Made hbond graph pyrosetta compatible (#99) You can't actually use the HBondGraph in pyrosetta because the LowMemGraph uses some crazy tricks that don't involve object inheritance. This adds 2 functions to bridge that gap.

• Summary
• integration 「1」
• scientific.protein_data_bank_diagnostic.cif

Modernize copy prevention in utility/graph EdgeList/Node/Edge to use = delete (#672) Replace old-style private-and-undefined copy constructor/assignment with explicit `= delete` in six internal classes across `Graph.hh` and `Digraph.hh`: - `Graph.hh`: `EdgeList`, `Node`, `Edge` - `Digraph.hh`: `DirectedEdgeList`, `DirectedNode`, `DirectedEdge` Also corrects the copy assignment signatures from the non-standard `T&` argument to the correct `T const &` form. The `Graph` class itself (which has a real, implemented copy constructor and assignment) is unchanged.

• Summary

Modernize copy prevention in KeyLookup to use = delete (#671) - Replace old-style private-and-undefined copy constructor/assignment in `utility/keys/KeyLookup` with explicit `= delete` - `KeyLookup` is a monostate singleton (all methods and data are static); copies are meaningless

• Summary
• integration.tensorflow 「1」
• integration.ubsan 「1」
• windows.build.release

Modernize copy prevention in factory/Registrant to use = delete (#670) - Replace old-style private-and-undefined copy constructor/assignment in `utility/factory/Registrant` with explicit `= delete` - Added a one-line comment explaining the non-obvious reason: each constructor calls `ProductFactory::add()`, so a copy would silently re-register the same key

• Summary
• integration.tensorflow 「1」
• integration 「1」

Modernize copy prevention in irstream to use = delete (#669) - Replace old-style private-and-undefined copy constructor/assignment in `utility/io/irstream` with explicit `= delete` - Mirrors the same treatment already applied to the sibling `orstream` class (PR #667)

• Summary
• integration 「1」

Modernize copy prevention in utility/signals classes to use = delete (#668) ## Summary - Replace old-style private-and-undefined copy constructor/assignment in five `utility/signals` classes with explicit `= delete` - Affected classes: `SignalHub`, `BufferedSignalHub`, `PausableSignalHub`, `TokenHub`, `LinkUnit` - Also explicitly deletes the `LinkUnit` default constructor (was previously also private-undefined) - Pure mechanical modernization — no behavioral change ## Motivation The pre-C++11 idiom of declaring copy ops private with no definition produces a linker error on misuse rather than a clear compile-time diagnostic. `= delete` gives an immediate, descriptive compiler error at the call site and is the modern idiomatic approach.

• Summary
• integration 「1」

Refactor ozstream raw pointers to unique_ptr; modernize orstream copy ops (#667) ## Summary - 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 in `open()`, `open_append()`, `open_append_if_existed()`, `close()`, and the buffer helpers - Modernize the private-undefined copy constructor/assignment in `orstream` to explicit `= delete`, consistent with the approach used in `irstream`/`izstream` (PR #664) ## Test plan - [x] Full debug build passes (`python3 ./scons.py -j16 mode=debug`) - [ ] No behavior change expected — ownership semantics are identical; `close()` still runs `zflush_finalize()` and `mpi_ostream::close()/clear()` before releasing the pointers

• Summary
• integration 「1」
• performance 「1」

Document mpistream rank-zero routing (#679) ## Summary - document that mpistream write messages intentionally route through rank 0 ## Testing - python3 ./scons.py -j16 mode=debug

• Summary
• integration.tutorials 「1」
• scientific.make_fragments.debug
• scientific.protein_data_bank_diagnostic.full

Explicitly delete copy constructor and assignment in Timer (#665) ## Summary `Timer::~Timer()` calls `Report()`, logging the elapsed time to a tracer or stdout. With no explicit copy policy, a copied `Timer` would produce a second `Report()` on its own destruction — silently logging a duplicate timing entry for the same measured interval. `tag_` and `t_` are non-owning pointers (no `delete` in the destructor), so there is no memory-safety risk. The issue is purely semantic, but it is a real hazard for callers who pass or store `Timer` by value. Explicitly `= delete` the copy constructor and copy assignment to make the non-copyable intent clear. ## Test plan - [x] `basic/gpu` builds cleanly in debug mode - [x] Full debug build passes with no errors

• Summary

Refactor izstream raw zip_stream_p_ pointer to unique_ptr (#664) ## Summary - `izstream` held a raw owning `zlib_stream::zip_istream*` managed by a custom destructor, with copy/assignment only blocked by inherited `private` declarations in `irstream` — no explicit policy on `izstream` itself - Replace `zip_stream_p_` with `std::unique_ptr<zlib_stream::zip_istream>`, eliminating the manual `delete` in the destructor - Explicitly `= delete` copy constructor and copy assignment directly on `izstream` - Update all allocation/reset sites in `izstream.hh` and `izstream.cc` to use `unique_ptr::reset()` ## Test plan - [x] `utility/io` builds cleanly in debug mode - [x] Full debug build passes with no errors

• Summary
• integration.release_debug 「1」

Hotfix of T919 and T920 tests for ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit test (#666) This PR removes a few built-in `hash()` function calls from the `T919` and `T920` unit tests, which are non-deterministic in Python-3.8.

• Summary
• integration.addsan 「1」
• integration.release_debug 「1」
• ubuntu.clang.python313.release.PyRosetta.MinSizeRel
• ubuntu.clang.python311.release.PyRosetta.Release
• ubuntu.clang.python312.release.PyRosetta.Release
• ubuntu.clang.python39.release.PyRosetta.Release
• scientific.protein_data_bank_diagnostic.cif

Fix memory leak in SimulateMPI: use unique_ptr for simulation_ ownership (#660) ## Summary - `initialize_simulation()` unconditionally assigned `new SimulateMPIData*` without deleting any previous allocation, leaking memory on re-initialization - `simulation_` was a raw owning static pointer with no cleanup path - Fixed by switching `simulation_` from `SimulateMPIData*` to `std::unique_ptr<SimulateMPIData>`, so `reset()` frees the old object on re-initialization and the static is properly cleaned up at program exit ## Test plan - [ ] Build `utility` library in debug mode: `cd source && ./scons.py -j16 mode=debug utility` - [ ] Run utility unit tests: `cd source && python test/run.py -j16 --mode=debug`

• Summary
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「2」
• integration.tutorials 「1」
• ubuntu.clang.python312.release.PyRosetta.Release
• release.PyRosetta.conda.Release 「2」
• scientific.glycan_dock
• scientific.make_fragments.debug

Fix memory leaks in Inline_File_Provider (#659) ## Summary - `clear_input_files()` and `remove_input_file()` were leaking `std::stringstream` objects by calling `vector::clear()`/`erase()` without deleting the raw pointers - `get_ostream()` also leaked a `new std::stringstream` on every call - Fixed by switching `input_files` and `output_files` members from `std::vector<std::pair<std::string, std::stringstream*>>` to `std::vector<std::pair<std::string, std::unique_ptr<std::stringstream>>>`, so the vector destructor and `erase()` handle cleanup automatically ## Test plan - [ ] Build `utility` library in debug mode: `cd source && ./scons.py -j16 mode=debug utility` - [ ] Run utility unit tests: `cd source && python test/run.py -j16 --mode=debug`

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

Clean up PyRosetta Sphinx documentation (#657) This is a very minor PR to fix a link in the PyRosetta Sphinx documentation and to properly format the PyRosetta initialization file docstrings for PyRosetta Sphinx documentation. Runtime functionality remains unchanged.

• Summary
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「2」
• integration.mpi 「2」
• integration.tensorflow 「1」
• integration.tutorials 「1」
• maintenance.documentation
• release.PyRosetta.conda.Release 「2」
• scientific.make_fragments.debug
• scientific.mp_lipid_acc
• windows.build.debug