{
  "name": "CodonTransformer",
  "version": "1.6.7",
  "layout": {
    "conf": "Repository configuration and auxiliary project files.",
    "model": "CodonTransformer Python package and bundled model resources.",
    "scripts": "Executable training, inference, SLURM, notebook, test, and demo files.",
    "weight": "Local model weights and checkpoints."
  },
  "entrypoints": {
    "prepare_pretrain_data": "scripts/slurm/prepare_pretrain_data.sh",
    "prepare_finetune_data": "scripts/slurm/prepare_finetune_data.sh",
    "export_finetuned_model": "scripts/slurm/export_finetuned_model.sh",
    "inference_finetuned": "scripts/slurm/run_inference_finetuned.sh",
    "finetune": "scripts/finetune.py",
    "pretrain": "scripts/pretrain.py",
    "inference_single": "scripts/slurm/run_inference_single.sh",
    "inference_multiple": "scripts/slurm/run_inference_multiple.sh",
    "inference_batch": "scripts/slurm/run_inference_batch.sh"
  },
  "resources": {
    "tokenizer": "model/src/CodonTransformerTokenizer.json",
    "demo_dataset": "scripts/demo/sample_dataset.csv",
    "raw_training_data": "scripts/data/raw",
    "processed_training_data": "scripts/data/processed",
    "checkpoints": "weight/checkpoints"
  }
}