Option to skip baseline variant sim_data

doc/workflows.rst

@@ -173,7 +173,11 @@ The name of each variant function is the name of the file containing its
 ``new_gene_internal_shift``. If the ``variants`` key points to an
 empty dictionary (no variants), then only the only "variant" saved
 by :py:mod:`runscripts.create_variants` is the unmodified simulation
-data object.
+data object. Thus, when running a workflow with :py:mod:`runscripts.workflow`,
+at least one lineage of cells will always be run with the baseline
+``sim_data``. To avoid this (e.g. when running many batches of simulations
+with the same variant function), set the top-level ``skip_baseline`` option
+to ``True``.
 
 .. warning::
     Only one variant function is supported at a time.
@@ -205,11 +209,12 @@ Output
 The generated variant simulation data objects are pickled and saved in the
 directory given in the ``outdir`` key of the configuration JSON.
 They all have file names of the format ``{index}.cPickle``, where
-index is an integer. The unmodified simulation data object is always
-saved as ``0.cPickle``. The identity of the other indices can be
-determined by referencing the ``metadata.json`` file that is also
-saved in ``outdir``. This JSON maps the variant function name to a
-mapping from each index to the exact parameter
+index is an integer. If the top-level ``skip_baseline`` option is not set
+to ``True``, the unmodified simulation data object is always
+saved as ``0.cPickle``. Otherwise, the 0 index is skipped. The identity of
+the other indices can be determined by referencing the ``metadata.json``
+file that is also saved in ``outdir``. This JSON maps the variant function
+name to a mapping from each index to the exact parameter
 dictionary passed to the variant function to create the
 variant simulation data saved with that index as its file name. See
 :py:func:`~runscripts.create_variants.apply_and_save_variants` for

ecoli/composites/ecoli_configs/default.json

@@ -25,6 +25,7 @@
     "fail_at_total_time": false,
 
     "variants": {},
+    "skip_baseline": false,
     "n_init_sims": 1,
     "generations": null,
     "single_daughters": true,

ecoli/experiments/ecoli_master_sim.py

@@ -150,8 +150,8 @@ def parse_key_value_args(args_list: list[str]) -> dict[str, str]:
     # Create an empty dictionary to store the parsed key-value pairs
     parsed_dict = {}
     for item in args_list:
-        if '=' in item:
-            key, value = item.split('=', 1)
+        if "=" in item:
+            key, value = item.split("=", 1)
             parsed_dict[key] = value
         else:
             raise ValueError(f"Argument '{item}' is not in the form key=value")

ecoli/experiments/tet_amp_sim.py

@@ -87,10 +87,7 @@ def run_sim(
             config["save_times"] = [11550]
         config["total_time"] = runtime
     if cloud:
-        config["emitter_arg"] = {
-            "host": "10.138.0.75:27017",
-            "emit_limit": 5000000
-        }
+        config["emitter_arg"] = {"host": "10.138.0.75:27017", "emit_limit": 5000000}
 
     run_simulation(config)
 

runscripts/create_variants.py

@@ -130,6 +130,7 @@ def apply_and_save_variants(
     param_dicts: list[dict[str, Any]],
     variant_name: str,
     outdir: str,
+    skip_baseline: bool,
 ):
     """
     Applies variant function to ``sim_data`` with each parameter dictionary
@@ -144,9 +145,12 @@ def apply_and_save_variants(
         param_dicts: Return value of :py:func:`~.parse_variants`
         variant_name: Name of variant function file in ``ecoli/variants`` folder
         outdir: Path to folder where variant ``sim_data`` pickles are saved
+        skip_baseline: Whether to save metadata for baseline sim_data
     """
     variant_mod = importlib.import_module(f"ecoli.variants.{variant_name}")
-    variant_metadata: dict[int, str | dict[str, Any]] = {0: "baseline"}
+    variant_metadata: dict[int, str | dict[str, Any]] = {}
+    if not skip_baseline:
+        variant_metadata[0] = "baseline"
     for i, params in enumerate(param_dicts):
         sim_data_copy = copy.deepcopy(sim_data)
         variant_metadata[i + 1] = params
@@ -280,9 +284,12 @@ def main():
     with open(os.path.join(config["kb"], "simData.cPickle"), "rb") as f:
         sim_data = pickle.load(f)
     os.makedirs(config["outdir"], exist_ok=True)
-    print("Saving baseline sim_data...")
-    with open(os.path.join(config["outdir"], "0.cPickle"), "wb") as f:
-        pickle.dump(sim_data, f)
+    if config["skip_baseline"]:
+        print("Skipping baseline sim_data...")
+    else:
+        print("Saving baseline sim_data...")
+        with open(os.path.join(config["outdir"], "0.cPickle"), "wb") as f:
+            pickle.dump(sim_data, f)
     variant_config = config.get("variants", {})
     if len(variant_config) > 1:
         raise RuntimeError(
@@ -296,7 +303,13 @@ def main():
         print("Parsing variants...")
         parsed_params = parse_variants(variant_params)
         print("Applying variants and saving variant sim_data...")
-        apply_and_save_variants(sim_data, parsed_params, variant_name, config["outdir"])
+        apply_and_save_variants(
+            sim_data,
+            parsed_params,
+            variant_name,
+            config["outdir"],
+            config["skip_baseline"],
+        )
     else:
         with open(os.path.join(config["outdir"], "metadata.json"), "w") as f:
             json.dump({None: {0: "baseline"}}, f)