Merge pull request #382 from AllenCellModeling/feature/manual_config_…

…save

Add save config function

cyto_dl/api/model.py

@@ -75,7 +75,6 @@ def load_default_experiment(
         output_dir.mkdir(parents=True, exist_ok=True)
 
         self.cfg = cfg
-        OmegaConf.save(self.cfg, output_dir / f'{"train" if train else "eval"}_config.yaml')
 
     def print_config(self):
         print_config_tree(self.cfg, resolve=True)
@@ -88,6 +87,13 @@ def override_config(self, overrides: Dict[str, Union[str, int, float, bool]]):
         for k, v in overrides.items():
             OmegaConf.update(self.cfg, k, v)
 
+    def save_config(self, path: Path) -> None:
+        """Save current config to provided path.
+
+        :param path: path at which to save config
+        """
+        OmegaConf.save(self.cfg, path)
+
     async def _train_async(self):
         return train_model(self.cfg)
 

pyproject.toml

@@ -43,7 +43,7 @@ dependencies = [
     "astropy>=5.2",
     "rich",
     "boto3",
-    "bioio",
+    "bioio>=1.0.1",
     "bioio-czi",
     "bioio-ome-tiff",
     "bioio-tifffile"

tests/api/test_model.py

@@ -14,7 +14,7 @@ def test_load_default_experiment_valid_exp_type(MockMkdir, MockSave):
     model: CytoDLModel = CytoDLModel()
     model.load_default_experiment(ExperimentType.SEGMENTATION.value, "fake_dir")
     MockMkdir.assert_called()
-    MockSave.assert_called()
+    MockSave.assert_not_called()
 
 
 @patch("cyto_dl.api.model.OmegaConf.save")