Merge pull request #6110 from RosettaCommons/vmullig/b2ec4c93907 Fix a bug with thioether lariat structure prediction. This fixes a bug in simple_cycpep_predict with thioether lariats with tails and a native structure. (There was a spot in the code where I was assuming that the last residue was the cysteine residue.)

• Summary
• code_quality.clang_tidy 「1」
• linux.gcc.mpi.serialization.integration.mpi 「23」
• linux.gcc.mpi.serialization.python310.integration.mpi 「23」
• linux.gcc.mpi.serialization.python36.integration.mpi 「6」
• linux.gcc.mpi.serialization.python38.integration.mpi 「6」
• linux.gcc.mpi.serialization.python39.integration.mpi 「6」
• integration.release_debug 「1」
• integration 「1」
• profile 「1」

Merge pull request #6082 from RosettaCommons/revert-6081-revert-5520-jyjwang/degreaser-fresh fixed things so that the tests that were broken passed. main culprits: unused variables / functions. annoying fix: indexing with Size instead of SSize. Thanks Sergey for checking in on the original PR ! Revert "Revert "Degreaser v 1.0""

• Summary
• code_quality.clang_tidy 「1」
• integration.addsan 「2」
• integration.mpi 「23」
• integration.release_debug 「4」
• integration.tutorials 「1」
• integration.ubsan 「1」
• integration 「3」
• profile 「2」
• scientific.make_fragments.debug
• scientific.make_fragments
• scientific.mp_lipid_acc
• scientific.sb_talaris13_relax_fast
• scientific.sb_talaris14_fast_design

increasing _merge_size_failure_threshold_bytes_ to 128KB

• Summary
• integration.mpi 「23」
• integration.release_debug 「3」
• integration.tensorflow 「1」
• integration 「1」
• profile 「3」

Merge pull request #6083 from RosettaCommons/sergey/binder fixing Rosetta and PyRosetta builds on Ubuntu-22.04

• Summary
• integration.addsan 「2」
• integration.mpi 「23」
• integration.release_debug 「2」
• integration.tensorflow 「1」
• integration.tutorials 「1」
• integration 「1」
• performance 「1」
• scientific.FlexPepDock.debug
• scientific.abinitio_RosettaNMR_rdc
• scientific.docking.debug
• scientific.loop_modeling_kic_12res
• scientific.mp_domain_assembly
• scientific.mp_symdock.debug
• scientific.peptide_pnear_vs_ic50

Merge pull request #6093 from RosettaCommons/vmullig/fix_thioether_cyclization_patch Fixing the oxygen atom placement in the AcetylatedProteinNtermConnection patch. The backbone carbon depended on the oxygen rather than the converse. This created bad geometry in GenKIC.

• Summary
• integration.addsan 「1」
• integration.mpi 「24」
• integration.release_debug 「11」
• integration.tensorflow 「2」
• integration.thread 「1」
• integration 「9」
• profile 「1」
• scientific.FlexPepDock
• scientific.design_fast
• scientific.ligand_docking.debug
• scientific.loop_modeling_ccd_12res.debug
• scientific.mp_f19_sequence_recovery
• scientific.mp_lipid_acc
• scientific.peptide_pnear_vs_ic50

Merge pull request #6087 from RosettaCommons/benchmark Fixing Mac builds, fixing Conda releases and updating default Python to 3.9.

• Summary
• integration.addsan 「1」
• integration.mpi 「22」
• integration.release_debug 「10」
• integration.tutorials 「1」
• integration.ubsan 「1」
• integration 「8」
• scientific.ddg_ala_scan
• scientific.docking.debug
• scientific.glycan_structure_prediction.debug
• scientific.ligand_docking.debug
• scientific.loop_modeling_ccd_12res.debug
• scientific.loop_modeling_ccd_12res
• scientific.mhc_epitope_energy.debug
• scientific.mp_domain_assembly.debug
• scientific.mp_domain_assembly
• scientific.mp_f19_ddG_of_mutation
• scientific.mp_f19_sequence_recovery
• scientific.mp_lipid_acc
• scientific.mp_symdock.debug
• scientific.peptide_pnear_vs_ic50

Merge pull request #6091 from RosettaCommons/roccomoretti/replica_dock_fix (Partially) Fix replica_docking integration test Looks like we need a pre-existing directory to put the logs into. We're still getting timeouts on the server, but we're not hard crashing anymore.

• Summary
• mac.clang.bcl.build.debug
• mac.clang.build.debug
• OpenCL
• mac.clang.python36.build.debug
• graphics
• mac.clang.build.release
• integration.mpi 「22」
• integration.release_debug 「4」
• integration 「12」
• scientific.FlexPepDock
• scientific.mp_f19_ddG_of_mutation
• scientific.mp_lipid_acc
• mac.clang.score
• mac.clang.unit.release
• gcc-9.gcc.unit 「54」
• mac.clang.unit