refactor: remove save methods from settings

Config files should be created/edited manually and version controlled,
not generated programmatically.

Author: claude

src/datajoint/settings.py

@@ -311,28 +311,6 @@ def get_store_spec(self, store: str) -> Dict[str, Any]:
 
         return spec
 
-    def save(self, filename: Optional[Union[str, Path]] = None, verbose: bool = False) -> None:
-        """
-        Save settings to a JSON file.
-
-        Args:
-            filename: Path to save the configuration. Defaults to datajoint.json in cwd.
-            verbose: If True, log the save operation.
-        """
-        if filename is None:
-            filename = Path.cwd() / CONFIG_FILENAME
-
-        data = self._to_flat_dict()
-        # Remove secrets from saved config
-        secrets_keys = ["database.password", "external.aws_secret_access_key"]
-        for key in secrets_keys:
-            data.pop(key, None)
-
-        with open(filename, "w") as f:
-            json.dump(data, f, indent=4, default=str)
-        if verbose:
-            logger.info(f"Saved settings to {filename}")
-
     def load(self, filename: Union[str, Path]) -> None:
         """
         Load settings from a JSON file.
@@ -352,31 +330,6 @@ def load(self, filename: Union[str, Path]) -> None:
         self._update_from_flat_dict(data)
         self._config_path = filepath
 
-    def _to_flat_dict(self) -> Dict[str, Any]:
-        """Convert settings to flat dict with dot notation keys."""
-        result: Dict[str, Any] = {}
-
-        def flatten(obj: Any, prefix: str = "") -> None:
-            if isinstance(obj, BaseSettings):
-                for name in obj.model_fields:
-                    if name.startswith("_"):
-                        continue
-                    value = getattr(obj, name)
-                    key = f"{prefix}.{name}" if prefix else name
-                    if isinstance(value, BaseSettings):
-                        flatten(value, key)
-                    elif isinstance(value, SecretStr):
-                        result[key] = value.get_secret_value() if value else None
-                    elif isinstance(value, Path):
-                        result[key] = str(value)
-                    else:
-                        result[key] = value
-            elif isinstance(obj, dict):
-                result[prefix] = obj
-
-        flatten(self)
-        return result
-
     def _update_from_flat_dict(self, data: Dict[str, Any]) -> None:
         """Update settings from a flat dict with dot notation keys."""
         for key, value in data.items():

tests/test_settings.py

@@ -1,6 +1,5 @@
 """Tests for DataJoint settings module."""
 
-import json
 from pathlib import Path
 
 import pytest
@@ -245,51 +244,26 @@ def test_override_restores_on_exception(self):
         assert dj.config.safemode == original
 
 
-class TestSaveLoad:
-    """Test saving and loading configuration."""
+class TestLoad:
+    """Test loading configuration."""
 
-    def test_save_and_load(self, tmp_path):
-        """Test saving and loading configuration."""
+    def test_load_config_file(self, tmp_path):
+        """Test loading configuration from file."""
         filename = tmp_path / "test_config.json"
+        filename.write_text('{"database": {"host": "loaded_host"}}')
         original_host = dj.config.database.host
 
         try:
-            dj.config.database.host = "saved_host"
-            dj.config.save(filename)
-            dj.config.database.host = "reset_host"
             dj.config.load(filename)
-
-            assert dj.config.database.host == "saved_host"
+            assert dj.config.database.host == "loaded_host"
         finally:
             dj.config.database.host = original_host
 
-    def test_save_excludes_secrets(self, tmp_path):
-        """Test that save() excludes secret values."""
-        filename = tmp_path / "test_config.json"
-        original_password = dj.config.database.password
-
-        try:
-            dj.config.database.password = "should_not_save"
-            dj.config.save(filename)
-
-            with open(filename) as f:
-                saved = json.load(f)
-
-            assert "database.password" not in saved
-        finally:
-            dj.config.database.password = original_password
-
     def test_load_nonexistent_file(self):
         """Test loading nonexistent file raises FileNotFoundError."""
         with pytest.raises(FileNotFoundError):
             dj.config.load("/nonexistent/path/config.json")
 
-    def test_save_default_filename(self, tmp_path, monkeypatch):
-        """Test save() uses datajoint.json in cwd by default."""
-        monkeypatch.chdir(tmp_path)
-        dj.config.save()
-        assert (tmp_path / CONFIG_FILENAME).exists()
-
 
 class TestStoreSpec:
     """Test external store configuration."""