21/08/2020 12:01:46.01 21/08/2020 12:01:51.45 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\ & ) 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 2ad2c1cc1..d56548eb0 master -> origin/master 12720ba97..7aca3ed82 diffBragg -> origin/diffBragg + b909e55f0...8d60f7e4a encapsulate_twodev -> origin/encapsulate_twodev (forced update) 37f3479fa..d56548eb0 releases/v2020.08 -> origin/releases/v2020.08 Updating 2ad2c1cc1..d56548eb0 Fast-forward boost_adaptbx/python_streambuf.h | 2 +- cctbx/development/create_models_or_maps.py | 24 +- cctbx/maptbx/box.py | 22 ++ cctbx_website/doc_model_manager.html | 2 +- iotbx/data_manager/restraint.py | 1 + iotbx/map_manager.py | 16 +- iotbx/map_model_manager.py | 24 +- iotbx/regression/tst_map_model_manager_3.py | 14 +- libtbx/auto_build/conda_envs/README.md | 21 +- .../auto_build/conda_envs/cctbx_py27_linux-64.txt | 356 ++++++++++----------- libtbx/auto_build/conda_envs/cctbx_py27_osx-64.txt | 299 +++++++++-------- libtbx/auto_build/conda_envs/cctbx_py27_win-64.txt | 245 +++++++------- .../auto_build/conda_envs/cctbx_py36_linux-64.txt | 347 ++++++++++---------- libtbx/auto_build/conda_envs/cctbx_py36_osx-64.txt | 297 +++++++++-------- libtbx/auto_build/conda_envs/cctbx_py36_win-64.txt | 250 +++++++-------- .../auto_build/conda_envs/cctbx_py37_linux-64.txt | 347 ++++++++++---------- libtbx/auto_build/conda_envs/cctbx_py37_osx-64.txt | 297 +++++++++-------- libtbx/auto_build/conda_envs/cctbx_py37_win-64.txt | 250 +++++++-------- .../auto_build/conda_envs/cctbx_py38_linux-64.txt | 338 +++++++++---------- libtbx/auto_build/conda_envs/cctbx_py38_osx-64.txt | 288 ++++++++--------- libtbx/auto_build/conda_envs/cctbx_py38_win-64.txt | 240 +++++++------- .../conda_envs/cctbxlite_py27_linux-64.txt | 286 +++++++++-------- .../conda_envs/cctbxlite_py27_osx-64.txt | 227 ++++++------- .../conda_envs/cctbxlite_py27_win-64.txt | 201 ++++++------ .../conda_envs/cctbxlite_py36_linux-64.txt | 286 +++++++++-------- .../conda_envs/cctbxlite_py36_osx-64.txt | 230 ++++++------- .../conda_envs/cctbxlite_py36_win-64.txt | 197 ++++++------ .../conda_envs/cctbxlite_py37_linux-64.txt | 286 +++++++++-------- .../conda_envs/cctbxlite_py37_osx-64.txt | 230 ++++++------- .../conda_envs/cctbxlite_py37_win-64.txt | 199 ++++++------ .../conda_envs/cctbxlite_py38_linux-64.txt | 283 ++++++++-------- .../conda_envs/cctbxlite_py38_osx-64.txt | 227 ++++++------- .../conda_envs/cctbxlite_py38_win-64.txt | 196 ++++++------ mmtbx/programs/rama_z.py | 4 + mmtbx/regression/tst_rama_z_01.py | 22 ++ simtbx/nanoBragg/sim_data.py | 2 +- xfel/command_line/cxi_display_metrology.py | 4 +- 37 files changed, 3335 insertions(+), 3225 deletions(-) Current branch master is up to date. Already up to date. Current branch master is up to date. From https://github.com/cctbx/dxtbx 979ede8..9e157b7 master -> origin/master bb8d150..0d3ffcd isort -> origin/isort Updating 979ede8..9e157b7 Fast-forward ext.py | 4 ++-- format/FormatBrukerPhotonII.py | 2 +- format/FormatCBFMini.py | 5 +++-- format/FormatGatanDM4.py | 2 +- format/FormatHDF5Sacla.py | 3 ++- format/FormatHDF5SaclaMPCCD.py | 3 ++- format/FormatHDF5SaclaRayonix.py | 3 ++- format/FormatSER.py | 2 +- format/FormatSMV.py | 2 +- format/FormatSMVCMOS1.py | 2 +- format/FormatSMVRigakuEiger.py | 2 +- format/FormatSMVRigakuPilatus.py | 2 +- format/FormatTIFFBruker.py | 2 +- format/FormatTIFFRayonix.py | 2 +- format/image.py | 2 +- format/nexus.py | 2 +- imageset.py | 8 ++++---- model/__init__.py | 14 +++++++------- model/spectrum.h | 3 ++- newsfragments/209.misc | 2 ++ newsfragments/212.misc | 1 + tests/format/test_FormatHDF5SaclaMPCCD.py | 8 ++++---- tests/model/test_spectrum.py | 4 +++- 23 files changed, 45 insertions(+), 35 deletions(-) create mode 100644 newsfragments/209.misc create mode 100644 newsfragments/212.misc Current branch master is up to date. 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: 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 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 ===== Running in modules\annlib_adaptbx: git pull --rebase Existing non-git directory -- don't know what to do. skipping: tntbx ===== Running in modules\dxtbx: git pull --rebase 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 218 files Bootstrap success: cleanup, hot, update 21/08/2020 12:31:57.07 21/08/2020 12:32:00.89 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 2630, in cold_start env.refresh() File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\env_config.py", line 1849, in refresh module.process_command_line_directories() File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\env_config.py", line 2170, 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 2067, 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 21/08/2020 12:36:48.77 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 2630, in cold_start env.refresh() File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\env_config.py", line 1849, in refresh module.process_command_line_directories() File "C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\modules\cctbx_project\libtbx\env_config.py", line 2170, 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 2067, 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 21/08/2020 12:42:54.59