Merge pull request #68 from respec/IOAbstraction

IO Abstraction

HSP2/ADCALC.py

@@ -18,7 +18,7 @@
 '''
 ERRMSG = []
 
-def adcalc(store, siminfo, uci, ts):
+def adcalc(io_manager, siminfo, uci, ts):
 	'''Prepare to simulate advection of fully entrained constituents'''
 
 	errorsV = zeros(len(ERRMSG), dtype=int)

HSP2/ATEMP.py

@@ -6,15 +6,17 @@
 
 from numba import njit
 from numpy import empty, zeros, int64
-from HSP2.utilities import hoursval, make_numba_dict
+from HSP2.utilities import hoursval, make_numba_dict, LAPSE
+
+from HSP2IO.protocols import SupportsReadTS, Category
 
 ERRMSGS = ()
 
 
-def atemp(store, siminfo, uci, ts):
+def atemp(io_manager:SupportsReadTS, siminfo, uci, ts):
     ''' high level driver for air temperature module'''
 
-    ts['LAPSE'] = hoursval(siminfo, store['TIMESERIES/LAPSE_Table'], lapselike=True)
+    ts['LAPSE'] = hoursval(siminfo, LAPSE, lapselike=True)
 
     ui = make_numba_dict(uci)   # Note: all values coverted to float automatically
     ui['k']      = siminfo['delt']  * 0.000833        # convert to in/timestep

HSP2/CONS.py

@@ -29,7 +29,7 @@
 
 ERRMSG = []
 
-def cons(store, siminfo, uci, ts):
+def cons(io_manager, siminfo, uci, ts):
 	''' Simulate behavior of conservative constituents; calculate concentration 
 	of conservative constituents after advection'''
 

HSP2/COPY.py

@@ -2,6 +2,8 @@
 import pandas as pd
 from typing import List, Dict
 
+from HSP2IO.protocols import SupportsReadTS
+
 class Copy():
     """
     Partial implementation of the COPY module. 
@@ -10,12 +12,12 @@ class Copy():
     This functionality is not currently implemented, presently only loading from EXT SOURCES
     """
 
-    def __init__(self, store: pd.HDFStore, sim_info: Dict, ext_sources: List) -> None:
+    def __init__(self, io:SupportsReadTS, sim_info: Dict, ext_sources: List) -> None:
         self._ts = {}
         self._ts['MEAN'] = {}
         self._ts['POINT'] = {}
 
-        ts = get_timeseries(store, ext_sources, sim_info)
+        ts = get_timeseries(io, ext_sources, sim_info)
         for source in ext_sources:
             themn = source.TMEMN
             themsb = source.TMEMSB

HSP2/GENER.py

@@ -1,9 +1,6 @@
-from numba import njit
 import numpy as np
 import pandas as pd
-from typing import Dict, List
-
-from HSP2.utilities import get_timeseries
+from typing import Dict
 
 class Gener():
     """

HSP2/GQUAL.py

@@ -22,7 +22,7 @@
 		  'GQUAL: the value of sdfg is 1, but timeseries SSED4 is not available as input',                #ERRMSG10
 		  'GQUAL: the value of phytfg is 1, but timeseries PHYTO is not available as input')              #ERRMSG11
 
-def gqual(store, siminfo, uci, ts):
+def gqual(io_manager, siminfo, uci, ts):
 	''' Simulate the behavior of a generalized quality constituent'''
 
 	errors = zeros(len(ERRMSGS)).astype(int64)

HSP2/HTRCH.py

@@ -36,7 +36,7 @@
 
 ERRMSGS =('HTRCH: Water temperature is above 66 C (150 F) -- In most cases, this indicates an instability in advection','')     #ERRMSG0
 
-def htrch(store, siminfo, uci, ts):
+def htrch(io_manager, siminfo, uci, ts):
 	'''Simulate heat exchange and water temperature'''
 
 	advectData = uci['advectData']

HSP2/HYDR.py

@@ -30,7 +30,7 @@
 MAXLOOPS  = 100     # newton method exit tolerance
 
 
-def hydr(store, siminfo, uci, ts):
+def hydr(io_manager, siminfo, uci, ts, ftables):
     ''' find the state of the reach/reservoir at the end of the time interval
     and the outflows during the interval
 
@@ -95,7 +95,8 @@ def hydr(store, siminfo, uci, ts):
     ts['CONVF'] = initm(siminfo, uci, 'VCONFG', 'MONTHLY_CONVF', 1.0)
 
     # extract key columns of specified FTable for faster access (1d vs. 2d)
-    rchtab = store[f"FTABLES/{uci['PARAMETERS']['FTBUCI']}"]
+    rchtab = ftables[f"{uci['PARAMETERS']['FTBUCI']}"]
+    #rchtab = store[f"FTABLES/{uci['PARAMETERS']['FTBUCI']}"]
     ts['volumeFT'] = rchtab['Volume'].to_numpy() * VFACT
     ts['depthFT']  = rchtab['Depth'].to_numpy()
     ts['sareaFT']  = rchtab['Area'].to_numpy()   * AFACT

HSP2/IQUAL.py

@@ -21,7 +21,7 @@
 
 ERRMSGS =('IQUAL: A constituent must be associated with overland flow in order to receive atmospheric deposition inputs','')     #ERRMSG0
 
-def iqual(store, siminfo, uci, ts):
+def iqual(io_manager, siminfo, uci, ts):
 	''' Simulate washoff of quality constituents (other than solids, Heat, dox, and co2)
 	using simple relationships with solids And/or water yield'''
 

HSP2/IWATER.py

@@ -16,7 +16,7 @@
   )
 
 
-def iwater(store, siminfo, uci, ts):
+def iwater(io_manager, siminfo, uci, ts):
     ''' Driver for IMPLND IWATER code. CALL: iwater(store, general, ui, ts)
        store is the Pandas/PyTable open store
        general is a dictionary with simulation info (OP_SEQUENCE for example)

HSP2/IWTGAS.py

@@ -30,7 +30,7 @@
 PCFLX3 = IGCF1(3,LEV) * MFACTA
 '''
 
-def iwtgas(store, siminfo, uci, ts):
+def iwtgas(io_manager, siminfo, uci, ts):
 	''' Estimate water temperature, dissolved oxygen, and carbon dioxide in the outflows
 	from a impervious land segment. calculate associated fluxes through exit gate'''
 

HSP2/PQUAL.py

@@ -24,7 +24,7 @@
 PFACTA = 1.0
 
 
-def pqual(store, siminfo, uci, ts):
+def pqual(io_manager, siminfo, uci, ts):
 	''' Simulate quality constituents (other than sediment, heat, dox, and co2)
 	using simple relationships with sediment and water yield'''
 

HSP2/PSTEMP.py

@@ -20,7 +20,7 @@
 MINTMP = -100
 MAXTMP = 100
 
-def pstemp(store, siminfo, uci, ts):
+def pstemp(io_manager, siminfo, uci, ts):
 	'''Estimate soil temperatures in a pervious land segment'''
 	simlen = siminfo['steps']
 

HSP2/PWATER.py

@@ -24,7 +24,7 @@
           'PWATER: High Water Table code not implemented', #ERRMSG9
           )
 
-def pwater(store, siminfo, uci, ts):
+def pwater(io_manager, siminfo, uci, ts):
     ''' PERLND WATER module
     CALL: pwater(store, general, ui, ts)
        store is the Pandas/PyTable open store

HSP2/PWTGAS.py

@@ -25,7 +25,7 @@
 MFACTB = 0.
 
 
-def pwtgas(store, siminfo, uci, ts):
+def pwtgas(io_manager, siminfo, uci, ts):
     ''' Estimate water temperature, dissolved oxygen, and carbon dioxide in the outflows
     from a pervious landsegment. calculate associated fluxes through exit gates'''
     simlen = siminfo['steps']

HSP2/RQUAL.py

@@ -24,7 +24,7 @@
 ERRMSGS_phcarb = ('PHCARB: Error -- Invalid CONS index specified for ALKCON (i.e., ALKCON > NCONS).',
 					'PHCARB: Error -- A satisfactory solution for pH has not been reached.')
 
-def rqual(store, siminfo, uci, uci_oxrx, uci_nutrx, uci_plank, uci_phcarb, ts):
+def rqual(io_manager, siminfo, uci, uci_oxrx, uci_nutrx, uci_plank, uci_phcarb, ts, monthdata):
 	''' Simulate constituents involved in biochemical transformations'''
 
 	# simulation information:
@@ -109,7 +109,7 @@ def rqual(store, siminfo, uci, uci_oxrx, uci_nutrx, uci_plank, uci_phcarb, ts):
 			NUADFX = zeros(simlen)
 
 			if nuadfg_dd > 0:
-				NUADFX = initmd(siminfo, store, 'MONTHDATA/MONTHDATA' + str(nuadfg_dd), 0.0)
+				NUADFX = initmd(siminfo, monthdata, 'MONTHDATA/MONTHDATA' + str(nuadfg_dd), 0.0)
 			elif nuadfg_dd == -1:
 				if 'NUADFX' + str(j) in ts:
 					NUADFX = ts['NUADFX' + str(j)]
@@ -124,7 +124,7 @@ def rqual(store, siminfo, uci, uci_oxrx, uci_nutrx, uci_plank, uci_phcarb, ts):
 			NUADCN = zeros(simlen)
 
 			if nuadfg_wd > 0:
-				NUADCN = initmd(siminfo, store, 'MONTHDATA/MONTHDATA' + str(nuadfg_wd), 0.0)
+				NUADCN = initmd(siminfo, monthdata, 'MONTHDATA/MONTHDATA' + str(nuadfg_wd), 0.0)
 			elif nuadfg_wd == -1:
 				if 'NUADCN' + str(j) in ts:
 					NUADCN = ts['NUADCN' + str(j)]
@@ -160,7 +160,7 @@ def rqual(store, siminfo, uci, uci_oxrx, uci_nutrx, uci_plank, uci_phcarb, ts):
 			pladfg_dd = int(ui_plank['PLADFG' + str(j)])
 
 			if pladfg_dd > 0:
-				PLADFX = initmd(siminfo, store, 'MONTHDATA/MONTHDATA' + str(pladfg_dd), 0.0)
+				PLADFX = initmd(siminfo, monthdata, 'MONTHDATA/MONTHDATA' + str(pladfg_dd), 0.0)
 			elif pladfg_dd == -1:
 				if 'PLADFX' + str(j) in ts:
 					PLADFX = ts['PLADFX' + str(j)]
@@ -175,7 +175,7 @@ def rqual(store, siminfo, uci, uci_oxrx, uci_nutrx, uci_plank, uci_phcarb, ts):
 			pladfg_wd = int(ui_plank['PLADFG' + str(n+1)])
 
 			if pladfg_wd > 0:
-				PLADCN = initmd(siminfo, store, 'MONTHDATA/MONTHDATA' + str(pladfg_wd), 0.0)
+				PLADCN = initmd(siminfo, monthdata, 'MONTHDATA/MONTHDATA' + str(pladfg_wd), 0.0)
 			elif pladfg_wd == -1:
 				if 'PLADCN' + str(j) in ts:
 					PLADCN = ts['PLADCN' + str(j)]

HSP2/SEDMNT.py

@@ -18,7 +18,7 @@
 PDETS= DETS*MFACTA # convert dimensional variables to external units
 '''
 
-def sedmnt(store, siminfo, uci, ts):
+def sedmnt(io_manager, siminfo, uci, ts):
 	''' Produce and remove sediment from the land surface'''
 
 	simlen = siminfo['steps']

HSP2/SEDTRN.py

@@ -17,7 +17,7 @@
           'SEDTRN: Simulation of sediment requires all 3 "auxiliary flags" (AUX1FG, etc) in section HYDR must be turned on', #ERRMSG5
           'SEDTRN: When specifying the initial composition of the bed, the fraction of sand, silt, and clay must sum to a value close to 1.0.')  #ERRMSG6
 
-def sedtrn(store, siminfo, uci, ts):
+def sedtrn(io_manager, siminfo, uci, ts):
 	''' Simulate behavior of inorganic sediment'''
 
 	# simlen = siminfo['steps']

HSP2/SNOW.py

@@ -16,13 +16,15 @@
 from numpy import zeros, ones, full, nan, int64
 from math import sqrt, floor
 from numba import njit
-from HSP2.utilities import hourflag, monthval, hoursval, make_numba_dict, initm
+from HSP2.utilities import hourflag, monthval, hoursval, make_numba_dict, initm, SEASONS, SVP
+
+from HSP2IO.protocols import SupportsReadTS, Category
 
 ERRMSGS = ('Snow simulation cannot function properly with delt> 360',   #ERRMSG0
  )
 
 
-def snow(store, siminfo, uci, ts):
+def snow(io_manager:SupportsReadTS, siminfo, uci, ts):
     ''' high level driver for SNOW module
     CALL: snow(store, general, ui, ts)
        store is the Pandas/PyTable open store
@@ -33,8 +35,8 @@ def snow(store, siminfo, uci, ts):
     steps   = siminfo['steps']                # number of simulation timesteps
     UUNITS  = siminfo['units']
 
-    ts['SVP']     = store['TIMESERIES/Saturated_Vapor_Pressure_Table'].to_numpy()
-    ts['SEASONS'] = monthval(siminfo, store['TIMESERIES/SEASONS_Table'])
+    ts['SVP'] = SVP
+    ts['SEASONS'] = monthval(siminfo, SEASONS)
 
     cloudfg = 'CLOUD' in ts
 

HSP2/SOLIDS.py

@@ -14,7 +14,7 @@
 ERRMSG = []
 
 
-def solids(store, siminfo, uci, ts):
+def solids(io_manager, siminfo, uci, ts):
 	'''Accumulate and remove solids from the impervious land segment'''
 
 	simlen = siminfo['steps']