08/07/2020 12:00:24.82 08/07/2020 12:00:25.26 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\ & ) 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 Existing non-git directory -- don't know what to do. skipping: scons ===== 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 83e468f62..fc9830b88 master -> origin/master + b57301129...178cfb643 azp -> origin/azp (forced update) * [new branch] dials-11 -> origin/dials-11 61bff1195..f66f792b4 diffBragg -> origin/diffBragg * [new branch] dxtbx-11 -> origin/dxtbx-11 * [new branch] flip_on -> origin/flip_on * [new branch] tidy-exercise-compression -> origin/tidy-exercise-compression Updating 83e468f62..fc9830b88 Fast-forward cbflib_adaptbx/run_tests.py | 10 +- cctbx/maptbx/auto_sharpen.py | 2 +- cctbx/maptbx/refine_sharpening.py | 2 +- cctbx/maptbx/segment_and_split_map.py | 28 +-- cctbx_website/__init__.py | 0 .../extract_script_from_html_cctbx_doc.py | 82 +++++++ cctbx_website/doc_data_manager.html | 153 +++++++++++++ cctbx_website/doc_high_level_objects.html | 94 ++++++++ cctbx_website/template.html | 18 +- iotbx/create_models_or_maps.py | 46 +++- iotbx/data_manager/model.py | 12 +- iotbx/map_manager.py | 5 +- iotbx/map_model_manager.py | 2 +- iotbx/regression/ncs/tst_ncs.py | 180 +++++++++++++++ iotbx/regression/tst_data_manager.py | 24 +- mmtbx/atomic_environment_vectors/__init__.py | 254 +++++++++++++++++++++ mmtbx/atomic_environment_vectors/tst.py | 71 ++++++ mmtbx/command_line/development.aev.py | 26 +++ .../LinkedResidues.py | 2 + mmtbx/conformation_dependent_library/__init__.py | 10 +- .../multi_residue_class.py | 21 +- .../tst_poly_ca_multi_residue.py | 146 ++++++++++++ mmtbx/pair_interaction/interaction.h | 26 +-- mmtbx/pair_interaction/tst_03.py | 34 ++- mmtbx/run_tests.py | 3 +- mmtbx/validation/experimental.py | 3 +- prime/postrefine/mod_gui_dialogs.py | 1 - prime/postrefine/mod_gui_frames.py | 9 +- 28 files changed, 1179 insertions(+), 85 deletions(-) create mode 100644 cctbx_website/__init__.py create mode 100644 cctbx_website/command_line/extract_script_from_html_cctbx_doc.py create mode 100644 cctbx_website/doc_data_manager.html create mode 100644 cctbx_website/doc_high_level_objects.html create mode 100644 mmtbx/atomic_environment_vectors/__init__.py create mode 100644 mmtbx/atomic_environment_vectors/tst.py create mode 100644 mmtbx/command_line/development.aev.py create mode 100644 mmtbx/conformation_dependent_library/tst_poly_ca_multi_residue.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 2a6b0d3..0e57e9f master -> origin/master Updating 2a6b0d3..0e57e9f Fast-forward format/FormatNexusEigerDLS.py | 2 +- format/nexus.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) 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 217 files Bootstrap success: cleanup, hot, update 08/07/2020 12:01:24.98 08/07/2020 12:01:25.04 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" mmtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\mmtbx" crys3d "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\crys3d" dxtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\dxtbx" iotbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\iotbx" 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" cbflib+adaptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cbflib" "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cbflib_adaptbx" 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 08/07/2020 12:02:32.91 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" mmtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\mmtbx" crys3d "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\crys3d" dxtbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\dxtbx" iotbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\iotbx" 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" cbflib+adaptbx "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cbflib" "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cbflib_adaptbx" 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 08/07/2020 12:04:08.46