Refactor: pySHiELD

.gitmodules

@@ -5,3 +5,6 @@
 [submodule "pyFV3"]
 	path = pyFV3
 	url = git@github.com:NOAA-GFDL/PyFV3.git
+[submodule "pySHiELD"]
+	path = pySHiELD
+	url = git@github.com:NOAA-GFDL/PySHiELD.git

.pre-commit-config.yaml

@@ -17,15 +17,6 @@ repos:
 -   repo: https://github.com/pre-commit/mirrors-mypy
     rev: v0.812
     hooks:
-    - id: mypy
-      name: mypy-fv3core
-      args: [--config-file, setup.cfg]
-      files: fv3core
-      exclude: |
-        (?x)^(
-        fv3core/pace/fv3core/stencils/fv_subgridz.py |
-        fv3core/tests/conftest.py
-        )$
     - id: mypy
       name: mypy-driver
       args: [--config-file, setup.cfg]
@@ -34,18 +25,6 @@ repos:
         (?x)^(
         tests/main/driver/__init__.py |
         )$
-    - id: mypy
-      name: mypy-physics
-      args: [--config-file, setup.cfg]
-      files: physics
-    - id: mypy
-      name: mypy-ndsl
-      args: [--config-file, setup.cfg]
-      files: ndsl
-      exclude: |
-        (?x)^(
-        ndsl/ndsl/gt4py_utils.py |
-        )$
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.3.0
     hooks:

constraints.txt

@@ -74,8 +74,6 @@ coverage==5.5
     # via pytest-cov
 cytoolz==0.12.1
     # via gt4py
-dace
-    # via ndsl
 dacite==1.6.0
     # via
     #   fv3config
@@ -113,8 +111,8 @@ f90nml==1.3.1
     # via
     #   -r requirements_dev.txt
     #   fv3config
-    #   pace-physics
     #   pyfv3
+    #   pyshield
 fasteners==0.16.3
     # via zarr
 fastjsonschema==2.16.2
@@ -147,8 +145,6 @@ gprof2dot==2021.2.21
     # via pytest-profiling
 gridtools-cpp==2.3.1
     # via gt4py
-gt4py
-    # via ndsl
 h5netcdf==1.1.0
     # via ndsl
 h5py==3.10.0
@@ -257,9 +253,9 @@ numpy==1.21.2
     #   netcdf4
     #   numcodecs
     #   pace-driver
-    #   pace-physics
     #   pandas
     #   pyfv3
+    #   pyshield
     #   scipy
     #   xarray
     #   zarr
@@ -477,8 +473,8 @@ xarray==0.19.0
     #   -r requirements_dev.txt
     #   ndsl
     #   pace-driver
-    #   pace-physics
     #   pyfv3
+    #   pyshield
 xxhash==2.0.2
     # via gt4py
 yarl==1.6.3

driver/examples/stencil_signatures.py

@@ -2,10 +2,10 @@
 import inspect
 from typing import Optional, TextIO
 
-import ndsl.dsl
-import ndsl.util
 import yaml
 
+import ndsl.dsl
+import ndsl.util
 import pace.driver
 
 

driver/pace/driver/configs/comm.py

@@ -4,6 +4,7 @@
 from typing import Any, ClassVar, List
 
 import dacite
+
 from ndsl.comm.caching_comm import CachingCommReader, CachingCommWriter
 from ndsl.comm.mpi import MPIComm
 from ndsl.comm.null_comm import NullComm

driver/pace/driver/diagnostics.py

@@ -11,7 +11,6 @@
 from ndsl.grid import GridData
 from ndsl.monitor import Monitor, NetCDFMonitor, ZarrMonitor
 from ndsl.quantity import Quantity
-
 from pyFV3.dycore_state import DycoreState
 
 from .state import DriverState

driver/pace/driver/driver.py

@@ -8,6 +8,9 @@
 import dace
 import dacite
 import yaml
+
+import pyFV3
+import pySHiELD
 from ndsl.comm.comm_abc import Comm
 from ndsl.comm.communicator import (
     Communicator,
@@ -28,14 +31,10 @@
 from ndsl.performance import PerformanceConfig
 from ndsl.performance.collector import PerformanceCollector
 from ndsl.performance.timer import Timer
-
-import pace.driver
-import pace.physics
-import pyFV3
 from pace.driver.safety_checks import SafetyChecker
 
 # TODO: move update_atmos_state into pace.driver
-from pace.physics.update import update_atmos_state
+from pySHiELD.update import update_atmos_state
 
 from . import diagnostics
 from .comm import CreatesCommSelector
@@ -116,8 +115,8 @@ class DriverConfig:
     dycore_config: pyFV3.DynamicalCoreConfig = dataclasses.field(
         default_factory=pyFV3.DynamicalCoreConfig
     )
-    physics_config: pace.physics.PhysicsConfig = dataclasses.field(
-        default_factory=pace.physics.PhysicsConfig
+    physics_config: pySHiELD.PhysicsConfig = dataclasses.field(
+        default_factory=pySHiELD.PhysicsConfig
     )
 
     days: int = 0
@@ -250,7 +249,7 @@ def from_dict(cls, kwargs: Dict[str, Any]) -> "DriverConfig":
 
         if isinstance(kwargs["physics_config"], dict):
             kwargs["physics_config"] = dacite.from_dict(
-                data_class=pace.physics.PhysicsConfig,
+                data_class=pySHiELD.PhysicsConfig,
                 data=kwargs.get("physics_config", {}),
                 config=dacite.Config(strict=True),
             )
@@ -505,7 +504,7 @@ def exit_instead_of_build(self):
 
             ndsl_log.info("setting up physics object started")
             if not config.dycore_only and not config.disable_step_physics:
-                self.physics = pace.physics.Physics(
+                self.physics = pySHiELD.Physics(
                     stencil_factory=self.stencil_factory,
                     quantity_factory=self.quantity_factory,
                     grid_data=self.state.grid_data,

driver/pace/driver/grid.py

@@ -4,6 +4,7 @@
 
 import f90nml
 import xarray as xr
+
 from ndsl.comm.communicator import Communicator
 from ndsl.comm.partitioner import get_tile_index
 from ndsl.constants import X_DIM, X_INTERFACE_DIM, Y_DIM, Y_INTERFACE_DIM

driver/pace/driver/initialization.py

@@ -6,6 +6,10 @@
 from typing import Callable, ClassVar, List, Type, TypeVar
 
 import f90nml
+
+import pyFV3
+import pyFV3.initialization.analytic_init as analytic_init
+import pySHiELD
 from ndsl.comm.communicator import Communicator
 from ndsl.constants import X_DIM, Y_DIM
 from ndsl.dsl.dace.orchestration import DaceConfig
@@ -15,11 +19,6 @@
 from ndsl.initialization.allocator import QuantityFactory
 from ndsl.namelist import Namelist
 from ndsl.stencils.testing import TranslateGrid, grid
-
-import pace.driver
-import pace.physics
-import pyFV3
-import pyFV3.initialization.analytic_init as analytic_init
 from pyFV3.testing import TranslateFVDynamics
 
 from .registry import Registry
@@ -40,7 +39,7 @@ def get_driver_state(
         damping_coefficients: DampingCoefficients,
         driver_grid_data: DriverGridData,
         grid_data: GridData,
-        schemes: List[pace.physics.PHYSICS_PACKAGES],
+        schemes: List[pySHiELD.PHYSICS_PACKAGES],
     ) -> DriverState:
         ...
 
@@ -78,7 +77,7 @@ def get_driver_state(
         damping_coefficients: DampingCoefficients,
         driver_grid_data: DriverGridData,
         grid_data: GridData,
-        schemes: List[pace.physics.PHYSICS_PACKAGES],
+        schemes: List[pySHiELD.PHYSICS_PACKAGES],
     ) -> DriverState:
         return self.config.get_driver_state(
             quantity_factory=quantity_factory,
@@ -112,7 +111,7 @@ def get_driver_state(
         damping_coefficients: DampingCoefficients,
         driver_grid_data: DriverGridData,
         grid_data: GridData,
-        schemes: List[pace.physics.PHYSICS_PACKAGES],
+        schemes: List[pySHiELD.PHYSICS_PACKAGES],
     ) -> DriverState:
         dycore_state = analytic_init.init_analytic_state(
             analytic_init_case=self.case,
@@ -123,7 +122,7 @@ def get_driver_state(
             moist_phys=True,
             comm=communicator,
         )
-        physics_state = pace.physics.PhysicsState.init_zeros(
+        physics_state = pySHiELD.PhysicsState.init_zeros(
             quantity_factory=quantity_factory, schemes=schemes
         )
         tendency_state = TendencyState.init_zeros(
@@ -156,7 +155,7 @@ def get_driver_state(
         damping_coefficients: DampingCoefficients,
         driver_grid_data: DriverGridData,
         grid_data: GridData,
-        schemes: List[pace.physics.PHYSICS_PACKAGES],
+        schemes: List[pySHiELD.PHYSICS_PACKAGES],
     ) -> DriverState:
         state = _restart_driver_state(
             self.path,
@@ -207,7 +206,7 @@ def get_driver_state(
         damping_coefficients: DampingCoefficients,
         driver_grid_data: DriverGridData,
         grid_data: GridData,
-        schemes: List[pace.physics.PHYSICS_PACKAGES],
+        schemes: List[pySHiELD.PHYSICS_PACKAGES],
     ) -> DriverState:
         state = _restart_driver_state(
             self.path,
@@ -280,14 +279,14 @@ def get_driver_state(
         damping_coefficients: DampingCoefficients,
         driver_grid_data: DriverGridData,
         grid_data: GridData,
-        schemes: List[pace.physics.PHYSICS_PACKAGES],
+        schemes: List[pySHiELD.PHYSICS_PACKAGES],
     ) -> DriverState:
         backend = quantity_factory.zeros(
             dims=[X_DIM, Y_DIM], units="unknown"
         ).gt4py_backend
 
         dycore_state = self._initialize_dycore_state(communicator, backend)
-        physics_state = pace.physics.PhysicsState.init_zeros(
+        physics_state = pySHiELD.PhysicsState.init_zeros(
             quantity_factory=quantity_factory,
             schemes=schemes,
         )
@@ -344,7 +343,7 @@ class PredefinedStateInit(Initializer):
     """
 
     dycore_state: pyFV3.DycoreState
-    physics_state: pace.physics.PhysicsState
+    physics_state: pySHiELD.PhysicsState
     tendency_state: TendencyState
     grid_data: GridData
     damping_coefficients: DampingCoefficients
@@ -358,7 +357,7 @@ def get_driver_state(
         damping_coefficients: DampingCoefficients,
         driver_grid_data: DriverGridData,
         grid_data: GridData,
-        schemes: List[pace.physics.PHYSICS_PACKAGES],
+        schemes: List[pySHiELD.PHYSICS_PACKAGES],
     ) -> DriverState:
         return DriverState(
             dycore_state=self.dycore_state,

driver/pace/driver/run.py

@@ -4,6 +4,7 @@
 
 import click
 import yaml
+
 from ndsl.logging import AVAILABLE_LOG_LEVELS, ndsl_log
 
 from .driver import Driver, DriverConfig

driver/pace/driver/safety_checks.py

@@ -1,8 +1,8 @@
 from typing import ClassVar, Dict, Optional
 
 import numpy as np
-from ndsl.quantity import Quantity
 
+from ndsl.quantity import Quantity
 from pyFV3.dycore_state import DycoreState
 
 

driver/pace/driver/state.py

@@ -2,8 +2,11 @@
 from dataclasses import fields
 from typing import List
 
-import ndsl.dsl.gt4py_utils as gt_utils
 import xarray as xr
+
+import ndsl.dsl.gt4py_utils as gt_utils
+import pyFV3
+import pySHiELD
 from ndsl.comm.communicator import Communicator
 from ndsl.constants import N_HALO_DEFAULT, X_DIM, Y_DIM, Z_DIM
 from ndsl.dsl.typing import Float
@@ -13,9 +16,6 @@
 from ndsl.initialization.sizer import SubtileGridSizer
 from ndsl.quantity import Quantity
 
-import pace.physics
-import pyFV3
-
 
 @dataclasses.dataclass()
 class TendencyState:
@@ -64,7 +64,7 @@ def init_zeros(cls, quantity_factory: QuantityFactory) -> "TendencyState":
 @dataclasses.dataclass
 class DriverState:
     dycore_state: pyFV3.DycoreState
-    physics_state: pace.physics.PhysicsState
+    physics_state: pySHiELD.PhysicsState
     tendency_state: TendencyState
     grid_data: GridData
     damping_coefficients: DampingCoefficients
@@ -81,7 +81,7 @@ def load_state_from_restart(
         damping_coefficients: DampingCoefficients,
         driver_grid_data: DriverGridData,
         grid_data: GridData,
-        schemes: List[pace.physics.PHYSICS_PACKAGES],
+        schemes: List[pySHiELD.PHYSICS_PACKAGES],
     ) -> "DriverState":
         comm = driver_config.comm_config.get_comm()
         communicator = Communicator.from_layout(comm=comm, layout=driver_config.layout)
@@ -182,7 +182,7 @@ def _restart_driver_state(
     damping_coefficients: DampingCoefficients,
     driver_grid_data: DriverGridData,
     grid_data: GridData,
-    schemes: List[pace.physics.PHYSICS_PACKAGES],
+    schemes: List[pySHiELD.PHYSICS_PACKAGES],
 ):
     fs = get_fs(path)
 
@@ -204,7 +204,7 @@ def _restart_driver_state(
             "restart_dycore_state",
         )
 
-    physics_state = pace.physics.PhysicsState.init_zeros(
+    physics_state = pySHiELD.PhysicsState.init_zeros(
         quantity_factory=quantity_factory, schemes=schemes
     )
 

driver/setup.py

@@ -7,8 +7,6 @@
 
 requirements = [
     "ndsl",
-    "pyFV3",
-    "pace-physics",
     "dacite",
     "pyyaml",
     "mpi4py",
@@ -41,7 +39,7 @@
     license="BSD license",
     packages=find_namespace_packages(include=["pace.*"]),
     include_package_data=True,
-    url="https://github.com/ai2cm/pace",
+    url="https://github.com/NOAA-GFDL/pace",
     version="0.2.0",
     zip_safe=False,
 )