Close file handles in writer.py instead of relying on GC - #249
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Changes made to run without errors on the Mac MPS device: torch.autocast, number of devices and workers to use on M1-5 chips, workaround for CUDA-specific code, handling of float64 incompatibilities for MPS.
Replace hardcoded torch.autocast("cuda") with device-agnostic
device_type=tensor.device.type in confidence_utils, inverse_fold,
and writer modules introduced in the upstream merge.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Python pickle does not preserve RDKit atom-level SetProp values. When PyTorch DataLoader spawns worker processes (default num_workers=1 on macOS), self.canonicals is pickled and all atom 'name' properties are lost, causing KeyError in process_atom_features. Fix: load all required molecules directly from the moldir zip inside each get_sample() / get_feat() call instead of using the pickled self.canonicals. The moldir zip handle is cached per-process by _get_zipfile(), so there is no repeated I/O overhead. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ders - Disable pin_memory on MPS (unsupported, causes UserWarning) - Enable persistent_workers when num_workers > 0 (avoids repeated worker init overhead and the PL suggestion warning) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Several output paths (refold cif, native cif, design cif, trajectory and x0-trajectory PDBs) opened files with a bare open(...).write(...) and never closed the handle, which spams ResourceWarning on CPython and can leave data unflushed until GC runs. Wrap them in `with`. Fixes HannesStark#204 Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Fixes #204.
Several output paths in
writer.py(refold cif, native cif, design cif, trajectory and x0-trajectory PDBs) opened files with a bareopen(...).write(...)and never closed the handle, which spamsResourceWarningon CPython and can leave data unflushed until GC runs. Wrapped each in awithblock.