Fixed CCMnet_py new usage

modules/ContactNetworkGenerator_CCMnetPy.py

@@ -8,7 +8,8 @@
 import FAVITES_GlobalContext as GC
 from gzip import open as gopen
 from os import chdir
-from os.path import expanduser
+from os.path import abspath, expanduser, isfile
+import json
 import math
 import random
 
@@ -611,6 +612,12 @@ def init():
             assert False, "Error loading NumPy. Install with: pip3 install numpy"
 
         # check user args
+        if hasattr(GC, "cn_config_file"):
+            assert isfile(GC.cn_config_file), "CCMnet_py config file not found: %s" % GC.cn_config_file
+            GC.cn_config_file = abspath(expanduser(GC.cn_config_file))
+        if hasattr(GC, "cn_config_dict"):
+            assert 'G' in GC.cn_config_dict, "CCMnet_py config dict must have 'G' key"
+            GC.cn_config_dict['G'] = abspath(expanduser(GC.cn_config_dict['G']))
         if hasattr(GC, "num_cn_nodes"):
             assert isinstance(GC.num_cn_nodes, int), "num_cn_nodes must be an integer"
             assert GC.num_cn_nodes >= 2, "Contact network must have at least 2 nodes"
@@ -651,8 +658,8 @@ def init():
             assert GC.cn_mcmc_burnin > 0, "cn_mcmc_burnin must be a positive integer"
 
     def get_edge_list():
-        if hasattr(GC, "cn_params_dict"):
-            cn = CCMnet_constr_py(**GC.cn_params_dict)
+        if hasattr(GC, "cn_config_dict"):
+            cn = CCMnet_constr_py(**GC.cn_config_dict)
         elif hasattr(GC, "cn_config_file"):
             cn = CCMnet_constr_py(config_file=GC.cn_config_file)
         else:

modules/FAVITES_ModuleFactory.py

@@ -37,8 +37,7 @@ def read_config(config, verbose):
         modules[module]() # instantiate to force check of abstract methods
         for req in sorted(module_implementations[module][config[module]]['req']):
             assert req in config, "Parameter %r of %s_%s module is not in the configuration file!" % (req, module, config[module])
-            reqs[req] = config[req]
-    GC.init(reqs)
+    GC.init(config)
     GC.VERBOSE = verbose
 
 def init(mod_dir):
@@ -85,4 +84,4 @@ def init(mod_dir):
     This function is just used for testing purposes. It has no actual function
     in the simulator tool.
     '''
-    init()
+    init()

modules/FAVITES_ModuleList.json

@@ -47,7 +47,7 @@
         },
 
         "CCMnetPy": {
-            "req": ["num_cn_nodes", "cn_network_stats", "cn_prob_dists", "cn_prob_dist_params", "cn_covariate_pattern", "cn_mcmc_burnin"]
+            "req": []
         },
 
         "Communities": {

run_favites.py

@@ -10,6 +10,10 @@
 from os import environ,getcwd
 from os.path import abspath,expanduser,isdir
 
+# for parsing booleans in JSON
+true = True
+false = False
+
 def parseArgs():
     '''
     Parse user arguments. As a developer, if you create any of your own module