batch file and cleans

main.bat

@@ -1,17 +1,26 @@
-PATH C:\LS\06_SOFT\conda\miniconda3
-PATH %PATH%;C:\LS\06_SOFT\conda\miniconda3\DLLs
-PATH %PATH%;C:\LS\06_SOFT\conda\miniconda3\lib
-PATH %PATH%;C:\LS\06_SOFT\conda\miniconda3\site-packages
-PATH %PATH%;C:\LS\06_SOFT\conda\miniconda3\site-packages\win32
-PATH %PATH%;C:\LS\06_SOFT\conda\miniconda3\site-packages\win32\lib
-PATH %PATH%;C:\LS\06_SOFT\conda\miniconda3\site-packages\Pythonwin
-PATH %PATH%;C:\LS\06_SOFT\conda\miniconda3\Library
-PATH %PATH%;C:\LS\06_SOFT\conda\miniconda3\Library\bin
-PATH %PATH%;C:\LS\06_SOFT\conda\miniconda3\Lib\R
-PATH %PATH%;C:\LS\06_SOFT\conda\miniconda3\Lib\R\library
+REM Setup the paths 
+set py_dir=C:\LS\06_SOFT\conda\miniconda3\
+PATH %py_dir%
+PATH %PATH%;%py_dir%\DLLs
+PATH %PATH%;%py_dir%\lib
+PATH %PATH%;%py_dir%\site-packages
+PATH %PATH%;%py_dir%\site-packages\win32
+PATH %PATH%;%py_dir%\site-packages\win32\lib
+PATH %PATH%;%py_dir%\site-packages\Pythonwin
+PATH %PATH%;%py_dir%\Library
+PATH %PATH%;%py_dir%\Library\bin
+PATH %PATH%;%py_dir%\Lib\R
+PATH %PATH%;%py_dir%\Lib\R\library
 ECHO %PATH%
 
-C:\LS\06_SOFT\conda\miniconda3\python.exe main_UT.py 2 NoNPI 5
+
+REM define the simulation parameters
+set sim_cnt=100
+set scen_nm=NoNPI
+set threads=4
+
+REM execute the script
+%py_dir%\python.exe main.py %sim_cnt% %scen_nm% %threads%
 
 pause
 

main.py

@@ -0,0 +1,134 @@
+#===============================================================================
+# call check
+#===============================================================================
+import sys
+print('called w/ %i args: \n%s'%(len(sys.argv), sys.argv))
+
+assert len(sys.argv) >2, 'failed to call w/ enough arguments'
+
+
+#==============================================================================
+# dependency check
+#==============================================================================
+# Let users know if they're missing any of our hard dependencies
+hard_dependencies = ('pandas', 'numpy','seaborn','matplotlib','geopy','tqdm', 'geopandas','shapely','numba','rpy2')
+missing_dependencies = []
+
+for dependency in hard_dependencies:
+    try:
+        __import__(dependency)
+    except ImportError as e:
+        missing_dependencies.append("{0}: {1}".format(dependency, str(e)))
+
+if missing_dependencies:
+    raise ImportError(
+        "Unable to import required dependencies:\n" + "\n".join(missing_dependencies)
+    )
+
+del hard_dependencies, dependency, missing_dependencies
+
+#===============================================================================
+# imports
+#===============================================================================
+
+
+
+import numpy as np
+import pandas as pd
+import datetime, time, multiprocessing, itertools, sys
+import matplotlib.pyplot as plt
+
+#===============================================================================
+# setup R
+#===============================================================================
+
+import os
+os.environ["R_USER"] = "R_USER"
+os.environ["R_HOME"] = r"C:\Program Files\R\R-3.6.3" #point to your R install
+
+#setup the rinterface
+import rpy2.rinterface as rinterface
+rinterface.initr()
+
+#===============================================================================
+# from rpy2.robjects.packages import importr
+# utils = importr('utils')
+# utils.install_packages('dplyr')
+#===============================================================================
+
+
+
+#===============================================================================
+# import custom modules
+#===============================================================================
+
+import seir_fix01 as seir
+import setup_fix01 as setup
+#from COVIDScenarioPipeline.SEIR import setup
+#from COVIDScenarioPipeline.SEIR import results
+
+class WestCoastSpatialSetup():
+    """
+        Setup for West Coast at the county scale.
+    """
+    def __init__(self):
+        self.setup_name = 'utah'
+        self.folder = f'data/{self.setup_name}/'
+
+        self.data = pd.read_csv(f'{self.folder}geodata.csv')
+        self.mobility = np.loadtxt(f'{self.folder}mobility.txt')
+        self.popnodes = self.data['pop2010'].to_numpy()
+        self.nnodes = len(self.data)
+
+if __name__ == '__main__':          # For windows thread
+    """
+    call this module from command line
+    
+    argv[1]:    number of s imulations
+    argv[2]:    scenario name (see below)
+    argv[3]:    number of threads to use
+    
+    """
+
+
+
+    #===========================================================================
+    # execute
+    #===========================================================================
+    s = setup.Setup(setup_name = 'mid_utah_'+sys.argv[2],
+                    spatial_setup = WestCoastSpatialSetup(),
+                    nsim = int(sys.argv[1]),
+                    ti = datetime.date(2020, 3, 6),
+                    tf = datetime.date(2020, 10, 1),
+                    interactive = False,
+                    write_csv = True,
+                    dt = 1/4)
+
+    if (sys.argv[2] == 'NoNPI'):
+        s.script_npi = 'COVIDScenarioPipeline/data/NPI_Scenario1_None.R'
+    elif (sys.argv[2] == 'SC'):
+        s.script_npi = 'COVIDScenarioPipeline/data/NPI_Scenario2_School_Closure.R'
+    elif (sys.argv[2] == 'BI1918'):
+        s.script_npi = 'COVIDScenarioPipeline/data/NPI_Scenario3_Bootsma_1918Influenza.R'
+    elif (sys.argv[2] == 'KansasCity'):
+        s.script_npi = 'COVIDScenarioPipeline/data/NPI_Scenario4_KansasCity.R'
+    elif (sys.argv[2] == 'Wuhan'):
+        s.script_npi = 'COVIDScenarioPipeline/data/NPI_Scenario5_Wuhan.R'
+    else:
+        raise IOError('unrecognized value %s'%sys.argv[2])
+
+
+
+    print(f">>> Starting {s.nsim} model runs on {sys.argv[3]} processes")
+    print(f">>> Setup *** {s.setup_name} *** from {s.ti} to {s.tf} !")
+    print(f">>> writing to folder : {s.datadir}{s.setup_name}")
+
+
+    tic = time.time()
+
+    res_l = seir.run_parallel(s, int(sys.argv[3]))
+    print(f">>> Runs done in {time.time()-tic} seconds...")
+
+
+
+

main_319PM.py → main_test.py

@@ -61,7 +61,7 @@
 import seir_fix01 as seir
 import setup_fix01 as setup
 #from COVIDScenarioPipeline.SEIR import setup
-from COVIDScenarioPipeline.SEIR import results
+#from COVIDScenarioPipeline.SEIR import results
 
 class WestCoastSpatialSetup():
     """

seir_fix01.py

@@ -31,6 +31,9 @@
 
 
 def onerun_SEIR(s, uid):
+    """
+    main function for simulating
+    """
     scipy.random.seed()
     #p = setup.COVID19Parameters(s)
     r_assign('ti_str', str(s.ti))
@@ -90,7 +93,9 @@ def onerun_SEIR(s, uid):
         out_df['comp'].replace(cumI,  'cumI', inplace=True)
         out_df['comp'].replace(ncomp, 'diffI', inplace=True)
         str(uuid.uuid4())[:2]
-        out_df.to_csv(f"{s.datadir}{s.timestamp}_{s.setup_name}_{str(uuid.uuid4())}.csv", index='time', index_label='time')
+        ofp = f"{s.datadir}{s.timestamp}_{s.setup_name}_{str(uuid.uuid4())}.csv"
+        out_df.to_csv(ofp, index='time', index_label='time')
+        print('    saving %i entries to %s'%(len(out_df), ofp))
 
     return 1