Fix hardcoded absolute paths causing FileNotFoundError on import

configs/dinotxt_stage.yaml

@@ -1,5 +1,5 @@
 # This version of the YAML uses processed patches
-project: /home/suraj/Repositories/DINOv2_3D
+project: "."
 run_name: "DINOv2_pretrain_primus"
 img_size: [160, 160, 160]
 hidden_size: 864

configs/predict.yaml

@@ -1,4 +1,4 @@
-project: /home/suraj/Repositories/DINOv2_3D
+project: "."
 num_workers: 8
 
 trainer:
@@ -16,7 +16,7 @@ trainer:
         name: "get_predictions"
     callbacks:
       - _target_: project.callbacks.prediction_saver.SavePredictions
-        path: /home/suraj/Repositories/DINOv2_3D/predictions.csv
+        path: ./predictions.csv
 
 lightning_module:
     _target_: project.models.DINOv2_3D_LightningModule

configs/train.yaml

@@ -1,5 +1,5 @@
 # This version of the YAML uses processed patches, optimized for low memory usage
-project: /home/suraj/Repositories/DINOv2_3D
+project: "."
 run_name: "DINOv2_pretrain_primus"
 img_size: [160, 160, 160]  # reduced spatial dims for lower mem
 hidden_size: 864

scripts/run.py

@@ -5,6 +5,7 @@
 """
 
 import os
+from pathlib import Path
 from torch.utils.data import DataLoader
 from monai.bundle import ConfigParser
 
@@ -34,7 +35,19 @@ def run(mode, config_file: str, **config_overrides):
     parser.update(config_overrides)
 
     project_path = parser.get("project")
-    import_module_from_path("project", project_path)
+
+    # Normalize and resolve project path
+    # If project_path is relative, resolve it relative to the repository root
+    project_path = Path(project_path).expanduser()
+
+    if not project_path.is_absolute():
+        # Get the repository root (parent of the scripts directory)
+        repo_root = Path(__file__).resolve().parent.parent
+        project_path = (repo_root / project_path).resolve()
+    else:
+        project_path = project_path.resolve()
+
+    import_module_from_path("project", str(project_path))
 
     trainer = parser.get_parsed_content("trainer")
     lightning_module = parser.get_parsed_content("lightning_module")

scripts/utility/export_ckpt_to_nnunet.py

@@ -8,6 +8,7 @@
 import torch
 import os
 import sys
+from pathlib import Path
 from typing import Dict, Any
 
 from utils.imports import import_module_from_path
@@ -30,12 +31,22 @@ def modify_state_dict(state_dict: Dict[str, Any]) -> Dict[str, Any]:
 
 def process_checkpoint(input_path: str, output_path: str, 
                       remove_cls_token: bool = True,
-                      arch_class_name: str = 'PrimusM') -> None:
+                      arch_class_name: str = 'PrimusM',
+                      project_path: str = '.') -> None:
     """Process checkpoint file and save in nnUNet format"""
 
     # Import project module to handle checkpoint dependencies
-    project_path = "/home/suraj/Repositories/DINOv2_3D"
-    import_module_from_path("project", project_path)
+    # Normalize and resolve project path
+    project_path = Path(project_path).expanduser()
+
+    if not project_path.is_absolute():
+        # Resolve relative to the repository root
+        script_dir = Path(__file__).resolve().parent.parent.parent
+        project_path = (script_dir / project_path).resolve()
+    else:
+        project_path = project_path.resolve()
+
+    import_module_from_path("project", str(project_path))
 
     print(f"Loading checkpoint from: {input_path}")
     try:
@@ -86,6 +97,8 @@ def main():
                        help="Architecture class name (default: PrimusM)")
     parser.add_argument("--keep-cls-token", action="store_true",
                        help="Keep CLS token in positional embeddings")
+    parser.add_argument("--project-path", default=".",
+                       help="Path to the project root (default: current directory)")
 
     args = parser.parse_args()
 
@@ -100,7 +113,8 @@ def main():
             input_path=args.input_path,
             output_path=args.output_path,
             remove_cls_token=not args.keep_cls_token,
-            arch_class_name=args.arch_class_name
+            arch_class_name=args.arch_class_name,
+            project_path=args.project_path
         )
         print("Checkpoint conversion completed successfully!")
     except Exception as e:

utils/imports.py

@@ -26,7 +26,12 @@ def import_module_from_path(module_name: str, module_path: str) -> None:
 
     module_path = Path(module_path).resolve() / "__init__.py"
     if not module_path.is_file():
-        raise FileNotFoundError(f"No `__init__.py` in `{module_path}`.")
+        raise FileNotFoundError(
+            f"No `__init__.py` found at `{module_path}`.\n"
+            f"If your config contains an absolute path like '/home/suraj/...', "
+            f"please update it to use a relative path (e.g., 'project: \".\"') "
+            f"or set it to your local repository root."
+        )
     spec = importlib.util.spec_from_file_location(module_name, str(module_path))
     module = importlib.util.module_from_spec(spec)
     spec.loader.exec_module(module)