Pull Request №707 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/fix/off-by-one-1-indexed-loops-batch Merge: c0fbd1cd0e786b420b817fd4f560a487ab05a307←349a3f409fdc85412cfd7cb6faf70c749b455300 Fix off-by-one loops over 1-indexed residue/atom/element ranges ---------------- Merge commit message: Fix off-by-one loops over 1-indexed residue/atom/element ranges Replace `i < container.size()` with `i <= container.size()` (or the matching `i < pose.size()` -> `i <= pose.size()`) across 35 loops where the body uses `i` as a direct 1-indexed element accessor (`pose.residue(i)`, `vec[i]`, etc.) — so the last residue/atom/element was silently being skipped. Also fixes two related copy-paste bugs in pose_sewing that surfaced during the audit: the distance check `pose.residue(upstream_res).xyz(2) .distance(pose.residue(upstream_res).xyz(2))` was self-distance (always zero, condition always satisfied) — should compare upstream vs downstream residue xyz. Affects helix_pair detection in BlockwiseAnalysisMover and OmnibusDisulfideAnalysisLabelerMover. Skipped candidates: loops with pair access `[i+1]` (correct stop at size-1), cutpoint-style "between residues" loops, MEM-chain-skipping loops in protocols/membrane, separator-style "all-but-last + last raw" patterns, suite/connection enumerations (N-1 connections for N segments), and commented-out code.

• Summary
• integration.mpi 「1」
• integration.release_debug 「5」
• integration.thread 「1」
• integration 「7」
• linux.clang.unit 「3」
• linux.gcc.cxx11thread.serialization.unit 「3」
• linux.gcc.unit 「3」
• mac.clang.unit 「3」

Apply Rule of Zero to utility/keys container family (corrected) (#705)

• Summary
• ubuntu-26.04.gcc.cxx11thread.serialization.python313.PyRosetta.unit
• ubuntu-26.04.gcc.cxx11thread.serialization.python314.PyRosetta.unit
• gcc-14.gcc.unit
• gcc-15.gcc.unit
• gcc-16.gcc.unit
• ubuntu-26.04.clang.unit
• ubuntu-26.04.gcc.unit

Pull Request №708 RosettaCommons/rosetta/main ← klimaj/rosetta/test_builds Merge: aeed26aa121b084f58f02bb9d358d1b285cfb78b←04669b474f1c71b9b3e00dd13ed083457b713e71 Testing Pose bindings/numeric unit tests with standard PyRosetta builds ---------------- Merge commit message: Setting default pickle protocol for Python 3.7

• Summary

Pull Request №708 RosettaCommons/rosetta/main ← klimaj/rosetta/test_builds Merge: aeed26aa121b084f58f02bb9d358d1b285cfb78b←a2e7defca066df604306886ee7f3d5b61f7f0e24 Testing Pose bindings/numeric unit tests with standard PyRosetta builds ---------------- Merge commit message: Skipping Pose object serialization for non-serialization builds

• Summary
• gcc-9.gcc.python37.PyRosetta.unit 「1」

Pull Request №708 RosettaCommons/rosetta/main ← klimaj/rosetta/test_builds Merge: aeed26aa121b084f58f02bb9d358d1b285cfb78b←bc91b523580212874e045fdd4ceae4ce1506f5f6 Testing Pose bindings/numeric unit tests with standard PyRosetta builds ---------------- Merge commit message: Remove scipy dependency via a numpy-only equivalent implementation

• Summary
• m1.clang.python38.PyRosetta.unit 「1」
• mac.clang.python38.PyRosetta.unit 「1」
• mac.clang.python39.PyRosetta.unit 「1」
• ubuntu.clang.python310.PyRosetta.unit 「1」
• ubuntu.gcc.python312.PyRosetta.unit 「1」

Pull Request №726 RosettaCommons/rosetta/main ← klimaj/rosetta/fix_diagnostics_port Merge: 9567e54bafdaf4697b28b6f4d41a07596e50ed5c←95c2adbe8956f58dae7537292165b853b3758e8e Update deprecated Dask `LocalCluster` method parameters in PyRosetta unit tests ---------------- Merge commit message: Revert "Add pyrosetta.tests.distributed.test_dask_worker test" This reverts commit 00e5dbe8a8e43beb35870f4ddfd5c070a00ad7bc.

• Summary

Pull Request №708 RosettaCommons/rosetta/main ← klimaj/rosetta/test_builds Merge: 9567e54bafdaf4697b28b6f4d41a07596e50ed5c←0dc2dbb66d24ef65da2d3302a6ddcc129b3042da Testing Pose bindings/numeric unit tests with standard PyRosetta builds ---------------- Merge commit message: Install numpy in non-serialization builds in get_required_pyrosetta_python_packages_for_testing

• Summary
• gcc-9.gcc.python37.PyRosetta.unit 「2」
• m1.clang.python310.PyRosetta.unit 「2」
• m1.clang.python311.PyRosetta.unit 「2」
• m1.clang.python312.PyRosetta.unit 「2」
• m1.clang.python313.PyRosetta.unit 「2」
• m1.clang.python314.PyRosetta.unit 「2」
• m1.clang.python38.PyRosetta.unit 「2」
• m1.clang.python39.PyRosetta.unit 「2」
• mac.clang.python310.PyRosetta.unit 「2」
• mac.clang.python311.PyRosetta.unit 「2」
• mac.clang.python312.PyRosetta.unit 「2」
• mac.clang.python313.PyRosetta.unit 「2」
• mac.clang.python314.PyRosetta.unit 「2」
• mac.clang.python38.PyRosetta.unit 「2」
• mac.clang.python39.PyRosetta.unit 「2」
• ubuntu-20.04.clang.cxx11thread.serialization.python310.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python311.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python312.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python313.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python314.PyRosetta.unit 「1」
• ubuntu-20.04.clang.python39.PyRosetta.unit 「2」
• ubuntu-20.04.gcc.cxx11thread.serialization.python310.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python311.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python312.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python313.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python314.PyRosetta.unit 「1」
• ubuntu-22.04.clang.python39.PyRosetta.unit 「2」
• ubuntu.clang.python310.PyRosetta.unit 「2」
• ubuntu.clang.python311.PyRosetta.unit 「2」
• ubuntu.clang.python312.PyRosetta.unit 「2」
• ubuntu.clang.python313.PyRosetta.unit 「2」
• ubuntu.clang.python314.PyRosetta.unit 「2」
• ubuntu.clang.python39.PyRosetta.unit 「2」
• ubuntu.gcc.python310.PyRosetta.unit 「2」
• ubuntu.gcc.python311.PyRosetta.unit 「2」
• ubuntu.gcc.python312.PyRosetta.unit 「2」
• ubuntu.gcc.python313.PyRosetta.unit 「2」
• ubuntu.gcc.python314.PyRosetta.unit 「2」
• ubuntu.gcc.python39.PyRosetta.unit 「2」

Pull Request №708 RosettaCommons/rosetta/main ← klimaj/rosetta/test_builds Merge: 9567e54bafdaf4697b28b6f4d41a07596e50ed5c←242a3b04fb5d314584d21ce58870674c8e085638 Testing Pose bindings/numeric unit tests with standard PyRosetta builds ---------------- Merge commit message: Remove exit on missing numpy requirement

• Summary
• m1.clang.python310.PyRosetta.unit 「2」
• m1.clang.python311.PyRosetta.unit 「2」
• m1.clang.python312.PyRosetta.unit 「2」
• m1.clang.python313.PyRosetta.unit 「2」
• m1.clang.python314.PyRosetta.unit 「2」
• m1.clang.python38.PyRosetta.unit 「2」
• m1.clang.python39.PyRosetta.unit 「2」

Pull Request №726 RosettaCommons/rosetta/main ← klimaj/rosetta/fix_diagnostics_port Merge: 9567e54bafdaf4697b28b6f4d41a07596e50ed5c←00e5dbe8a8e43beb35870f4ddfd5c070a00ad7bc Update deprecated Dask `LocalCluster` method parameters in PyRosetta unit tests ---------------- Merge commit message: Add pyrosetta.tests.distributed.test_dask_worker test

• Summary
• ubuntu-20.04.gcc.cxx11thread.serialization.python312.PyRosetta.unit
• ubuntu-20.04.gcc.cxx11thread.serialization.python313.PyRosetta.unit

Pull Request №717 RosettaCommons/rosetta/main ← roccomoretti/rosetta/bcif_mmjson Merge: bbb6a2d27c70be05b2fb2409f3920b5894967d60←72ee12c45b6c16268f1b03f1dab2190623a10051 BinaryCIF and mmJSON input support for Rosetta. ---------------- Merge commit message: Remove unintended files.

• Summary
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mpi
• mpi.serialization
• build.levels
• build.ninja_debug
• beautification
• code_quality.merge_size
• integration.mpi
• integration.release_debug 「2」
• integration.thread
• integration 「2」
• linux.gcc.cxx11thread.serialization.unit
• linux.gcc.unit
• windows.build.debug
• windows.build.release

Pull Request №723 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/fix/numeric-gcc15-template-id-cdtor Merge: 9567e54bafdaf4697b28b6f4d41a07596e50ed5c←5f88382e5242482039bed0812b890a38fbd85dae Drop template-id from MathVector/MathMatrix ctor/dtor names (GCC 15 -Werror=template-id-cdtor) ---------------- Merge commit message: Drop template-id from MathVector/MathMatrix ctor/dtor names (GCC 15) GCC 15 enforces -Werror=template-id-cdtor: a class template may not name its own constructors or destructors with explicit template arguments (the injected-class-name must be used without <...>). MathVector and MathMatrix declared several ctors and their dtor as e.g. 'MathVector< T>()' and '~MathVector< T>()', which fails to compile under GCC 15 in C++20 mode and broke the debug build before it reached any core/ code. Drop the '< T>' so these match the injected-class-name form already used by the copy constructors in the same classes. No semantic change.

• Summary
• beautification
• integration.mpi 「2」

Pull Request №725 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/protocols-rule-of-zero-redundant-dtors Merge: 9567e54bafdaf4697b28b6f4d41a07596e50ed5c←d674c6a338a087e57a3e277f0dced0cf781119a4 Apply Rule of Zero to protocols/ classes with redundant destructors ---------------- Merge commit message: Apply Rule of Zero to protocols/ classes with redundant destructors Removes user-declared destructors that are equivalent to the implicitly generated one (either '= default' or an empty '{}' body), letting the compiler generate them. In every case the class holds only non-owning raw pointers (back-references it does not allocate or free), so no destructor logic is lost and ownership semantics are unchanged. Classes: - antibody/clusters/CDRClusterSet - hbnet/NetworkState - jobdist/AtomTreeDiffJobDistributor - nmr/pcs/AtomGridPoint - noesy_assign/FloatingResonance - noesy_assign/PeakAssignment - peptide_deriver/PeptideDeriverBasicStreamOutputter (also drops its user-declared copy constructor, which did a plain memberwise copy identical to the implicit one) For classes deriving from a base with a virtual destructor, the implicit destructor is virtual and inherited, so polymorphic destruction is unchanged. A few now-moot 'auto-generated destructor' doc comments were removed alongside their declarations. Other rule_of_zero scan hits in protocols/ were intentionally left out: they own their pointers (freed in the destructor), are singletons/ factories that legitimately prevent copying, are observers whose destructors detach from a subject, or have intentionally partial copy constructors.

• Summary
• integration.mpi 「1」

Pull Request №722 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/fix/membrane-info-slab-arg-order Merge: f8a8eab4344af49c25e1e5db84ce25fec05eea27←87aafb70e6d09e8a333fac5418df8fd5c9552384 Fix Slab geometry thickness/steepness argument order in MembraneInfo (#719) ---------------- Merge commit message: Fix Slab geometry thickness/steepness argument order in MembraneInfo Slab's constructor is Slab(steepness, thickness), but two MembraneInfo constructors called it with the arguments swapped (see issue #719): - The plain 6-arg constructor passed Slab(thickness, steepness), so the Slab geometry stored thickness and steepness swapped. Because the fa_2012 energy methods (FaMPEnv/FaMPSolv -> mpframework_smooth_fa_2012) read thickness/steepness off the geometry, this silently changed scores. Now passes Slab(steepness, thickness). - The implicit-lipid constructor passed Slab(thickness, steepness) where the bare 'thickness' was not the member just set from water_thickness() but the unscoped MEM::thickness enum (== 1) from MembraneParams.hh, so the call was effectively Slab(1, steepness) and the lipid water thickness was dropped. Now passes Slab(steepness, thickness_), matching the sibling lipid + MP_GEOMETRY_TRANSITION constructor's SLAB case.

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

Pull Request №720 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/roccomoretti-pyjobdistributor Merge: bbb6a2d27c70be05b2fb2409f3920b5894967d60←e3751361009dba8c0071735914215864538210c5 Fix restart behavior in PyJobDistributor ---------------- Merge commit message: Fix restart behavior in PyJobDistributor The PyJobDistributor can result in an infinite loop if one of the entries are already completed (e.g. from a prior run) or is in progress from another run. Fixes #347

• Summary
• ubuntu-20.04.clang.cxx11thread.serialization.python310.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python311.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python312.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python313.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python314.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python310.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python311.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python312.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python313.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python314.PyRosetta.unit 「1」

Pull Request №716 RosettaCommons/rosetta/main ← roccomoretti/rosetta/fix_bcl Merge: bbb6a2d27c70be05b2fb2409f3920b5894967d60←ea721e3f202dcc2d7b99c53032e5aa99789b6be4 Fix the extras=bcl compilation. ---------------- Merge commit message: Fix the extras=bcl compilation. I accidentally broke it with the multi-chainletter PR.

• Summary

Pull Request №698 RosettaCommons/rosetta/main ← roccomoretti/rosetta/change_chirality_loading Merge: 8f55d1556a33b9d485bc33f6e788ddf6f5216669←3dcd35ef3b290a2461db2f870b1048350163baef Rework chirality detection in restype determination for PDB loading ---------------- Merge commit message: Merge remote-tracking branch 'origin/main' into change_chirality_loading

• Summary
• integration.mpi 「3」
• integration.release_debug 「6」

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