Pull Request №663 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/variant-option-key-unique-ptr Merge: 068bd85322153b1ddc5a354f8cf0633a5631e9fa←237432f9eebcac8bb7a0e46347ae2c7283ba279c Refactor VariantKey and VariantOption raw pointers to unique_ptr ---------------- Merge commit message: Refactor VariantKey and VariantOption raw pointers to unique_ptr Both classes held a raw owning pointer and manually defined copy-constructor, copy-assignment, and destructor, but lacked move constructor and move-assignment (Rule of Five violation). Replacing the raw pointer with std::unique_ptr eliminates the manual destructor and adds correct move semantics via = default; the copy operations are preserved using unique_ptr::reset with the existing clone() deep-copy logic.

• Summary
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「2」
• integration.mpi 「22」
• integration.release_debug 「1」
• integration.tensorflow 「1」

Pull Request №662 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/svm-rosetta-unique-ptr Merge: 068bd85322153b1ddc5a354f8cf0633a5631e9fa←62c1e29ac2e17961b916c01f36ecbbfef3304ca8 Refactor Svm_rosetta raw pointer to unique_ptr with custom deleter ---------------- Merge commit message: Refactor Svm_rosetta raw pointer to unique_ptr with custom deleter Replaces the bare svm_model* in Svm_rosetta with std::unique_ptr<svm_model, SvmModelDeleter> to make ownership explicit and eliminate the latent double-free from compiler-generated copy operations. Deletes copy constructor and assignment. Removes the unnecessary = default destructor from Svm_node_rosetta.

• Summary
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「2」
• integration.mpi 「2」
• integration.tensorflow 「1」
• integration 「1」

Pull Request №99 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/bcov/hbond_graph_pyrosetta Merge: 068bd85322153b1ddc5a354f8cf0633a5631e9fa←9cfeafbca0d32d55f153024809fcde2236eb50b5 Made hbond graph pyrosetta compatible ---------------- Merge commit message: Whitespace

• Summary
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「2」
• code_quality.submodule_regression
• integration.mpi 「2」

Pull Request №661 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/pimpl-unique-ptr-xml-schema Merge: 068bd85322153b1ddc5a354f8cf0633a5631e9fa←9b302e32e1eda33df31b186c33ea081c097ac445 Refactor pimpl pointers in XMLSchemaComplexTypeGenerator and XMLValidator to unique_ptr ---------------- Merge commit message: Refactor pimpl pointers in XMLSchemaComplexTypeGenerator and XMLValidator to unique_ptr Replace raw owning `class Impl*` members with `std::unique_ptr<class Impl>`, allowing destructors to be defaulted and making ownership explicit in the type system.

• Summary
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「2」
• integration.mpi 「2」
• integration.tensorflow 「1」

Pull Request №660 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/fix/simulate-mpi-memory-leak Merge: 068bd85322153b1ddc5a354f8cf0633a5631e9fa←8e107b58d4261b849c1987b2ce35860ec09eb427 Fix memory leak in SimulateMPI: use unique_ptr for simulation_ ownership ---------------- Merge commit message: Fix memory leak in SimulateMPI: use unique_ptr for simulation_ ownership initialize_simulation() unconditionally assigned a new SimulateMPIData* without deleting any previous allocation, leaking memory on re-initialization. Switch simulation_ from a raw pointer to unique_ptr so reset() properly frees the old object and the static is cleaned up at program exit.

• Summary
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「2」
• integration.mpi 「2」
• integration.tensorflow 「1」

Pull Request №659 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/fix/inline-file-provider-memory-leak Merge: 068bd85322153b1ddc5a354f8cf0633a5631e9fa←7bbc4a6638240c9abc2a15a733d9931cb50a231f Fix memory leaks in Inline_File_Provider ---------------- Merge commit message: Fix memory leaks in Inline_File_Provider: use unique_ptr for stream ownership clear_input_files() and remove_input_file() were leaking stringstream objects by calling vector::clear()/erase() without deleting the raw pointers. get_ostream() also leaked on every call. Switch input_files and output_files to store unique_ptr<stringstream> so the vector destructor and erase() handle cleanup automatically.

• Summary
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「2」
• integration.mpi 「2」
• integration.tensorflow 「1」

Pull Request №658 RosettaCommons/rosetta/main ← klimaj/rosetta/cache_efficiency Merge: 068bd85322153b1ddc5a354f8cf0633a5631e9fa←2f8ba23f9a4bb78a6da6d54e6c0c53b0a59c7994 Improving `Pose.cache` dictionary getter and setter performance ---------------- Merge commit message: Clean up API; update docstring

• Summary
• mac.clang.cxx11thread.serialization.python38.PyRosetta.unit 「7」
• mac.clang.cxx11thread.serialization.python39.PyRosetta.unit 「7」
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「2」
• mpi.serialization
• integration.mpi 「2」
• integration.tensorflow 「1」

Pull Request №658 RosettaCommons/rosetta/main ← klimaj/rosetta/cache_efficiency Merge: 068bd85322153b1ddc5a354f8cf0633a5631e9fa←66b0d28dfe545a6914a0091669329be4b7fd8bc4 Improving `Pose.cache` dictionary getter and setter performance ---------------- Merge commit message: Initial commit

• Summary
• ubuntu-20.04.clang.cxx11thread.serialization.python310.PyRosetta.unit 「5」
• ubuntu-20.04.clang.cxx11thread.serialization.python311.PyRosetta.unit 「5」
• ubuntu-20.04.clang.cxx11thread.serialization.python312.PyRosetta.unit 「5」
• ubuntu-20.04.clang.cxx11thread.serialization.python313.PyRosetta.unit 「5」
• ubuntu-20.04.clang.cxx11thread.serialization.python314.PyRosetta.unit 「5」
• ubuntu-20.04.clang.cxx11thread.serialization.python39.PyRosetta.unit 「5」
• ubuntu-20.04.gcc.cxx11thread.serialization.python310.PyRosetta.unit 「5」
• ubuntu-20.04.gcc.cxx11thread.serialization.python311.PyRosetta.unit 「5」
• ubuntu-20.04.gcc.cxx11thread.serialization.python312.PyRosetta.unit 「5」
• ubuntu-20.04.gcc.cxx11thread.serialization.python313.PyRosetta.unit 「5」
• ubuntu-20.04.gcc.cxx11thread.serialization.python314.PyRosetta.unit 「5」
• ubuntu-20.04.gcc.cxx11thread.serialization.python39.PyRosetta.unit 「5」

Pull Request №99 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/bcov/hbond_graph_pyrosetta Merge: 068bd85322153b1ddc5a354f8cf0633a5631e9fa←ddf7f266d6f8416a677818c4fc4127f1fd59e49a Made hbond graph pyrosetta compatible ---------------- Merge commit message: Merge remote-tracking branch 'origin/main' into bcov/hbond_graph_pyrosetta

• Summary
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「2」
• integration.mpi 「2」
• integration.tensorflow 「1」

Pull Request №627 RosettaCommons/rosetta/main ← jderiz/rosetta/jderiz/feature/add_interface_AB_HL_option_to_cartesian_ddg Merge: 597b55d6600c3939574ffee30a4469b26c3337bd←8867af51577392850881227fcc4305c68a368114 Jderiz/feature/add Docking Protocol-like interface definition option to cartesian ddg ---------------- Merge commit message: Merge branch 'RosettaCommons:main' into jderiz/feature/add_interface_AB_HL_option_to_cartesian_ddg

• Summary
• integration.mpi 「2」
• integration.release_debug 「0」
• integration.tensorflow 「1」
• integration.thread 「0」
• integration.torch
• integration 「0」
• performance 「0」
• profile 「0」
• linux.clang.score 「0」
• linux.gcc.score 「0」
• mac.clang.score 「0」
• scripts.pyrosetta

Pull Request №657 RosettaCommons/rosetta/main ← klimaj/rosetta/docstrings2 Merge: ac1c89d42bb0c2942c3a91382a8ec42d65e96275←d37c3d550cf404034d90b65ea58c557655395d75 Clean up PyRosetta Sphinx documentation ---------------- Merge commit message: Initial commit

• Summary

Pull Request №655 RosettaCommons/rosetta/main ← klimaj/rosetta/security_patch Merge: ea526b88894f2552c8fa2e3efd3603716034cd6a←87d8e415bb38ef536a1765ec0f37d2c81af29baf Quick update: change which HKDF function is used by HMAC-SHA256 verification machinery in PyRosettaCluster ---------------- Merge commit message: git pull origin main

• Summary

Pull Request №655 RosettaCommons/rosetta/main ← klimaj/rosetta/security_patch Merge: b166af21f0776040bd54a021d8c7fd264cd99bfa←b493fcbb63beffbeeddbe3ba6dd25b90a61ba5c4 Quick update: change which HKDF function is used by HMAC-SHA256 verification machinery in PyRosettaCluster ---------------- Merge commit message: Update version

• Summary

Pull Request №648 RosettaCommons/rosetta/main ← klimaj/rosetta/unittests3 Merge: b166af21f0776040bd54a021d8c7fd264cd99bfa←bb803ff3a4ce2ffd2662d6bdea80ef847511e387 Split T900_distributed.py module into separate sub-tests ---------------- Merge commit message: Update warning/error messages in relevant unit tests from merged PR #646

• Summary

Pull Request №648 RosettaCommons/rosetta/main ← klimaj/rosetta/unittests3 Merge: 47f3ee8eecf722cf09d8adbc44898160976e9f8a←7fabb1c946e94cc85ea21cdb3880a6124f321952 Testing PR #636 variant: non-streaming grandchild processes (with subprocess.getstatusoutput) with os.fork model in self-test.py ---------------- Merge commit message: Revert "Disable T914 tests" This reverts commit 0cabcf55f3c6e19454444800a9f1779439a2cac1.

• Summary

Pull Request №648 RosettaCommons/rosetta/main ← klimaj/rosetta/unittests3 Merge: 47f3ee8eecf722cf09d8adbc44898160976e9f8a←0cabcf55f3c6e19454444800a9f1779439a2cac1 Testing PR #636 variant: non-streaming grandchild processes (with subprocess.getstatusoutput) with os.fork model in self-test.py ---------------- Merge commit message: Disable T914 tests

• Summary

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