steal sim run from imod-python, stub write on base component (#135)

Close #132. Also simplify how Component implements MutableMapping, it can just use children from xattree

Author: wpbonelli

docs/examples/quickstart.py

@@ -30,6 +30,8 @@
     save_budget={"*": "all"},
 )
 
+sim.run(verbose=True)
+
 # check CHD
 assert chd.data["head"][0, 0] == 1.0
 assert chd.data.head.sel(per=0)[99] == 0.0

flopy4/mf6/component.py

@@ -13,30 +13,22 @@ class Component(ABC, MutableMapping):
     def __attrs_init_subclass__(cls):
         COMPONENTS[cls.__name__.lower()] = cls
 
-    def __attrs_post_init__(self):
-        self._where = type(self).__xattree__["where"]
-
     def __getitem__(self, key):
-        data = getattr(self, self._where)
-        return data.children[key]
+        return self.children[key]  # type: ignore
 
     def __setitem__(self, key, value):
-        data = getattr(self, self._where)
-        if key in data.children:
-            data.update({key: value})
-        else:
-            data = data.assign({key: value})
-        setattr(self, self._where, data)
+        self.children[key] = value  # type: ignore
 
     def __delitem__(self, key):
-        data = getattr(self, self._where)
-        data = data.drop_nodes(key)
-        setattr(self, self._where, data)
+        del self.children[key]  # type: ignore
 
     def __iter__(self):
-        data = getattr(self, self._where)
-        return iter(data.children)
+        return iter(self.children)  # type: ignore
 
     def __len__(self):
-        data = getattr(self, self._where)
-        return len(data.children)
+        return len(self.children)  # type: ignore
+
+    def write(self) -> None:
+        # TODO: write with jinja to file
+        for child in self.children.values():  # type: ignore
+            child.write()

flopy4/mf6/simulation.py

@@ -1,6 +1,8 @@
+from os import PathLike
 from pathlib import Path
 
 from flopy.discretization.modeltime import ModelTime
+from modflow_devtools.misc import run_cmd, set_dir
 from xattree import field, xattree
 
 from flopy4.mf6.component import Component
@@ -31,3 +33,15 @@ class Simulation(Component):
     @property
     def time(self) -> ModelTime:
         return self.tdis.to_time()
+
+    def run(self, exe: str | PathLike = "mf6", verbose: bool = False) -> None:
+        """Run the simulation using the given executable."""
+        if self.path is None:
+            raise ValueError(f"Simulation {self.name} has no workspace path.")
+        with set_dir(self.path):
+            stdout, stderr, retcode = run_cmd(exe, verbose=verbose)
+            if retcode != 0:
+                raise RuntimeError(
+                    f"Simulation {self.name}: {exe} failed to run with returncode "  # type: ignore
+                    f"{retcode}, and error message:\n\n{stdout + stderr} "
+                )