Enable switching service availability in healthsystem module

resources/healthsystem/ResourceFile_HealthSystem_parameters.csv

@@ -3,6 +3,8 @@ policy_name,Naive
 year_mode_switch,2100
 scale_to_effective_capabilities,FALSE
 Service_Availability,"[""*""]"
+year_service_availability_switch,2100
+service_availability_postSwitch,"[""*""]"
 use_funded_or_actual_staffing,funded_plus
 mode_appt_constraints,1
 mode_appt_constraints_postSwitch,1

src/scripts/lcoa_inputs_from_tlo_analyses/combine_suspended_and_resumed_pickles.py

@@ -0,0 +1,132 @@
+"""CLI helper to combine suspended and resumed pickle outputs."""
+
+# python src/scripts/lcoa_inputs_from_tlo_analyses/combine_suspended_and_resumed_pickles.py --suspended_results_folder outputs/s.bhatia@imperial.ac.uk/effect_of_each_treatment_id-2026-02-12T120859Z --resumed_results_folder outputs/s.bhatia@imperial.ac.uk/effect_of_each_treatment_id-2026-02-16T154500Z_folder --output_folder outputs/s.bhatia@imperial.ac.uk/effect_of_each_treatment_id-combined
+
+
+import argparse
+import pickle
+import warnings
+from pathlib import Path
+from typing import Any
+
+import pandas as pd
+
+def _validate_input_output_paths(
+    suspended_results_folder: Path,
+    resumed_results_folder: Path,
+    output_folder: Path,
+) -> None:
+    """Validate input/output path constraints for pickle combination helper."""
+    suspended_resolved = suspended_results_folder.resolve()
+    resumed_resolved = resumed_results_folder.resolve()
+    output_resolved = output_folder.resolve()
+
+    if output_resolved == suspended_resolved or output_resolved == resumed_resolved:
+        raise ValueError(
+            "output_folder must be different from both suspended_results_folder and resumed_results_folder."
+        )
+
+def _combine_pickled_objects(suspended_obj: Any, resumed_obj: Any, context: str = "root") -> Any:
+    """Combine suspended and resumed objects with suspended object first."""
+    if suspended_obj is None and resumed_obj is None:
+        return None
+    if isinstance(suspended_obj, dict) and isinstance(resumed_obj, dict):
+        combined = {}
+        for key, suspended_value in suspended_obj.items():
+            if key in resumed_obj:
+                combined[key] = _combine_pickled_objects(
+                    suspended_value, resumed_obj[key], context=f"{context}.{key}"
+                )
+            else:
+                combined[key] = suspended_value
+        for key, resumed_value in resumed_obj.items():
+            if key not in combined:
+                combined[key] = resumed_value
+        return combined
+    if isinstance(suspended_obj, pd.DataFrame) and isinstance(resumed_obj, pd.DataFrame):
+        return pd.concat([suspended_obj, resumed_obj], axis=0)
+    if isinstance(suspended_obj, pd.Series) and isinstance(resumed_obj, pd.Series):
+        return pd.concat([suspended_obj, resumed_obj], axis=0)
+    if isinstance(suspended_obj, list) and isinstance(resumed_obj, list):
+        return suspended_obj + resumed_obj
+    if isinstance(suspended_obj, tuple) and isinstance(resumed_obj, tuple):
+        return suspended_obj + resumed_obj
+    try:
+        return suspended_obj + resumed_obj
+    except TypeError as exc:
+        raise TypeError(
+            f"Unsupported combine operation at {context}: "
+            f"{type(suspended_obj).__name__} and {type(resumed_obj).__name__}."
+        ) from exc
+
+
+def combine_suspended_and_resumed_pickles(
+    suspended_results_folder: Path,
+    resumed_results_folder: Path,
+    output_folder: Path,
+) -> None:
+    """Combine corresponding suspended and resumed pickles into output folder."""
+    _validate_input_output_paths(suspended_results_folder, resumed_results_folder, output_folder)
+
+    draw_dirs = sorted([p for p in resumed_results_folder.iterdir() if p.is_dir()], key=lambda p: p.name)
+    for draw_dir in draw_dirs:
+        print(f"Processing draw directory: {draw_dir}...")
+        run_dirs = sorted([p for p in draw_dir.iterdir() if p.is_dir()], key=lambda p: p.name)
+        for run_dir in run_dirs:
+            print(f"  Processing run directory: {run_dir}...")
+            pickles = sorted(run_dir.glob("*.pickle"), key=lambda p: p.name)
+            for resumed_pickle_path in pickles:
+                print(f"    Processing pickle file: {resumed_pickle_path}...")
+                with resumed_pickle_path.open("rb") as resumed_file:
+                    resumed_obj = pickle.load(resumed_file)
+
+                suspended_pickle_path = (
+                    suspended_results_folder / "0" / run_dir.name / resumed_pickle_path.name
+                )
+                if suspended_pickle_path.exists():
+                    with suspended_pickle_path.open("rb") as suspended_file:
+                        suspended_obj = pickle.load(suspended_file)
+                    try:
+                        combined_obj = _combine_pickled_objects(suspended_obj, resumed_obj)
+                    except TypeError as exc:
+                        raise TypeError(
+                            "Could not combine pickled objects for "
+                            f"{resumed_pickle_path} with types "
+                            f"{type(suspended_obj).__name__} and {type(resumed_obj).__name__}."
+                        ) from exc
+                else:
+                    warnings.warn(
+                        "No suspended counterpart found for "
+                        f"{resumed_pickle_path} (expected at {suspended_pickle_path}); "
+                        "copying resumed object to output unchanged.",
+                        stacklevel=2,
+                    )
+                    combined_obj = resumed_obj
+
+                output_pickle_path = output_folder / draw_dir.name / run_dir.name / resumed_pickle_path.name
+                output_pickle_path.parent.mkdir(parents=True, exist_ok=True)
+                with output_pickle_path.open("wb") as output_file:
+                    pickle.dump(combined_obj, output_file)
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(
+        description=(
+            "Combine suspended and resumed pickle outputs into a new output folder, "
+            "with suspended content prepended where counterparts exist."
+        )
+    )
+    parser.add_argument("suspended_results_folder", type=Path)
+    parser.add_argument("resumed_results_folder", type=Path)
+    parser.add_argument("output_folder", type=Path)
+    args = parser.parse_args()
+
+    combine_suspended_and_resumed_pickles(
+        suspended_results_folder=args.suspended_results_folder,
+        resumed_results_folder=args.resumed_results_folder,
+        output_folder=args.output_folder,
+    )
+
+
+if __name__ == "__main__":
+    main()