Migration script

pyproject.toml

@@ -70,6 +70,7 @@ check-domain = "workflow.scripts.check_domain:app"
 gcmt-auto-simulate = "workflow.scripts.gcmt_auto_simulate:app"
 import-realisation = "workflow.scripts.import_realisation:app"
 lf-to-xarray = "workflow.scripts.lf_to_xarray:app"
+migrate = "workflow.scripts.migrate:app"
 
 [tool.setuptools.package-dir]
 workflow = "workflow"

workflow/defaults.py

@@ -3,11 +3,11 @@
 import importlib
 from enum import StrEnum
 from importlib import resources
-from typing import Any
 
 import yaml
 
 import workflow.default_parameters.root as root
+from workflow import utils
 
 
 class DefaultsVersion(StrEnum):
@@ -19,30 +19,6 @@ class DefaultsVersion(StrEnum):
     develop = "develop"
 
 
-def _merge_defaults(defaults_a: dict[str, Any], defaults_b: dict[str, Any]) -> None:
-    """Deep-merge dictionaries in place, updating the first with values from the second.
-
-    Parameters
-    ----------
-    defaults_a : dict[str, Any]
-        Base dictionary to be updated. This dictionary is modified in place with
-        merged values.
-    defaults_b : dict[str, Any]
-        Dictionary providing overriding values. Keys in this dictionary are
-        preferred when keys conflict. This dictionary is not modified.
-    """
-
-    for key, value in defaults_b.items():
-        if (
-            key in defaults_a
-            and isinstance(defaults_a[key], dict)
-            and isinstance(value, dict)
-        ):
-            _merge_defaults(defaults_a[key], defaults_b[key])
-        else:
-            defaults_a[key] = value
-
-
 def load_defaults(version: DefaultsVersion) -> dict[str, int | float | str]:
     """Load default parameters for EMOD3D simulation from a YAML file.
 
@@ -72,5 +48,5 @@ def load_defaults(version: DefaultsVersion) -> dict[str, int | float | str]:
     defaults_path = resources.files(defaults_package) / "defaults.yaml"
     with defaults_path.open(encoding="utf-8") as emod3d_defaults_file_handle:
         defaults = yaml.safe_load(emod3d_defaults_file_handle)
-    _merge_defaults(root_defaults, defaults)
+    utils.merge_dictionaries(root_defaults, defaults)
     return root_defaults