Pull Request №667 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/ozstream-unique-ptr Merge: 8556abcecef09877257656a5144b1902b5f7c699←d06df99ede8699393ad8a30e570bcaeede24699d Refactor ozstream raw pointers to unique_ptr; modernize orstream copy ops ---------------- Merge commit message: Refactor ozstream raw pointers to unique_ptr; modernize orstream copy ops Replace three raw owning pointers in ozstream (char_buffer_p_, zip_stream_p_, mpi_stream_p_) with std::unique_ptr, eliminating manual delete/nullptr pairs throughout open(), open_append(), open_append_if_existed(), close(), and the buffer helpers. Also replace the old private-undefined copy ctor/assignment in orstream with explicit = delete, consistent with the irstream/izstream refactor.

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

Pull Request №665 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/timer-delete-copy Merge: f9c5b025aa6240de1105fd6cdcf04f7a535ea67d←776a3e20b99c27214dd542508fbf49c8056c617f Explicitly delete copy constructor and assignment in Timer ---------------- Merge commit message: Explicitly delete copy constructor and assignment in Timer Timer's destructor calls Report(), printing the elapsed time. Without explicit copy deletion, a copied Timer would silently produce a second Report() call on destruction, logging a duplicate timing entry for the same measured interval. Both tag_ and t_ are non-owning pointers so there is no memory-safety risk, but the semantic hazard is real. Deleting copy constructor and copy assignment makes the non-copyable intent explicit.

• Summary

Pull Request №663 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/variant-option-key-unique-ptr Merge: 068bd85322153b1ddc5a354f8cf0633a5631e9fa←28a846a04cea64e67d633086273b0ce57e64417e Refactor VariantKey and VariantOption raw pointers to unique_ptr ---------------- Merge commit message: Remove unnecessary = default move ctor/assignment from VariantKey and VariantOption Both classes have user-declared copy constructor and copy-assignment, which suppress implicit move generation (C++11). The explicit = default moves were performance-only; without them, moves fall back to deep-clone copies, which is semantically correct. Per project policy, this performance-only benefit is not worth the added noise.

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

Pull Request №658 RosettaCommons/rosetta/main ← klimaj/rosetta/cache_efficiency Merge: 8556abcecef09877257656a5144b1902b5f7c699←7a890e29801f48255fa91816222235a3bc123518 Improving `Pose.cache` dictionary getter and setter performance ---------------- Merge commit message: Merge branch 'main' of github.com:klimaj/rosetta into cache_efficiency

• Summary

Pull Request №666 RosettaCommons/rosetta/main ← klimaj/rosetta/test_t919 Merge: f9c5b025aa6240de1105fd6cdcf04f7a535ea67d←ef261e0dd1e7c6c9688369fa184d1b21dbfa6022 Testing T919 and T920 unit tests with ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit ---------------- Merge commit message: Clean up

• Summary

Pull Request №666 RosettaCommons/rosetta/main ← klimaj/rosetta/test_t919 Merge: f9c5b025aa6240de1105fd6cdcf04f7a535ea67d←4312038e3b987a511533c4cbacf293037bb97ea8 Testing T919 and T920 unit tests with ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit ---------------- Merge commit message: Remove hash functions

• Summary

Pull Request №666 RosettaCommons/rosetta/main ← klimaj/rosetta/test_t919 Merge: f9c5b025aa6240de1105fd6cdcf04f7a535ea67d←052b421cbf02f7ea251d60948195eaf7f1a3fe9c Testing T919 and T920 unit tests with ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit ---------------- Merge commit message: Initial commit

• Summary
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「2」

Pull Request №664 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/izstream-unique-ptr Merge: f9c5b025aa6240de1105fd6cdcf04f7a535ea67d←986182c8292578b08c4c38889ed079bc23b064a1 Refactor izstream raw zip_stream_p_ pointer to unique_ptr ---------------- Merge commit message: Fix inaccurate comments on deleted copy ops in izstream

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

Pull Request №664 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/izstream-unique-ptr Merge: f9c5b025aa6240de1105fd6cdcf04f7a535ea67d←2371147ec5067102b18bc01e0529261a8d4797ad Refactor izstream raw zip_stream_p_ pointer to unique_ptr ---------------- Merge commit message: Refactor izstream raw zip_stream_p_ pointer to unique_ptr zip_stream_p_ was a raw owning pointer managed by a custom destructor with no corresponding copy/move declarations — the inherited private copy ops from irstream prevented copying, but this relied on an implicit base-class mechanism rather than explicit class policy. Replace the raw pointer with std::unique_ptr, explicitly delete copy constructor and copy assignment in izstream itself, and update all reset/allocation sites to use unique_ptr::reset(). The redundant manual delete in the destructor is eliminated; the if_stream_ cleanup calls are kept.

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

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」

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