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branch: master 「№61944」
Commited by: Sergey Lyskov
GitHub commit link: 「5a073af94d2c9fde」 「№6226」
Difference from previous tested commit:  code diff
Commit date: 2022-10-01 19:08:06
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook aarch64.clang.python39.PyRosetta.unit gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python38.PyRosetta.unit mac.clang.python39.PyRosetta.unit ubuntu-20.04.clang.python39.PyRosetta.unit ubuntu-22.04.clang.python39.PyRosetta.unit build.clean.debug aarch64.gcc.python39.build.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.build.debug gcc-9.gcc.build.debug icc.icc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization mac.clang.bcl.build.debug OpenCL ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics aarch64.gcc.python39.build.release gcc-10.gcc.build.release gcc-11.gcc.build.release gcc-9.gcc.build.release static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration.valgrind integration performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug mac.clang.python310.release.PyRosetta.Debug mac.clang.python38.release.PyRosetta.Debug mac.clang.python39.release.PyRosetta.Debug linux.clang.python310.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel mac.clang.python310.release.PyRosetta.MinSizeRel mac.clang.python38.release.PyRosetta.MinSizeRel mac.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python310.release.PyRosetta.Release linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python310.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python310.release.PyRosetta.Release mac.clang.python38.release.PyRosetta.Release mac.clang.python39.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.PyRosetta.conda.Release release.source scientific.FlexPepDock linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release unit.ubsan unit.valgrind aarch64.gcc.python39.unit gcc-10.gcc.unit gcc-11.gcc.unit gcc-9.gcc.unit m1.clang.python39.unit ubuntu-20.04.clang.python39.unit ubuntu-20.04.gcc.python39.unit ubuntu-22.04.clang.python39.unit ubuntu-22.04.gcc.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #6226 from RosettaCommons/benchmark adding aarch64 support

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Test: ubuntu.gcc.integration.addsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: linux.gcc.mpi.serialization.integration.mpi

Failed sub-tests (click for more details):
replica_docking
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: ubuntu.gcc.integration.ubsan

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


branch: master 「№61943」
Commited by: Rocco Moretti
GitHub commit link: 「d8d9982120b445e6」 「№5360」
Difference from previous tested commit:  code diff
Commit date: 2022-09-28 18:13:34
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python38.PyRosetta.unit mac.clang.python39.PyRosetta.unit ubuntu-20.04.clang.python39.PyRosetta.unit ubuntu-22.04.clang.python39.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.build.debug gcc-9.gcc.build.debug icc.icc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization mac.clang.bcl.build.debug OpenCL ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics gcc-10.gcc.build.release gcc-11.gcc.build.release gcc-9.gcc.build.release static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration.valgrind integration performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug mac.clang.python310.release.PyRosetta.Debug mac.clang.python38.release.PyRosetta.Debug mac.clang.python39.release.PyRosetta.Debug linux.clang.python310.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel mac.clang.python310.release.PyRosetta.MinSizeRel mac.clang.python38.release.PyRosetta.MinSizeRel mac.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python310.release.PyRosetta.Release linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python310.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python310.release.PyRosetta.Release mac.clang.python38.release.PyRosetta.Release mac.clang.python39.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.PyRosetta.conda.Release release.source scientific.FlexPepDock scientific.antibody_grafting.debug scientific.antibody_grafting linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release unit.ubsan unit.valgrind gcc-10.gcc.unit gcc-11.gcc.unit gcc-9.gcc.unit m1.clang.python39.unit ubuntu-20.04.clang.python39.unit ubuntu-20.04.gcc.python39.unit ubuntu-22.04.clang.python39.unit ubuntu-22.04.gcc.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #5360 from RosettaCommons/roccomoretti/chemistry_objects Add "Chemistry" Objects, which are like Movers, but for ResidueTypes. This is part of the process of merging my the drug_design branch piecemeal. The Chemisty objects come in two parts. The first is a simple core-level one, which defines the basic interface. The second is a protocols-level one which extents the interface to be XML parsable and Pose-aware. (That is, you can potentially have chemistries which are aware of the residue context in the Pose.) Chemistries occupy a new section in the input XML. With this PR comes some simple Chemistries, such as PatchChemistry, which allows you to apply the same manipulations you could in a patch. I also add an ApplyChemistyMover, which allows you to apply one or more Chemistries to a Pose from an XML context.

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Test: ubuntu.gcc.integration.addsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: linux.gcc.mpi.serialization.integration.mpi

Failed sub-tests (click for more details):
replica_docking
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
database_md5 output_schema


branch: master 「№61942」
Commited by: Sergey Lyskov
GitHub commit link: 「42f63275dedaa6cb」 「№6217」
Difference from previous tested commit:  code diff
Commit date: 2022-09-28 14:42:57
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python38.PyRosetta.unit mac.clang.python39.PyRosetta.unit ubuntu-20.04.clang.python39.PyRosetta.unit ubuntu-22.04.clang.python39.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.build.debug gcc-9.gcc.build.debug icc.icc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization mac.clang.bcl.build.debug OpenCL ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics gcc-10.gcc.build.release gcc-11.gcc.build.release gcc-9.gcc.build.release static beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.PyRosetta.Debug m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel mac.clang.python38.release.PyRosetta.MinSizeRel mac.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.Release mac.clang.python39.release.PyRosetta.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release unit.ubsan gcc-10.gcc.unit gcc-11.gcc.unit gcc-9.gcc.unit m1.clang.python39.unit ubuntu-20.04.clang.python39.unit ubuntu-20.04.gcc.python39.unit ubuntu-22.04.clang.python39.unit ubuntu-22.04.gcc.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #6217 from RosettaCommons/benchmark updating release scripts - adding release.rosetta.documentation - refactoring release.binary script so release-as-git repository became optional

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

Failed sub-tests (click for more details):
replica_docking
Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
rnp_ddg_finalize
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
database_md5


branch: master 「№61941」
Commited by: Sergey Lyskov
GitHub commit link: 「7ee89691fa724d69」 「№6208」
Difference from previous tested commit:  code diff
Commit date: 2022-09-23 00:32:54
scientific.fragments_picking.debug

Merge pull request #6208 from RosettaCommons/benchmark Porting Rosetta/PyRosetta to Linux arm64 platform

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Test: ubuntu-20.04.clang.python36.scientific.fragments_picking.debug

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branch: master 「№61940」
Commited by: Sergey Lyskov
GitHub commit link: 「4c51f714cd413ab5」 「№6201」
Difference from previous tested commit:  code diff
Commit date: 2022-09-16 19:05:06
maintenance.documentation

Merge pull request #6201 from RosettaCommons/benchmark fixing 15.02-Membrane-Protein-ddG-of-mutation notebook

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Test: linux.clang.maintenance.documentation

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branch: master 「№61939」
Commited by: Sergey Lyskov
GitHub commit link: 「717883cf62544f62」 「№6199」
Difference from previous tested commit:  code diff
Commit date: 2022-09-16 17:09:16

Merge pull request #6199 from RosettaCommons/benchmark updating PyRosetta.notebooks module to fix 02.06-Visualization-and-PyMOL-Mover.PyRosetta-ColabPyMOL-integration notebook

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branch: master 「№61938」
Commited by: Sergey Lyskov
GitHub commit link: 「f8d1edff335ebf03」 「№6195」
Difference from previous tested commit:  code diff
Commit date: 2022-09-14 20:40:19

Merge pull request #6195 from RosettaCommons/benchmark Benchmark scripts update

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branch: master 「№61937」
Commited by: Sergey Lyskov
GitHub commit link: 「f438a55714bb05ec」 「№6193」
Difference from previous tested commit:  code diff
Commit date: 2022-09-14 14:43:57

Merge pull request #6193 from RosettaCommons/sergey/binder PyRosetta, improving template bindings

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branch: master 「№61936」
Commited by: Andy Watkins
GitHub commit link: 「7f68ebd7b1940762」 「№6170」
Difference from previous tested commit:  code diff
Commit date: 2022-09-03 18:00:32

Merge pull request #6170 from RosettaCommons/everyday847/update_docs Bump docs submodule

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branch: master 「№61935」
Commited by: Sergey Lyskov
GitHub commit link: 「6079c70fa16855c0」 「№6167」
Difference from previous tested commit:  code diff
Commit date: 2022-08-31 20:05:32

Merge pull request #6167 from RosettaCommons/sergey/binder fixing PyRosetta package name calculation

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branch: master 「№61934」
Commited by: Sergey Lyskov
GitHub commit link: 「aa46261401fad3f4」 「№6163」
Difference from previous tested commit:  code diff
Commit date: 2022-08-30 19:12:16
maintenance.documentation

Merge pull request #6163 from RosettaCommons/sergey/binder adding `fixedsizearrayX_add_on_binder`

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Test: linux.clang.maintenance.documentation

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branch: master 「№61933」
Commited by: Sergey Lyskov
GitHub commit link: 「febec3c2d35cfc9f」 「№6154」
Difference from previous tested commit:  code diff
Commit date: 2022-08-25 19:59:15

Merge pull request #6154 from RosettaCommons/benchmark fixing fixing `calculate_extension` function

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branch: master 「№61932」
Commited by: Sergey Lyskov
GitHub commit link: 「b098d5406e565f7d」 「№6147」
Difference from previous tested commit:  code diff
Commit date: 2022-08-24 16:38:39

Merge pull request #6147 from RosettaCommons/sergey/f switching integration.mpi test to run in release_debug mode

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branch: master 「№61931」
Commited by: P. Douglas Renfrew
GitHub commit link: 「9ec33c9fe00427e5」 「№6148」
Difference from previous tested commit:  code diff
Commit date: 2022-08-24 09:49:27
maintenance.documentation

Merge pull request #6148 from RosettaCommons/dougrenfrew/remove_legacy_dunbrack_functions Remove legacy rotlib functions that caused array bounds warnings with GCC v10.3

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Test: linux.clang.maintenance.documentation

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branch: master 「№61930」
Commited by: Rocco Moretti
GitHub commit link: 「26e7887ec7bd82f0」 「№6146」
Difference from previous tested commit:  code diff
Commit date: 2022-08-19 16:22:05

Merge pull request #6146 from RosettaCommons/roccomoretti/fix_master_tests2 Fix clang_tidy warning in master Be explicit about which virtual function is being called during constructor. (This is easy, as it's the most-derived class which is calling things.)

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branch: master 「№61929」
Commited by: David P. Nannemann
GitHub commit link: 「8ffafd6497fa6765」 「№6142」
Difference from previous tested commit:  code diff
Commit date: 2022-08-19 12:12:16
maintenance.documentation

Merge pull request #6142 from RosettaCommons/nannemdp/vicinity_sampling_by_LoopRelaxMover Added if statement to LoopRelaxMover to bypass centroid setup when not remodeling the loop.

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Test: linux.clang.maintenance.documentation

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