Fix compatibility with newer PyTorch Lightning, torch_geometric, and SciPy#1
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supergolem wants to merge 1 commit into
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Fix compatibility with newer PyTorch Lightning, torch_geometric, and SciPy#1supergolem wants to merge 1 commit into
supergolem wants to merge 1 commit into
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…SciPy - abstract_datatype.py: replace removed LightningDataset (torch_geometric) with pl.LightningDataModule; fix validation hook name validation_dataloader -> val_dataloader (correct PL API); add None guard for missing val dataset - setup.py: use check_val_every_n_epoch=None (not 0) to disable validation in newer PL; add num_sanity_val_steps=0 when validation is off - evaluation_statistics.py: drop return_sensitivity=True which raises ValueError in newer SciPy versions; catch ValueError alongside LinAlgError - MERFISH_mouse_cortex.ipynb: restore relative data path, remove machine-specific training cell, clear execution outputs Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Changes
utils/data/abstract_datatype.pyLightningDataset(torch_geometric) has been removed in newer versions.pl.LightningDataModulewith manual dataloader wiring.validation_dataloader->val_dataloader(the original was silently never called by PyTorch Lightning).
Noneguard so the module works when no validation set is provided.utils/diffusion_model/setup/setup.pycheck_val_every_n_epoch=0no longer disables validation in newer PL —changed to
None.num_sanity_val_steps=0to suppress the sanity check when validation is disabled.metrics/evaluation_statistics.pyreturn_sensitivity=TrueraisesValueErrorin newer SciPy versions(documented in the README as "use SciPy 1.9.1").
ValueErrorexplicitly.example/MERFISH_mouse_cortex.ipynbTested on Python 3.10, PyTorch 2.x, PyTorch Lightning 2.x, torch_geometric 2.x.