Added multiple models convection model

Added new functionality: Multiple species pressure based convection model for biomass propagation. v.0.5.0 06/22/24 ID

cometspy/comets.py

@@ -17,13 +17,13 @@
 import numpy as np
 import platform
 
-__author__ = "Djordje Bajic, Jean Vila, Jeremy Chacon"
+__author__ = "Djordje Bajic, Jean Vila, Jeremy Chacon, Ilija Dukovski"
 __copyright__ = "Copyright 2024, The COMETS Consortium"
-__credits__ = ["Djordje Bajic", "Jean Vila", "Jeremy Chacon"]
+__credits__ = ["Djordje Bajic", "Jean Vila", "Jeremy Chacon", "Ilija Dukovski"]
 __license__ = "MIT"
-__version__ = "0.4.20"
-__comets_compatibility__ = "2.11.1" # version of comets this was tested with (except signaling)
-__comets_compatibility_signaling__ = "2.11.1" # version signaling was tested with
+__version__ = "0.5.0"
+__comets_compatibility__ = "2.12.0" # version of comets this was tested with (except signaling)
+__comets_compatibility_signaling__ = "2.12.0" # version signaling was tested with
 
 __maintainer__ = "Djordje Bajic"
 __email__ = "[email protected]"
@@ -347,6 +347,7 @@ def run(self, delete_files : bool = True):
 
         """
         print('\nRunning COMETS simulation ...')
+        print('\nDebug Here ...')
 
         # If evolution is true, write the biomass but not the total biomass log
         if self.parameters.all_params['evolution']:
@@ -389,10 +390,10 @@ def run(self, delete_files : bool = True):
                      shell=True, stdout=sp.PIPE, stderr=sp.STDOUT)
 
         self.run_output, self.run_errors = p.communicate()
-        self.run_output = self.run_output.decode()
+        self.run_output = self.run_output.decode('ascii','ignore')
 
         if self.run_errors is not None:
-            self.run_errors = self.run_errors.decode()
+            self.run_errors = self.run_errors.decode('ascii','ignore')
         else:
             self.run_errors = "STDERR empty."
 

cometspy/layout.py

@@ -111,6 +111,9 @@ def __init__(self, input_obj : list = None):
         self.region_map = None
         self.region_parameters = {}
 
+        self.models_pairs_frictions =[]
+        self.models_substrate_frictions =[]
+
         self.__local_media_flag = False
         self.__diffusion_flag = False
         self.__refresh_flag = False
@@ -119,6 +122,8 @@ def __init__(self, input_obj : list = None):
         self.__region_flag = False
         self.__ext_rxns_flag = False
         self.__periodic_media_flag = False
+        self.__models_frictions_flag = False
+        self.__models_pairs_frictions_flag = False
 
         if input_obj is None:
             print('building empty layout model\nmodels will need to be added' +
@@ -701,7 +706,7 @@ def add_barriers(self, barriers : list):
         if len(self.barriers) > 0:
             self.__barrier_flag = True
             self.barriers = list(set(self.barriers))
-    
+
     def set_metabolite_diffusion(self, diffusion_constant : float):
         """
         sets the default diffusion constant for all metabolites
@@ -967,6 +972,44 @@ def set_specific_static_at_location(self, met : str,
             self.local_static[location] = {}
         self.local_static[location][met] = amount
 
+    def set_models_substrate_frictions(self, 
+                                        friction : list):
+        """
+        sets the values of the friction paremeters between the organisms and substrate
+
+        Parameters
+        ----------
+        model : int
+            the order of the model
+        location : tuple
+            the (x, y) location of the fixed metabolite amount. x, y are int
+        amount : float
+            the amount, in mmol, that is in each box at each time step
+
+
+        """
+        self.__models_frictions_flag = True
+        self.models_substrate_frictions=friction
+
+    def set_models_pairs_frictions(self, 
+                                        pairs_frictions : list):
+        """
+        sets the values of the friction paremeters between the organisms and substrate
+
+        Parameters
+        ----------
+        model : int
+            the order of the model
+        location : tuple
+            the (x, y) location of the fixed metabolite amount. x, y are int
+        amount : float
+            the amount, in mmol, that is in each box at each time step
+
+
+        """
+        self.__models_pairs_frictions_flag = True
+        self.models_pairs_frictions=pairs_frictions
+
     def add_typical_trace_metabolites(self, amount : float=1000.0, 
                                       static : bool =True):
         """
@@ -1055,6 +1098,8 @@ def write_layout(self, working_dir : str, to_append = ""):
         self.__write_barrier_chunk(lyt)
         self.__write_regions_chunk(lyt)
         self.__write_periodic_media_chunk(lyt)
+        self.__write_models_frictions_chunk(lyt)
+        self.__write_models_pairs_frictions_chunk(lyt)
         lyt.write(r'  //' + '\n')
 
         self.__write_initial_pop_chunk(lyt)
@@ -1300,6 +1345,27 @@ def __write_initial_pop_chunk(self, lyt):
         lyt.write(r'  //' + '\n')
         lyt.write(r'//' + '\n')
 
+    def __write_models_frictions_chunk(self, lyt):
+        """ writes the models frictions to the open
+        lyt file and adds the closing //s """
+        if self.__models_frictions_flag:
+            print('HERE')
+            lyt.write('  modelsFriction\n')
+            for i in self.models_substrate_frictions:
+                print('HERE1')
+                lyt.write('    ' + str(self.models_substrate_frictions.index(i))+ ' ' + str(i) + '\n')
+            lyt.write(r'  //' + '\n')
+
+    def __write_models_pairs_frictions_chunk(self, lyt):
+        """ writes the intermodels pairs frictions to the open
+        lyt file and adds the closing //s """
+        if self.__models_pairs_frictions_flag:
+            lyt.write('  interModelPairsFriction\n')
+            for i in range(len(self.models_pairs_frictions)):
+                for j in range(len(self.models_pairs_frictions)):
+                    lyt.write('    ' + str(i) + ' ' +str(j) + ' ' + str(self.models_pairs_frictions[i][j]) + '\n')
+            lyt.write(r'  //' + '\n')
+
     def update_models(self):
         """ updates layout properties when models are added / removed
         

cometspy/model.py

@@ -495,6 +495,18 @@ def change_hill(self, reaction, hill):
         self.reactions.loc[self.reactions[
             'REACTION_NAMES'] == reaction, 'HILL'] = hill
 
+    def change_optimizer(self, optimizer):
+        """ changes the optimizer to a specified one. 
+        
+            Parameters
+            ----------
+            
+            optimizer : str
+                the name of the optimizer
+        
+        """
+        self.optimizer = optimizer
+
     def read_cobra_model(self, path : str, randomtag : bool = False):
         """ reads a cobra model from a file and loads it into this model