initiating clean rebuild

• Summary
• code_quality.clang_tidy 「1」
• integration.addsan 「1」
• integration.mpi 「1」
• integration.release_debug 「1」
• integration.tutorials 「1」
• integration.ubsan 「1」
• integration 「3」
• maintenance.documentation
• profile 「1」

Merge pull request #6144 from RosettaCommons/jyjwang/degreaser-documentation-1 updating documentation

• Summary
• code_quality.clang_tidy 「1」
• integration.addsan 「2」
• integration.mpi 「1」
• integration.release_debug 「4」
• integration.tutorials 「1」
• integration.ubsan 「1」
• integration 「3」
• scientific.glycan_dock
• mac.clang.unit.release 「4」
• linux.gcc.cxx11thread.serialization.unit 「4」
• m1.clang.python39.unit 「4」
• mac.clang.unit 「4」
• ubuntu-20.04.gcc.python39.unit 「3」
• ubuntu-22.04.gcc.python39.unit 「3」

Merge pull request #6122 from RosettaCommons/roccomoretti/update_rdkit Update RDKit Due to interest, update the version of RDKit to 2021.03.5. This version is the same one being used in Foldit (PR #5590) and should be C++14 compatible. Compilation issues seem to be sorted out if I explicitly ignore some of the new subdirectories in RDKit, which should be okay-ish, as they aren't used elsewhere in RDKit, and aren't used currently by Rosetta. (More extensive fixes may be necessary if we start to use those features.)

• Summary
• code_quality.clang_tidy 「3」
• integration.mpi 「1」
• integration.release_debug 「2」
• integration.tutorials 「1」
• integration.ubsan 「1」
• integration 「2」
• mac.clang.unit.release 「4」
• gcc-11.gcc.python39.unit 「4」
• gcc-9.gcc.unit 「4」
• linux.clang.unit 「4」
• m1.clang.python39.unit 「4」
• mac.clang.unit 「4」
• ubuntu-20.04.gcc.python39.unit 「4」

initiating clean rebuild

• Summary
• code_quality.clang_tidy 「1」
• integration.mpi 「6」
• integration 「2」

Merge pull request #6139 from RosettaCommons/jtseffer/ERMS_prediction_app_steepness Fixed typo in rigid dimer steepness for app SID_ERMS_prediction.

• Summary
• code_quality.clang_tidy 「3」
• integration.mpi 「6」
• integration 「2」
• profile 「13」
• mac.clang.unit.release 「3」
• linux.clang.unit 「4」
• linux.gcc.unit 「4」
• mac.clang.unit 「4」

Merge pull request #5867 from RosettaCommons/roccomoretti/packer_task_thresholds Make Dunbrack probability thresholds non-global. Right now, the -packing::dunbrack_prob_buried options and the like are a set-once option in the dunbrack/RotamerLibrary singleton. It looks like it doesn't need to be. Instead, as it controls the Rotamer generation logic (e.g. which rotamers are selected). we can move these options to the PackerTask. It's not 100% clean, as to preserve the current behavior we can't put the option reading under the same control as the other command line options, but at least it allows us to change these thresholds on a per-packing run basis, rather than a once-per-program-launch basis. (This will help with certain use cases in Foldit and PyRosetta.)

• Summary
• code_quality.clang_tidy 「1」
• integration.addsan 「2」
• integration.mpi 「23」
• integration.release_debug 「1」
• integration.tutorials 「1」
• integration.ubsan 「1」
• integration 「2」
• m1.clang.performance
• linux.clang.profile 「1」
• m1.clang.profile
• scientific.make_fragments.debug
• scientific.make_fragments
• scientific.mp_f19_tilt_angle
• scientific.mp_lipid_acc
• mac.clang.unit.release 「3」
• unit.valgrind 「4」
• linux.gcc.cxx11thread.serialization.unit 「4」
• mac.clang.unit 「4」

Merge pull request #5926 from RosettaCommons/roccomoretti/scratch_space_reorg_master Reduce dependency on RotamerLibraryScratchSpace The SingleResidueRotamerLibrary functions had dunbrack::RotamerLibraryScratchSpace as a parameter dependency. This was a little bit of an annoyance for non-Dunbrack rotamer libraries, particularly as there's fixed numbers of torsions within the scratch space. (Which results in some jiggery-pokery on the derivatives for non-canonicals.) It turns out that we don't actually make much use of the ScratchSpace for the general SingleResidueRotamerLibrary member interface. (In particular, we don't really re-use the scratch space at all.) We can re-write the interface to exclude it (letting the Dunbrack library create a new one), using a new TorsionEnergy class for the return-by-reference of the score components. For derivatives, we can push the torsion selection into the interface, avoiding having to return all the torsion derivatives. I cleaned up/condensed the usage of Scratch Space for the Dunbrack libraries. Not knowing the full complexities which have been layered on here, I stopped at a certain point. In particular, there's probably some room for efficiency improvements by skipping derivative calculations for unneeded torsions, though I leave that to a future PR by someone else.

• Summary
• integration.mpi 「23」
• integration 「2」
• m1.clang.performance
• linux.clang.profile 「1」
• m1.clang.profile
• linux.clang.unit.release 「4」
• linux.gcc.unit.release 「4」
• mac.clang.unit.release 「3」
• unit.valgrind 「4」
• linux.clang.unit 「4」
• mac.clang.unit 「4」

Merge pull request #6123 from RosettaCommons/vmullig/update_gcc_10_3 Add build settings for GCC 10.3.

• Summary
• integration.addsan 「2」
• integration.mpi 「3」
• integration.tutorials 「1」
• integration.ubsan 「1」
• m1.clang.performance
• m1.clang.profile
• ubuntu-20.04.gcc.python39.unit 「3」

beautifying

• Summary
• integration.addsan 「2」
• integration.mpi 「23」
• integration.tutorials 「1」
• integration.ubsan 「1」
• m1.clang.performance
• m1.clang.profile
• scientific.mp_f19_tilt_angle
• gcc-9.gcc.unit 「3」

Merge pull request #6124 from RosettaCommons/smturzo/parcs_update PARCS update: Modified to read silent files too. The integration test fail is expected because the TR now outputs the number of pose along with name of pose and CCS value.

• Summary
• beautification
• integration.mpi 「23」
• integration.release_debug 「3」
• integration 「1」
• m1.clang.performance
• m1.clang.profile

Merge pull request #6101 from RosettaCommons/roccomoretti/named_constraint_activation Enable NamedAtomPairConstraints in constraint file It looks like the creator wasn't being registered.

• Summary
• integration.addsan 「2」
• integration.mpi 「23」
• integration.release_debug 「2」
• integration.tutorials 「1」
• integration.ubsan 「1」
• m1.clang.performance
• m1.clang.profile

Merge pull request #6113 from RosettaCommons/roccomoretti/python3_fixes Make integration tests which need Python2 into Python3 compatible Various Python2 ->Python3 fixes for scripts which are used by integration tests. This should now make it such that all integration tests can run with Python3.

• Summary
• integration.addsan 「2」
• integration.mpi 「6」
• integration.release_debug 「6」
• integration 「6」
• m1.clang.performance
• m1.clang.profile
• scientific.ligand_scoring_ranking