Added in-code documentation.

run.py

@@ -19,18 +19,18 @@
 
     # Instantiate the parser
     parser = argparse.ArgumentParser()
-    parser.add_argument('--location', action="store", default="brent")
-    parser.add_argument('-m','--measures_yml', action="store", default="measures_uk")
-    parser.add_argument('-d','--disease_yml', action="store", default="disease_covid19")
-    parser.add_argument('-v','--vaccinations_yml', action="store", default="vaccinations")
-    parser.add_argument('--output_dir', action="store", default=".")
-    parser.add_argument('--data_dir', action="store", default="covid_data")
-    parser.add_argument('-s','--starting_infections', action="store", default="500")
-    parser.add_argument('--start_date', action="store", default="1/3/2020")
+    parser.add_argument('--location', action="store", default="brent", help="Name of location to load.")
+    parser.add_argument('-m','--measures_yml', action="store", default="measures_uk", help="Input YML file containing interventions.")
+    parser.add_argument('-d','--disease_yml', action="store", default="disease_covid19", help="Input YML file containing disease specification.")
+    parser.add_argument('-v','--vaccinations_yml', action="store", default="vaccinations", help="Input YML file containing vaccine strategy specification.")
+    parser.add_argument('--output_dir', action="store", default=".", help="directory to write output to."))
+    parser.add_argument('--data_dir', action="store", default="covid_data", help="subdirectory containing simulation input data.")
+    parser.add_argument('-s','--starting_infections', action="store", default="500", help="Starting # of infections. Values below 1.0 are interpreted as a ratio of population.")
+    parser.add_argument('--start_date', action="store", default="1/3/2020", help="Start date, format = %d/%m/%Y")
     parser.add_argument('-q', '--quicktest', action="store_true", help="set house_ratio to 100 to do quicker (but less accurate) runs for populous regions.")
     parser.add_argument('-g', '--generic_outfile', action="store_true", help="Write main output to out.csv instead of a scenario-specific named file.")
     parser.add_argument('--dbg', action="store_true", help="Write additional outputs to help debugging")
-    parser.add_argument('-t', '--simulation_period', action="store",type=int, default='-1')
+    parser.add_argument('-t', '--simulation_period', action="store",type=int, default='-1', help="Simulation duration [days].")
     args = parser.parse_args()
     print(args)