Fix path resolution for configs and cache

pyproject.toml

@@ -64,3 +64,7 @@ hest = { git = "https://github.com/mahmoodlab/HEST.git", rev = "2c777630b1e8a74d
 
 [tool.hatch.metadata]
 allow-direct-references = true
+
+[tool.hatch.build.targets.wheel.force-include]
+"conf" = "seal/conf"
+"cache" = "seal/cache"

seal/models/encoder_factory.py

@@ -14,7 +14,22 @@
 import shutil
 import os
 
+from pathlib import Path
+import argparse
 
+def find_config_yaml():
+    # 1. Check for local override first (preserves original behavior)
+    local_config = Path("conf/config.yaml")
+    if local_config.exists():
+        return str(local_config)
+
+    # 2. Fall back to the bundled package config
+    package_config = Path(__file__).resolve().parent.parent / "conf" / "config.yaml"
+    if package_config.exists():
+        return str(package_config)
+
+    # 3. Last resort fallback to avoid a silent failure
+    raise FileNotFoundError("Could not find config.yaml locally or in the installed package.")
 
 def get_constants(norm='imagenet'):
     IMAGENET_MEAN = [0.485, 0.456, 0.406]
@@ -781,7 +796,7 @@ def load_img_model_from_checkpoint(
     import argparse
     from seal.models.load_model import ModelMixin
 
-    default_config_path = argparse.Namespace(config='conf/config.yaml')
+    default_config_path = argparse.Namespace(config=find_config_yaml())
 
     if checkpoint_path is None:
         print(f"Warning: No image checkpoint provided for checkpoint_dir={checkpoint_dir}")
@@ -842,7 +857,7 @@ def load_gene_model_from_checkpoint(
     """
     from seal.models.load_model import ModelMixin
 
-    default_config_path = argparse.Namespace(config='conf/config.yaml')
+    default_config_path = argparse.Namespace(config=find_config_yaml())
     model_config = update_config(default_config_path)
     default_config = update_config(default_config_path)
 

seal/models/load_model.py

@@ -31,11 +31,21 @@
 import torch.nn as nn
 from seal.models.da_model import AdversarialDiscriminator
 from seal.models.encoder_factory import encoder_factory
-
+from pathlib import Path
 
 HF_API_KEY = os.getenv("HF_API_KEY")
 
+def find_organ_ids():
+    rel_path = "cache/organ_ids.json"
+    id_file = Path(rel_path)
 
+    if not id_file.exists():
+        id_file = Path(__file__).resolve().parent.parent / rel_path
+        if not id_file.exists():
+            raise FileNotFoundError(f'Could not locate {rel_path} locally or in package.')
+
+    with open(id_file, 'r') as f: 
+        return json.load(f) # You can return this directly without assigning it to a variable
 
 class ModelMixin(): 
 
@@ -533,8 +543,7 @@ def __init__(self, encoder, out_dim, rec_dim, eval_transforms, precision,
         if self.use_adapter: 
             self.adapter = self.encoder.adapter
 
-        with open("cache/organ_ids.json", 'r') as f: 
-            organ_ids = json.load(f)
+        organ_ids = find_organ_ids()
         num_organs = len(organ_ids)
 
         if self.organ_token: