Restructure data files into package data dir

Author: RalfG

deeplc/__init__.py

@@ -1,3 +1,5 @@
+"""DeepLC: Retention time prediction for peptides carrying any modification."""
+
 from importlib.metadata import version
 
 from deeplc.core import calibrate_and_predict, finetune_and_predict, predict

deeplc/_argument_parser.py

@@ -228,4 +228,4 @@ def _predict_epoch(
             features = [feature_tensor.to(device) for feature_tensor in features]
             outputs = model(*features)
             predictions.append(outputs.cpu())
-    return torch.cat(predictions, dim=0)
+    return torch.cat(predictions, dim=0).squeeze()

deeplc/_model_ops.py

@@ -22,7 +22,7 @@
 
 DEEPLC_DIR = Path(__file__).resolve().parent
 DEFAULT_MODEL_NAME = "full_hc_PXD005573_pub_1fd8363d9af9dcad3be7553c39396960.pt"
-DEFAULT_MODEL = DEEPLC_DIR / "models" / DEFAULT_MODEL_NAME
+DEFAULT_MODEL = DEEPLC_DIR / "package_data" / "models" / DEFAULT_MODEL_NAME
 
 
 def predict(
@@ -156,7 +156,7 @@ def finetune_and_predict(
 
     """
     # Fine-tune the model
-    LOGGER.info("Fine-tuning model...")s
+    LOGGER.info("Fine-tuning model...")
     reference_dataset = DeepLCDataset.from_psm_list(psm_list_reference)
     # TODO: Allow model to be saved or exported after fine-tuning
     finetuned_model = _model_ops.train(