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* Upgrade PyTorch Lightning from 1.9.5 to 2.5.1 This commit implements the following changes: - Update imports from pytorch_lightning to lightning.pytorch - Replace deprecated CombinedLoader import path - Change *_epoch_end hooks to on_*_epoch_end hooks - Add step output collection for epoch-end processing - Update trainer.fit() to use ckpt_path - Update requirements.in to use lightning>=2.5.1,<2.6 - Remove pytorch-lightning package dependency * single gpu training test passing * fix import style * remove -e from requirements.txt * uv (#23) * specify deps in pyproject.toml and add uv.lock * pre-commit and lint * update github actions configuration * add missing dep * update readme * remove setup.cfg * cleanup * relax some version bounds --------- Co-authored-by: Samuel Stanton <stanton.samuel@gene.com> Co-authored-by: Joseph Kleinhenz <kleinhej@gene.com>
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