fixing maintenance.documentation test

• Summary
• code_quality.clang_analysis 「1」
• code_quality.clang_tidy 「5」
• integration.addsan 「10」
• integration.mpi 「1」
• integration.release_debug 「6」
• integration.tutorials 「1」
• integration.ubsan 「4」
• integration.valgrind 「5」
• integration 「2」
• maintenance.documentation
• profile 「1」
• gcc-10.gcc.unit 「3」
• gcc-11.gcc.unit 「3」
• gcc-9.gcc.unit 「3」

Merge pull request #6427 from RosettaCommons/benchmark fixing PyRosetta Conda releases on Mac

• Summary
• code_quality.clang_analysis 「1」
• code_quality.clang_tidy 「5」
• integration.addsan 「2」
• integration.mpi 「1」
• integration.release_debug 「3」
• integration.tutorials 「1」
• integration.ubsan 「2」
• integration.valgrind 「5」
• integration 「2」
• maintenance.documentation
• scientific.fragments_picking.debug
• gcc-10.gcc.unit 「3」
• gcc-11.gcc.unit 「3」

Merge pull request #6021 from RosettaCommons/woodsh17/mem_geo_pore MP pore compatible with FaMPEnv and FaMPSolv score terms New membrane geometries compatible with franklin2019 score function

• Summary
• code_quality.clang_analysis 「1」
• integration.addsan 「13」
• integration.mpi 「1」
• integration.release_debug 「15」
• integration.ubsan 「2」
• integration 「15」
• scientific.ligand_scoring_ranking
• scientific.mp_f19_decoy_discrimination.debug
• scientific.mp_f19_decoy_discrimination
• linux.clang.score 「5」
• linux.gcc.score 「5」
• mac.clang.score 「5」
• gcc-10.gcc.unit 「3」
• gcc-11.gcc.unit 「3」

Merge pull request #6426 from RosettaCommons/everyday847/fix_mpdock_itest Fix bug where sfxn memory address was written to tracer output

• Summary
• code_quality.clang_tidy 「4」
• integration.addsan 「1」
• integration.mpi 「1」
• integration.release_debug 「4」
• integration.tensorflow 「1」
• integration.tutorials 「1」
• integration.ubsan 「4」
• integration.valgrind 「5」
• integration 「4」
• maintenance.documentation
• mac.clang.python311.release.PyRosetta.MinSizeRel
• mac.clang.python311.release.PyRosetta.Release

Merge pull request #6425 from RosettaCommons/guangfeng/galiganddock_vsx_update Added options to report the number of hydrogen bonds between the ligand and selected residues.

• Summary
• code_quality.clang_tidy 「4」
• integration.mpi 「1」
• integration.release_debug 「6」
• integration.tensorflow 「1」
• integration.tutorials 「1」
• integration 「5」
• mac.clang.python311.release.PyRosetta.MinSizeRel
• mac.clang.python311.release.PyRosetta.Release
• scientific.ligand_scoring_ranking

Merge pull request #6424 from RosettaCommons/peisenhuth/PyTorchCmake Adding build support for PyTorch in CMake

• Summary
• integration.mpi 「1」
• integration.release_debug 「4」
• integration.tensorflow 「1」
• integration 「4」
• maintenance.documentation
• mac.clang.python311.release.PyRosetta.MinSizeRel
• mac.clang.python311.release.PyRosetta.Release
• scientific.ligand_scoring_ranking

Merge pull request #6420 from RosettaCommons/everyday847/nmethyl_cys_chi Fix chi scheme for N-methyl CYS and DCYS

• Summary
• code_quality.clang_tidy 「6」
• integration.addsan 「2」
• integration.mpi 「2」
• integration.release_debug 「6」
• integration.tensorflow 「2」
• integration.thread 「1」
• integration.tutorials 「1」
• integration.ubsan 「4」
• integration.valgrind 「5」
• integration 「5」
• maintenance.documentation
• mac.clang.python311.release.PyRosetta.MinSizeRel
• mac.clang.python311.release.PyRosetta.Release
• scientific.make_fragments.debug
• scientific.make_fragments
• scientific.mp_lipid_acc

Merge pull request #6421 from RosettaCommons/vmullig/update_layer_selector_xsd Update the XSD for the Layer selector. It drives me nuts having to search through the code for the default values. This fills in some "XRW TO DO" lines.

• Summary
• code_quality.clang_tidy 「4」
• integration.addsan 「1」
• integration.mpi 「1」
• integration.release_debug 「6」
• integration.tensorflow 「1」
• integration.tutorials 「1」
• integration.ubsan 「4」
• integration 「6」
• mac.clang.python311.release.PyRosetta.MinSizeRel
• mac.clang.python311.release.PyRosetta.Release

Merge pull request #6419 from RosettaCommons/guangfeng/galiganddock_vsx_update Added the following major updates in GALigandDock: 1. Added template docking in GALigandDock. When a template complex structure is provided, GALigandDock will align ligands to the template ligand using maximum common substructure from RDKit with slight perturbation in non-aligned torsions and rigid body. Atom feature alignment is also performed after template alignment; 2. Added a simple entropy model to estimate the ligand entropy using the number of rotational bonds in a ligand; 3. Added buried unsatisfied hydrogen bonds estimation in GALigandDock; 4. A few minor bugfixes and code improvements.

• Summary
• code_quality.clang_tidy 「4」
• integration.addsan 「1」
• integration.mpi 「1」
• integration.release_debug 「7」
• integration.tutorials 「1」
• integration.ubsan 「4」
• integration.valgrind 「5」
• integration 「6」
• maintenance.documentation
• mac.clang.python311.release.PyRosetta.MinSizeRel
• mac.clang.python311.release.PyRosetta.Release

attaching glycans to other residues (#6415) * An edit of the SimpleGlycosylateMover so that a linker atom can be specified on the residue to be glycosylated. Even the wrong atom, so long as it is in the residue, triggers a change in the code pathway so users will need to be cautious. Rosetta still finds the right patch for the residue if it exists and is functional (and it is the only glycosylation-related patch for that residue). There is an onus on the user to check functionality when using the new feature; old features perform the same. * Adding an integration test to test the functionality of the mover.

• Summary
• code_quality.clang_tidy 「6」
• integration.addsan 「1」
• integration.mpi 「1」
• integration.release_debug 「5」
• integration.tutorials 「1」
• integration.ubsan 「1」
• integration.valgrind 「2」
• integration 「5」
• maintenance.documentation
• mac.clang.python311.release.PyRosetta.MinSizeRel
• mac.clang.python311.release.PyRosetta.Release
• scientific.FlexPepDock
• scientific.antibody_h3_modeling
• scientific.fragments_picking.debug
• scientific.ligand_scoring_ranking
• scientific.make_fragments.debug
• scientific.make_fragments
• scientific.mp_f19_tilt_angle
• scientific.mp_lipid_acc

updating copyright info

• Summary
• integration.mpi 「1」
• integration.release_debug 「3」
• integration 「3」

Merge pull request #6418 from RosettaCommons/roccomoretti/gcc13 Fix compilation for GCC 13.1 Address a bunch of warnings which popped up. GCC 13 seems to have some more aggressive settings on warnings, which resulted in a number of warnings which can't directly be fixed. For now I've just turned off treating those warnings as errors in the compilation settings. If other people want to take a look at figuring out a work-around, I encourage them to do so.

• Summary
• integration.mpi 「1」
• integration.release_debug 「4」
• integration 「4」
• mac.clang.python311.release.PyRosetta.MinSizeRel
• scientific.ligand_scoring_ranking