Pull Request №676 RosettaCommons/rosetta/main ← everyday847/rosetta/origin/everyday847/parametric_helpers Merge: 5c9f6db69d1a20db6353738e3724092516415bd3←3fec048183eb354c26030092edabd404582c57bf Factor common logic out of add_*_parameter methods ---------------- Merge commit message: Factor common logic out of add_*_parameter methods Extract a private configure_and_add_parameter() helper that handles the shared configuration steps (name, description, units, type, capabilities, global flag) and add_parameter() call. Each add_*_parameter() and add_custom_parameter() now only constructs the type-specific object, sets any conditional default value, and delegates to the helper. Also replace bare new with make_shared.

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

Pull Request №677 RosettaCommons/rosetta/main ← everyday847/rosetta/origin/everyday847/parametric_make_shared Merge: 5c9f6db69d1a20db6353738e3724092516415bd3←2ab90802a27b283be4fd87d779276b092a0b0c26 Use make_shared in ParametrizationCalculator ---------------- Merge commit message: Use make_shared in ParametrizationCalculator

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

Pull Request №681 RosettaCommons/rosetta/main ← everyday847/rosetta/differentiable-parametric Merge: cf532f89b6bbb7e67fd75031f3cc2aa95fb5ce19←f84a8d234b4b9854783474b432ca98d0cba1aa82 Add differentiable parametric backbone minimization ---------------- Merge commit message: Add differentiable parametric backbone minimization Enables MinMover to co-optimize parametric DOFs (r0, omega0, delta_omega0, etc.) alongside standard atom-tree DOFs (chi angles, backbone torsions for non-parametric residues, jumps). Components: - Analytical Crick equation derivatives (dXYZ/dParam) in numeric/crick_equations/BundleParams_derivatives for r0, omega0, delta_omega0, delta_omega1, and delta_t - MoveMap::set_parametric(true) flag to enable parametric DOFs - ParametricAtomTreeMultifunc: extends the DOF vector with parametric variables, computes gradients via Jacobian chain rule (dE/dParam = sum_atoms dE/dXYZ . dXYZ/dParam) - AtomTreeMinimizer dispatch: detects parametric poses and automatically excludes backbone torsions of parametric residues to prevent redundant DOF control - Integration test: 3-helix ELLKAIA bundle minimized with and without chi angle co-optimization

• Summary
• mac.clang.python38.PyRosetta.unit
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mpi
• mpi.serialization
• mac.clang.build.debug
• build.levels
• build.ninja_debug
• linux.clang.build.release
• linux.gcc.build.release
• mac.clang.build.release
• beautification
• serialization 「1」
• integration.mpi
• integration.release_debug
• integration.tensorflow
• integration.thread
• integration.torch
• integration
• performance
• profile
• linux.clang.score
• linux.gcc.score
• mac.clang.score
• scripts.pyrosetta
• scripts.rosetta.parse
• scripts.rosetta.validate
• scripts.rosetta.verify
• linux.clang.unit
• linux.gcc.cxx11thread.serialization.unit
• linux.gcc.unit
• mac.clang.unit
• windows.build.debug
• windows.build.release

Pull Request №682 RosettaCommons/rosetta/main ← everyday847/rosetta/beta-barrel-parametrization Merge: cf532f89b6bbb7e67fd75031f3cc2aa95fb5ce19←67de64cd94e3716afd4856bf7b80e108c9548c3d Beta barrel parametrization ---------------- Merge commit message: Add README documenting barrel, solenoid, and TIM barrel configurations

• Summary
• mac.clang.python38.PyRosetta.unit
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mpi
• mpi.serialization
• mac.clang.build.debug
• build.ninja_debug
• linux.clang.build.release
• linux.gcc.build.release
• mac.clang.build.release
• beautification
• code_quality.cppcheck 「1」
• serialization 「1」
• integration.mpi
• integration.release_debug
• integration.tensorflow
• integration.thread
• integration.torch
• integration
• performance
• profile
• linux.clang.score
• linux.gcc.score
• mac.clang.score
• scripts.pyrosetta
• scripts.rosetta.parse
• scripts.rosetta.validate
• scripts.rosetta.verify
• linux.clang.unit
• linux.gcc.cxx11thread.serialization.unit
• linux.gcc.unit
• mac.clang.unit

Pull Request №683 RosettaCommons/rosetta/main ← everyday847/rosetta/correlated-perturbation Merge: cf532f89b6bbb7e67fd75031f3cc2aa95fb5ce19←bb306f5089bb1aadf8c93971dc2d2b928c5d3142 Add correlated parameter perturbation to PerturbBundle ---------------- Merge commit message: Add correlated parameter perturbation to PerturbBundle Introduces <Correlation> sub-tags for PerturbBundle that specify Pearson correlation coefficients between bundle parameters. When present, correlated parameters are perturbed jointly via multivariate Gaussian sampling (Cholesky decomposition of the covariance matrix). Parameters not involved in correlations continue to be perturbed independently. Adds a Cholesky decomposition wrapper in numeric/linear_algebra/ backed by Eigen::LLT, exposing only vector1-based types.

• Summary
• beautification
• integration.mpi 「1」
• integration.release_debug 「2」
• linux.clang.unit 「8」
• linux.gcc.cxx11thread.serialization.unit 「8」
• linux.gcc.unit 「8」
• mac.clang.unit 「8」

Pull Request №680 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/fix/key-map-range-indexing Merge: cf532f89b6bbb7e67fd75031f3cc2aa95fb5ce19←0e93096452d3c2190bc781f1c29b0923ad3d07df Fix key map range indexing ---------------- Merge commit message: Fix key map range indexing

• Summary
• integration.mpi 「22」

Pull Request №679 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/docs/mpistream-rank-zero-comment Merge: cf532f89b6bbb7e67fd75031f3cc2aa95fb5ce19←1108e0764642a00d284c10e75657911a6c5db0cb Document mpistream rank-zero routing ---------------- Merge commit message: Document mpistream rank-zero routing

• Summary
• integration.mpi 「1」

Pull Request №674 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/basic-otstream-copy-prevention Merge: 5c9f6db69d1a20db6353738e3724092516415bd3←77f1ba2d66e0e1ec62e5d9dd75cc9bb7c64eb770 Modernize copy prevention in basic_otstream and TracerImpl ---------------- Merge commit message: Modernize copy prevention in basic_otstream and TracerImpl basic_otstream: replace private undefined copy ctor with explicit = delete in the public section for both copy ctor and copy assignment. Add a comment explaining why: the destructor calls delete this->rdbuf(), so a copy sharing the same buffer would cause a double-free. TracerImpl: move the already-deleted copy ctor from private to public and add the missing copy assignment = delete.

• Summary
• integration.mpi 「1」

Pull Request №678 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/basic-emitter-copy-prevention Merge: 5c9f6db69d1a20db6353738e3724092516415bd3←a02c82e50df8c1a7a3a93d80ee50f7b5b122e322 Modernize copy prevention in Emitter, YamlEmitter, and JsonEmitter ---------------- Merge commit message: Modernize copy prevention in Emitter, YamlEmitter, and JsonEmitter Replace private/protected undefined copy ctor declarations with explicit = delete in the public section, and add the missing copy assignment = delete. Also remove the redundant undefined null-ctor declarations (suppressed automatically in C++11 by the presence of user-declared non-default ctors).

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

Pull Request №669 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/irstream-modernize-copy-prevention Merge: 5c9f6db69d1a20db6353738e3724092516415bd3←56292bf7c603504d2f187fef7e3981440511b307 Modernize copy prevention in irstream to use = delete ---------------- Merge commit message: Modernize copy prevention in irstream to use = delete Replace old-style private-and-undefined copy constructor/assignment with explicit = delete in the public section. Matches the treatment already applied to the sibling orstream class.

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

Pull Request №670 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/registrant-modernize-copy-prevention Merge: 5c9f6db69d1a20db6353738e3724092516415bd3←61c9a26d96c83d65f054961f4dae132e43c4b090 Modernize copy prevention in factory/Registrant to use = delete ---------------- Merge commit message: Modernize copy prevention in Registrant to use = delete Replace old-style private-and-undefined copy constructor/assignment with explicit = delete. A comment explains the non-obvious reason: each constructor calls ProductFactory::add(), so a copy would silently re-register the same key.

• Summary
• integration.mpi 「1」

Pull Request №671 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/keylookup-modernize-copy-prevention Merge: 5c9f6db69d1a20db6353738e3724092516415bd3←102fc88740667713fe7d03f5e62820dc103d2fb0 Modernize copy prevention in KeyLookup to use = delete ---------------- Merge commit message: Modernize copy prevention in KeyLookup to use = delete Replace old-style private-and-undefined copy constructor/assignment with explicit = delete. KeyLookup is a monostate singleton (all methods and data are static), so copies are meaningless.

• Summary
• integration.mpi 「1」

Pull Request №672 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/graph-modernize-copy-prevention Merge: 5c9f6db69d1a20db6353738e3724092516415bd3←0ccc000fb7c5f72b3a1f502bd5835647e3df5a8e Modernize copy prevention in utility/graph EdgeList/Node/Edge to use = delete ---------------- Merge commit message: Modernize copy prevention in graph EdgeList/Node/Edge to use = delete Replace old-style private-and-undefined copy constructor/assignment in Graph.hh (EdgeList, Node, Edge) and Digraph.hh (DirectedEdgeList, DirectedNode, DirectedEdge) with explicit = delete. Also corrects the copy assignment signatures from non-const T& to const T& to match the standard copy assignment operator form.

• Summary
• integration.mpi 「1」

Pull Request №673 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/basic-modernize-copy-prevention Merge: 5c9f6db69d1a20db6353738e3724092516415bd3←aa9828ef329b75e624b5d314be79edd69207c8d0 Modernize copy prevention in basic/ComparingTracer and MessageListenerFactory ---------------- Merge commit message: Modernize copy prevention in basic/ComparingTracer and MessageListenerFactory ComparingTracer: replace private-undefined copy ctor with public = delete; also explicitly delete copy assignment (std::fstream member makes copies impossible anyway, but = delete documents the intent clearly). MessageListenerFactory: remove redundant private-undefined copy ctor and assignment -- SingletonBase already deletes them via inheritance.

• Summary
• integration.mpi 「1」

Pull Request №668 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/signals-modernize-copy-prevention Merge: 8556abcecef09877257656a5144b1902b5f7c699←45ad271fbf7645713af9216c17f1f187d246729c Modernize copy prevention in utility/signals classes to use = delete ---------------- Merge commit message: Modernize copy prevention in utility/signals classes to use = delete Replace old-style private-and-undefined copy constructor/assignment declarations with explicit = delete in SignalHub, BufferedSignalHub, PausableSignalHub, TokenHub, and LinkUnit. Also deletes the LinkUnit default constructor the same way.

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

Pull Request №665 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/timer-delete-copy Merge: f9c5b025aa6240de1105fd6cdcf04f7a535ea67d←10241cb3bfbfba45df7c00c7064e6ebdb328df3b Explicitly delete copy constructor and assignment in Timer ---------------- Merge commit message: Add comment explaining why Timer copy ops are deleted

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

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