batch runs setup

main.bat

@@ -1,23 +1,29 @@
 REM Setup the paths 
-set py_dir=C:\LS\06_SOFT\conda\miniconda3\
+@ECHO off
+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%\lib\site-packages
+PATH %PATH%;%py_dir%\lib\site-packages\win32
+PATH %PATH%;%py_dir%\lib\site-packages\win32\lib
+PATH %PATH%;%py_dir%\lib\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%
 
+REM set R environment variables
+set R_USER=MyName
+set R_HOME=C:\Program Files\R\R-3.6.3
 
+
+@ECHO on
 REM define the simulation parameters
-set sim_cnt=100
+set sim_cnt=2
 set scen_nm=NoNPI
-set threads=4
+set threads=2
 
 REM execute the script
 %py_dir%\python.exe main.py %sim_cnt% %scen_nm% %threads%

main.py

@@ -1,17 +1,18 @@
-#===============================================================================
-# call check
-#===============================================================================
-import sys
-print('called w/ %i args: \n%s'%(len(sys.argv), sys.argv))
+"""
+call this module from command line
+
+main runner for Utah SEIR model
+
+"""
+
 
-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')
+hard_dependencies = ('pandas', 'numpy','seaborn','geopy','tqdm', 'geopandas','shapely','numba','rpy2')
 missing_dependencies = []
 
 for dependency in hard_dependencies:
@@ -34,17 +35,21 @@
 
 
 import numpy as np
+
+"""supress FutureWarning: from_items is deprecated"""
+import warnings
+warnings.simplefilter(action='ignore', category=FutureWarning)
+
+
 import pandas as pd
-import datetime, time, multiprocessing, itertools, sys
-import matplotlib.pyplot as plt
+import datetime, time, multiprocessing, itertools, sys, os
+#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
@@ -79,56 +84,142 @@ def __init__(self):
         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
+
+
+
+def run(pars, #parameter files
+        #directory of scenario files
+        scen_dir = r'C:\LS\03_TOOLS\_git\COVID_01\scenarios',
+
+        #map to scenario files
+        scen_d = {
+        'NoNPI':'NPI_Scenario1_None.R',
+        'BI1918':'NPI_Scenario2_Bootsma_1918Influenza.R',
+        'SouthKorea':'NPI_Scenario3_SouthKorea.R',
+        'Reduced':'NPI_Scenario4_ReducedGamma.R',       
+        }
+        ):
+
     """
-    call this module from command line
+    convience fucntion for running simulations
+    
+        
     
     argv[1]:    number of s imulations
     argv[2]:    scenario name (see below)
     argv[3]:    number of threads to use
     
+    
     """
+
+
+
+    #===========================================================================
+    # precheck 
+    #===========================================================================
+    assert len(pars)==4, 'unexpected inputs count'
+    print('pars: \n%s'%pars)
+
+    #check the R Environment variables
+    assert 'R_USER' in os.environ
+    assert 'R_HOME' in os.environ
+
+    #print('R_USER=%s \nR_HOME=%s'%(os.getenv('R_USER'), os.getenv('R_HOME')))
 
-
-
+
+
+
+
     #===========================================================================
-    # execute
+    # setup
     #===========================================================================
-    s = setup.Setup(setup_name = 'mid_utah_'+sys.argv[2],
+    s = setup.Setup(setup_name = 'mid_utah_'+pars[2],
                     spatial_setup = WestCoastSpatialSetup(),
-                    nsim = int(sys.argv[1]),
+                    nsim = int(pars[1]),
                     ti = datetime.date(2020, 3, 6),
                     tf = datetime.date(2020, 10, 1),
                     interactive = False,
                     write_csv = True,
                     dt = 1/4)
+
+    #===========================================================================
+    # set the scenario parmaters
+    #===========================================================================
 
-    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])
 
+
+    assert pars[2] in scen_d, 'unrecognized scenario: %s'%pars[2]
+
+    rfp = os.path.join(scen_dir, scen_d[pars[2]])
+    assert os.path.exists(rfp)
+
+    s.script_npi = rfp
+
+    print('set script_npi=%s'%s.script_npi)
 
+    #===========================================================================
+    # execute
+    #===========================================================================
 
-    print(f">>> Starting {s.nsim} model runs on {sys.argv[3]} processes")
+    print()
+    print()
+    print(f">>> Starting {s.nsim} model runs on {pars[3]} processes")
     print(f">>> Setup *** {s.setup_name} *** from {s.ti} to {s.tf} !")
     print(f">>> writing to folder : {s.datadir}{s.setup_name}")
-
-
+    print()
+    print()
+
     tic = time.time()
 
-    res_l = seir.run_parallel(s, int(sys.argv[3]))
+    res_l = seir.run_parallel(s, int(pars[3]))
     print(f">>> Runs done in {time.time()-tic} seconds...")
 
 
+
+if __name__ == '__main__':          # For windows thread
+
+
+
+
+
+    if len(sys.argv)<=1:
+
+        import os
+        #setup the R environment
+        os.environ["R_USER"] = "R_USER"
+        os.environ["R_HOME"] = r"C:\Program Files\R\R-3.6.3" #point to your R install
+
+
+        for indxr, sname in enumerate([
+            'NoNPI', 
+            'SouthKorea',  
+            'Reduced', 
+            #'BI1918'
+            ]):
+            print('\n \nrun %i: %s \n \n'%(indxr, sname))
+
+            try:
+                run({
+                0:'placeholder',
+                1: 1000, #number of s imulations
+                2: sname,
+                3: 5, #number of threadas
+                })
+            except Exception as e:
+                print('FAILED on %s w/ \n%s'%(sname, e))
+    else:
+
+
+        print('called w/ %i args: \n%s'%(len(sys.argv), sys.argv))
+
+        assert len(sys.argv) >2, 'failed to call w/ enough arguments'
+
+        run(sys.argv)
+
+    print('finished')
+
+
+
+
 
 

main_all.bat

@@ -0,0 +1,48 @@
+REM Setup the paths 
+@ECHO off
+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%\lib\site-packages
+PATH %PATH%;%py_dir%\lib\site-packages\win32
+PATH %PATH%;%py_dir%\lib\site-packages\win32\lib
+PATH %PATH%;%py_dir%\lib\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%
+
+REM set R environment variables
+set R_USER=MyName
+set R_HOME=C:\Program Files\R\R-3.6.3
+
+
+@ECHO on
+REM define the simulation parameters
+set sim_cnt=2
+
+set threads=2
+
+REM execute the script 1
+set scen_nm=NoNPI
+%py_dir%\python.exe main.py %sim_cnt% %scen_nm% %threads%
+
+
+REM execute the script 1
+set scen_nm=BI1918
+%py_dir%\python.exe main.py %sim_cnt% %scen_nm% %threads%
+
+
+REM execute the script 1
+set scen_nm=SouthKorea
+%py_dir%\python.exe main.py %sim_cnt% %scen_nm% %threads%
+
+
+REM execute the script 1
+set scen_nm=Reduced
+%py_dir%\python.exe main.py %sim_cnt% %scen_nm% %threads%
+
+pause
+

main_test.py

@@ -40,7 +40,7 @@
 
 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
+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
@@ -92,7 +92,7 @@ def __init__(self):
 
 
     #===========================================================================
-    # execute
+    # setup
     #===========================================================================
     s = setup.Setup(setup_name = 'mid_utah_'+pars[2],
                     spatial_setup = WestCoastSpatialSetup(),
@@ -103,35 +103,30 @@ def __init__(self):
                     write_csv = True,
                     dt = 1/4)
 
-
+    #===========================================================================
+    # set the scenario parmaters
+    #===========================================================================
     scen_d = {
         'NoNPI':'NPI_Scenario1_None.R',
         'BI1918':'NPI_Scenario2_Bootsma_1918Influenza.R',
         'SouthKorea':'NPI_Scenario3_SouthKorea.R',
-        'ReducedGamma':'NPI_Scenario4_ReducedGamma.R',       
+        'Reduced':'NPI_Scenario4_ReducedGamma.R',       
         }
 
 
-
-
-
+    assert pars[2] in scen_d, 'unrecognized scenario: %s'%pars[2]
+
+    rfp = os.path.join(scen_dir, scen_d[pars[2]])
+    assert os.path.exists(rfp)
+
+    s.script_npi = rfp
+
+    print('set script_npi=%s'%s.script_npi)
 
     #===========================================================================
-    # if (pars[2] == 'NoNPI'):
-    #     s.script_npi = 'COVIDScenarioPipeline/data/NPI_Scenario1_None.R'
-    # if (pars[2] == 'SC'):
-    #     s.script_npi = 'COVIDScenarioPipeline/data/NPI_Scenario2_School_Closure.R'
-    # if (pars[2] == 'BI1918'):
-    #     s.script_npi = 'COVIDScenarioPipeline/data/NPI_Scenario3_Bootsma_1918Influenza.R'
-    # if (pars[2] == 'KansasCity'):
-    #     s.script_npi = 'COVIDScenarioPipeline/data/NPI_Scenario4_KansasCity.R'
-    # if (pars[2] == 'Wuhan'):
-    #     s.script_npi = 'COVIDScenarioPipeline/data/NPI_Scenario5_Wuhan.R'
+    # execute
     #===========================================================================
-
-    #s.script_import = 'COVIDScenarioPipeline/R/distribute_airport_importations_to_counties.R'
 
-    #s.set_filter(np.loadtxt('data/west-coast-AZ-NV/filtergithub.txt'))
     print()
     print()
     print(f">>> Starting {s.nsim} model runs on {pars[3]} processes")