09/09/2019 12:00:27.67 09/09/2019 12:00:30.14 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 ===== 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 9792adf46..5cf1a68e8 master -> origin/master + 914c6fc21...5a316d07c LS49_exp -> origin/LS49_exp (forced update) + c08468193...77f5876e5 conda_boost -> origin/conda_boost (forced update) 97712a57d..5793d54f2 dependencies -> origin/dependencies * [new branch] deprecate_injector -> origin/deprecate_injector 8b7f3c21d..d0519a5a0 diffBragg -> origin/diffBragg a316b3dc1..756d8e60e iotbx-mtz-batch-tuning -> origin/iotbx-mtz-batch-tuning * [new branch] issue_380 -> origin/issue_380 c1df5348d..6c113fab4 py3rst -> origin/py3rst * [new branch] ratchet1 -> origin/ratchet1 * [new branch] xfel_deprecations -> origin/xfel_deprecations Updating 9792adf46..5cf1a68e8 Fast-forward .azure-pipelines/azure-pipelines-base.yml | 53 ++ .azure-pipelines/azure-pipelines-linux.yml | 3 +- .azure-pipelines/azure-pipelines-osx.yml | 4 +- .azure-pipelines/base-linux.yml | 53 ++ .azure-pipelines/base-osx.yml | 40 ++ .azure-pipelines/unix-base-build.yml | 60 ++ .../{unix-build.yml => unix-conda-build.yml} | 27 +- .azure-pipelines/unix-install-miniconda.yml | 15 - boost/python.py | 33 +- boost_adaptbx/SConscript | 736 +++++++++++---------- boost_adaptbx/libtbx_refresh.py | 14 +- boost_adaptbx/meta_ext.cpp | 1 + cctbx/command_line/cctbx_test_nightly.py | 2 - cctbx/examples/ccp4_map.py | 14 + cctbx/geometry_restraints/__init__.py | 5 +- cctbx/geometry_restraints/base_geometry.py | 2 +- cctbx/geometry_restraints/manager.py | 18 +- cctbx/maptbx/boost_python/maptbx_ext.cpp | 19 + cctbx/maptbx/segment_and_split_map.py | 64 +- cctbx/maptbx/utils.h | 188 ++++-- cctbx/miller/__init__.py | 12 +- cctbx/miller/display2.py | 13 +- cctbx/regression/tst_loc_res.py | 2 +- crys3d/hklview/NGL_HKLviewerGui.py | 68 +- crys3d/hklview/cmdlineframes.py | 87 ++- crys3d/hklview/jsview_3d.py | 674 +++++++++++-------- iotbx/bioinformatics/local_blast.py | 28 +- iotbx/bioinformatics/pdb_info.csv.gz | Bin 0 -> 1215926 bytes iotbx/bioinformatics/pdb_info.py | 15 +- iotbx/bioinformatics/structure.py | 8 +- iotbx/data_manager/model.py | 29 + iotbx/detectors/detectors_ext.cpp | 1 + iotbx/detectors/display.h | 13 + iotbx/regression/tst_data_manager.py | 14 + libtbx/SConscript | 7 +- libtbx/auto_build/bootstrap.py | 10 +- libtbx/env_config.py | 40 +- mmtbx/command_line/map_box.py | 56 +- mmtbx/model/model.py | 2 +- mmtbx/model/statistics.py | 2 +- mmtbx/monomer_library/pdb_interpretation.py | 57 +- mmtbx/pair_interaction/tst_01.py | 1 - mmtbx/regression/pdb_interpretation/tst_edits.py | 94 +-- .../pdb_interpretation/tst_edits_actions.py | 169 +++++ mmtbx/regression/tst_add_arrows_on_plot.py | 2 +- mmtbx/regression/tst_utils.py | 39 ++ mmtbx/run_tests.py | 1 + mmtbx/utils/__init__.py | 34 +- mmtbx/utils/rotatable_bonds.py | 16 +- rstbx/indexing_api/tools.py | 172 ++--- scitbx/array_family/boost_python/SConscript | 5 +- scitbx/boost_python/SConscript | 5 +- simtbx/SConscript | 8 +- simtbx/nanoBragg/nanoBragg.cpp | 2 +- xfel/merging/application/mpi_logger.py | 14 +- xfel/merging/application/phil/phil.py | 5 + .../application/postrefine/postrefinement.py | 37 +- xfel/mono_simulation/max_like.py | 17 +- xfel/ui/db/xfel_db.py | 5 - 59 files changed, 1995 insertions(+), 1120 deletions(-) create mode 100644 .azure-pipelines/azure-pipelines-base.yml create mode 100644 .azure-pipelines/base-linux.yml create mode 100644 .azure-pipelines/base-osx.yml create mode 100644 .azure-pipelines/unix-base-build.yml rename .azure-pipelines/{unix-build.yml => unix-conda-build.yml} (80%) delete mode 100644 .azure-pipelines/unix-install-miniconda.yml create mode 100644 iotbx/bioinformatics/pdb_info.csv.gz create mode 100644 mmtbx/regression/pdb_interpretation/tst_edits_actions.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 5a8bb5b..7aa36b6 master -> origin/master + c731dbc...b68ddf7 XTC_timestamp_identifier -> origin/XTC_timestamp_identifier (forced update) * [new branch] add-dlsnxs2cbf -> origin/add-dlsnxs2cbf + 90e3131...b7f7ead beam-get-sample-to-source-direction -> origin/beam-get-sample-to-source-direction (forced update) * [new branch] nexus-refactor -> origin/nexus-refactor + ad38801...6e4a5d2 travis -> origin/travis (forced update) Updating 5a8bb5b..7aa36b6 Fast-forward .pre-commit-config.yaml | 7 +- .travis.yml | 65 +++-- .travis/check-working-directory-is-clean | 7 + .travis/clean-cctbx | 10 + .travis/update-cctbx | 19 ++ CONTRIBUTING.md | 143 ++++++++++ SConscript | 5 +- boost_python/imageset_ext.cc | 7 +- command_line/dlsnxs2cbf.py | 199 ++++++++++++++ command_line/print_sweep.py | 2 +- datablock.py | 93 ++++--- example/resolution_corners.py | 2 +- example/to_xds.py | 6 +- filecache.py | 7 +- format/Format.py | 17 +- format/FormatBruker.py | 6 +- format/FormatBrukerFixedChi.py | 12 - format/FormatBrukerPhotonII.py | 11 - format/FormatCBF.py | 7 +- format/FormatCBFFull.py | 35 ++- format/FormatCBFFullPilatus.py | 45 --- format/FormatCBFFullPilatusDLS300KSN104.py | 18 +- format/FormatCBFFullPilatusDLS6MSN100.py | 19 +- format/FormatCBFFullPilatusDLS6MSN126.py | 35 +-- format/FormatCBFMini.py | 11 +- format/FormatCBFMiniADSCHF4M.py | 16 -- format/FormatCBFMiniEiger.py | 43 --- format/FormatCBFMiniEigerDLS16MSN160.py | 17 -- format/FormatCBFMiniEigerPetraP14.py | 13 - format/FormatCBFMiniEigerPhotonFactory.py | 16 -- format/FormatCBFMiniPilatus.py | 42 --- format/FormatCBFMiniPilatus3APS19ID6MSN132.py | 13 - format/FormatCBFMiniPilatusCHESS_6MSN127.py | 13 - format/FormatCBFMiniPilatusDLS12M.py | 27 +- format/FormatCBFMiniPilatusDLS6MSN100.py | 22 +- format/FormatCBFMiniPilatusDLS6MSN114.py | 13 - format/FormatCBFMiniPilatusDLS6MSN114DMM.py | 5 - format/FormatCBFMiniPilatusDLS6MSN119.py | 13 - format/FormatCBFMiniPilatusDLS6MSN126.py | 8 +- format/FormatCBFMiniPilatusSOLEILPX16MSN106.py | 13 - format/FormatCBFMiniPilatusSPring8_6MSN125.py | 13 - format/FormatCBFMiniPilatusXXX.py | 11 - format/FormatCBFMultiTile.py | 11 - format/FormatCBFMultiTileHierarchy.py | 22 +- format/FormatDIP2030b.py | 6 +- format/FormatEDFALS733.py | 5 +- format/FormatEiger0MQDump.py | 3 - format/FormatGatanDM4.py | 3 +- format/FormatHDF5.py | 3 +- format/FormatHDF5Dectris.py | 9 - format/FormatHDF5EigerNearlyNexus.py | 7 - format/FormatHDF5Lambda.py | 7 - format/FormatHDF5PAL.py | 7 - format/FormatHDF5RawData.py | 7 - format/FormatHDF5Sacla.py | 7 - format/FormatHDF5SaclaMPCCD.py | 26 +- format/FormatHDF5SaclaRayonix.py | 8 +- format/FormatMultiImage.py | 14 +- format/FormatNexus.py | 7 - format/FormatNexusEigerDLS16M.py | 27 -- format/FormatNexusExternalDataFile.py | 7 - format/FormatPY.py | 5 +- format/FormatPYmultitile.py | 9 - format/FormatPYunspecified.py | 31 +-- format/FormatPYunspecifiedStill.py | 21 +- format/FormatPilatusHelpers.py | 2 +- format/FormatSER.py | 3 +- format/FormatSEReBIC.py | 6 - format/FormatSMV.py | 6 +- format/FormatSMVADSC.py | 15 - format/FormatSMVADSCNoDateStamp.py | 15 - format/FormatSMVADSCSN.py | 11 +- format/FormatSMVADSCSN445.py | 11 - format/FormatSMVADSCSN457.py | 11 - format/FormatSMVADSCSN905.py | 11 - format/FormatSMVADSCSN915.py | 11 - format/FormatSMVADSCSN920.py | 11 - format/FormatSMVADSCSN926.py | 11 - format/FormatSMVADSCSN928.py | 11 - format/FormatSMVADSCSNAPSID19.py | 11 - format/FormatSMVADSCmlfsom.py | 11 - format/FormatSMVCMOS1.py | 10 +- format/FormatSMVHamamatsu.py | 4 - format/FormatSMVJHSim.py | 17 -- format/FormatSMVNOIR.py | 8 +- format/FormatSMVRigaku.py | 11 - format/FormatSMVRigakuA200.py | 12 - format/FormatSMVRigakuA200SPring8BL26B1.py | 16 -- format/FormatSMVRigakuEiger.py | 11 - format/FormatSMVRigakuPilatus.py | 11 - format/FormatSMVRigakuSaturn.py | 12 - format/FormatSMVRigakuSaturnNoTS.py | 12 - format/FormatSMVTimePix_SU.py | 15 - format/FormatTIFF.py | 5 +- format/FormatTIFFBruker.py | 13 +- format/FormatTIFFRayonix.py | 11 +- format/FormatTIFFRayonixESRF.py | 12 - format/FormatTIFFRayonixSPring8.py | 10 - format/FormatTIFFRayonixXPP.py | 7 +- format/FormatXDS.py | 7 +- format/FormatXTC.py | 2 +- format/FormatXTCCspad.py | 5 +- format/FormatXTCJungfrau.py | 5 +- format/FormatXTCMultipleDetectors.py | 4 - format/FormatXTCRayonix.py | 5 +- format/boost_python/cbf_read_buffer.cpp | 72 +++++ format/boost_python/cbf_read_buffer.h | 8 + format/boost_python/image_ext.cc | 4 + format/doc/adding_new_formats.txt | 301 --------------------- format/image.py | 23 +- format/nexus.py | 51 +++- imageset.py | 33 ++- libtbx_config | 7 +- model/__init__.py | 258 +++++++++++------- model/beam.h | 12 +- model/boost_python/beam.cc | 6 +- model/experiment_list.py | 12 +- newsfragments/72.feature | 1 + newsfragments/73.feature | 4 + newsfragments/75.bugfix | 1 + newsfragments/76.misc | 9 + newsfragments/81.feature | 2 + serialize/xds.py | 4 +- tests/command_line/test_dlsnxs2cbf.py | 22 ++ tests/command_line/test_to_xds.py | 44 +-- .../format/test_FormatCBFFullPilatusDLS6MSN126.py | 42 +++ tests/format/test_FormatCBFMiniEigerDLS16MSN160.py | 29 ++ tests/format/test_FormatHDF5EigerNearlyNexus.py | 6 +- .../test_FormatHDF5EigerNearlyNexusSPring8.py | 6 +- tests/format/test_FormatHDF5SaclaMPCCD.py | 142 ++++++++++ tests/format/test_FormatNexus.py | 6 +- tests/format/test_FormatNexusEigerDLS16M.py | 33 ++- tests/format/test_FormatPYunspecified.py | 47 ++++ tests/image_001.dat | 1 - tests/image_002.dat | 1 - tests/image_003.dat | 1 - tests/image_004.dat | 1 - tests/image_005.dat | 1 - tests/image_006.dat | 1 - tests/image_007.dat | 1 - tests/image_008.dat | 1 - tests/image_009.dat | 1 - tests/image_010.dat | 1 - tests/image_011.dat | 1 - tests/image_012.dat | 1 - tests/image_013.dat | 1 - tests/image_014.dat | 1 - tests/image_015.dat | 1 - tests/image_016.dat | 1 - tests/image_017.dat | 1 - tests/image_018.dat | 1 - tests/image_019.dat | 1 - tests/image_020.dat | 1 - tests/model/test_beam.py | 8 +- tests/model/test_crystal_model.py | 40 ++- tests/serialize/test_serialize.py | 2 +- tests/serialize/test_xds.py | 15 +- tests/test_image_readers.py | 18 +- tests/test_imageset.py | 4 +- tests/test_regression_images.py | 49 ++++ tests/test_scan.py | 36 ++- 161 files changed, 1450 insertions(+), 1647 deletions(-) create mode 100755 .travis/check-working-directory-is-clean create mode 100755 .travis/clean-cctbx create mode 100755 .travis/update-cctbx create mode 100644 CONTRIBUTING.md create mode 100644 command_line/dlsnxs2cbf.py create mode 100644 format/boost_python/cbf_read_buffer.cpp create mode 100644 format/boost_python/cbf_read_buffer.h delete mode 100644 format/doc/adding_new_formats.txt create mode 100644 newsfragments/72.feature create mode 100644 newsfragments/73.feature create mode 100644 newsfragments/75.bugfix create mode 100644 newsfragments/76.misc create mode 100644 newsfragments/81.feature create mode 100644 tests/command_line/test_dlsnxs2cbf.py create mode 100644 tests/format/test_FormatCBFFullPilatusDLS6MSN126.py create mode 100644 tests/format/test_FormatCBFMiniEigerDLS16MSN160.py create mode 100644 tests/format/test_FormatHDF5SaclaMPCCD.py create mode 100644 tests/format/test_FormatPYunspecified.py delete mode 100644 tests/image_001.dat delete mode 100644 tests/image_002.dat delete mode 100644 tests/image_003.dat delete mode 100644 tests/image_004.dat delete mode 100644 tests/image_005.dat delete mode 100644 tests/image_006.dat delete mode 100644 tests/image_007.dat delete mode 100644 tests/image_008.dat delete mode 100644 tests/image_009.dat delete mode 100644 tests/image_010.dat delete mode 100644 tests/image_011.dat delete mode 100644 tests/image_012.dat delete mode 100644 tests/image_013.dat delete mode 100644 tests/image_014.dat delete mode 100644 tests/image_015.dat delete mode 100644 tests/image_016.dat delete mode 100644 tests/image_017.dat delete mode 100644 tests/image_018.dat delete mode 100644 tests/image_019.dat delete mode 100644 tests/image_020.dat 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 431 files Bootstrap success: cleanup, hot, update 09/09/2019 12:15:30.75 09/09/2019 12:15:30.83 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. Using default conda installation Base conda installation: C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\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 Python3 migration warning policy: None 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" 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" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\boost_adaptbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\fable\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\scitbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cctbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cbflib_adaptbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\smtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_projecDEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. t\iotbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\dxtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\mmtbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\gltbx\command_line" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\wxtbx\command_line" requirement dials-data>=2.0.30 is not currently met, package not installed attempting install of dials-data>=2.0.30... Collecting dials-data>=2.0.30 Downloading https://files.pythonhosted.org/packages/e3/7e/a58b6a6d3b7cbd734ab7540d5bf2af6777dbac0a87633ec002239ee4d1e1/dials_data-2.0.40-py2.py3-none-any.whl (105kB) Requirement already satisfied: pytest in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from dials-data>=2.0.30) (3.10.1) Collecting pyyaml (from dials-data>=2.0.30) Using cached https://files.pythonhosted.org/packages/da/7e/b82dad5d7343eb3d53cf84aaefb53515a659c55b1cb7c328287256c1c156/PyYAML-5.1.2-cp27-cp27m-win_amd64.whl Requirement already satisfied: setuptools in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from dials-data>=2.0.30) (40.8.0) Requirement already satisfied: six in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from dials-data>=2.0.30) (1.12.0) Requirement already satisfied: py>=1.5.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (1.7.0) Requirement already satisfied: attrs>=17.4.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (18.2.0) Requirement already satisfied: more-itertools>=4.0.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (4.3.0) Requirement already satisfied: atomicwrites>=1.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (1.3.0) Requirement already satisfied: pluggy>=0.7 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (0.8.1) Requirement already satisfied: pathlib2>=2.2.0 in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (2.3.3) Requirement already satisfied: funcsigs in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (1.0.2) Requirement already satisfied: colorama in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pytest->dials-data>=2.0.30) (0.4.1) Requirement already satisfied: scandir; python_version < "3.5" in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from pathlib2>=2.2.0->pytest->dials-data>=2.0.30) (1.9.0) Installing collected packages: pyyaml, dials-data The script dials.data.exe is installed in 'C:\Users\phaserbuilder\NightlyBuilds\CCTBXVC2008\x64\Current\conda_base\Scripts' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Successfully installed dials-data-2.0.40 pyyaml-5.1.2 install successful requires mock>=2.0, has 2.0.0 requirement procrunner>=1.0 is not currently met, current version 0.9.0 attempting update of procrunner>=1.0... Collecting procrunner>=1.0 Using cached https://files.pythonhosted.org/packages/66/16/de3bb5b86261d41e7910c38409d90dd36c15e8398e791c6cffb78fcd9801/procrunner-1.0.2-py2.py3-none-any.whl Requirement already satisfied: six in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from procrunner>=1.0) (1.12.0) Requirement already satisfied: pywin32; sys_platform == "win32" and python_version == "2.7" in c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\conda_base\lib\site-packages (from procrunner>=1.0) (221) Installing collected packages: procrunner Found existing installation: procrunner 0.9.0 Uninstalling procrunner-0.9.0: Successfully uninstalled procrunner-0.9.0 Successfully installed procrunner-1.0.2 update successful requires pytest>=3.10.1, has 3.10.1 Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\boost_adaptbx\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\scitbx\libtbx_refresh.py" Generating C++ header files in: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build\include\scitbx\array_family" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build\include\scitbx\array_family\boost_python" Using fable to convert scitbx\lbfgs.f Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cctbx\libtbx_refresh.py" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build\cctbx\eltbx" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build\include\cctbx\boost_python" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\cbflib_adaptbx\libtbx_refresh.py" Copying to lib: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cbflib\pycbf\pycbf.py" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\smtbx\libtbx_refresh.py" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build\include\smtbx\boost_python" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\iotbx\libtbx_refresh.py" Using fable to convert iotbx\pdb\hybrid_36_f.f Writing: iotbx\pdb\hybrid_36_fem.cpp Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\dxtbx\libtbx_refresh.py" Enumerating format classes: found FormatBruker based on ['Format'] found FormatBrukerFixedChi based on ['FormatBruker'] found FormatBrukerPhotonII based on ['FormatBruker'] found FormatCBF based on ['Format'] found FormatCBFCspad based on ['FormatCBFMultiTileHierarchyStill'] found FormatCBFFullStillInMemory based on ['FormatCBFFullStill'] found FormatCBFMultiTileHierarchyStillInMemory based on ['FormatCBFFullStillInMemory', 'FormatCBFMultiTileHierarchyStill'] found FormatCBFCspadInMemory based on ['FormatCBFMultiTileHierarchyStillInMemory', 'FormatCBFCspad'] found FormatCBFFull based on ['FormatCBF'] found FormatCBFFullStill based on ['FormatStill', 'FormatCBFFull'] found FormatCBFFullPilatus based on ['FormatCBFFull'] found FormatCBFFullPilatusDLS300KSN104 based on ['FormatCBFFullPilatus'] found FormatCBFFullPilatusDLS6MSN100 based on ['FormatCBFFullPilatus'] found FormatCBFFullPilatusDLS6MSN126 based on ['FormatCBFFullPilatus'] found FormatCBFMini based on ['FormatCBF'] found FormatCBFMiniADSCHF4M based on ['FormatCBFMini'] found FormatCBFMiniEiger based on ['FormatCBFMini'] found FormatCBFMiniEigerDLS16MSN160 based on ['FormatCBFMiniEiger'] found FormatCBFMiniEigerMaxIVBio based on ['FormatCBFMiniEiger'] found FormatCBFMiniEigerPetraP14 based on ['FormatCBFMiniEiger'] found FormatCBFMiniEigerPhotonFactory based on ['FormatCBFMini'] found FormatCBFMiniPilatus based on ['FormatCBFMini'] found FormatCBFMiniPilatus3AOS19ID6MSN132 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusCHESS_6MSN127 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusDESY6MSN115 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusDLS12M based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusDLS6MSN100 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusDLS6MSN114 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusDLS6MSN114DMM based on ['FormatCBFMiniPilatus', 'FormatStill'] found FormatCBFMiniPilatusDLS6MSN119 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusDLS6MSN126 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusSOLEILPX16MSN106 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusSPring8_6MSN125 based on ['FormatCBFMiniPilatus'] found FormatCBFMiniPilatusXXX based on ['FormatCBFMiniPilatus'] found FormatCBFMultiTile based on ['FormatCBFFull'] found FormatCBFMultiTileStill based on ['FormatStill', 'FormatCBFMultiTile'] found FormatCBFMultiTileHierarchy based on ['FormatCBFMultiTile'] found FormatCBFMultiTileHierarchyStill based on ['FormatCBFMultiTileStill', 'FormatCBFMultiTileHierarchy'] found FormatDIP2030b based on ['Format'] found FormatEDFALS733 based on ['Format'] found FormatEiger0MQDump based on ['Format'] found FormatEigerStream based on ['FormatMultiImage', 'Format'] found FormatGatanDM4 based on ['FormatMultiImage', 'Format'] found FormatHDF5 based on ['FormatMultiImage', 'Format'] found FormatHDF5Dectris based on ['FormatHDF5'] found FormatHDF5EigerNearlyNexus based on ['FormatHDF5'] found FormatHDF5EigerNearlyNexusSPring8 based on ['FormatHDF5EigerNearlyNexus'] found FormatHDF5Lambda based on ['FormatHDF5'] found FormatHDF5PAL based on ['FormatHDF5'] found FormatRawData based on ['FormatHDF5'] found FormatHDF5Sacla based on ['FormatHDF5', 'FormatStill'] found FormatHDF5SaclaMPCCD based on ['FormatHDF5', 'FormatStill'] found FormatHDF5SaclaRayonix based on ['FormatHDF5', 'FormatStill'] found FormatMarIP based on ['Format'] found FormatMultiImage based on ['Format'] found FormatMultiImageLazy based on ['FormatMultiImage'] found FormatNexus based on ['FormatHDF5'] found FormatNexusStill based on ['FormatMultiImageLazy', 'FormatNexus', 'FormatStill'] found FormatNexusEigerDLS16M based on ['FormatNexus'] found FormatNexusExternalDataFile based on ['FormatHDF5'] found FormatPY based on ['Format'] found FormatPYmultitile based on ['FormatPY'] found FormatPYunspecified based on ['FormatPY'] found FormatPYunspecifiedInMemory based on ['FormatPYunspecified'] found FormatPYunspecifiedStill based on ['FormatStill', 'FormatPYunspecified'] found FormatPYunspecifiedStillInMemory based on ['FormatStill', 'FormatPYunspecifiedInMemory'] found FormatRAXIS based on ['Format'] found FormatRAXISII based on ['Format'] found FormatRAXISIVSPring8 based on ['Format'] found FormatSER based on ['FormatMultiImage', 'Format'] found FormatSEReBIC based on ['FormatSER'] found FormatSMV based on ['Format'] found FormatSMVADSC based on ['FormatSMV'] found FormatSMVADSCDBG based on ['FormatSMVADSC'] found FormatSMVADSCNoDateStamp based on ['FormatSMVADSC'] found FormatSMVADSCSN based on ['FormatSMVADSC'] found FormatSMVADSCSN445 based on ['FormatSMVADSCSN'] found FormatSMVADSCSNSN457 based on ['FormatSMVADSCSN'] found FormatSMVADSCSN905 based on ['FormatSMVADSCSN'] found FormatSMVADSCSN915 based on ['FormatSMVADSCSN'] found FormatSMVADSCSN920 based on ['FormatSMVADSCSN'] found FormatSMVADSCSN926 based on ['FormatSMVADSCSN'] found FormatSMVADSCSN928 based on ['FormatSMVADSCSN'] found FormatSMVADSCSNAPSID19 based on ['FormatSMVADSCSN'] found FormatSMVADSCmlfsom based on ['FormatSMVADSC'] found FormatSMVCMOS1 based on ['FormatSMV'] found FormatSMVHamamatsu based on ['FormatSMVADSC'] found FormatSMVHamamatsuSPring8BL32XU based on ['FormatSMVHamamatsu'] found FormatSMVJHSim based on ['FormatSMV'] found FormatSMVNOIR based on ['FormatSMVRigaku'] found FormatSMVRigaku based on ['FormatSMV'] found FormatSMVRigakuA200 based on ['FormatSMVRigaku'] found FormatSMVRigakuA200SPring8BL26B1 based on ['FormatSMVRigakuA200'] found FormatSMVRigakuEiger based on ['FormatSMVRigaku'] found FormatSMVRigakuPilatus based on ['FormatSMVRigaku'] found FormatSMVRigakuSaturn based on ['FormatSMVRigaku'] found FormatSMVRigakuSaturnNoTS based on ['FormatSMVRigaku'] found FormatSMVRigakuSaturnSN07400090 based on ['FormatSMVRigakuSaturn'] found FormatSMVRigakuSaturn09040159 based on ['FormatSMVRigakuSaturnNoTS'] found FormatSMVRigakuSaturnSN11480296 based on ['FormatSMVRigakuSaturn'] found FormatSMVTimePix_SU based on ['FormatSMV'] found FormatSMVTimePix_SU_512x512 based on ['FormatSMVTimePix_SU'] found FormatSMVTimePix_SU_516x516 based on ['FormatSMVTimePix_SU'] found FormatStill based on ['Format'] found FormatTIFF based on ['Format'] found FormatTIFFBruker based on ['FormatTIFF'] found FormatTIFFRayonix based on ['FormatTIFF'] found FormatTIFFRayonixESRF based on ['FormatTIFFRayonix'] found FormatTIFFRayonixSPring8 based on ['FormatTIFFRayonix'] found FormatTIFFRayonixXPP based on ['FormatTIFFRayonix'] found FormatXDS based on ['Format'] found FormatXTC based on ['FormatMultiImageLazy', 'FormatStill', 'Format'] found FormatXTCCspad based on ['FormatXTC'] found FormatXTCJungfrau based on ['FormatXTC'] found FormatXTCJungfrauMonolithic based on ['FormatXTCJungfrau'] found FormatXTCMultipleDetectors based on ['FormatXTCRayonix', 'FormatXTCCspad', 'FormatXTCJungfrau'] found FormatXTCRayonix based on ['FormatXTC'] Updating entry points for dxtbx 117 entries for entry point dxtbx.format Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\mmtbx\libtbx_refresh.py" Processing: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\modules\cctbx_project\gltbx\libtbx_refresh.py" Generating C++ files in: "c:\users\phaserbuilder\nightlybuilds\cctbxvc2008\x64\current\build\gltbx" fonts: 8x13 9x15 10x20 Done. usr+sys time: 0.75 seconds wall clock time: 0.75 seconds usage: scons [OPTION] [TARGET] ... SCons Error: option -j: invalid integer value: 'getbootstrap' Performing actions: base build Installing base packages using: python modules\cctbx_project\libtbx\auto_build\install_conda.py --builder=cctbx ===== 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 ===== Running in build: save configure command ===== Running in build: libtbx.scons.bat Process failed with return code 2 09/09/2019 12:21:36.43