15/10/2019 12:00:24.45 15/10/2019 12:00:24.76 C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current>((ROBOCOPY empty dist /MIR /COPYALL 1>nul ) & rmdir /S /Q dist\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current>((ROBOCOPY empty tests /MIR /COPYALL 1>nul ) & rmdir /S /Q tests\ & ) C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current>((ROBOCOPY empty doc /MIR /COPYALL 1>nul ) & rmdir /S /Q doc\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current>((ROBOCOPY empty tmp /MIR /COPYALL 1>nul ) & rmdir /S /Q tmp\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current>((ROBOCOPY empty base /MIR /COPYALL 1>nul ) & rmdir /S /Q base\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\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\CCTBXVC2008\x64\Current>((ROBOCOPY empty build /MIR /COPYALL 1>nul ) & rmdir /S /Q build\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\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 ===== Running in .: deleting dist, tests, doc, tmp, base, base_tmp, build, conda_base ===== Downloading http://cci.lbl.gov/repositories/annlib.gz: 0.5 MB [0%.........20%.........40%.........60%.........80%.........100%] ===== Running in modules: extracting files from annlib.gz ===== Downloading http://cci.lbl.gov/repositories/scons.gz: 0.6 MB [0%.........20%.........40%.........60%.........80%.........100%] ===== Running in modules: extracting files from scons.gz ===== Downloading http://cci.lbl.gov/repositories/ccp4io.gz: 1.4 MB [0%.........20%.........40%.........60%.........80%.........100%] ===== Running in modules: extracting files from ccp4io.gz ===== Downloading http://cci.lbl.gov/repositories/eigen.gz: 1.5 MB [0%.........20%.........40%.........60%.........80%.........100%] ===== Running in modules: extracting files from eigen.gz ===== Downloading http://cci.lbl.gov/repositories/clipper.gz: 0.6 MB [0%.........20%.........40%.........60%.........80%.........100%] Already up to date. Current branch master is up to date. From https://github.com/cctbx/cctbx_project 54344b84c..8ddf49c09 master -> origin/master 40ec2f73e..3bc17a7fd LS49_exp -> origin/LS49_exp 6d76c2292..ae60ea87a diffBragg -> origin/diffBragg + 14d82acca...042400897 test -> origin/test (forced update) Updating 54344b84c..8ddf49c09 Fast-forward .azure-pipelines/unix-conda-build.yml | 1 + cctbx/geometry_restraints/__init__.py | 4 +- cctbx/geometry_restraints/auto_linking_types.py | 24 +- cctbx/geometry_restraints/manager.py | 25 +- cctbx/regression/tst_geometry_restraints_2.py | 13 +- crys3d/hklview/NGL_HKLviewerGui.py | 2 +- crys3d/hklview/jsview_3d.py | 42 +- libtbx/auto_build/bootstrap.py | 43 +- libtbx/auto_build/install_conda.py | 44 ++ mmtbx/model/statistics.py | 2 +- mmtbx/monomer_library/tst_carbo_linking.py | 151 ++++ mmtbx/monomer_library/tst_paral_geo.py | 794 +++++++++++++++++++++ .../ncs/tst_minimization_ncs_constraints.py | 3 +- mmtbx/run_tests.py | 2 + mmtbx/secondary_structure/nucleic_acids.py | 14 +- 15 files changed, 1103 insertions(+), 61 deletions(-) create mode 100644 mmtbx/monomer_library/tst_carbo_linking.py create mode 100644 mmtbx/monomer_library/tst_paral_geo.py Current branch master is up to date. Already up to date. Current branch master is up to date. ===== Running in modules: extracting files from clipper.gz ===== Running in modules\cbflib: git pull --rebase ===== Running in modules\cctbx_project: git pull --rebase ===== Running in modules\annlib_adaptbx: git pull --rebase ===== Downloading http://cci.lbl.gov/repositories/tntbx.gz: 38.0 kB [0%.........20%.........40%.........60%.........80%.........100%] From https://github.com/cctbx/dxtbx 3e448d4..a317a41 master -> origin/master Updating 3e448d4..a317a41 Fast-forward README.md | 2 +- boost_python/imageset_ext.cc | 70 ++++---- command_line/import_datablock.py | 22 +-- command_line/print_beam_centre.py | 8 +- command_line/print_matching_images.py | 2 +- command_line/{print_sweep.py => print_sequence.py} | 22 +-- ...rint_sweep_check.py => print_sequence_check.py} | 8 +- command_line/{read_sweep.py => read_sequence.py} | 18 +- command_line/to_ewald_sphere.py | 16 +- command_line/to_xds.py | 8 +- datablock.py | 107 ++++++----- example/to_xds.py | 20 +-- format/Format.py | 36 ++-- format/FormatMultiImage.py | 32 ++-- format/FormatMultiImageLazy.py | 4 +- format/nexus.py | 8 +- format/test_cbf_mini_as_file.py | 5 +- imageset.h | 56 +++--- imageset.py | 90 +++++----- model/__init__.py | 21 +-- model/boost_python/experiment.cc | 4 +- model/experiment.h | 2 +- model/experiment_list.py | 41 +++-- newsfragments/89.bugfix | 2 +- sweep_filenames.py => sequence_filenames.py | 4 +- serialize/imageset.py | 63 +++---- serialize/xds.py | 19 +- tests/command_line/test_to_xds.py | 9 +- tests/format/test_FormatHDF5EigerNearlyNexus.py | 2 - tests/model/test_experiment_list.py | 31 ++-- tests/model/test_scan_helpers.py | 2 +- tests/serialize/test_xds.py | 14 +- tests/test_datablock.py | 67 ++++--- tests/test_imageset.py | 195 ++++++++++----------- ...eep_filenames.py => test_sequence_filenames.py} | 2 +- 35 files changed, 505 insertions(+), 507 deletions(-) rename command_line/{print_sweep.py => print_sequence.py} (62%) rename command_line/{print_sweep_check.py => print_sequence_check.py} (54%) rename command_line/{read_sweep.py => read_sequence.py} (52%) rename sweep_filenames.py => sequence_filenames.py (98%) rename tests/{test_sweep_filenames.py => test_sequence_filenames.py} (91%) Current branch master is up to date. ===== Running in modules: extracting files from tntbx.gz ===== Running in modules\dxtbx: git pull --rebase ===== Downloading http://cci.lbl.gov/repositories/ccp4io_adaptbx.gz: 203.9 kB [0%.........20%.........40%.........60%.........80%.........100%] Already up to date. Current branch master is up to date. ===== Running in modules: extracting files from ccp4io_adaptbx.gz ===== Running in modules\boost: git pull --rebase ===== Downloading http://cci.lbl.gov/repositories/gui_resources.gz: 2.1 MB [0%.........20%.........40%.........60%.........80%.........100%] ===== Running in modules: extracting files from gui_resources.gz removing .pyc files in C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules, walk? True removed 0 files Bootstrap success: cleanup, hot, update 15/10/2019 12:01:21.48 15/10/2019 12:01:21.56 Performing actions: base build Installing base packages using: python modules\cctbx_project\libtbx\auto_build\install_conda.py --builder=cctbx Traceback (most recent call last): File "bootstrap.py", line 2721, in run() File "bootstrap.py", line 2716, in run use_conda=options.use_conda, File "bootstrap.py", line 1119, in __init__ self.add_configure() File "bootstrap.py", line 1753, in add_configure self.python_base = self._get_conda_python() File "bootstrap.py", line 1513, in _get_conda_python m = self._get_conda_manager() File "bootstrap.py", line 1503, in _get_conda_manager check_file=check_file, log=log) File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\auto_build\install_conda.py", line 327, in __init__ env=self.env)) File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\auto_build\install_conda.py", line 57, in check_output returncode = subprocess.check_call(command_list, stdout=f, *args, **kwargs) File "C:\Python27amd64\lib\subprocess.py", line 190, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['cmd', '/c', 'C:\\Users\\phaserbuilder\\PhaserTng2\\mc3\\Scripts\\conda.exe', 'info', '--json']' returned non-zero exit status 1 15/10/2019 12:01:25.55