Merge pull request #5 from NOAA-GFDL/feature/init_standard

Standardizing module import method for pyFV3

examples/standalone/runfile/acoustics.py

@@ -15,9 +15,7 @@
 from ndsl.dsl.dace.orchestration import DaceConfig
 from ndsl.dsl.stencil import CompilationConfig
 from ndsl.stencils.testing.grid import Grid
-from pyFV3._config import DynamicalCoreConfig
-from pyFV3.stencils.dyn_core import AcousticDynamics
-from pyFV3.testing import TranslateDynCore
+from pyFV3 import AcousticDynamics, DynamicalCoreConfig, TranslateDynCore
 
 
 try:

examples/standalone/runfile/compile.py

@@ -10,7 +10,7 @@
 
 import ndsl.dsl.stencil  # noqa: F401
 from ndsl.comm.null_comm import NullComm
-from pyFV3._config import DynamicalCoreConfig
+from pyFV3 import DynamicalCoreConfig
 
 
 try:

examples/standalone/runfile/dynamics.py

@@ -25,10 +25,8 @@
 from ndsl.grid import DampingCoefficients, GridData, MetricTerms
 from ndsl.stencils.testing import dataset_to_dict
 from ndsl.stencils.testing.grid import Grid
-from pyFV3 import DynamicalCore, DynamicalCoreConfig
-from pyFV3.dycore_state import DycoreState
-from pyFV3.initialization.baroclinic import init_baroclinic_state
-from pyFV3.testing import TranslateFVDynamics
+from pyFV3 import DycoreState, DynamicalCore, DynamicalCoreConfig, TranslateFVDynamics
+from pyFV3.initialization.test_cases import init_baroclinic_state
 
 
 def parse_args() -> Namespace:

pyFV3/__init__.py

@@ -1,8 +1,14 @@
 from ._config import DynamicalCoreConfig
 from .dycore_state import DycoreState
-from .stencils.fv_dynamics import DynamicalCore
-from .stencils.fv_subgridz import DryConvectiveAdjustment
-from .wrappers.geos_wrapper import GeosDycoreWrapper
+from .stencils import DryConvectiveAdjustment, DynamicalCore
 
 
+"""
+DynamicalCoreConfig: Configuration for the FV3 dynamical core
+DycoreState: Dataclass containing state of the dynamical core
+DryConvectiveAdjustment: Sub-grid dry convective adjustment
+DynamicalCore: The FV3 dynamical core
+GeosDycoreWrapper: Interface to the dycore for the GEOS model
+"""
+
 __version__ = "0.2.0"

pyFV3/initialization/__init__.py

@@ -1 +1,6 @@
 from .analytic_init import init_analytic_state
+
+
+"""
+init_analytic_state: Creates dycore state object out of analytic initial conditions
+"""

pyFV3/stencils/__init__.py

@@ -0,0 +1,65 @@
+from .a2b_ord4 import AGrid2BGridFourthOrder
+from .c_sw import CGridShallowWaterDynamics
+from .d2a2c_vect import DGrid2AGrid2CGridVectors
+from .d_sw import DGridShallowWaterLagrangianDynamics
+from .del2cubed import HyperdiffusionDamping
+from .delnflux import DelnFlux, DelnFluxNoSG
+from .divergence_damping import DivergenceDamping
+from .dyn_core import AcousticDynamics
+from .fillz import FillNegativeTracerValues
+from .fv_dynamics import DynamicalCore
+from .fv_subgridz import DryConvectiveAdjustment
+from .fvtp2d import FiniteVolumeTransport
+from .fxadv import FiniteVolumeFluxPrep
+from .map_single import MapSingle
+from .mapn_tracer import MapNTracer
+from .neg_adj3 import AdjustNegativeTracerMixingRatio
+from .nh_p_grad import NonHydrostaticPressureGradient
+from .pk3_halo import PK3Halo
+from .ray_fast import RayleighDamping
+from .remap_profile import RemapProfile
+from .remapping import LagrangianToEulerian
+from .riem_solver3 import NonhydrostaticVerticalSolver
+from .riem_solver_c import NonhydrostaticVerticalSolverCGrid
+from .saturation_adjustment import SatAdjust3d
+from .sim1_solver import Sim1Solver
+from .tracer_2d_1l import TracerAdvection
+from .updatedzc import UpdateGeopotentialHeightOnCGrid
+from .updatedzd import UpdateHeightOnDGrid
+from .xppm import XPiecewiseParabolic
+from .yppm import YPiecewiseParabolic
+
+
+"""
+AGrid2BGridFourthOrder: Converts field from A grid to B grid
+CGridShallowWaterDynamics: C-grid shallow water solver
+DGrid2AGrid2CGridVectors: Converts velocities from the D-grid to the A-grid and C-grid
+DGridShallowWaterLagrangianDynamics: D-grid shallow water solver
+HyperdiffusionDamping: Performs hyper diffusion filtering
+DelnFlux: Computes damping fluxes and applies them to a field
+DelnFluxNoSG: Only computes damping fluxes, but does not apply them
+DivergenceDamping: Diffusively damps the divergence field
+AcousticDynamics: Acoustic loop of the dynamical core
+FillNegativeTracerValues: Fixes negative tracer values
+DynamicalCore: The FV3 dynamical core
+DryConvectiveAdjustment: Performs subgrid dry convective adjustment mixing
+FiniteVolumeTransport: Calculates fluxes for finite volume transport
+FiniteVolumeFluxPrep: Prepares fluxes for finite volume transport
+MapSingle: Remaps vertical layers for one field
+MapNTracer: Remaps vertical layers for all tracer species
+AdjustNegativeTracerMixingRatio: Updates winds from pressure gradients
+PK3Halo: Calculates pressure raised to kappa power in halos
+RayleighDamping: Applies Rayleigh damping
+RemapProfile: Calculates cubic spline interpolation for vertical remapping
+LagrangianToEulerian: Remaps Lagrangian surfaces onto Eulerian coordinates
+NonhydrostaticVerticalSolver: Calculates nonhydrostatic w and p after advection
+NonhydrostaticVerticalSolverCGrid: Calculates nonhydrostatic w and p after
+                                   C-grid advection
+SatAdjust3d: Fast microphysical phase changes
+Sim1Solver: Semi-implict method solver
+TracerAdvection: Advects tracers
+UpdateGeopotentialHeightOnCGrid: Updates cell heights on C-grid
+UpdateHeightOnDGrid: Updates cell heights on D-grid
+XPiecewiseParabolic: Piecewise parabolic method advection in x-direction
+YPiecewiseParabolic: Piecewise parabolic method advection in y-direction
+"""

pyFV3/testing/__init__.py

@@ -3,3 +3,12 @@
 from .translate_dyncore import TranslateDynCore
 from .translate_fvdynamics import TranslateDycoreFortranData2Py, TranslateFVDynamics
 from .validation import enable_selective_validation
+
+
+"""
+MapSingleFactory: Pool of objects to apply vertical remapping to multiple fields
+TranslateDynCore: Translate test for dynamical core
+TranslateDycoreFortranData2Py: Infrastructure to format serialized fortran data for translate tests
+TranslateFVDynamics: Translate test of acoustic dynamics
+enable_selective_validation: Allows for selection of data for translate tests
+"""

pyFV3/testing/translate_dyncore.py

@@ -5,7 +5,8 @@
 from ndsl.namelist import Namelist
 from ndsl.quantity import Quantity
 from ndsl.stencils.testing import ParallelTranslate2PyState
-from pyFV3 import DycoreState, DynamicalCoreConfig
+from pyFV3._config import DynamicalCoreConfig
+from pyFV3.dycore_state import DycoreState
 
 
 class TranslateDynCore(ParallelTranslate2PyState):

pyFV3/wrappers/__init__.py

@@ -0,0 +1,10 @@
+from .geos_wrapper import GeosDycoreWrapper, MemorySpace, StencilBackendCompilerOverride
+
+
+"""
+GeosDycoreWrapper: Main class, wrap the digest the GEOS interface call
+                   and execute the pyFV3 numerics
+MemorySpace: Flag describing the memory space for both side of the interface
+StencilBackendCompilerOverride: Custom workaround to align gt backends
+                                build with orchestrated backends
+"""

tests/mpi/test_doubly_periodic.py

@@ -3,8 +3,6 @@
 
 import ndsl.dsl.stencil
 import ndsl.stencils.testing
-import pyFV3
-import pyFV3._config
 import pyFV3.initialization.test_cases.initialize_baroclinic as baroclinic_init
 from ndsl.comm.communicator import CubedSphereCommunicator, TileCommunicator
 from ndsl.comm.mpi import MPIComm
@@ -13,12 +11,13 @@
 from ndsl.grid import DampingCoefficients, GridData, MetricTerms
 from ndsl.initialization.allocator import QuantityFactory
 from ndsl.initialization.sizer import SubtileGridSizer
+from pyFV3 import DynamicalCore, DynamicalCoreConfig
 
 
-def setup_dycore() -> Tuple[pyFV3.DynamicalCore, List[Any]]:
+def setup_dycore() -> Tuple[DynamicalCore, List[Any]]:
     backend = "numpy"
     layout = (3, 3)
-    config = pyFV3.DynamicalCoreConfig(
+    config = DynamicalCoreConfig(
         layout=layout,
         npx=13,
         npy=13,
@@ -117,7 +116,7 @@ def setup_dycore() -> Tuple[pyFV3.DynamicalCore, List[Any]]:
         grid_indexing=grid_indexing,
     )
 
-    dycore = pyFV3.DynamicalCore(
+    dycore = DynamicalCore(
         comm=communicator,
         grid_data=grid_data,
         stencil_factory=stencil_factory,

tests/savepoint/translate/translate_a2b_ord4.py

@@ -4,7 +4,7 @@
 from ndsl.dsl.dace.orchestration import orchestrate
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
-from pyFV3.stencils.divergence_damping import DivergenceDamping
+from pyFV3.stencils import DivergenceDamping
 from pyFV3.testing import TranslateDycoreFortranData2Py
 
 

tests/savepoint/translate/translate_c_sw.py

@@ -1,7 +1,7 @@
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.initialization.allocator import QuantityFactory
 from ndsl.namelist import Namelist
-from pyFV3.stencils.c_sw import CGridShallowWaterDynamics
+from pyFV3.stencils import CGridShallowWaterDynamics
 from pyFV3.testing import TranslateDycoreFortranData2Py
 
 

tests/savepoint/translate/translate_d2a2c_vect.py

@@ -1,6 +1,6 @@
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
-from pyFV3.stencils.d2a2c_vect import DGrid2AGrid2CGridVectors
+from pyFV3.stencils import DGrid2AGrid2CGridVectors
 from pyFV3.testing import TranslateDycoreFortranData2Py
 
 

tests/savepoint/translate/translate_del2cubed.py

@@ -2,7 +2,7 @@
 
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
-from pyFV3.stencils.del2cubed import HyperdiffusionDamping
+from pyFV3.stencils import HyperdiffusionDamping
 from pyFV3.testing import TranslateDycoreFortranData2Py
 
 

tests/savepoint/translate/translate_divergencedamping.py

@@ -3,7 +3,7 @@
 from ndsl.constants import Z_DIM
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
-from pyFV3.stencils.divergence_damping import DivergenceDamping
+from pyFV3.stencils import DivergenceDamping
 from pyFV3.testing import TranslateDycoreFortranData2Py
 
 

tests/savepoint/translate/translate_fvsubgridz.py

@@ -1,11 +1,11 @@
 from types import SimpleNamespace
 
 import ndsl.dsl.gt4py_utils as utils
-import pyFV3.stencils.fv_subgridz as fv_subgridz
 from ndsl.constants import X_DIM, Y_DIM, Z_DIM, Z_INTERFACE_DIM
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
 from ndsl.stencils.testing import ParallelTranslateBaseSlicing
+from pyFV3 import DryConvectiveAdjustment
 
 
 # NOTE, does no halo updates, does not need to be a Parallel test,
@@ -181,7 +181,7 @@ def __init__(
 
     def compute_parallel(self, inputs, communicator):
         state = self.state_from_inputs(inputs)
-        fvsubgridz = fv_subgridz.DryConvectiveAdjustment(
+        fvsubgridz = DryConvectiveAdjustment(
             self.stencil_factory,
             self.grid.quantity_factory,
             self.namelist.nwat,
@@ -201,7 +201,7 @@ def compute_parallel(self, inputs, communicator):
     def compute_sequential(self, inputs_list, communicator_list):
         state_list = self.state_list_from_inputs_list(inputs_list)
         for state in state_list:
-            fvsubgridz = fv_subgridz.DryConvectiveAdjustment(
+            fvsubgridz = DryConvectiveAdjustment(
                 self.stencil_factory,
                 self.grid.quantity_factory,
                 self.namelist.nwat,

tests/savepoint/translate/translate_fvtp2d.py

@@ -3,7 +3,7 @@
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.dsl.typing import Float
 from ndsl.namelist import Namelist
-from pyFV3.stencils.fvtp2d import FiniteVolumeTransport
+from pyFV3.stencils import FiniteVolumeTransport
 from pyFV3.testing import TranslateDycoreFortranData2Py
 
 

tests/savepoint/translate/translate_fxadv.py

@@ -3,7 +3,7 @@
 from ndsl.constants import X_DIM, Y_DIM, Z_DIM
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
-from pyFV3.stencils.fxadv import FiniteVolumeFluxPrep
+from pyFV3.stencils import FiniteVolumeFluxPrep
 from pyFV3.testing import TranslateDycoreFortranData2Py
 from pyFV3.utils.functional_validation import get_subset_func
 

tests/savepoint/translate/translate_neg_adj3.py

@@ -3,7 +3,7 @@
 import ndsl.dsl.gt4py_utils as utils
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
-from pyFV3.stencils.neg_adj3 import AdjustNegativeTracerMixingRatio
+from pyFV3.stencils import AdjustNegativeTracerMixingRatio
 from pyFV3.testing import TranslateDycoreFortranData2Py
 
 

tests/savepoint/translate/translate_pk3_halo.py

@@ -1,6 +1,6 @@
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
-from pyFV3.stencils.pk3_halo import PK3Halo
+from pyFV3.stencils import PK3Halo
 from pyFV3.testing import TranslateDycoreFortranData2Py
 
 

tests/savepoint/translate/translate_pressureadjustedtemperature_nonhydrostatic.py

@@ -1,8 +1,8 @@
 from typing import Any, Dict
 
-import pyFV3
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
+from pyFV3 import DynamicalCoreConfig
 from pyFV3.stencils import temperature_adjust
 from pyFV3.stencils.dyn_core import get_nk_heat_dissipation
 from pyFV3.testing import TranslateDycoreFortranData2Py
@@ -18,7 +18,7 @@ def __init__(
         stencil_factory: StencilFactory,
     ):
         super().__init__(grid, namelist, stencil_factory)
-        dycore_config = pyFV3.DynamicalCoreConfig.from_namelist(namelist)
+        dycore_config = DynamicalCoreConfig.from_namelist(namelist)
         self.namelist = dycore_config
         n_adj = get_nk_heat_dissipation(
             config=dycore_config.d_grid_shallow_water,

tests/savepoint/translate/translate_ray_fast.py

@@ -1,6 +1,6 @@
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
-from pyFV3.stencils.ray_fast import RayleighDamping
+from pyFV3.stencils import RayleighDamping
 from pyFV3.testing import TranslateDycoreFortranData2Py
 
 

tests/savepoint/translate/translate_remapping.py

@@ -3,7 +3,7 @@
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
 from pyFV3 import DynamicalCoreConfig
-from pyFV3.stencils.remapping import LagrangianToEulerian
+from pyFV3.stencils import LagrangianToEulerian
 from pyFV3.testing import TranslateDycoreFortranData2Py
 
 

tests/savepoint/translate/translate_riem_solver3.py

@@ -1,7 +1,7 @@
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
 from pyFV3 import _config as spec
-from pyFV3.stencils.riem_solver3 import NonhydrostaticVerticalSolver
+from pyFV3.stencils import NonhydrostaticVerticalSolver
 from pyFV3.testing import TranslateDycoreFortranData2Py
 
 

tests/savepoint/translate/translate_riem_solver_c.py

@@ -1,6 +1,6 @@
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
-from pyFV3.stencils.riem_solver_c import NonhydrostaticVerticalSolverCGrid
+from pyFV3.stencils import NonhydrostaticVerticalSolverCGrid
 from pyFV3.testing import TranslateDycoreFortranData2Py
 
 

tests/savepoint/translate/translate_satadjust3d.py

@@ -1,8 +1,7 @@
-import pyFV3
 from ndsl.dsl.stencil import StencilFactory
 from ndsl.namelist import Namelist
 from pyFV3 import DynamicalCoreConfig
-from pyFV3.stencils.saturation_adjustment import SatAdjust3d
+from pyFV3.stencils import SatAdjust3d
 from pyFV3.testing import TranslateDycoreFortranData2Py
 
 
@@ -61,7 +60,7 @@ def __init__(
             },
             "cappa": {},
         }
-        self.namelist = pyFV3.DynamicalCoreConfig.from_namelist(namelist)
+        self.namelist = DynamicalCoreConfig.from_namelist(namelist)
         self.stencil_factory = stencil_factory
 
     def compute_from_storage(self, inputs):