array converter (#103)

More complete draft of an array conversion function to expand sparse dictionary representations to a full array. Also some housekeeping, move things into their own modules.

Conversion function still needs testing, only the barest minimum here.

Author: wpbonelli

.github/workflows/ci.yml

@@ -30,6 +30,9 @@ jobs:
       - name: Run ruff
         run: pixi run lint
 
+      - name: Run mypy
+        run: pixi run mypy flopy4
+
   build:
     name: Build
     runs-on: ubuntu-latest

flopy4/mf6/__init__.py

@@ -1,101 +0,0 @@
-from abc import ABC
-from datetime import datetime
-from pathlib import Path
-from typing import Optional
-
-import numpy as np
-from attrs import define
-from numpy.typing import NDArray
-from xattree import ROOT, array, dim, field, xattree
-
-__all__ = [
-    "Component",
-    "Package",
-    "Model",
-    "Simulation",
-    "Solution",
-    "Exchange",
-    "COMPONENTS",
-]
-
-COMPONENTS = {}
-"""MF6 component registry."""
-
-
-class Component(ABC):
-    @classmethod
-    def __attrs_init_subclass__(cls):
-        COMPONENTS[cls.__name__.lower()] = cls
-
-
-@define
-class Package(Component):
-    pass
-
-
-@define
-class Model(Component):
-    pass
-
-
-@define
-class Solution(Package):
-    pass
-
-
-@define
-class Exchange(Package):
-    exgtype: type = field()
-    exgfile: Path = field()
-    exgmnamea: Optional[str] = field(default=None)
-    exgmnameb: Optional[str] = field(default=None)
-
-
-@xattree
-class Tdis(Package):
-    @define
-    class PeriodData:
-        perlen: float
-        nstp: int
-        tsmult: float
-
-    nper: int = dim(
-        name="per",
-        default=1,
-        scope=ROOT,
-        metadata={"block": "dimensions"},
-    )
-    time_units: Optional[str] = field(
-        default=None, metadata={"block": "options"}
-    )
-    start_date_time: Optional[datetime] = field(
-        default=None, metadata={"block": "options"}
-    )
-    # perioddata: NDArray[np.object_] = array(
-    #     PeriodData,
-    #     dims=("per",),
-    #     metadata={"block": "perioddata"},
-    # )
-    perlen: NDArray[np.floating] = array(
-        default=1.0,
-        dims=("per",),
-        metadata={"block": "perioddata"},
-    )
-    nstp: NDArray[np.integer] = array(
-        default=1,
-        dims=("per",),
-        metadata={"block": "perioddata"},
-    )
-    tsmult: NDArray[np.floating] = array(
-        default=1.0,
-        dims=("per",),
-        metadata={"block": "perioddata"},
-    )
-
-
-@xattree
-class Simulation(Component):
-    models: dict[str, Model] = field()
-    exchanges: dict[str, Exchange] = field()
-    solutions: dict[str, Solution] = field()
-    tdis: Tdis = field()

flopy4/mf6/component.py

@@ -0,0 +1,10 @@
+from abc import ABC
+
+COMPONENTS = {}
+"""MF6 component registry."""
+
+
+class Component(ABC):
+    @classmethod
+    def __attrs_init_subclass__(cls):
+        COMPONENTS[cls.__name__.lower()] = cls

flopy4/mf6/constants.py

@@ -0,0 +1,4 @@
+import numpy as np
+
+FILL_DEFAULT = np.nan
+FILL_DNODATA = 1e30

flopy4/mf6/converters.py

@@ -0,0 +1,66 @@
+
+import numpy as np
+from numpy.typing import NDArray
+from xattree import _get_xatspec
+
+from flopy4.mf6.constants import FILL_DNODATA
+
+
+def convert_array(value, self_, field) -> NDArray:
+    if not isinstance(value, dict):
+        # if not a dict, assume it's a numpy array
+        # and let xarray deal with it if it isn't
+        return value
+
+    # get spec
+    spec = _get_xatspec(type(self_))
+    field = spec.arrays[field.name]
+    if not field.dims:
+        raise ValueError(f"Field {field} missing dims")
+
+    # resolve dims
+    explicit_dims = self_.__dict__.get("dims", {})
+    inherited_dims = self_.parent.data.dims if self_.parent else {}
+    dims = inherited_dims | explicit_dims
+    shape = [dims.get(d, d) for d in field.dims]
+    unresolved = [d for d in shape if isinstance(d, str)]
+    if any(unresolved):
+        raise ValueError(f"Couldn't resolve dims: {unresolved}")
+
+    # create array
+    a = np.full(shape, fill_value=FILL_DNODATA, dtype=field.dtype)
+
+    def _get_nn(cellid):
+        match len(cellid):
+            case 1:
+                return cellid[0]
+            case 2:
+                k, j = cellid
+                return k * dims["ncpl"] + j
+            case 3:
+                k, i, j = cellid
+                return k * dims["row"] * dims["col"] + i * dims["col"] + j
+            case _:
+                raise ValueError(f"Invalid cellid: {cellid}")
+
+    # populate array. TODO: is there a way to do this
+    # without hardcoding awareness of kper and cellid?
+    if "per" in dims:
+        for kper, period in value.items():
+            if kper == "*":
+                kper = 0
+            match len(shape):
+                case 1:
+                    a[kper] = value
+                case _:
+                    for cellid, v in period.items():
+                        nn = _get_nn(cellid)
+                        a[kper, nn] = v
+            if kper == "*":
+                break
+    else:
+        for cellid, v in value.items():
+            nn = _get_nn(cellid)
+            a[nn] = v
+
+    return a

flopy4/mf6/exchange.py

@@ -0,0 +1,15 @@
+from pathlib import Path
+from typing import Optional
+
+from attrs import define
+from xattree import field
+
+from flopy4.mf6.package import Package
+
+
+@define
+class Exchange(Package):
+    exgtype: type = field()
+    exgfile: Path = field()
+    exgmnamea: Optional[str] = field(default=None)
+    exgmnameb: Optional[str] = field(default=None)

flopy4/mf6/gwf/__init__.py

@@ -4,12 +4,12 @@
 from attrs import define
 from xattree import field, xattree
 
-from flopy4.mf6 import Model
 from flopy4.mf6.gwf.chd import Chd
 from flopy4.mf6.gwf.dis import Dis
 from flopy4.mf6.gwf.ic import Ic
 from flopy4.mf6.gwf.npf import Npf
 from flopy4.mf6.gwf.oc import Oc
+from flopy4.mf6.model import Model
 
 __all__ = ["Gwf", "Chd", "Dis", "Ic", "Npf", "Oc"]
 

flopy4/mf6/gwf/chd.py

@@ -1,44 +1,16 @@
 from pathlib import Path
 from typing import Optional
 
-import attrs
 import numpy as np
-from attrs import define
+from attrs import Converter, define
 from numpy.typing import NDArray
-from xattree import _get_xatspec, array, field, xattree
+from xattree import array, field, xattree
 
-from flopy4.mf6 import Package
+from flopy4.mf6.converters import convert_array
+from flopy4.mf6.package import Package
 
-dnodata = 1e30
 
-
-def _get_nn(ncol, nrow, k, i, j):
-    return k * nrow * ncol + i * ncol + j
-
-
-def _convert_array(value, self_, field):
-    if not isinstance(value, dict):
-        return value
-
-    inherited_dims = self_.__dict__.get("dims", {})
-    spec = _get_xatspec(type(self_))
-    field = spec.arrays["head"]
-    shape = field.dims
-    if not shape:
-        raise ValueError()
-    dims = [inherited_dims.get(d, d) for d in shape]
-    # TODO pull out dtype from annotation
-    a = np.full(dims, fill_value=dnodata, dtype=np.float64)
-    for kper, period in value.items():
-        if kper == "*":
-            kper = 0
-        for cellid, v in period.items():
-            nn = _get_nn(inherited_dims["col"], inherited_dims["row"], *cellid)
-            a[kper, nn] = v
-    return a
-
-
-@xattree(multi="list")
+@xattree
 class Chd(Package):
     @define(slots=False)
     class Steps:
@@ -75,9 +47,7 @@ class Steps:
         ),
         default=None,
         metadata={"block": "period"},
-        converter=attrs.Converter(
-            _convert_array, takes_self=True, takes_field=True
-        ),
+        converter=Converter(convert_array, takes_self=True, takes_field=True),
     )
     aux: Optional[NDArray[np.floating]] = array(
         dims=(
@@ -86,6 +56,7 @@ class Steps:
         ),
         default=None,
         metadata={"block": "period"},
+        converter=Converter(convert_array, takes_self=True, takes_field=True),
     )
     boundname: Optional[NDArray[np.str_]] = array(
         dims=(
@@ -94,7 +65,12 @@ class Steps:
         ),
         default=None,
         metadata={"block": "period"},
+        converter=Converter(convert_array, takes_self=True, takes_field=True),
     )
     steps: Optional[NDArray[np.object_]] = array(
-        Steps, dims=("per", "node"), default=None, metadata={"block": "period"}
+        Steps,
+        dims=("per", "node"),
+        default=None,
+        metadata={"block": "period"},
+        converter=Converter(convert_array, takes_self=True, takes_field=True),
     )

flopy4/mf6/gwf/dis.py

@@ -1,8 +1,10 @@
 import numpy as np
+from attrs import Converter
 from numpy.typing import NDArray
 from xattree import array, dim, field, xattree
 
-from flopy4.mf6 import Package
+from flopy4.mf6.converters import convert_array
+from flopy4.mf6.package import Package
 
 
 @xattree
@@ -46,26 +48,31 @@ class Dis(Package):
         dims=("col",),
         default=1.0,
         metadata={"block": "griddata"},
+        converter=Converter(convert_array, takes_self=True, takes_field=True),
     )
     delc: NDArray[np.floating] = array(
         dims=("row",),
         default=1.0,
         metadata={"block": "griddata"},
+        converter=Converter(convert_array, takes_self=True, takes_field=True),
     )
     top: NDArray[np.floating] = array(
         dims=("col", "row"),
         default=1.0,
         metadata={"block": "griddata"},
+        converter=Converter(convert_array, takes_self=True, takes_field=True),
     )
     botm: NDArray[np.floating] = array(
         dims=("col", "row", "lay"),
         default=0.0,
         metadata={"block": "griddata"},
+        converter=Converter(convert_array, takes_self=True, takes_field=True),
     )
     idomain: NDArray[np.integer] = array(
         dims=("col", "row", "lay"),
         default=1,
         metadata={"block": "griddata"},
+        converter=Converter(convert_array, takes_self=True, takes_field=True),
     )
     nnodes: int = dim(name="node", scope="gwf", init=False)
 

flopy4/mf6/gwf/ic.py

@@ -1,8 +1,10 @@
 import numpy as np
+from attrs import Converter
 from numpy.typing import NDArray
 from xattree import array, field, xattree
 
-from flopy4.mf6 import Package
+from flopy4.mf6.converters import convert_array
+from flopy4.mf6.package import Package
 
 
 @xattree
@@ -11,6 +13,7 @@ class Ic(Package):
         dims=("node",),
         default=1.0,
         metadata={"block": "packagedata"},
+        converter=Converter(convert_array, takes_self=True, takes_field=True),
     )
     export_array_ascii: bool = field(
         default=False, metadata={"block": "options"}