Fix pytests and reduce warnings

ecoli/processes/environment/derive_globals.py

@@ -147,7 +147,7 @@ def get_default_global_state():
             'mmol_to_counts': mmol_to_counts.to('L/mmol')}}
 
 
-def test_deriver(total_time=10):
+def test_deriver(total_time=10, return_data=False):
 
     growth_rate = 6e-3
 
@@ -183,9 +183,10 @@ def test_deriver(total_time=10):
         # save state
         saved_state[time] = copy.deepcopy(state)
 
-    return saved_state
+    if return_data:
+        return saved_state
 
 
 if __name__ == '__main__':
-    saved_data = test_deriver(100)
+    saved_data = test_deriver(100, return_data=True)
     print(saved_data)

ecoli/processes/environment/lysis.py

@@ -287,7 +287,8 @@ def test_lysis(
         emit_step=1,
         bounds=[25, 25] * units.um,
         n_bins=[5, 5],
-        uptake_rate_max=25
+        uptake_rate_max=25,
+        return_data=False
 ):
     from ecoli.composites.environment.lattice import Lattice
 
@@ -360,7 +361,9 @@ def test_lysis(
         emit_step=emit_step)
     sim.update(total_time)
     data = sim.emitter.get_data_unitless()
-    return data
+
+    if return_data:
+        return data
 
 
 def main():
@@ -377,6 +380,7 @@ def main():
         emit_step=10,
         bounds=bounds,
         n_bins=[11, 11],
+        return_data=True
     )
 
     # format the data for plot_snapshots

ecoli/processes/environment/multibody_physics.py

@@ -348,7 +348,7 @@ def get(self, timeout=0):
         return self.update
 
 # tests and simulations
-def test_multibody(n_agents=1, time=10):
+def test_multibody(n_agents=1, time=10, return_data=False):
     agent_ids = [
         str(agent_id)
         for agent_id in range(n_agents)]
@@ -369,7 +369,9 @@ def test_multibody(n_agents=1, time=10):
         'timestep': 1,
         'total_time': time,
         'return_raw_data': True}
-    return simulate_experiment(experiment, settings)
+    data = simulate_experiment(experiment, settings)
+    if return_data:
+        return data
 
 
 def test_growth_division(
@@ -380,6 +382,7 @@ def test_growth_division(
         total_time=10,
         timestep=1,
         experiment_settings=None,
+        return_data=False
 ):
     if not experiment_settings:
         experiment_settings = {}
@@ -460,7 +463,8 @@ def test_growth_division(
         experiment._send_updates(invoked_update)
 
     experiment.end()
-    return experiment.emitter.get_data_unitless()
+    if return_data:
+        return experiment.emitter.get_data_unitless()
 
 
 def run_growth_division(
@@ -495,7 +499,8 @@ def run_growth_division(
         growth_rate_noise=0.001,
         division_volume=volume_from_length(4, 1) * units.fL,
         total_time=100,
-        experiment_settings=experiment_settings)
+        experiment_settings=experiment_settings,
+        return_data=True)
 
     agents, fields = format_snapshot_data(gd_data)
     return plot_snapshots(

ecoli/processes/membrane/membrane_potential.py

@@ -202,7 +202,7 @@ def next_update(self, timestep, states):
                 'PMF': PMF}}
 
 
-def test_mem_potential():
+def test_mem_potential(return_data=False):
     """
     test :module: ecoli.processes.membrane.membrane_potential.MembranePotential
     by running it with changing external Na concentrations.
@@ -219,15 +219,17 @@ def test_mem_potential():
 
     PMF_timeseries = timeseries['membrane']['PMF']
     assert PMF_timeseries[-1] > PMF_timeseries[2]
-    return timeseries
+
+    if return_data:
+        return timeseries
 
 
 def main():
     out_dir = os.path.join(PROCESS_OUT_DIR, NAME)
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
 
-    timeseries = test_mem_potential()
+    timeseries = test_mem_potential(return_data=True)
     settings = {
         'remove_first_timestep': True
     }

ecoli/processes/metabolism_redux.py

@@ -793,7 +793,8 @@ def solve(self,
             constr.append(v[self.maintenance_idx] >= ngam_target)
         # If enzymes not present, constrain rxn flux to 0
         if binary_kinetic_idx is not None:
-            constr.append(v[binary_kinetic_idx] == 0)
+            if len(binary_kinetic_idx) > 0:
+                constr.append(v[binary_kinetic_idx] == 0)
         # TODO (Cyrus) - make this a parameter
         constr.extend([v >= 0, v <= upper_flux_bound, e >= 0, e <= upper_flux_bound])
 

ecoli/processes/spatiality/spatial_geometry.py

@@ -180,7 +180,7 @@ def run_spatial_geometry_process():
     return output
 
 
-def test_spatial_geometry_process():
+def test_spatial_geometry_process(return_data=False):
     """
     Test that the process runs correctly.
 
@@ -189,7 +189,8 @@ def test_spatial_geometry_process():
     output = run_spatial_geometry_process()
     # TODO(vivarium): Add assert statements to ensure correct performance.
 
-    return output
+    if return_data:
+        return output
 
 
 def main():
@@ -199,7 +200,7 @@ def main():
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
 
-    output = test_spatial_geometry_process()
+    output = test_spatial_geometry_process(return_data=True)
 
 
 

ecoli/states/wcecoli_state.py

@@ -31,7 +31,9 @@ def numpy_molecules(states):
     if 'environment' in states:
         if 'exchange_data' in states['environment']:
             states['environment']['exchange_data']['constrained'
-                ] *= units.mmol / (units. g * units.h)
+                ] = {mol: units.mmol / (units. g * units.h) * rate
+                for mol, rate in states['environment']['exchange_data'][
+                    'constrained']}
         else:
             # Load aerobic minimal media exchange data by default
             states['environment']['exchange_data'] = {