v1.2.1, check changelog.md .

README.md

@@ -718,8 +718,8 @@ _Keyword arguments:_
 - **kwargs -- setup parameters and values, which may include the following:
 - num_loci -- length of each pathogen genome string (int > 0)
 - possible_alleles -- set of possible characters in all genome string, or
-    at each position in genome string (String or list of Strings with
-    num_loci elements)
+    at each position in genome string; to specify lists in parameter files, use
+    prefix `#LIST:` (String or list of Strings with num_loci elements)
 - fitnessHost -- function that evaluates relative fitness in head-to-head
     competition for different genomes within the same host
     (function object, takes a String argument and returns a number >= 0)
@@ -860,28 +860,28 @@ _Keyword arguments:_
 #### saveSetup
 
 ```python
-saveSetup(setup_name, save_to_file)
+saveSetup(setup_id, save_to_file)
 ```
 
 
 Saves Setup parameters to given file location as a CSV file.
 Functions (e.g. fitness functions) cannot be saved in this format.
 
 _Arguments:_
-- setup_name -- name of setup used as a key in setups dictionary
+- setup_id -- name of setup used as a key in setups dictionary
 - save_to_file -- file path and name to save  parameters under (String)
 
 #### loadSetup
 
 ```python
-loadSetup(setup_name, file, preset=None)
+loadSetup(setup_id, file, preset=None)
 ```
 
 
 Loads Setup parameters from CSV file at given location.
 
 _Arguments:_
-- setup_name -- name of setup to be used as a key in setups dictionary
+- setup_id -- name of setup to be used as a key in setups dictionary
 - file -- file path to CSV file with parameters (String)
 
 _Keyword arguments:_
@@ -1541,7 +1541,7 @@ _Returns:_
 #### newPopulation
 
 ```python
-newPopulation(id, setup_name, num_hosts=100, num_vectors=100)
+newPopulation(id, setup_id, num_hosts=100, num_vectors=100)
 ```
 
 
@@ -1551,7 +1551,7 @@ If population ID is already in use, appends _2 to it
 
 _Arguments:_
 - id -- unique identifier for this population in the model (String)
-- setup_name -- setup object with parameters for this population (Setup)
+- setup_id -- setup object with parameters for this population (Setup)
 
 _Keyword Arguments:_
 - num_hosts -- number of hosts to initialize population with (default 100;
@@ -1648,7 +1648,7 @@ _Arguments:_
 
 ```python
 createInterconnectedPopulations(
-      num_populations, id_prefix, setup_name,
+      num_populations, id_prefix, setup_id,
       host_migration_rate=0, vector_migration_rate=0,
       host_host_contact_rate=0,
       host_vector_contact_rate=0, vector_host_contact_rate=0,
@@ -1667,7 +1667,7 @@ _Arguments:_
 - num_populations -- number of populations to be created (int)
 - id_prefix -- prefix for IDs to be used for this population in the model,
     (String)
-- setup_name -- setup object with parameters for all populations (Setup)
+- setup_id -- setup object with parameters for all populations (Setup)
 
 _Keyword arguments:_
 - host_migration_rate -- host migration rate between populations;

changelog.md

@@ -1,6 +1,15 @@
 
 # Opqua Changelog
 
+## v1.2.1
+## 1 Feb 2024
+Fixed some bugs in function importing (or lack thereof; recommended practice is 
+to declare function parameters as Python code in same scope as simulation and
+pass function names as arguments to `newSetup()` or `loadSetup()`).
+
+Also corrected small bug in which `importlib_resources` wasn't being imported in
+`Setup` class.
+
 ## v1.2.0
 ## 1 Feb 2024
 Woke up and decided yesterday's changes were significant enough to warrant a

opqua/internal/setup.py

@@ -2,9 +2,10 @@
 """Contains class Setup."""
 
 # import importlib.util
-# import importlib_resources
+import importlib_resources
 import sys
 import io
+import ast
 import pandas as pd
 
 class Setup(object):
@@ -65,6 +66,13 @@ def setParameters(self,**kwargs):
             setattr( self, parameter, value )
 
         self.num_loci = int(self.num_loci)
+        if self.population_threshold <= 0 and self.selection_threshold <= 0:
+            self.population_threshold = 0
+            self.selection_threshold = 100 # arbitrarily large
+        if self.population_threshold <= 0:
+            self.population_threshold = 1 / self.selection_threshold
+        elif self.selection_threshold <= 0:
+            self.selection_threshold = 1 / self.population_threshold
 
         if isinstance(self.possible_alleles, list):
             self.possible_alleles = self.possible_alleles
@@ -89,6 +97,10 @@ def save(self,save_to_file):
                     # checks if parameter is function
                 out = out + parameter + ',#FUNCTION:'+parameter+'Function\n'
                 function_counter += 1
+            elif isinstance( getattr(self,parameter), list ):
+                out = out + parameter + ',#LIST:' + str(
+                    getattr(self,parameter)
+                    )+'\n'
             else:
                 out = out + parameter + ',' + str( getattr(self,parameter) )+'\n'
 
@@ -114,6 +126,9 @@ def load(self,file,preset=None,**kwargs):
             (String, default None)
         **kwargs -- setup parameters and values
         """
+        self.population_threshold = -1
+        self.selection_threshold = -1
+
         if preset is None:
             df = pd.read_csv(file)
         else:
@@ -133,15 +148,21 @@ def load(self,file,preset=None,**kwargs):
         #     spec.loader.exec_module(function_params)
 
         for i,row in df.iterrows():
-            if '#FUNCTION:' in str(row['Value']): # checks if parameter is function
+            if '#FUNCTION:' in str( row['Value'] ):
+                    # checks if parameter is function
                 function_name = row['Value'][len('#FUNCTION'):].strip()
-                if ( #function_file_path is None or
-                        not hasattr(function_params, function_name) ):
+                # if ( function_file_path is None or
+                #         not hasattr(function_params, function_name) ):
+                if len( str( row['Value'] ).strip() ) == len('#FUNCTION:'):
                     setattr( self, row['Parameter'], lambda g:1 )
                 else:
                     setattr( self, row['Parameter'], getattr(
                             function_params, function_name
                             ) )
+            elif '#LIST:' in str(row['Value']):
+                setattr( self, row['Parameter'], ast.literal_eval(
+                    row['Value'][ len('#LIST:'): ]
+                    ) )
             elif not isinstance(row['Value'], str) and pd.isna(row['Value']):
                 setattr( self, row['Parameter'], None )
             elif isinstance(row['Value'], str) and (

opqua/model.py

@@ -215,35 +215,35 @@ def newSetup(self, name, preset=None, **kwargs):
         elif len(kwargs) > 0:
             self.setups[name].setParameters(**kwargs)
 
-    def saveSetup(self, setup_name, save_to_file):
+    def saveSetup(self, setup_id, save_to_file):
         """
         Saves Setup parameters to given file location as a CSV file.
 
         Functions (e.g. fitness functions) cannot be saved in this format.
 
         Arguments:
-        setup_name -- name of setup used as a key in setups dictionary
+        setup_id -- name of setup used as a key in setups dictionary
         save_to_file -- file path and name to save  parameters under (String)
         """
-        self.setups[setup_name].save(save_to_file)
+        self.setups[setup_id].save(save_to_file)
 
-    def loadSetup(self, setup_name, file, preset=None, **kwargs):
+    def loadSetup(self, setup_id, file, preset=None, **kwargs):
         """
         Loads Setup parameters from CSV file at given location.
 
         Arguments:
-        setup_name -- name of setup to be used as a key in setups dictionary
+        setup_id -- name of setup to be used as a key in setups dictionary
         file -- file path to CSV file with parameters (String)
 
         Keyword arguments:
         preset -- if using preset parameters, 'host-host' or 'vector-borne'
             (String, default None)
         **kwargs -- setup parameters and values
         """
-        if setup_name not in self.setups.keys():
-            self.setups[setup_name] = Setup()
+        if setup_id not in self.setups.keys():
+            self.setups[setup_id] = Setup()
 
-        self.setups[setup_name].load(file, preset=preset, **kwargs)
+        self.setups[setup_id].load(file, preset=preset, **kwargs)
 
     def newIntervention(self, time, method_name, args):
         """Create a new intervention to be carried out at a specific time.
@@ -1116,14 +1116,14 @@ def getCompositionData(
 
     ### Model interventions: ###
 
-    def newPopulation(self, id, setup_name, num_hosts=0, num_vectors=0):
+    def newPopulation(self, id, setup_id, num_hosts=0, num_vectors=0):
         """Create a new Population object with setup parameters.
 
         If population ID is already in use, appends _2 to it
 
         Arguments:
         id -- unique identifier for this population in the model (String)
-        setup_name -- setup object with parameters for this population (Setup)
+        setup_id -- setup object with parameters for this population (Setup)
 
         Keyword arguments:
         num_hosts -- number of hosts to initialize population with (default 100;
@@ -1136,7 +1136,7 @@ def newPopulation(self, id, setup_name, num_hosts=0, num_vectors=0):
             id = id+'_2'
 
         self.populations[id] = Population(
-            self, id, self.setups[setup_name], num_hosts, num_vectors
+            self, id, self.setups[setup_id], num_hosts, num_vectors
             )
 
         for p in self.populations:
@@ -1251,7 +1251,7 @@ def linkPopulationsVectorHostContact(self, pop1_id, pop2_id, rate):
             )
 
     def createInterconnectedPopulations(
-            self, num_populations, id_prefix, setup_name,
+            self, num_populations, id_prefix, setup_id,
             host_migration_rate=0, vector_migration_rate=0,
             host_host_contact_rate=0,
             host_vector_contact_rate=0, vector_host_contact_rate=0,
@@ -1267,7 +1267,7 @@ def createInterconnectedPopulations(
         num_populations -- number of populations to be created (int)
         id_prefix -- prefix for IDs to be used for this population in the model,
             (String)
-        setup_name -- setup object with parameters for all populations (Setup)
+        setup_id -- setup object with parameters for all populations (Setup)
 
         Keyword arguments:
         host_migration_rate -- host migration rate between populations;
@@ -1288,7 +1288,7 @@ def createInterconnectedPopulations(
 
         new_pops = [
             Population(
-                self, str(id_prefix) + str(i), self.setups[setup_name],
+                self, str(id_prefix) + str(i), self.setups[setup_id],
                 num_hosts, num_vectors
                 ) for i in range(num_populations)
             ]

opqua/parameters/host-host.csv

@@ -2,28 +2,28 @@ Parameter,Value
 id,my_setup
 num_loci,10
 possible_alleles,ATCG
-fitnessHost,#FUNCTION:fitnessHostFunction
-contactHost,#FUNCTION:contactHostFunction
-receiveContactHost,#FUNCTION:receiveContactHostFunction
-mortalityHost,#FUNCTION:mortalityHostFunction
-natalityHost,#FUNCTION:natalityHostFunction
-recoveryHost,#FUNCTION:recoveryHostFunction
-migrationHost,#FUNCTION:migrationHostFunction
-populationContactHost,#FUNCTION:populationContactHostFunction
-receivePopulationContactHost,#FUNCTION:receivePopulationContactHostFunction
-mutationHost,#FUNCTION:mutationHostFunction
-recombinationHost,#FUNCTION:recombinationHostFunction
-fitnessVector,#FUNCTION:fitnessVectorFunction
-contactVector,#FUNCTION:contactVectorFunction
-receiveContactVector,#FUNCTION:receiveContactVectorFunction
-mortalityVector,#FUNCTION:mortalityVectorFunction
-natalityVector,#FUNCTION:natalityVectorFunction
-recoveryVector,#FUNCTION:recoveryVectorFunction
-migrationVector,#FUNCTION:migrationVectorFunction
-populationContactVector,#FUNCTION:populationContactVectorFunction
-receivePopulationContactVector,#FUNCTION:receivePopulationContactVectorFunction
-mutationVector,#FUNCTION:mutationVectorFunction
-recombinationVector,#FUNCTION:recombinationVectorFunction
+fitnessHost,#FUNCTION:
+contactHost,#FUNCTION:
+receiveContactHost,#FUNCTION:
+mortalityHost,#FUNCTION:
+natalityHost,#FUNCTION:
+recoveryHost,#FUNCTION:
+migrationHost,#FUNCTION:
+populationContactHost,#FUNCTION:
+receivePopulationContactHost,#FUNCTION:
+mutationHost,#FUNCTION:
+recombinationHost,#FUNCTION:
+fitnessVector,#FUNCTION:
+contactVector,#FUNCTION:
+receiveContactVector,#FUNCTION:
+mortalityVector,#FUNCTION:
+natalityVector,#FUNCTION:
+recoveryVector,#FUNCTION:
+migrationVector,#FUNCTION:
+populationContactVector,#FUNCTION:
+receivePopulationContactVector,#FUNCTION:
+mutationVector,#FUNCTION:
+recombinationVector,#FUNCTION:
 contact_rate_host_vector,0
 transmission_efficiency_host_vector,0
 transmission_efficiency_vector_host,0

opqua/parameters/vector-borne.csv

@@ -2,28 +2,28 @@ Parameter,Value
 id,my_setup
 num_loci,10
 possible_alleles,ATCG
-fitnessHost,#FUNCTION:fitnessHostFunction
-contactHost,#FUNCTION:contactHostFunction
-receiveContactHost,#FUNCTION:receiveContactHostFunction
-mortalityHost,#FUNCTION:mortalityHostFunction
-natalityHost,#FUNCTION:natalityHostFunction
-recoveryHost,#FUNCTION:recoveryHostFunction
-migrationHost,#FUNCTION:migrationHostFunction
-populationContactHost,#FUNCTION:populationContactHostFunction
-receivePopulationContactHost,#FUNCTION:receivePopulationContactHostFunction
-mutationHost,#FUNCTION:mutationHostFunction
-recombinationHost,#FUNCTION:recombinationHostFunction
-fitnessVector,#FUNCTION:fitnessVectorFunction
-contactVector,#FUNCTION:contactVectorFunction
-receiveContactVector,#FUNCTION:receiveContactVectorFunction
-mortalityVector,#FUNCTION:mortalityVectorFunction
-natalityVector,#FUNCTION:natalityVectorFunction
-recoveryVector,#FUNCTION:recoveryVectorFunction
-migrationVector,#FUNCTION:migrationVectorFunction
-populationContactVector,#FUNCTION:populationContactVectorFunction
-receivePopulationContactVector,#FUNCTION:receivePopulationContactVectorFunction
-mutationVector,#FUNCTION:mutationVectorFunction
-recombinationVector,#FUNCTION:recombinationVectorFunction
+fitnessHost,#FUNCTION:
+contactHost,#FUNCTION:
+receiveContactHost,#FUNCTION:
+mortalityHost,#FUNCTION:
+natalityHost,#FUNCTION:
+recoveryHost,#FUNCTION:
+migrationHost,#FUNCTION:
+populationContactHost,#FUNCTION:
+receivePopulationContactHost,#FUNCTION:
+mutationHost,#FUNCTION:
+recombinationHost,#FUNCTION:
+fitnessVector,#FUNCTION:
+contactVector,#FUNCTION:
+receiveContactVector,#FUNCTION:
+mortalityVector,#FUNCTION:
+natalityVector,#FUNCTION:
+recoveryVector,#FUNCTION:
+migrationVector,#FUNCTION:
+populationContactVector,#FUNCTION:
+receivePopulationContactVector,#FUNCTION:
+mutationVector,#FUNCTION:
+recombinationVector,#FUNCTION:
 contact_rate_host_vector,0.2
 transmission_efficiency_host_vector,1
 transmission_efficiency_vector_host,1

setup.py

@@ -9,7 +9,7 @@
 
 setup(
     name='opqua',
-    version='v1.2.0',
+    version='v1.2.1',
     description='An epidemiological modeling framework for population ' \
         + 'genetics and evolution.',
     long_description='Opqua is an epidemiological modeling framework for ' \
@@ -22,7 +22,7 @@
         + 'github.com/pablocarderam/opqua for more information.',
     description_file='README.md',
     url='https://github.com/pablocarderam/opqua',
-    download_url='https://github.com/pablocarderam/opqua/archive/v1.2.0.tar.gz',
+    download_url='https://github.com/pablocarderam/opqua/archive/v1.2.1.tar.gz',
     author='Pablo Cardenas',
     author_email='pablocarderam@gmail.com',
     keywords=['epidemiology','evolution','biology'],