fix tests, use model_dump for pydantic base model

Author: lucidrains

alphafold3_pytorch/alphafold3.py

@@ -3069,7 +3069,7 @@ def save(self, path: str | Path, overwrite = False):
         if isinstance(path, str):
             path = Path(path)
 
-        assert path.is_file() and (not path.exists() or overwrite)
+        assert not path.is_dir() and (not path.exists() or overwrite)
 
         path.parent.mkdir(exist_ok = True, parents = True)
 

alphafold3_pytorch/configs.py

@@ -68,9 +68,12 @@ def from_yaml_file(path: str | Path):
         return Alphafold3Config(**config_dict)
 
     def create_instance(self) -> Alphafold3:
-        alphafold3 = Alphafold3(**self.dict())
+        alphafold3 = Alphafold3(**self.model_dump())
         return alphafold3
 
     def create_instance_from_yaml_file(path: str | Path) -> Alphafold3:
         af3_config = Alphafold3Config.from_yaml_file(path)
         return af3_config.create_instance()
+
+class TrainerConfig(BaseModelWithExtra):
+    pass

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "alphafold3-pytorch"
-version = "0.1.22"
+version = "0.1.23"
 description = "Alphafold 3 - Pytorch"
 authors = [
     { name = "Phil Wang", email = "[email protected]" }