take args processing into __main__

covid_ode.py

@@ -180,15 +180,13 @@ def plot_age_attack_rate(ax, sim, N, label):
     ax.plot(age_groups, attack_rate, 'o-', label=label)
 
 
-if __name__ == '__main__':
+    
+def main(configfile):
 
-    parser = optparse.OptionParser()
-    parser.add_option("--config", "-c", dest="config",
-                      help="configuration file")
-    options, args = parser.parse_args()
-    with open(options.config, 'r') as ymlfile:
+    with open(configfile, 'r') as ymlfile:
         config = yaml.load(ymlfile)
 
+    global age_groups
     K_tt, age_groups = load_age_mixing(config['data']['age_mixing_matrix_term'])
     K_hh, _ = load_age_mixing(config['data']['age_mixing_matrix_hol'])
 
@@ -232,3 +230,11 @@ if __name__ == '__main__':
     fig_uk.gca().grid(True)
     plt.show()
 
+
+if __name__ == '__main__':
+
+    parser = optparse.OptionParser()
+    parser.add_option("--config", "-c", dest="config",
+                      help="configuration file")
+    options, args = parser.parse_args()
+    main(options.config)