Fixed issue with not being able to run basic sim.

CovertLab · Jan 10, 2024 · a0ca4b5 · a0ca4b5
1 parent 7994957
commit a0ca4b5
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Showing 3 changed files with 6,640 additions and 6,366 deletions.
diff --git a/ecoli/experiments/metabolism_redux_sim.py b/ecoli/experiments/metabolism_redux_sim.py
@@ -62,9 +62,9 @@ def run_ecoli_with_metabolism_redux_classic(
         name='metabolism-redux-classic',
         raw_output=False,
         save=True,
-        save_times=[1, 200, 400, 600, 800, 1000, 1200, 1300, 1400],
-        condition = "with_aa", # basal, with_aa
-        fixed_media = "minimal_plus_amino_acids" # minimal, minimal_plus_amino_acids
+        save_times=[1, 200, 400, 600, 800, 1000, 1200, 1300, 1400, 1800, 2200, 2400],
+        # condition = "with_aa", # basal, with_aa
+        # fixed_media = "minimal_plus_amino_acids" # minimal, minimal_plus_amino_acids
 ):
     # filename = 'default'
     sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + ".json")
@@ -75,11 +75,11 @@ def run_ecoli_with_metabolism_redux_classic(
     sim.emitter = emitter
     # sim.initial_state = get_state_from_file(path=f'data/{initial_state_file}.json')
     sim.raw_output = raw_output
-    # sim.save = save
-    # sim.save_times = save_times
+    sim.save = save
+    sim.save_times = save_times
 
-    sim.condition = condition
-    sim.fixed_media = fixed_media
+    # sim.condition = condition
+    # sim.fixed_media = fixed_media
 
 
     # # simplify working with uptake

diff --git a/ecoli/library/sim_data.py b/ecoli/library/sim_data.py
@@ -34,8 +34,8 @@ def __init__(
         jit=False,
         total_time=10,
         fixed_media = None,
-        media_timeline=((0, 'minimal'),),   # have to change both media_timeline and condition
-        condition = 'basal',
+        media_timeline= ((0, 'minimal'),),   # e.g. minimal_plus_amino_acids,  have to change both media_timeline and condition
+        condition = None, # e.g. basal, with_aa
         operons=True,
         trna_charging=True,
         ppgpp_regulation=True,
@@ -68,10 +68,13 @@ def __init__(
         self.total_time = total_time
         self.random_state = np.random.RandomState(seed = seed)
         # Iterable of tuples with the format (time, media_id)
-        self.condition = condition
+        if condition is not None:
+            self.condition = condition
+            self.sim_data.condition = condition
 
         if fixed_media is not None and media_timeline is not None:
             media_timeline = ((0, fixed_media),)
+
         self.media_timeline = media_timeline
 
         self.trna_charging = trna_charging
@@ -101,7 +104,6 @@ def __init__(
         with open(sim_data_path, 'rb') as sim_data_file:
             self.sim_data = pickle.load(sim_data_file)
 
-        self.sim_data.condition = condition
 
         # Used by processes to apply submass updates to correct unique attr
         self.submass_indices = {