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branch: release 「№238」
Commited by: Sergey Lyskov
GitHub commit link: 「fc8ab401178f6f09」 「№4341」
Difference from previous tested commit:  code diff
Commit date: 2019-11-05 17:46:43
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Merge pull request #4341 from RosettaCommons/benchmark Adding `--disable-new-dtags` linker option to default GCC settings, this should allow proper linking to Rosetta sqlite on Ubuntu.

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Test: linux.clang.profile

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AnchoredDesign
Test: linux.clang.python37.release.PyRosetta4.Release

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branch: release 「№237」
Commited by: Rebecca Alford
GitHub commit link: 「5aed75f2e796a33a」 「№4327」
Difference from previous tested commit:  code diff
Commit date: 2019-10-29 08:37:43
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Merge pull request #4327 from RosettaCommons/rfalford12/find-optimal-hydrophobic-thk Adding application for finding the lowest energy hydrophobic thickness

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Test: linux.clang.profile

Failed sub-tests (click for more details):
AnchoredDesign
Test: mac.clang.python36.release.PyRosetta4.conda.Release

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branch: release 「№236」
Commited by: Vikram K. Mulligan
GitHub commit link: 「36665092fdf1cd84」 「№4291」
Difference from previous tested commit:  code diff
Commit date: 2019-10-19 15:21:32
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Merge pull request #4291 from RosettaCommons/vmullig/bind_fragmentstore_vartypes_to_python Bind FragmentStore variables to allow access to Python. This incorporates changes from Brian Weitzner and Bobby Langan, and suggestions from Sergey Lyskov.

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Test: mac.clang.python36.release.PyRosetta4.conda.Release

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branch: release 「№235」
Commited by: Daniel Farrell
GitHub commit link: 「94f6040c83f5106f」 「№4267」
Difference from previous tested commit:  code diff
Commit date: 2019-10-11 19:34:08
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Merge pull request #4267 from RosettaCommons/danpf/denovo_dump_pdb make debug denovo_density dump pdb not text

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Test: linux.clang.performance

Failed sub-tests (click for more details):
core_scoring_Score_100x_envsmooth
Test: mac.clang.python36.release.PyRosetta4.conda.Release

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branch: release 「№234」
Commited by: Brian Coventry
GitHub commit link: 「513cc22d17d203e9」 「№4132」
Difference from previous tested commit:  code diff
Commit date: 2019-10-04 14:07:07
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Merge pull request #4132 from RosettaCommons/bcov/super_bugfix Super bugfix and arbitrary mover change pr



branch: release 「№233」
Commited by: Jack Maguire
GitHub commit link: 「93456a567a8125ca」 「№4242」
Difference from previous tested commit:  code diff
Commit date: 2019-09-26 14:24:44
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Merge pull request #4242 from RosettaCommons/JackMaguire/floats_core Revive extras=rosetta_float, part 2 Sequel to #4241 , partial replacement of #4240 Just modifying src/core in this PR

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Test: mac.clang.python36.release.PyRosetta4.conda.Release

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Test: mac.clang.static.release.binary

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branch: release 「№232」
Commited by: Daniel Farrell
GitHub commit link: 「f3cd88e4837a35eb」 「№4233」
Difference from previous tested commit:  code diff
Commit date: 2019-09-19 02:40:11
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Merge pull request #4233 from RosettaCommons/danpf/fix_static_build update static builds to core.6 split



branch: release 「№231」
Commited by: Andrew Leaver-Fay
GitHub commit link: 「767c1ea25c572fbc」
Difference from previous tested commit:  code diff
Commit date: 2019-08-22 09:19:33
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Fix bug: InterfaceGroupByVector order dependency (#4142) The InterfaceGroupByVector selector was sensitive to the order in which residues were presented it, failing to detect interactions between residue i in group 1 and residue j in group 2 if j < i. Why? The UpperEdgeGraph stores only the edges to higher- indexed nodes and is used for neighbor detection because it is fast to add edges to this kind of graph. It's not the right choice, however, if you're trying to iterate across all neighbors of a particular set of residues. Because the InterfaceGroupByVector class used this graph, it would miss residues at the interface between two sets if the lower-indexed residues were listed second; e.g. if you have a pose w/ chains A and B (and A comes first) and you created an IGBV where you said the two groups were chain B and chain A (in that order), then the IGBV would find no residues at the interface.



branch: release 「№230」
Commited by: Sergey Lyskov
GitHub commit link: 「1e60c63beb532fd4」 「№4094」
Difference from previous tested commit:  code diff
Commit date: 2019-08-09 17:19:57
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Merge pull request #4094 from RosettaCommons/sergey/binder adding PyRosetta.notebooks submodule, fixing PyRosetta thread build

...
Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol
Test: linux.clang.profile

Failed sub-tests (click for more details):
AnchoredDesign


branch: release 「№229」
Commited by: Rocco Moretti
GitHub commit link: 「9a323bc72ca18d3a」 「№4072」
Difference from previous tested commit:  code diff
Commit date: 2019-07-29 17:16:04
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Merge pull request #4072 from RosettaCommons/roccomoretti/component_loading_both Fix CCD component loading such that it is more complete. We're now providing the CCD for reading of arbitrary wwPDB recognized ligands, but we're doing it incompletely. Right now we have an odd system where we'll load a CCD version, but only if there isn't a Rosetta residue type which has the same three letter code. This is a bit silly, as there's a large number of Rosetta residue types with three letter codes which are not equivalent to the wwPDB residue with that three letter code, and these will obscure the CCD version. We already have a mechanism for removing CCD types that are equivalent to Rosetta types. This is the exclude_pdb_component_list.txt in the Rosetta database. (And associated facilities for -extra_res_fa etc.) If a three letter code is listed there, we don't load the CCD version. If the CCD version isn't excluded, and has the same three letter code as the (chemically non-equivalent) Rosetta version, we can load both and then let the atom name heuristic (or other such facility) pick the best residue type match. (The CCD types should come after the Rosetta types, so all else being equal, Rosetta should prefer the database version.) If, for some reason, this behavior doesn't work for you, you can always add -check_all_PDB_components false (now defaults true) to the command line, or call rtf.set_no_CCD_on_name3_match(true) in-code for your ResidueTypeFinder, and this should re-enable the old behavior. With this, I've dug through the centroid and fa_standard residue type sets, and updated their exclude_pdb_component_list.txt to be more complete.

...
Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol
Test: linux.clang.python36.release.PyRosetta4.conda.Release

Failed sub-tests (click for more details):
T900_distributed
Test: linux.clang.python37.release.PyRosetta4.conda.Release

Failed sub-tests (click for more details):
T900_distributed
Test: mac.clang.python36.release.PyRosetta4.conda.Release

Failed sub-tests (click for more details):
T900_distributed
Test: mac.clang.python37.release.PyRosetta4.conda.Release

Failed sub-tests (click for more details):
T900_distributed


branch: release 「№228」
Commited by: Vikram K. Mulligan
GitHub commit link: 「0da57b43256586e7」 「№4104」
Difference from previous tested commit:  code diff
Commit date: 2019-07-21 15:08:17
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Merge pull request #4104 from RosettaCommons/vmullig/rename_scorefunction_tracer Renaming ScoreFunction tracer to actually reflect the class name and not just the namespace. This will unfortunately change a bunch of integration tests. It brings the tracer in line with Rosetta conventions, though.

...
Test: linux.clang.python36.release.PyRosetta4.documentation

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branch: release 「№227」
Commited by: Labonte
GitHub commit link: 「03208cbfaffeda72」 「№4068」
Difference from previous tested commit:  code diff
Commit date: 2019-07-04 11:00:19
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Merge pull request #4068 from RosettaCommons/JWLabonte/quick_fix Bug Fix: ligand_motif_design integration test This merge will hopefully correct the `ligand_motif_design` integration test, which I accidentally broke when adding ATP to the database. (:rat: is sorry.) The test formerly used its own ATP `.params` file, and Rosetta will not allow there to be two ATPs in a `ResidueTypeSet`. I am simply making the test use the database version, which also involves renaming the atoms in the input `.pdb` file to their correct PDB names. All tests pass, but there are naturally differences in the `ligand_motif_design` test.

...
Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol


branch: release 「№226」
Commited by: Labonte
GitHub commit link: 「98bf209eda57a650」 「№4037」
Difference from previous tested commit:  code diff
Commit date: 2019-06-25 14:01:49
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Merge pull request #4037 from RosettaCommons/Blair980728-patch-1 PTMs: Adding 2 more enzymes to database

...
Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol


branch: release 「№225」
Commited by: Jack Maguire
GitHub commit link: 「d24aa6a89229a158」 「№4025」
Difference from previous tested commit:  code diff
Commit date: 2019-06-16 09:23:37
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug mac.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release mac.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.conda.Release linux.clang.python37.release.PyRosetta4.conda.Release mac.clang.python36.release.PyRosetta4.conda.Release mac.clang.python37.release.PyRosetta4.conda.Release release.PyRosetta4.documentation linux.gcc.static.release.binary mac.clang.static.release.binary release.source linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps

Merge pull request #4025 from RosettaCommons/JackMaguire/ClangCxx14 Correcting extras=cxx... flags for clang #3992 added options to compile with std=c++1y and later versions of c++. To do this, I needed to remove std=c++1x from those builds but failed to notice that clang uses std=c++11 instead. This PR simply corrects the flag being removed. Thanks for the review Sergey!

...
Test: linux.gcc.mpi.serialization.integration.mpi

Failed sub-tests (click for more details):
recon_design_mpi
Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol


branch: release 「№224」
Commited by: Jaume Bonet
GitHub commit link: 「b0c18bd01c0dd36a」 「№4001」
Difference from previous tested commit:  code diff
Commit date: 2019-06-07 07:40:47
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels static linux.ui mac.ui serialization integration.mpi performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug