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Revisions №62169

branch: rosetta:main 「№62169」
Commited by: Jason C. Klima
GitHub commit link: 「931f7d9046b1ae0a」
Difference from previous tested commit:  code diff
Commit date: 2025-06-29 10:57:49
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
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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

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