Fix Parquet emitter issues for colony simulations

ecoli/experiments/ecoli_engine_process.py

@@ -452,6 +452,7 @@ def run_simulation(config):
     metadata.pop("initial_state", None)
     metadata["git_hash"] = get_git_revision_hash()
     metadata["git_diff"] = get_git_diff()
+    metadata = serialize_value(metadata)
 
     # Since unique numpy updater is an class method, internal
     # deepcopying in vivarium-core causes this warning to appear
@@ -467,11 +468,20 @@ def run_simulation(config):
         topology=composite.topology,
         initial_state=initial_state,
         experiment_id=experiment_id,
+        emit_config=config.get("emit_config", False),
         emitter=emitter_config,
         progress_bar=config["progress_bar"],
         metadata=metadata,
         profile=config["profile"],
         initial_global_time=config.get("start_time", 0.0),
+        emit_topology=config.get("emit_topology", True),
+        emit_processes=config.get("emit_processes", False),
+        emit_step=config.get("emit_step", 1),
+        display_info=config.get("display_info", True),
+        global_time_precision=config.get("global_time_precision", None),
+        store_schema=config.get("store_schema", None),
+        description=config.get("description", ""),
+        experiment_name=config.get("experiment_name", None),
     )
     # Unnecessary reference to initial_state
     engine.initial_state = None

ecoli/library/serialize.py

@@ -1,6 +1,7 @@
 import numpy as np
 import orjson
 import re
+import ast
 from unum import Unum
 from vivarium.core.registry import Serializer
 from vivarium.library.topology import convert_path_style, normalize_path
@@ -80,9 +81,12 @@ def deserialize(self, data):
         matched_regex = self.regex_for_serialized.fullmatch(data)
         if matched_regex:
             data = matched_regex.group(1)
-        data = orjson.loads(data)
+        if data.startswith("("):
+            data = ast.literal_eval(data)
+        else:
+            data = orjson.loads(data)
         rng = np.random.RandomState()
-        rng.set_state(data)
+        rng.set_state(tuple(data))
         return rng