adding species_names property and garbage collector

synbio_morpher/utils/circuit/agnostic_circuits/circuit.py

@@ -51,6 +51,7 @@ def init_refcircuit(self, config: dict):
         self.use_prod_and_deg = config.get('include_prod_deg', True)
         self.model = construct_bioreaction_model(
             config.get('data'), config.get('molecular_params'), include_prod_deg=self.use_prod_and_deg)
+        self.species_names = [s.name for s in self.model.species]
         self.circuit_size = len(self.model.species)
         self.data: DataManager = config.get('data')
         self.qreactions = self.init_reactions(self.model, config)

synbio_morpher/utils/circuit/agnostic_circuits/circuit_manager.py

@@ -11,6 +11,7 @@
 from datetime import datetime
 import inspect
 import os
+import gc
 # import sys
 import logging
 import diffrax as dfx
@@ -129,6 +130,30 @@ def compute_interactions(self, circuit: Circuit):
                 filename_addon=filename_addon, subfolder=filename_addon)
         return circuit
 
+    def compute_interactions_batch(self, circuits, batch=True):
+        # Make sure multi-threading is on
+        assert self.simulator_args[''] > 1, 'Set the IntaRNA nu'
+        if self.simulator_args['name'] == 'IntaRNA':
+            if self.simulator_args['threads'] == 1:
+                logging.warning(
+                    'For batch-computation of interaction strengths with IntaRNA, multi-threading is recommended. Set `threads` in the config file within the simulator arguments (`interaction_simulator`) kwargs.')
+        # And that raw_stdout is set to true, otherwise IntaRNA will only return the first interaction
+            if self.simulator_args['raw_stdout'] == False:
+                logging.warning('For batching IntaRNA, setting raw_stdout to True, otherwise the output from the Python API will only return one interaction')
+                self.simulator_args['raw_stdout'] = True
+
+        # Write temporary fasta file with all interactions
+
+
+        # Run simulator with fasta as input
+
+        # Process output from string into csv into numpy
+
+        # Fill in the species that didn't get returned with IntaRNA non-interaction default parameters
+
+        # Delete fasta file
+        pass
+
     def run_interaction_simulator(self, species: List[Species], quantities, filename=None) -> InteractionDataHandler:
         data = {s: s.physical_data for s in species}
         # if filename is not None:
@@ -153,7 +178,7 @@ def find_steady_states(self, circuits: List[Circuit], batch=True) -> List[Circui
                 category='time_series',
                 vis_func=VisODE().plot,
                 vis_kwargs={'t': t,
-                            'legend': [s.name for s in circuit.model.species],
+                            'legend': circuit.species_names,
                             'out_type': 'svg'},
                 analytics_kwargs={'labels': [
                     s.name for s in circuit.model.species]},
@@ -414,7 +439,7 @@ def prepare_batch_params(circuits: List[Circuit]):
                 vis_func=VisODE().plot,
                 analytics=analytics,
                 vis_kwargs={'t': t,
-                            'legend': [s.name for s in circuit.model.species],
+                            'legend': circuit.species_names,
                             'out_type': 'svg'})
         # return {top_name: {subname: circuits[len(v)*i + j] for j, subname in enumerate(v.keys())}
         #         for i, (top_name, v) in enumerate(.items())}
@@ -446,9 +471,10 @@ def load_mutations(self, circuit: Circuit):
             subcircuits[i].circuit_size = circuit.circuit_size
             subcircuits[i].signal: Signal = circuit.signal
             subcircuits[i].use_prod_and_deg = circuit.use_prod_and_deg
-
+            
             # Cannot be by ref
             subcircuits[i].model = deepcopy(circuit.model)
+            subcircuits[i].species_names = circuit.species_name
             subcircuits[i].qreactions = deepcopy(circuit.qreactions)
             subcircuits[i] = implement_mutation(subcircuits[i], m)
         return subcircuits
@@ -590,6 +616,7 @@ def batch_circuits(self,
         viable_circuit_nums = [0]
         next_viable = 0
         i = 0
+        assert num_subcircuits[0] < self.max_circuits, f'The number of subcircuits {num_subcircuits[0]} in the first circuit is less than the max circuits specified ({self.max_circuits}).'
         while i < len(num_subcircuits):
             while (i < len(num_subcircuits)) and (next_viable + num_subcircuits[i] < self.max_circuits):
                 next_viable += num_subcircuits[i]
@@ -645,6 +672,7 @@ def batch_circuits(self,
             logging.warning(
                 f'Single batch: {single_batch_time} \nProjected time: {single_batch_time.total_seconds() * len(subcircuits)/tot_subcircuits}s \nTotal time: {str(datetime.now() - start_time)}')
             del subcircuits
+            gc.collect()
         return circuits
 
     def run_batch(self,

synbio_morpher/utils/evolution/evolver.py

@@ -103,12 +103,12 @@ def make_species_iter(circuit: Circuit):
                 if type(self.concurrent_species_to_mutate) == str:
                     if self.concurrent_species_to_mutate == 'single_species_at_a_time':
                         spec_iter = circuit.model.species
-                    elif self.concurrent_species_to_mutate in [s.name for s in circuit.model.species]:
+                    elif self.concurrent_species_to_mutate in circuit.species_names:
                         spec_iter = [
                             s for s in circuit.model.species if s.name == self.concurrent_species_to_mutate]
                     else:
                         logging.warning(f'Could not find {self.concurrent_species_to_mutate} among the circuit species:')
-                        logging.warning([s.name for s in circuit.model.species])
+                        logging.warning(circuit.species_names)
                 elif type(self.concurrent_species_to_mutate) == list:
                     spec_iter = []
                     for c in self.concurrent_species_to_mutate:
@@ -239,7 +239,7 @@ def write_mutations(self, mutations: Mutations, overwrite=False):
 def load_mutations(circuit, filename=None):
     table = load_csv(filename, load_as='pandas')
     circuit.mutations = {}
-    species_names = [s.name for s in circuit.model.species]
+    species_names = circuit.species_names
     for i in range(len(table)):
         mutating_species = circuit.model.species[species_names.index(
             table.iloc[i]['template_name'])]

synbio_morpher/utils/evolution/mutation.py

@@ -125,8 +125,8 @@ def reverse_mut_mapping(self, mut_encoding: int):
 
 def implement_mutation(circuit: Circuit, mutation: Mutations):
 
-    if mutation.template_name in [s.name for s in circuit.model.species]:
-        sidx = [s.name for s in circuit.model.species].index(mutation.template_name)
+    if mutation.template_name in circuit.species_names:
+        sidx = circuit.species_names.index(mutation.template_name)
         # circuit.model.species[sidx].name = mutation.mutation_name
         circuit.model.species[sidx].physical_data = mutation.get_sequence()
     else: