25/06/2020 12:00:25.17 25/06/2020 12:00:25.52 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\ & ) 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 6c7bfc2f1..c2f346416 master -> origin/master * [new branch] cjw_poly_ca -> origin/cjw_poly_ca 2c266ef07..04d40d16a diffBragg -> origin/diffBragg * [new branch] jpb/gpu -> origin/jpb/gpu + 4d5dd6ac8...0b10b461c test -> origin/test (forced update) Updating 6c7bfc2f1..c2f346416 Fast-forward .azure-pipelines/azure-pipelines-build-cache.yml | 7 + .azure-pipelines/ci-build.yml | 2 + .azure-pipelines/conda-linux.yml | 11 +- .azure-pipelines/conda-osx.yml | 9 +- .azure-pipelines/conda-win.yml | 1 + .azure-pipelines/full-build.yml | 9 + .azure-pipelines/xfel/azure-pipelines-xfel.yml | 20 +- .azure-pipelines/xfel/conda-linux.yml | 115 ++++++- .azure-pipelines/xfel/conda-osx.yml | 97 +++++- .azure-pipelines/xfel/conda-psana.yml | 38 --- .azure-pipelines/xfel/download-source.yml | 8 +- .azure-pipelines/xfel/unix-conda-build.yml | 8 +- .azure-pipelines/xfel/unix-psana-build.yml | 8 +- .azure-pipelines/xfel/xfel-ci-build.yml | 22 ++ cctbx/maptbx/box.py | 5 +- cctbx/maptbx/connectivity.h | 6 +- cctbx/maptbx/segment_and_split_map.py | 24 +- cctbx/regression/tst_connectivity.py | 32 +- cctbx/regression/tst_fcalc_fft_stability.py | 58 ++++ cctbx/run_tests.py | 4 + iotbx/map_manager.py | 196 +++++++++-- iotbx/map_model_manager.py | 284 +++++++++++----- iotbx/mrcfile/__init__.py | 6 + iotbx/ncs/__init__.py | 10 +- iotbx/regression/tst_map_manager.py | 51 ++- iotbx/regression/tst_r_model.py | 20 +- mmtbx/command_line/map_box.py | 1 + mmtbx/ncs/ncs.py | 364 ++++++++++++++++++++- mmtbx/ncs/ncs_restraints_group_list.py | 12 +- .../ncs/tst_ncs_restraints_group_list.py | 99 ++++++ mmtbx/scaling/plan_sad_experiment.py | 2 +- scitbx/suffixtree/boost_python/edge_exports.hpp | 258 +++++---------- .../suffixtree/boost_python/iterator_wrapper.hpp | 64 ++++ .../suffixtree/boost_python/object_extensions.cpp | 3 +- .../boost_python/suffixtree_single_ext.cpp | 18 +- scitbx/suffixtree/edge.hpp | 118 +++---- scitbx/suffixtree/edge.hxx | 215 +++++------- scitbx/suffixtree/iterator.hpp | 90 +++-- scitbx/suffixtree/iterator.hxx | 18 +- scitbx/suffixtree/matching_statistics.hpp | 18 +- scitbx/suffixtree/test/tst_single.py | 150 +-------- scitbx/suffixtree/tree.hpp | 13 +- scitbx/suffixtree/tree.hxx | 25 +- scitbx/suffixtree/word.hpp | 52 +-- scitbx/suffixtree/word.hxx | 81 +---- xfel/conda_envs/psana_environment.yml | 2 +- 46 files changed, 1680 insertions(+), 974 deletions(-) delete mode 100644 .azure-pipelines/xfel/conda-psana.yml create mode 100644 .azure-pipelines/xfel/xfel-ci-build.yml create mode 100644 cctbx/regression/tst_fcalc_fft_stability.py create mode 100644 scitbx/suffixtree/boost_python/iterator_wrapper.hpp 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 b0d1792..3850bbd master -> origin/master 3fa983a..139a4e9 dls-eiger-0xffff -> origin/dls-eiger-0xffff Updating b0d1792..3850bbd Fast-forward CHANGELOG.rst | 9 +++++++++ pyproject.toml | 1 + 2 files changed, 10 insertions(+) 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 1 files Bootstrap success: cleanup, hot, update 25/06/2020 12:01:18.12 25/06/2020 12:01:18.21 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 25/06/2020 12:02:44.51 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\ & ) 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 25/06/2020 12:04:19.06