12c5 master -> origin/master Updating 2a620f7..65f12c5 Fast-forward html_files/doc_fit_ligand.html | 22 +- .../doc_high_level_model_building_intro.html | 77 ++++ html_files/doc_model_building_1.html | 36 +- html_files/doc_model_building_2.html | 29 +- ...ding_segment.html => doc_model_building_3.html} | 73 +++- html_files/doc_model_building_morphing.html | 177 ++++++++ html_files/doc_model_building_read_files.html | 6 +- html_files/doc_model_building_sequence.html | 99 +++++ html_files/doc_quick_reference.html | 473 +++++++++++++++++++++ html_files/template.html | 6 +- regression/__init__.py | 0 regression/exercise.py | 49 +++ regression/tst_doc_fit_ligand.py | 11 + regression/tst_doc_model_building_1.py | 11 + regression/tst_doc_model_building_2.py | 11 + regression/tst_doc_model_building_3.py | 11 + regression/tst_doc_model_building_morphing.py | 11 + regression/tst_doc_model_building_read_files.py | 54 +++ regression/tst_doc_model_building_sequence.py | 11 + regression/tst_doc_quick_reference.py | 11 + run_tests.py | 9 +- 21 files changed, 1154 insertions(+), 33 deletions(-) create mode 100644 html_files/doc_high_level_model_building_intro.html rename html_files/{doc_model_building_segment.html => doc_model_building_3.html} (52%) create mode 100644 html_files/doc_model_building_morphing.html create mode 100644 html_files/doc_model_building_sequence.html create mode 100644 html_files/doc_quick_reference.html create mode 100644 regression/__init__.py create mode 100644 regression/exercise.py create mode 100644 regression/tst_doc_fit_ligand.py create mode 100644 regression/tst_doc_model_building_1.py create mode 100644 regression/tst_doc_model_building_2.py create mode 100644 regression/tst_doc_model_building_3.py create mode 100644 regression/tst_doc_model_building_morphing.py create mode 100644 regression/tst_doc_model_building_read_files.py create mode 100644 regression/tst_doc_model_building_sequence.py create mode 100644 regression/tst_doc_quick_reference.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\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