Add copy to sim_config in psimulate (#278)

* add copies, make job specific non-overwriting

* rever job specific change

* fully revert

* formatting

* add unit test

* format

* add docstring and comment

Ensure that the branch_configuration remains unchanged during simulation configuration.

* format

* add changelog

Author: patricktnast

CHANGELOG.rst

@@ -1,3 +1,7 @@
+**2.1.23 - 10/27/25**
+
+  - Bugfix: Deep copy branch_configuration when making sim_config property
+
 **2.1.22 - 10/22/25**
 
   - Bugfix: Move model spec missing error to only raise for run command

src/vivarium_cluster_tools/psimulate/jobs.py

@@ -6,6 +6,7 @@
 """
 
 from collections import defaultdict
+from copy import deepcopy
 from pathlib import Path
 from typing import Any, NamedTuple
 
@@ -48,7 +49,7 @@ def job_specific(self) -> dict[str, Any]:
     @property
     def sim_config(self) -> dict[str, Any]:
         """Parameters for the simulation configuration."""
-        config = defaultdict(dict, self.branch_configuration)
+        config = defaultdict(dict, deepcopy(self.branch_configuration))
         config["randomness"]["random_seed"] = self.random_seed
         config["input_data"]["input_draw_number"] = self.input_draw
         return dict(config)

tests/psimulate/test_jobs.py

@@ -0,0 +1,19 @@
+from copy import deepcopy
+
+from vivarium_cluster_tools.psimulate.jobs import JobParameters
+
+
+def test_branch_config_immutable() -> None:
+    "Test that the branch_configuration doesn't get mutated in place."
+    original_branch_config = {"foo": "bar", "input_data": {"spam": "eggs"}}
+    params = JobParameters(
+        model_specification="model_spec.yaml",
+        branch_configuration=deepcopy(original_branch_config),
+        input_draw=0,
+        random_seed=1,
+        results_path="results",
+        backup_configuration={},
+        extras={},
+    )
+    params.sim_config  # This was previously causing branch_config to change
+    assert params.branch_configuration == original_branch_config