reactor: StorageUnit renamed to Process, before going to Conservative…

…Process subclass Process is conservative

pywatershed/__init__.py

@@ -9,7 +9,7 @@
 from .base.control import Control
 from .base.model import Model
 from .base.parameters import Parameters
-from .base.storage_unit import StorageUnit
+from .base.process import Process
 from .base.timeseries import TimeseriesArray
 from .hydrology.PRMSCanopy import PRMSCanopy
 from .hydrology.PRMSChannel import PRMSChannel

pywatershed/analysis/process_plot.py

@@ -11,7 +11,7 @@
 
 from ..base import meta
 from ..base.model import Model
-from ..base.storage_unit import StorageUnit
+from ..base.process import Process
 from ..utils.optional_import import import_optional_dependency
 
 
@@ -51,7 +51,7 @@ def __init__(
 
         return
 
-    def plot(self, var_name: str, process: StorageUnit, cmap: str = None):
+    def plot(self, var_name: str, process: Process, cmap: str = None):
         var_dims = list(meta.get_vars(var_name)[var_name]["dims"])
         if "nsegment" in var_dims:
             if not cmap:
@@ -62,7 +62,7 @@ def plot(self, var_name: str, process: StorageUnit, cmap: str = None):
         else:
             raise ValueError()
 
-    def plot_seg_var(self, var_name: str, process: StorageUnit, cmap="cool"):
+    def plot_seg_var(self, var_name: str, process: Process, cmap="cool"):
         ccrs = import_optional_dependency("cartopy.crs")
 
         data_df = pd.DataFrame(
@@ -158,7 +158,7 @@ def get_hru_var(self, var_name: str, model: Model):
     def plot_hru_var(
         self,
         var_name: str,
-        process: StorageUnit,
+        process: Process,
         data: np.ndarray = None,
         data_units: str = None,
         nhm_id: np.ndarray = None,

pywatershed/atmosphere/PRMSAtmosphere.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-from pywatershed.base.storage_unit import StorageUnit
+from pywatershed.base.process import Process
 from pywatershed.utils.netcdf_utils import NetCdfWrite
 
 from ..base.adapter import adaptable
@@ -23,7 +23,7 @@ def tile_time_to_space(arr: np.ndarray, n_space) -> np.ndarray:
     return np.transpose(np.tile(arr, (n_space, 1)))
 
 
-class PRMSAtmosphere(StorageUnit):
+class PRMSAtmosphere(Process):
     """PRMS atmospheric boundary layer model.
 
     Implementation based on PRMS 5.2.1 with theoretical documentation based on

pywatershed/atmosphere/PRMSSolarGeometry.py

@@ -4,8 +4,7 @@
 
 import numpy as np
 
-# would like to not subclass storageUnit but it is much simpler to do so
-from pywatershed.base.storage_unit import StorageUnit
+from pywatershed.base.process import Process
 from pywatershed.utils.netcdf_utils import NetCdfWrite
 
 from ..base.control import Control
@@ -36,7 +35,7 @@ def tile_space_to_time(arr: np.ndarray) -> np.ndarray:
 #    return np.transpose(np.tile(arr, (n_hru, 1)))
 
 
-class PRMSSolarGeometry(StorageUnit):
+class PRMSSolarGeometry(Process):
     """PRMS solar geometry."""
 
     def __init__(
@@ -56,7 +55,7 @@ def __init__(
         self._set_budget(budget_type)
         self.netcdf_output_dir = netcdf_output_dir
 
-        # self._time is needed by storageUnit for timeseries arrays
+        # self._time is needed by Process for timeseries arrays
         # TODO: this is redundant because the parameter doy is set
         #       on load of prms file. Could pass the name to use for
         #       self._time to super or come up with some other work around.

pywatershed/base/__init__.py

@@ -4,5 +4,5 @@
 from .control import Control
 from .model import Model
 from .parameters import Parameters
-from .storage_unit import StorageUnit
+from .process import Process
 from .timeseries import TimeseriesArray

pywatershed/base/storage_unit.py → pywatershed/base/process.py

@@ -16,10 +16,10 @@
 from .control import Control
 
 
-class StorageUnit(Accessor):
-    """StorageUnit base class
+class Process(Accessor):
+    """Process base class
 
-    The StorageUnit is a base class for conserving mass and energy.
+    Process is a base class for physical processes.
 
     It has budgets that can optionally be established for mass an energy and
     these can be enforced or simply diagnosed with the model run.
@@ -32,8 +32,8 @@ class StorageUnit(Accessor):
 
         inputs/get_inputs():
             List the names of variables required from external sources.
-            Still working on conventions if these are to be modified but
-            the storageUnit. For an input to be successfully inicluded,
+            Still working on conventions if these are to be modified.
+            For an input to be successfully inicluded,
             that variable must be defined in the metadata
             (pywatershed/static/metadata/variables.yaml).
             Efforts should be made to not use diagnostic variables as input
@@ -100,7 +100,7 @@ def __init__(
         metadata_patches: dict[dict] = None,
         metadata_patch_conflicts: Literal["ignore", "warn", "error"] = "error",
     ):
-        self.name = "StorageUnit"
+        self.name = "Process"
         self.control = control
 
         missing_params = set(self.parameters).difference(
@@ -152,7 +152,7 @@ def output(self) -> None:
         return
 
     def finalize(self) -> None:
-        """Finalize storageUnit
+        """Finalize Process
 
         Finalizes the object, including output methods.
 
@@ -381,7 +381,7 @@ def set_input_to_adapter(self, input_variable_name: str, adapter: Adapter):
 
         # Using a pointer between boxes means that the same pointer has to
         # be used for the budget, so there's no way to have a preestablished
-        # pointer between storageUnit and its budget. So this stuff...
+        # pointer between Process and its budget. So this stuff...
         if self.budget is not None:
             for comp in self.budget.components:
                 if input_variable_name in self.budget[comp].keys():
@@ -439,7 +439,7 @@ def _calculate(self):
         raise Exception("This must be overridden")
 
     def calculate(self, time_length: float, **kwargs) -> None:
-        """Calculate storageUnit terms for a time step
+        """Calculate Process terms for a time step
 
         Args:
             simulation_time: current simulation time

pywatershed/hydrology/PRMSCanopy.py

@@ -3,7 +3,7 @@
 
 from ..base.adapter import adaptable
 from ..base.control import Control
-from ..base.storage_unit import StorageUnit
+from ..base.process import Process
 from ..constants import CovType, HruType, numba_num_threads, zero
 from ..parameters import Parameters
 
@@ -28,7 +28,7 @@
 ACTIVE = 1
 
 
-class PRMSCanopy(StorageUnit):
+class PRMSCanopy(Process):
     """PRMS canopy."""
 
     def __init__(

pywatershed/hydrology/PRMSChannel.py

@@ -3,7 +3,7 @@
 import networkx as nx
 import numpy as np
 
-from pywatershed.base.storage_unit import StorageUnit
+from pywatershed.base.process import Process
 
 from ..base.adapter import adaptable
 from ..base.control import Control
@@ -18,7 +18,7 @@
     has_prmschannel_f = False
 
 
-class PRMSChannel(StorageUnit):
+class PRMSChannel(Process):
     """PRMS channel flow (muskingum_mann).
 
     The muskingum module was originally developed for the Precipitation Runoff

pywatershed/hydrology/PRMSEt.py

@@ -1,7 +1,7 @@
 import numpy as np
 
 from pywatershed.base.budget import Budget
-from pywatershed.base.storage_unit import StorageUnit
+from pywatershed.base.process import Process
 
 from ..base.adapter import adaptable
 from ..base.control import Control
@@ -17,7 +17,7 @@
 #       end of each time calculation.
 
 
-class PRMSEt(StorageUnit):
+class PRMSEt(Process):
     def __init__(
         self,
         control: Control,

pywatershed/hydrology/PRMSGroundwater.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from pywatershed.base.storage_unit import StorageUnit
+from pywatershed.base.process import Process
 
 from ..base.adapter import adaptable
 from ..base.control import Control
@@ -15,7 +15,7 @@
     has_prmsgroundwater_f = False
 
 
-class PRMSGroundwater(StorageUnit):
+class PRMSGroundwater(Process):
     """PRMS groundwater reservoir."""
 
     def __init__(

pywatershed/hydrology/PRMSRunoff.py

@@ -1,7 +1,7 @@
 import numpy as np
 from numba import prange
 
-from pywatershed.base.storage_unit import StorageUnit
+from pywatershed.base.process import Process
 
 from ..base.adapter import adaptable
 from ..base.control import Control
@@ -24,7 +24,7 @@
 LAKE = HruType.LAKE.value
 
 
-class PRMSRunoff(StorageUnit):
+class PRMSRunoff(Process):
     """PRMS surface runoff."""
 
     def __init__(

pywatershed/hydrology/PRMSSnow.py

@@ -1,7 +1,7 @@
 import numpy as np
 from numba import prange
 
-from pywatershed.base.storage_unit import StorageUnit
+from pywatershed.base.process import Process
 
 from ..base.adapter import adaptable
 from ..base.control import Control
@@ -68,7 +68,7 @@
 dbgind = 434
 
 
-class PRMSSnow(StorageUnit):
+class PRMSSnow(Process):
     """PRMS snow pack."""
 
     def __init__(

pywatershed/hydrology/PRMSSoilzone.py

@@ -1,7 +1,7 @@
 import numpy as np
 from numba import prange
 
-from pywatershed.base.storage_unit import StorageUnit
+from pywatershed.base.process import Process
 
 from ..base.adapter import adaptable
 from ..base.control import Control
@@ -21,7 +21,7 @@
 TWOTHIRDS = 2 / 3
 
 
-class PRMSSoilzone(StorageUnit):
+class PRMSSoilzone(Process):
     """PRMS soil zone.
 
     Args:

pywatershed/hydrology/Starfit.py

@@ -1,14 +1,14 @@
 import numpy as np
 
-from pywatershed.base.storage_unit import StorageUnit
+from pywatershed.base.process import Process
 
 from ..base.adapter import adaptable
 from ..base.control import Control
 from ..constants import nan, one, zero
 from ..parameters import Parameters
 
 
-class Starfit(StorageUnit):
+class Starfit(Process):
     """starfit: Storage Targets And Release Function Inference Tool
 
     Sean W.D. Turner, Jennie Clarice Steyaert, Laura Condon, Nathalie Voisin,

test_data/drb_2yr/control.yml

@@ -19,6 +19,7 @@ load_n_time_batches: 1
 # still used by snow and soilzone, but should be removed
 init_vars_from_file: 0
 
+
 dprst_flag: True
 
 # boolean
@@ -28,3 +29,11 @@ netcdf_output_var_names:
   - albedo
   - cap_infil_tot
   - contrib_fraction
+
+
+# candidates from PRMS style control files to HONOR or keep
+# modules listing: could be used to create model_dict
+# parameter_file: single (multiple?) parameter file
+# model.out: log file
+# paths to input files (e.g. cbh files, with names)
+# output frequency and output dir

test_data/drb_2yr/nhm_model.yml

@@ -8,32 +8,32 @@ solargeometry:
   class: PRMSSolarGeometry
   parameters: parameters_PRMSSolarGeometry.nc
   dis: dis_hru
-  
+
 atmosphere:
   class: PRMSAtmosphere
   parameters: parameters_PRMSAtmosphere.nc
   dis: dis_hru
-  
+
 canopy:
   class: PRMSCanopy
   parameters: parameters_PRMSCanopy.nc
   dis: dis_hru
-  
+
 snow:
   class: PRMSSnow
   parameters: parameters_PRMSSnow.nc
   dis: dis_hru
-  
+
 runoff:
   class: PRMSRunoff
   parameters: parameters_PRMSRunoff.nc
   dis: dis_hru
-  
+
 soilzone:
   class: PRMSSoilzone
   parameters: parameters_PRMSSoilzone.nc
   dis: dis_hru
-  
+
 groundwater:
   class: PRMSGroundwater
   parameters: parameters_PRMSGroundwater.nc
@@ -53,4 +53,3 @@ model_order:
   - soilzone
   - groundwater
   - channel
-