Refactor "uci" names.

* In some places "uci" would describe "parameters" and in other
  places would describe "model".  Changed as appropriate.
* Applied "ruff check --fix ." safe fixes.
* Applied "ruff format .".

Author: timcera

src/hsp2/__init__.py

@@ -1,16 +1,16 @@
-"""The Hydrologic Simulation Program - Python (HSP2) watershed model is is a 
- port of the well-established Hydrological Simulation Program - FORTRAN (HSPF),
- re-coded with modern scientific Python and data formats.
+"""The Hydrologic Simulation Program - Python (HSP2) watershed model is is a
+port of the well-established Hydrological Simulation Program - FORTRAN (HSPF),
+re-coded with modern scientific Python and data formats.
 
- Modules:
-    - HSP2 contains the hydrology and water quality code modules converted from 
-    HSPF, along with the main programs to run HSP2.
-    - HSP2tools contains supporting software modules such as the code to convert 
-    legacy WDM and UCI files to HDF5 files for HSP2, and to provide additional 
-    new and legacy capabilities.
-    - HSP2IO is new in v0.10 and contains an abstracted approach to getting data 
-    in and out of HSP2 for flexibility and performance and also to support future 
-    automation and model coupling. 
+Modules:
+   - HSP2 contains the hydrology and water quality code modules converted from
+   HSPF, along with the main programs to run HSP2.
+   - HSP2tools contains supporting software modules such as the code to convert
+   legacy WDM and UCI files to HDF5 files for HSP2, and to provide additional
+   new and legacy capabilities.
+   - HSP2IO is new in v0.10 and contains an abstracted approach to getting data
+   in and out of HSP2 for flexibility and performance and also to support future
+   automation and model coupling.
 """
 
 from importlib.metadata import version, PackageNotFoundError
@@ -19,5 +19,8 @@
     __version__ = version("hsp2")
 except PackageNotFoundError:
     import os
-    with open(os.path.join(os.path.dirname(__file__),"../..", "VERSION"), encoding="ascii") as version_file:
+
+    with open(
+        os.path.join(os.path.dirname(__file__), "../..", "VERSION"), encoding="ascii"
+    ) as version_file:
         __version__ = version_file.read().strip()

src/hsp2/hsp2/ADCALC.py

@@ -8,7 +8,7 @@
 """
 
 from numba import njit
-from numpy import array, zeros
+from numpy import zeros
 
 from hsp2.hsp2.utilities import make_numba_dict
 
@@ -18,14 +18,14 @@
 ERRMSG = []
 
 
-def adcalc(io_manager, siminfo, uci, ts):
+def adcalc(io_manager, siminfo, parameter, ts):
     """Prepare to simulate advection of fully entrained constituents"""
 
     errorsV = zeros(len(ERRMSG), dtype=int)
 
     simlen = siminfo["steps"]
 
-    ui = make_numba_dict(uci)
+    ui = make_numba_dict(parameter)
     nexits = int(ui["NEXITS"])  # table type GEN-INFO
     ui["simlen"] = siminfo["steps"]
     ui["delts"] = siminfo["delt"] * 60.0  # delts is the simulation interval in seconds
@@ -55,7 +55,7 @@ def adcalc(io_manager, siminfo, uci, ts):
         SOVOL[:, i] = ts["SOVOL" + str(i + 1)]
         EOVOL[:, i] = ts["EOVOL" + str(i + 1)]
 
-    uci["adcalcData"] = (nexits, vol, VOL, SROVOL, EROVOL, SOVOL, EOVOL)
+    parameter["adcalcData"] = (nexits, vol, VOL, SROVOL, EROVOL, SOVOL, EOVOL)
 
     return errorsV, ERRMSG
 

src/hsp2/hsp2/ATEMP.py

@@ -7,17 +7,17 @@
 from numpy import empty, int64, zeros
 
 from hsp2.hsp2.utilities import LAPSE, hoursval, make_numba_dict
-from hsp2.hsp2io.protocols import Category, SupportsReadTS
+from hsp2.hsp2io.protocols import SupportsReadTS
 
 ERRMSGS = ()
 
 
-def atemp(io_manager: SupportsReadTS, siminfo, uci, ts):
+def atemp(io_manager: SupportsReadTS, siminfo, parameters, ts):
     """high level driver for air temperature module"""
 
     ts["LAPSE"] = hoursval(siminfo, LAPSE, lapselike=True)
 
-    ui = make_numba_dict(uci)  # Note: all values coverted to float automatically
+    ui = make_numba_dict(parameters)  # Note: all values coverted to float automatically
     ui["k"] = siminfo["delt"] * 0.000833  # convert to in/timestep
     ui["steps"] = siminfo["steps"]
     ui["errlen"] = len(ERRMSGS)

src/hsp2/hsp2/CONS.py

@@ -26,7 +26,7 @@
 ERRMSG = []
 
 
-def cons(io_manager, siminfo, uci, ts):
+def cons(io_manager, siminfo, parameters, ts):
     """Simulate behavior of conservative constituents; calculate concentration
     of conservative constituents after advection"""
 
@@ -40,7 +40,7 @@ def cons(io_manager, siminfo, uci, ts):
         # si units conversion constants, 1 hectare is 10000 sq m
         AFACT = 1000000.0
 
-    advectData = uci["advectData"]
+    advectData = parameters["advectData"]
     (nexits, vol, VOL, SROVOL, EROVOL, SOVOL, EOVOL) = advectData
     svol = vol * AFACT
 
@@ -51,7 +51,7 @@ def cons(io_manager, siminfo, uci, ts):
         ts["SOVOL" + str(i + 1)] = SOVOL[:, i]
         ts["EOVOL" + str(i + 1)] = EOVOL[:, i]
 
-    ui = make_numba_dict(uci)
+    ui = make_numba_dict(parameters)
     nexits = int(ui["NEXITS"])
 
     ui["simlen"] = siminfo["steps"]
@@ -63,13 +63,13 @@ def cons(io_manager, siminfo, uci, ts):
     # conactive = ui['CONACTIVE']   # dict
 
     ncons = 1
-    if "PARAMETERS" in uci:
-        if "NCONS" in uci["PARAMETERS"]:
-            ncons = uci["PARAMETERS"]["NCONS"]
+    if "PARAMETERS" in parameters:
+        if "NCONS" in parameters["PARAMETERS"]:
+            ncons = parameters["PARAMETERS"]["NCONS"]
 
     for index in range(ncons):
         icon = str(index + 1)
-        parms = uci["CONS" + icon]
+        parms = parameters["CONS" + icon]
         conid = parms["CONID"]  # string name of the conservative constituent
         con = parms["CON"]  # initial concentration of the conservative
         concid = parms[
@@ -92,21 +92,29 @@ def cons(io_manager, siminfo, uci, ts):
         # COADFG2 = ui['COADFG2']    # table-type cons-ad-flags
         # COADCN = getit()            # flag: COADFG; monthly COACNM; value COADCN
 
-        if "FLAGS" in uci:
-            u = uci["FLAGS"]
+        if "FLAGS" in parameters:
+            u = parameters["FLAGS"]
             # get atmos dep timeseries
             coadfg1 = u["COADFG" + str((index * 2) - 1)]
             if coadfg1 > 0:
                 ts["COADFX"] = initm(
-                    siminfo, uci, coadfg1, "CONS" + str(index) + "_MONTHLY/COADFX", 0.0
+                    siminfo,
+                    parameters,
+                    coadfg1,
+                    "CONS" + str(index) + "_MONTHLY/COADFX",
+                    0.0,
                 )
             elif coadfg1 == -1:
                 ts["COADFX"] = ts["COADFX" + str(index)]
 
             coadfg2 = u["COADFG" + str(index * 2)]
             if coadfg2 > 0:
                 ts["COADCN"] = initm(
-                    siminfo, uci, coadfg2, "CONS" + str(index) + "_MONTHLY/COADCN", 0.0
+                    siminfo,
+                    parameters,
+                    coadfg2,
+                    "CONS" + str(index) + "_MONTHLY/COADCN",
+                    0.0,
                 )
             elif coadfg2 == -1:
                 ts["COADCN"] = ts["COADCN" + str(index)]
@@ -121,7 +129,7 @@ def cons(io_manager, siminfo, uci, ts):
         ############################################################################
 
         if nexits > 1:
-            u = uci["SAVE"]
+            u = parameters["SAVE"]
             key1 = name + "_OCON"
             for i in range(nexits):
                 u[f"{key1}{i + 1}"] = u["OCON"]
@@ -226,12 +234,12 @@ def _cons_(ui, ts):
     return
 
 
-def expand_CONS_masslinks(flags, uci, dat, recs):
+def expand_CONS_masslinks(flags, parameters, dat, recs):
     if flags["CONS"]:
         ncons = 1
-        if "PARAMETERS" in uci:
-            if "NCONS" in uci["PARAMETERS"]:
-                ncons = uci["PARAMETERS"]["NCONS"]
+        if "PARAMETERS" in parameters:
+            if "NCONS" in parameters["PARAMETERS"]:
+                ncons = parameters["PARAMETERS"]["NCONS"]
         for i in range(1, ncons + 1):
             # ICONS                        loop for each cons
             rec = {}

src/hsp2/hsp2/GENER.py

@@ -78,7 +78,7 @@ def __init__(
                     self.ts_input_1 = tsin["ONE"]
                 if "TWO" in tsin:
                     self.ts_input_2 = tsin["TWO"]
-                if not "ONE" in tsin and not "TWO" in tsin:
+                if "ONE" not in tsin and "TWO" not in tsin:
                     raise NotImplementedError(f"Invalid SVOL for '{link.SVOLNO}'")
 
             if link.SVOL == "COPY" or link.SVOL == "GENER":
@@ -153,9 +153,17 @@ def _opcode7(self) -> pd.Series:
     def _opcode8(self) -> pd.Series:
         # K(1) + K(2) * A + K(3) * A ** 2
         # The user supplies the number of terms and the values of coefficients (K)
-        return ((self.k1 + (self.k2 * self.ts_input_1) + (self.k3 * (self.ts_input_1 ** 2))
-                + (self.k4 * (self.ts_input_1 ** 3))) + (self.k5 * (self.ts_input_1 ** 4))
-                + (self.k6 * (self.ts_input_1 ** 7)) + (self.k7 * (self.ts_input_1 ** 8)))
+        return (
+            (
+                self.k1
+                + (self.k2 * self.ts_input_1)
+                + (self.k3 * (self.ts_input_1**2))
+                + (self.k4 * (self.ts_input_1**3))
+            )
+            + (self.k5 * (self.ts_input_1**4))
+            + (self.k6 * (self.ts_input_1**7))
+            + (self.k7 * (self.ts_input_1**8))
+        )
 
     def _opcode9(self) -> pd.Series:
         return np.power(self.k, self.ts_input_1)