Attempt to fix failing tests in main. (#299) This PR attempts to address (in part) the following failures: * code_template_tests_src integration -- Update test (and script documentation) for the new scheme * unit valgrind -- fix for Python3 * clang tidy -- update NULL/nullptr * mp_f19_tilt_angle scientific -- Make more robust, and remove unneeded (for the scientific test) repacking step added with RosettaCommons/main#5551 * protein_data_bank_diagnostic scientific -- Errors are due to running out of pseudotty handles, attempt to recognize that situation and use a fall-back approach. * glycan_structure_prediction scientific -- Adjust number of processors and runtime to run on single node. I've also made some changes to better support the GCC 11 & Rocky9 build I'm now doing locally. I've also attempted to fix the replica_docking MPI integration test timeout, but there some additional issues which mean it's not quite working correctly.

• Summary

Pull Request №299 RosettaCommons/rosetta/main ← roccomoretti/rosetta/master_fix Merge: a1e0e9908af05092868be83ae85c6c7c4b04fcf6←65d53cb5c48ce3098a0fa59fab7e4ae71d327e6b Attempt to fix failing tests in main. ---------------- Merge commit message: Beautify

• Summary
• integration.mpi 「1」
• integration.release_debug 「3」
• integration 「4」

fix make_fragments test (#302)

• Summary

Pull Request №299 RosettaCommons/rosetta/main ← roccomoretti/rosetta/master_fix Merge: a1e0e9908af05092868be83ae85c6c7c4b04fcf6←017e21b0edf79019cc8936d4f0520e66cdcf7f55 Attempt to fix failing tests in main. ---------------- Merge commit message: Attempt to fix edge case in replica_dock integration test.

• Summary
• beautification
• integration.mpi 「1」
• integration.release_debug 「4」
• integration 「4」

Pull Request №299 RosettaCommons/rosetta/main ← roccomoretti/rosetta/master_fix Merge: a1e0e9908af05092868be83ae85c6c7c4b04fcf6←a16059d3dd31ed66fad030a4cf819ab203d60c1e Attempt to fix failing tests in main. ---------------- Merge commit message: Fix mp_f19_tilt_angle due to new column added.

• Summary
• integration.mpi 「1」

switch to HTTPS URL for pdb_seqres.txt

• Summary

Pull Request №295 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/roccomoretti-patch-2 Merge: 1f5080a079a5261122c0e532c46f61a4f7e20df8←1b4aff6bb90488cf540e909be178f468746a0b4e Attempt to fix simple_cycpep_predict ---------------- Merge commit message: restrict SLURM MPI jobs to use single node

• Summary

Pull Request №299 RosettaCommons/rosetta/main ← roccomoretti/rosetta/master_fix Merge: 1f5080a079a5261122c0e532c46f61a4f7e20df8←e0398398937d58b94046a1d85973853b8036bbf2 Attempt to fix failing tests in main. ---------------- Merge commit message: Can't double-close file handles.

• Summary
• integration.mpi 「1」
• integration 「2」
• scientific.mp_f19_tilt_angle
• scientific.protein_data_bank_diagnostic.full

Pull Request №299 RosettaCommons/rosetta/main ← roccomoretti/rosetta/master_fix Merge: 1f5080a079a5261122c0e532c46f61a4f7e20df8←e3950ef0f6e22f1874b013d3400b454212f3d496 Attempt to fix failing tests in main. ---------------- Merge commit message: Remove unneeded (for the scientific test) repacking stage.

• Summary
• code_quality.clang_tidy
• integration.mpi
• integration
• unit.valgrind

Merge branch 'main' into benchmark

• Summary

Pull Request №295 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/roccomoretti-patch-2 Merge: 1f5080a079a5261122c0e532c46f61a4f7e20df8←f14cfde15403352a976dafc427f084304c5fc5b9 Attempt to fix simple_cycpep_predict ---------------- Merge commit message: Fix spacing, address similar issue in other script.

• Summary
• scientific.peptide_pnear_vs_ic50

Pull Request №295 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/roccomoretti-patch-2 Merge: 1f5080a079a5261122c0e532c46f61a4f7e20df8←90ea6fad7b4f251891e3c0561e616c5e3372d641 Attempt to fix simple_cycpep_predict ---------------- Merge commit message: Attempt to fix simple_cycpep_predict

• Summary
• scientific.simple_cycpep_predict.debug

Pull Request №243 RosettaCommons/rosetta/main ← lyskov/rosetta/pyrosetta Merge: 4e95d564dc8b93fbe830018d2f295f3f69a70dfd←259ea7e252a19d4012e421d8052343b66f4fff50 Update Conda setup ---------------- Merge commit message: mitigate error if no `defaults` channel was set

• Summary
• mac.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• release.rosetta.conda.release

Pull Request №243 RosettaCommons/rosetta/main ← lyskov/rosetta/pyrosetta Merge: 4e95d564dc8b93fbe830018d2f295f3f69a70dfd←d8c6c48f0b7bb42fcb33bc7b497c0e26ddd0783f Update Conda setup ---------------- Merge commit message: remove `defaults` channel

• Summary
• m1.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• m1.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• m1.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• m1.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• m1.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• release.rosetta.conda.release

remove conda `defaults` and add `conda-forge` channel

• Summary
• ubuntu.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• release.rosetta.conda.release

Fix issue related to PackerTask usage in homodimer_design. (#115) With a -pack_min_runs of 2 or greater, there's a chance that the sequence of the structure changes. This is a problem for a fixed PackerTask run, as `task_is_valid( pose )` fails if the base residue types don't match up properly. This is an issue found in Discussion #112 The fix is simple -- just use the TaskFactory which we already have lying around instead of manually generating the packer task. (The PackRotamersMover will properly re-apply the TaskFactory.) We can also make the interface of PackRotamersMover a bit nicer.

• Summary

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