Broaden PyRosetta conda package dependency version requirements for NumPy (#496)

• Summary
• icc.icc.build.debug
• ubuntu-24.04.clang.cxx11thread.serialization.build.debug
• ubuntu-24.04.clang.build.release
• ubuntu-24.04.clang.cxx11thread.serialization.build.release
• code_quality.clang_tidy 「1」
• integration.mpi 「1」
• integration.thread 「1」
• integration.tutorials 「1」
• maintenance.documentation
• scientific.sb_talaris13_fast_design
• ubuntu-24.04.clang.cxx11thread.serialization.unit
• ubuntu-24.04.clang.unit

Refactor PyRosetta unit tests to always run in fresh venv, temporary disable distributed tests for Python-3.12 builds. (#478)

• Summary
• icc.icc.build.debug
• ubuntu-24.04.clang.build.debug
• ubuntu-24.04.clang.cxx11thread.serialization.build.debug
• ubuntu-24.04.clang.build.release
• ubuntu-24.04.clang.cxx11thread.serialization.build.release
• code_quality.clang_tidy 「1」
• integration.addsan 「1」
• integration.mpi 「1」
• integration.thread 「1」
• integration.tutorials 「1」
• maintenance.documentation
• ubuntu.clang.python311.release.PyRosetta.MinSizeRel
• scientific.FlexPepDock
• scientific.abinitio_RosettaNMR_pcs
• scientific.glycan_dock
• scientific.mp_lipid_acc
• scientific.peptide_pnear_vs_ic50.debug
• scientific.protein_data_bank_diagnostic.cif
• scientific.protein_data_bank_diagnostic.full
• scripts.pyrosetta
• ubuntu-24.04.clang.cxx11thread.serialization.unit
• ubuntu-24.04.clang.unit

Set correct scope for automatic protocol detection in PyRosettaCluster reproduction (#484)

• Summary
• ubuntu-24.04.clang.build.debug
• ubuntu-24.04.clang.cxx11thread.serialization.build.release
• code_quality.clang_tidy 「1」
• integration.mpi 「1」
• integration.tutorials 「1」
• maintenance.documentation
• release.PyRosetta.conda.Release
• ubuntu-24.04.clang.cxx11thread.serialization.unit

Add the deterministic_flag option to the ProteinMPNNProbabilitiesMetric SimpleMetric (#485) This PR adds the `deterministic_flag` option to the `ProteinMPNNProbabilitiesMetric` PerResidueProbabilitiesMetric. After some evidence provided in #429, the `ProteinMPNNMover` already has the `deterministic_flag` option set to `false` by default, and therefore due to Torch randomness the `ProteinMPNNProbabilitiesMetric` can return non-deterministic PSSM tables, even with the `-run:constant_seed 1` Rosetta option enabled. This PR just adds some control of the `ProteinMPNNMover` from the `ProteinMPNNProbabilitiesMetric` to enable deterministic mode when calculating per-residue ProteinMPNN probabilities.

• Summary
• integration.mpi 「2」
• integration.release_debug 「2」
• integration 「1」

Initial commit (#483) If using the local `OptionsCollection` in the `ProtocolSettingsMetric` CompositeStringMetric, the `get_script_vars` and `get_user_options` arguments are swapped relative to the `parse_options` signature. These options are both `true` by default, so this bug has likely gone unnoticed, but would only have an effect when `get_script_vars` and `get_user_options` have different values.

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

Support yielding PackedPose objects in memory from PyRosettaCluster (#452) * Initial commit * Refactor * Fix import * Fix import * Update typing * Update unit tests * Support str inputs * Update typing and docstrings * Clean up * Refactor yield_results * Refactor __call__ method * Add warning and update docstring * Update docstring * Enable runtime tests for evaluation * Update logging in runtime tests * Set logging stream handler * Disable runtime tests

• Summary
• icc.icc.build.debug
• ubuntu-24.04.clang.build.debug
• ubuntu-24.04.clang.cxx11thread.serialization.build.debug
• ubuntu-24.04.clang.build.release
• ubuntu-24.04.clang.cxx11thread.serialization.build.release
• code_quality.clang_tidy 「1」
• integration.addsan 「1」
• integration.mpi 「2」
• integration.tutorials 「1」
• maintenance.documentation
• release.PyRosetta.conda.Release
• scientific.ligand_scoring_ranking
• scientific.protein_data_bank_diagnostic.cif
• scientific.protein_data_bank_diagnostic.full
• linux.gcc.python310.unit
• linux.gcc.python38.unit
• linux.gcc.python39.unit
• ubuntu-24.04.clang.cxx11thread.serialization.unit
• ubuntu-24.04.clang.unit

Enable Pose.scores dictionary to store arbitrary python objects (#430) * Fix KeyError for string objects * Serialize and deserialize values in pose scores dictionary * Update TypeError message * Maybe deserialize ScoreMap.get_arbitrary_string_data_from_pose data * Test PyJobDistributor with arbitrary scoretypes * Test SimpleMetric implementation * Fix NotImplementedError * Update unit tests that assert that float values are rounded upon score set/get round trips * Add warnings for setPoseExtraScore float value precision change, type casting, and possible UnicodeDecodeError * Update import * Update reserved scoretypes * Add rounding difference to warning message * Update imports * Initial refactor of pose.cache dictionary * Add pose.cache unit tests * Remove numpy dependency for non-serialization builds * Change pose.scores to pose.cache * Move pose.cache into modules for comprehensibility * Use pose.cache instead of packed_pose.update_scores * Set clobber warnings in pose.scores * Add deprecation warning to pose.scores * Add warning if key in immutable SimpleMetrics data exists * Clean up * Setting PackedPose.scores to Pose.cache * Set cache with packed_pose.update_scores * Fix warning * Reserve pose.cache keys * Update warning messages * Update warning message * Update PackedPose.scores dictionary with pose.cache * Update logging message test * Update reserve_scores decorator to be using pose.cache * Add update_scores in reserve_scores * Update version * Add syntax warning for setting PackedPose.scores items * Test saving detached scores in the PackedPose.scores dictionary * Improve docstring example * Update docstrings * Clean up * Split into separate warnings when deleting reserved scoretypes * Return nested MappingProxyType read-only data by pose.cache.all_scores * Update docstrings * Minor tweaks to docstrings * Clean up applying SimpleMetrics to the pose * Validate strict base64

• Summary
• icc.icc.build.debug
• ubuntu-24.04.clang.build.debug
• ubuntu-24.04.clang.cxx11thread.serialization.build.debug
• ubuntu-24.04.clang.build.release
• ubuntu-24.04.clang.cxx11thread.serialization.build.release
• code_quality.clang_tidy 「1」
• integration.addsan 「1」
• integration.mpi 「1」
• integration.tutorials 「1」
• maintenance.documentation
• scientific.mp_lipid_acc
• ubuntu-24.04.clang.cxx11thread.serialization.unit
• ubuntu-24.04.clang.unit