18/10/2020 12:00:46.86 18/10/2020 12:00:48.78 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\ & ) The system cannot find the file specified. 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\ & ) Already up to date. Current branch master is up to date. From https://github.com/cctbx/cctbx_project eeb1a7159b..440c1ebf4d master -> origin/master b4e2bb9ee9..551ef9e652 NGL_HKLviewer2 -> origin/NGL_HKLviewer2 + 0f1b2f7614...88f98797c1 boost172 -> origin/boost172 (forced update) * [new branch] cctbx -> origin/cctbx + d3b7f2cc23...3b99ed926f diffBragg -> origin/diffBragg (forced update) db7bf59f27..18dd2ecdc4 exafel_api -> origin/exafel_api + 2b0dd9257c...6999769387 fixed-width-int-types -> origin/fixed-width-int-types (forced update) * [new branch] hydrogenate -> origin/hydrogenate * [new branch] model_box_cs -> origin/model_box_cs * [new branch] new_phi_psi_2_rama_restraints -> origin/new_phi_psi_2_rama_restraints 862e03f58c..38ca59f920 psana_api -> origin/psana_api * [new branch] r_friedel -> origin/r_friedel + b386c1a62c...827ae638fc shifter-fixes-2 -> origin/shifter-fixes-2 (forced update) f0ea15d47e..42e5688e80 xfel_unit_cell -> origin/xfel_unit_cell Updating eeb1a7159b..440c1ebf4d Fast-forward .azure-pipelines/conda-linux.yml | 5 + .azure-pipelines/conda-osx.yml | 5 + .azure-pipelines/conda-win.yml | 4 + .azure-pipelines/download-conda.yml | 9 + .azure-pipelines/syntax.yml | 5 +- .azure-pipelines/xfel/conda-linux.yml | 1 + .github/workflows/mirror.yml | 18 +- .../geometry_restraints/tst_nonbonded_overlaps.py | 12 +- cctbx/maptbx/asymmetric_map.h | 6 +- cctbx/maptbx/box.py | 13 +- cctbx/maptbx/refine_sharpening.py | 353 +++++++-- cctbx/maptbx/segment_and_split_map.py | 1 - cctbx/regression/tst_maptbx_box.py | 6 +- cctbx/regression/tst_twin_target.py | 10 +- cctbx/sgtbx/direct_space_asu/proto/tst_asu.cpp | 4 +- gltbx/gl_managed.py | 16 +- gltbx/opengl_specs.txt | 4 +- iotbx/cif/__init__.py | 1 + iotbx/cif/model.py | 6 +- iotbx/cli_parser.py | 3 - iotbx/data_manager/__init__.py | 2 + iotbx/data_manager/common.py | 8 + iotbx/map_manager.py | 1 - iotbx/map_model_manager.py | 829 +++++++++++++++------ iotbx/merging_statistics.py | 15 +- iotbx/pdb/__init__.py | 13 +- iotbx/pdb/hierarchy.py | 4 +- iotbx/pdb/tst_mmcif_hierarchy_2.py | 14 + iotbx/regression/tst_map_model_manager_4.py | 70 +- .../tst_map_model_manager_call_consistency.py | 9 +- iotbx/regression/tst_merging_statistics.py | 7 +- .../auto_build/conda_envs/cctbx_py39_linux-64.txt | 73 ++ libtbx/auto_build/conda_envs/cctbx_py39_osx-64.txt | 70 ++ libtbx/auto_build/conda_envs/cctbx_py39_win-64.txt | 62 ++ libtbx/auto_build/conda_envs/py39_basic.yml | 33 + libtbx/command_line/pytest_launcher.py | 12 - libtbx/containers.py | 8 +- libtbx/introspection.py | 3 +- libtbx/program_template.py | 5 +- mmtbx/building/__init__.py | 10 +- mmtbx/command_line/find_tls_groups.py | 5 +- mmtbx/command_line/geometry_minimization.py | 8 +- mmtbx/command_line/hydrogenate.py | 6 + mmtbx/command_line/simulate_low_res_data.py | 8 +- mmtbx/hydrogens/__init__.py | 164 +--- mmtbx/hydrogens/parameterization.py | 9 +- mmtbx/hydrogens/reduce.py | 257 +++++++ mmtbx/hydrogens/riding.py | 6 +- mmtbx/hydrogens/specialised_hydrogen_atoms.py | 4 +- mmtbx/hydrogens/tst_add_hydrogen.py | 42 +- mmtbx/hydrogens/tst_add_hydrogen_2.py | 280 ++++++- mmtbx/ions/svm/__init__.py | 5 +- mmtbx/ligands/__init__.py | 87 --- mmtbx/ligands/hierarchy_utils.py | 36 +- mmtbx/ligands/ready_set_basics.py | 35 + mmtbx/ligands/ready_set_utils.py | 89 ++- mmtbx/masks/atom_mask.cpp | 54 +- mmtbx/model/model.py | 137 ++-- mmtbx/monomer_library/pdb_interpretation.py | 2 +- mmtbx/monomer_library/tst_linking.py | 2 +- mmtbx/monomer_library/tst_paral_geo.py | 2 +- mmtbx/ncs/ncs.py | 4 + mmtbx/programs/hydrogenate.py | 55 ++ mmtbx/regression/pdbs/ligand_before_prot.pdb | 47 ++ mmtbx/regression/tst_pdbtools.py | 1 - mmtbx/run_tests.py | 2 +- mmtbx/validation/molprobity/__init__.py | 2 +- .../regression/tst_do_flips_clashscore.py | 3 +- mmtbx/validation/regression/tst_symmetry_SS.py | 3 +- scitbx/array_family/accessors/c_interval_grid.h | 2 +- scitbx/math/breakpoint.py | 10 +- wxtbx/anomalous_scattering.py | 4 +- xfel/lcls_api/__init__.py | 0 xfel/lcls_api/exercise_api.py | 72 ++ xfel/lcls_api/psana_cctbx.py | 157 ++++ xfel/merging/application/balance/load_balancer.py | 13 + xfel/merging/application/integrate/integrate.py | 28 +- xfel/merging/application/model/crystal_model.py | 22 +- xfel/merging/application/phil/phil.py | 3 + xfel/merging/command_line/mpi_integrate.py | 9 +- xfel/pal/__init__.py | 0 xfel/pal/jf4m_geom2nexus.py | 253 +++++++ xfel/ui/components/xfel_gui_controls.py | 5 +- xfel/ui/components/xfel_gui_dialogs.py | 8 +- xfel/ui/db/job.py | 2 + xfel/ui/db/schema.sql | 3 +- xfel/ui/db/xfel_db.py | 11 + 87 files changed, 2810 insertions(+), 877 deletions(-) create mode 100644 libtbx/auto_build/conda_envs/cctbx_py39_linux-64.txt create mode 100644 libtbx/auto_build/conda_envs/cctbx_py39_osx-64.txt create mode 100644 libtbx/auto_build/conda_envs/cctbx_py39_win-64.txt create mode 100644 libtbx/auto_build/conda_envs/py39_basic.yml delete mode 100644 libtbx/command_line/pytest_launcher.py create mode 100644 mmtbx/command_line/hydrogenate.py create mode 100644 mmtbx/hydrogens/reduce.py create mode 100644 mmtbx/programs/hydrogenate.py create mode 100644 mmtbx/regression/pdbs/ligand_before_prot.pdb create mode 100644 xfel/lcls_api/__init__.py create mode 100644 xfel/lcls_api/exercise_api.py create mode 100644 xfel/lcls_api/psana_cctbx.py create mode 100644 xfel/pal/__init__.py create mode 100644 xfel/pal/jf4m_geom2nexus.py Current branch master is up to date. Already up to date. Current branch master is up to date. From https://github.com/dials/dxtbx 59c8db7..e85f4ec dials-3.1 -> origin/dials-3.1 5eab062..19169d3 dials-next -> origin/dials-next f227287..6c70ce6 master -> origin/master Already up to date. Current branch dials-2.2 is up to date. Your branch is up to date with 'origin/dials-2.2'. Already on 'dials-2.2' Branch 'dials-2.2' set up to track remote branch 'dials-2.2' from 'origin'. Already up to date. Current branch master is up to date. Performing actions: cleanup hot update ===== Running in .: deleting dist, tests, doc, tmp, base, base_tmp, build, conda_base Existing non-git directory -- don't know what to do. skipping: scons Existing non-git directory -- don't know what to do. skipping: annlib Existing non-git directory -- don't know what to do. skipping: clipper ===== Running in modules\cbflib: git pull --rebase ===== Running in modules\cctbx_project: git pull --rebase Existing non-git directory -- don't know what to do. skipping: eigen ===== Running in modules\annlib_adaptbx: git pull --rebase Existing non-git directory -- don't know what to do. skipping: ccp4io Existing non-git directory -- don't know what to do. skipping: tntbx ===== Running in modules\dxtbx: git pull --rebase ===== Running in modules\dxtbx: git remote set-url origin https://github.com/dials/dxtbx.git ===== Running in modules\dxtbx: git fetch origin ===== Running in modules\dxtbx: git checkout dials-2.2 ===== Running in modules\dxtbx: git branch --set-upstream-to=origin/dials-2.2 dials-2.2 Existing non-git directory -- don't know what to do. skipping: ccp4io_adaptbx ===== Running in modules\boost: git pull --rebase Existing non-git directory -- don't know what to do. skipping: gui_resources removing .pyc files in C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules, walk? True removed 1 files Bootstrap success: cleanup, hot, update 18/10/2020 12:41:58.14 18/10/2020 12:42:09.51 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\ & ) 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. Base conda installation: C:\Users\phaserbuilder\NightlyBuilds\PhaserVC2015\Current\mc3 Installing cctbx environment with: C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\auto_build\conda_envs\cctbx_py27_win-64.txt Completed installation into: C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base Python: 2.7.15 "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\python.exe" Compiler: default Build mode: release Warning level: 0 Precompiled Headers: False Static libraries: False Static exe: False Scan Boost headers: False Write full flex_fwd.h files: False Build Boost.Python extensions: True Define BOOST_PYTHON_NO_PY_SIGNATURES: False Define BOOST_PYTHON_BOOL_INT_STRICT: True Enable OpenMP if possible: False Boost threads enabled: True Enable CUDA: False Use conda: True Use opt_resources if available: False Use environment flags: False Enable C++11: False command_version_suffix: None Relocatable paths anchored at: c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build Top-down list of all modules involved: wxtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\wxtbx" gltbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\gltbx" crys3d "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\crys3d" cctbx_website "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cctbx_website" mmtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\mmtbx" iotbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\iotbx" dxtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\dxtbx" cbflib+adaptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cbflib" "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cbflib_adaptbx" ccp4io+adaptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\ccp4io" "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\ccp4io_adaptbx" smtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\smtbx" ucif "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\ucif" cctbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cctbx" scitbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\scitbx" fable "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\fable" omptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\omptbx" boost+adaptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\boost" "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\boost_adaptbx" tbxx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\tbxx" chiltbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\chiltbx" libtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\libtbx" Creating files in build directory: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build" dispatcher_include_template.bat setpaths.bat setpaths_all.bat setpaths_debug.bat unsetpaths.bat SConstruct Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\libtbx\command_line" Traceback (most recent call last): File "..\modules\cctbx_project\libtbx\configure.py", line 34, in if not run(): File "..\modules\cctbx_project\libtbx\configure.py", line 29, in run libtbx.env_config.cold_start(sys.argv) File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\env_config.py", line 3011, in cold_start env.refresh() File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\env_config.py", line 2227, in refresh module.process_command_line_directories() File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\env_config.py", line 2551, in process_command_line_directories scan_for_libtbx_set_dispatcher_name=True) File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\env_config.py", line 2448, in write_dispatcher try: import IPython File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\IPython\__init__.py", line 49, in from .terminal.embed import embed File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\IPython\terminal\embed.py", line 17, in from IPython.core.interactiveshell import DummyMod, InteractiveShell File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\IPython\core\interactiveshell.py", line 199, in class InteractiveShell(SingletonConfigurable): File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\IPython\core\interactiveshell.py", line 261, in InteractiveShell help="Set the color scheme (NoColor, Neutral, Linux, or LightBG)." File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\traitlets\traitlets.py", line 2151, in __init__ values = [cast_unicode_py2(value) for value in values] File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\ipython_genutils\py3compat.py", line 26, in cast_unicode return decode(s, encoding) File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\ipython_genutils\py3compat.py", line 17, in decode return s.decode(encoding, "replace") LookupError: unknown encoding: cp65001 Performing actions: base build Installing base packages using: python modules\cctbx_project\libtbx\auto_build\install_conda.py --builder=cctbx --install_conda --python=27 ===== Running in .: deleting dist, tests, tmp removing .pyc files in C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules, walk? True removed 2 files ===== Running in .: base ===== Running in build: run configure.py Process failed with return code 1 18/10/2020 13:02:43.41 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 tmp /MIR /COPYALL 1>nul ) & rmdir /S /Q tmp\ & ) The system cannot find the file specified. Python: 2.7.15 "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\python.exe" Compiler: default Build mode: release Warning level: 0 Precompiled Headers: False Static libraries: False Static exe: False Scan Boost headers: False Write full flex_fwd.h files: False Build Boost.Python extensions: True Define BOOST_PYTHON_NO_PY_SIGNATURES: False Define BOOST_PYTHON_BOOL_INT_STRICT: True Enable OpenMP if possible: False Boost threads enabled: True Enable CUDA: False Use conda: True Use opt_resources if available: False Use environment flags: False Enable C++11: False command_version_suffix: None Relocatable paths anchored at: c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build Top-down list of all modules involved: wxtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\wxtbx" gltbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\gltbx" crys3d "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\crys3d" cctbx_website "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cctbx_website" mmtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\mmtbx" iotbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\iotbx" dxtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\dxtbx" cbflib+adaptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cbflib" "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cbflib_adaptbx" ccp4io+adaptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\ccp4io" "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\ccp4io_adaptbx" smtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\smtbx" ucif "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\ucif" cctbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cctbx" scitbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\scitbx" fable "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\fable" omptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\omptbx" boost+adaptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\boost" "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\boost_adaptbx" tbxx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\tbxx" chiltbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\chiltbx" libtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\libtbx" Creating files in build directory: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build" dispatcher_include_template.bat setpaths.bat setpaths_all.bat setpaths_debug.bat unsetpaths.bat SConstruct Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\libtbx\command_line" Traceback (most recent call last): File "..\modules\cctbx_project\libtbx\configure.py", line 34, in if not run(): File "..\modules\cctbx_project\libtbx\configure.py", line 29, in run libtbx.env_config.cold_start(sys.argv) File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\env_config.py", line 3011, in cold_start env.refresh() File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\env_config.py", line 2227, in refresh module.process_command_line_directories() File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\env_config.py", line 2551, in process_command_line_directories scan_for_libtbx_set_dispatcher_name=True) File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\env_config.py", line 2448, in write_dispatcher try: import IPython File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\IPython\__init__.py", line 49, in from .terminal.embed import embed File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\IPython\terminal\embed.py", line 17, in from IPython.core.interactiveshell import DummyMod, InteractiveShell File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\IPython\core\interactiveshell.py", line 199, in class InteractiveShell(SingletonConfigurable): File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\IPython\core\interactiveshell.py", line 261, in InteractiveShell help="Set the color scheme (NoColor, Neutral, Linux, or LightBG)." File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\traitlets\traitlets.py", line 2151, in __init__ values = [cast_unicode_py2(value) for value in values] File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\ipython_genutils\py3compat.py", line 26, in cast_unicode return decode(s, encoding) File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\lib\site-packages\ipython_genutils\py3compat.py", line 17, in decode return s.decode(encoding, "replace") LookupError: unknown encoding: cp65001 Performing actions: build ===== Running in .: deleting dist, tests, tmp removing .pyc files in C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules, walk? True removed 2 files ===== Running in build: run configure.py Process failed with return code 1 18/10/2020 13:17:54.69