Enhance pyrosetta and pyrosetta.distributed I/O interfaces (#431) * Fix DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) * Update imports * Update pyrosetta.io and pyrosetta.distributed.io interfaces * Add unit tests for pyrosetta.io updates * Add unit tests for pyrosetta.distributed.io updates * Update pyrosetta.distributed.io interface * Test PackedPose generators * Set place for assertAlmostEqual * Update @unittest.skip message * Support dump_file and dump_scored_pdb * Update syntax for Python <3.8 compatibility * Duplicate import * Reformat imports for readability * Define create_score_function, get_fa_scorefxn, and get_score_function helper functions * Add support for ScorePoseTask and string instances in dump_scored_pdb * Test different parameter types to io.dump_scored_pdb * Support ScorePoseTask instantiation in io namespace * Test ScorePoseTask instantiation * Add warnings when dumping poses with nonstandard file extensions * Support .pdb.gz and .pdb.xz file I/O * Test .pdb.gz and .pdb.xz file I/O * Update gzip I/O so .pdb.gz files open in PyMOL * Support bz2, gzip, and xz compression in dump_pdb function * Support dumping scored PDB files with bz2, gzip, and xz compression * Support decompression of PDB files for pose_from_pdb and pose_from_file in pyrosetta.io namespace * Fix pose_from_none * Move pose_from_pdbstring to pyrosetta.io namespace * Test io.dump_pdb function * Update tests to include PDB/CIF/MMTF I/O * Support getting score functions from pyrosetta.io namespace * Update filename in unit test * Skip if xz is not installed * Parse filename * Update poses_from_multimodel_pdb with new pose_from_pdbstring function * Clean up; Redefine pose_from_pdbstring for backward compatibility * Test args and kwargs with pose_from_pdbstring

• Summary

Add RosettaLigand docking scores to the Pose when JD2 is not active. (#456) People running RosettaLigand jobs under PyRosetta keep having problems that the computed docking scores don't show up. This is because the current RosettaLigand code was written for RosettaScripts and assumes the use of JD2. The scores get stuck in a JD2 job, which is hard to access when you're not running a command line JD2 job. We can change the code to stick the scores into the pose instead of (in addition to) the job when not running under JD2 (e.g. PyRosetta) Hopefully this should make the access easier.

• Summary

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

Pull Request №478 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/lyskov-pyrosetta-tests Merge: fce88fc4bd527d5f2e5903499b30e7c1c401b2f1←89dfeb5d2db1e69efda36fdd0e2ef127811e9248 dummy PR to trigger test run for main ---------------- Merge commit message: dummy commit to trigger test run

• Summary
• ubuntu-20.04.gcc.cxx11thread.serialization.python312.PyRosetta.unit 「1」
• ubuntu-24.04.gcc.cxx11thread.serialization.python312.PyRosetta.unit 「1」

Pull Request №459 RosettaCommons/rosetta/main ← klimaj/rosetta/filter_empty Merge: fce88fc4bd527d5f2e5903499b30e7c1c401b2f1←268ee7aac176c96a2cb23433a74afcb6ad191b63 Add support for filtering results in PyRosettaCluster ---------------- Merge commit message: Set filter_results=False and simulation names in unit tests

• Summary
• ubuntu-20.04.clang.cxx11thread.serialization.python312.PyRosetta.unit 「1」

Pull Request №459 RosettaCommons/rosetta/main ← klimaj/rosetta/filter_empty Merge: fce88fc4bd527d5f2e5903499b30e7c1c401b2f1←a742cc43b38fd22ad05b098eff71300ee4c74887 Add support for filtering results in PyRosettaCluster ---------------- Merge commit message: Set filter_results=False in unit tests

• Summary
• ubuntu-20.04.clang.cxx11thread.serialization.python312.PyRosetta.unit 「1」

Set filter_results=False in unit tests

• Summary
• ubuntu-20.04.clang.cxx11thread.serialization.python312.PyRosetta.unit
• ubuntu-20.04.gcc.cxx11thread.serialization.python312.PyRosetta.unit
• ubuntu-22.04.clang.cxx11thread.serialization.python312.PyRosetta.unit
• ubuntu-22.04.gcc.cxx11thread.serialization.python312.PyRosetta.unit
• ubuntu-24.04.clang.cxx11thread.serialization.python312.PyRosetta.unit

Pull Request №459 RosettaCommons/rosetta/main ← klimaj/rosetta/filter_empty Merge: fce88fc4bd527d5f2e5903499b30e7c1c401b2f1←70d9b21631492e80817b82d062c00a86ce9a4694 Add support for filtering results in PyRosettaCluster ---------------- Merge commit message: git pull origin main

• Summary
• ubuntu-20.04.clang.cxx11thread.serialization.python312.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python312.PyRosetta.unit 「1」
• ubuntu-24.04.clang.cxx11thread.serialization.python312.PyRosetta.unit 「1」

Pull Request №462 RosettaCommons/rosetta/main ← klimaj/rosetta/cluster_io Merge: c07e51cae6c8448b25147b861092087346bd001e←c2c970ee478d4cbdcc493c551d886ae11694c055 Support saving PackedPose objects and arbitrary score data in PyRosettaCluster ---------------- Merge commit message: git pull origin main

• Summary

Pull Request №452 RosettaCommons/rosetta/main ← klimaj/rosetta/yield_poses Merge: c07e51cae6c8448b25147b861092087346bd001e←0b8cb7045302b61088d5afeb1f2fb360e7a4f7d6 Support yielding PackedPose objects in memory from PyRosettaCluster ---------------- Merge commit message: git pull origin main

• Summary

Pull Request №459 RosettaCommons/rosetta/main ← klimaj/rosetta/filter_empty Merge: c07e51cae6c8448b25147b861092087346bd001e←8c5935169b67bb218146ffda1342936b03d5033b Add support for filtering results in PyRosettaCluster ---------------- Merge commit message: git pull origin main

• Summary

Pull Request №419 RosettaCommons/rosetta/main ← roccomoretti/rosetta/foldamers Merge: 495e869888bb4b295294209edc0c8bee13039138←ce63a6b1ed4d6be64de79a311ccecece77ac0f11 Updates to molfile_to_params_polymer.py to better accomodate non-alpha residues. ---------------- Merge commit message: Merge with recent main. Fix merge conflict with Eric's changes.

• Summary

Pull Request №349 RosettaCommons/rosetta/main ← ewbell94/FakeRotLib/FakeRotLib Merge: 029c6a159b896477003a14f78f472d4cd2cead46←41dc373e8f9fb14dd066c4d9ef0bba623809b7c7 FakeRotLib and minor tweaks to m2pp.py ---------------- Merge commit message: Added stereochemistry call in rdkitConf

• Summary
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit
• integration.mpi 「1」
• integration.release_debug 「0」
• integration.tensorflow 「0」
• integration.thread 「0」
• integration.torch
• integration 「0」
• performance 「0」
• profile 「0」
• linux.clang.score 「0」
• linux.gcc.score 「0」
• mac.clang.score 「0」

Pull Request №456 RosettaCommons/rosetta/main ← roccomoretti/rosetta/rl_scores_to_pose Merge: 931f7d9046b1ae0a0b62c826dea7edc4a33f52ab←6507ccd6a7dbaef81462828b7b729be23c012beb Add RosettaLigand docking scores to the Pose when JD2 is not active. ---------------- Merge commit message: Update comments around behavior.

• Summary
• code_quality.merge_size
• integration.mpi 「2」
• integration.release_debug 「2」
• integration 「3」

Pull Request №457 RosettaCommons/rosetta/main ← roccomoretti/rosetta/fm_cartesian Merge: 931f7d9046b1ae0a0b62c826dea7edc4a33f52ab←83a0f71f71c0c546a132b0c90f34cd311f534c8e Add cartesian option to RosettaLigand FinalMinimizer. ---------------- Merge commit message: Fixes from PR review.

• Summary
• integration.mpi 「1」
• integration.release_debug 「3」
• integration 「2」
• linux.gcc.cxx11thread.serialization.unit

Pull Request №462 RosettaCommons/rosetta/main ← klimaj/rosetta/cluster_io Merge: 931f7d9046b1ae0a0b62c826dea7edc4a33f52ab←c3be21f624567d4a7ae13431d27998ef82512240 Support saving PackedPose objects and arbitrary score data in PyRosettaCluster ---------------- Merge commit message: Set full unit test

• Summary

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