cattrs converter with hook factory using xattree.asdict

flopy4/mf6/codec/__init__.py

@@ -3,6 +3,8 @@
 from typing import Any
 
 import numpy as np
+import xattree
+from cattrs import Converter
 from jinja2 import Environment, PackageLoader
 
 from flopy4.mf6 import filters
@@ -29,13 +31,13 @@
     "threshold": sys.maxsize,
 }
 
+_CONVERTER = Converter()
+_CONVERTER.register_unstructure_hook_factory(
+    lambda cls: xattree.has(cls), lambda cls: xattree.asdict
+)
 
-def unstructure(data):
-    # TODO unstructure arrays into sparse dicts
-    # TODO combine OC fields into list input as defined in the MF6 dfn
-    # TODO return a dictionary instead of the component itself, then
-    # update filters to use dictinoary access instead of getattr()
-    return data
+# TODO unstructure arrays into sparse dicts
+# TODO combine OC fields into list input as defined in the MF6 dfn
 
 
 def loads(data: str) -> Any:
@@ -51,12 +53,12 @@ def load(path: str | PathLike) -> Any:
 def dumps(data) -> str:
     template = _JINJA_ENV.get_template(_JINJA_TEMPLATE_NAME)
     with np.printoptions(**_PRINT_OPTIONS):  # type: ignore
-        return template.render(dfn=type(data).dfn, data=unstructure(data))
+        return template.render(dfn=type(data).dfn, data=_CONVERTER.unstructure(data))
 
 
 def dump(data, path: str | PathLike) -> None:
     template = _JINJA_ENV.get_template(_JINJA_TEMPLATE_NAME)
-    iterator = template.generate(dfn=type(data).dfn, data=unstructure(data))
+    iterator = template.generate(dfn=type(data).dfn, data=_CONVERTER.unstructure(data))
     with np.printoptions(**_PRINT_OPTIONS), open(path, "w") as f:  # type: ignore
         f.writelines(iterator)
 

flopy4/mf6/filters.py

@@ -35,7 +35,7 @@ def field_type(field: Field) -> str:
 @pass_context
 def field_value(ctx, field: Field):
     """Get a field's value via the template context."""
-    return getattr(ctx["data"], field["name"])
+    return ctx["data"][field["name"]]
 
 
 def array_how(value: xr.DataArray) -> str:

flopy4/mf6/simulation.py

@@ -44,20 +44,20 @@ def time(self) -> ModelTime:
 
     def run(self, exe: str | PathLike = "mf6", verbose: bool = False) -> None:
         """Run the simulation using the given executable."""
-        if self.workspace is None:
-            raise ValueError(f"Simulation {self.name} has no workspace path.")
         with cd(self.workspace):
-            stdout, stderr, retcode = run_cmd(exe, verbose=verbose)
-            if retcode != 0:
+            out, err, ret = run_cmd(exe, verbose=verbose)
+            if ret != 0:
                 raise RuntimeError(
-                    f"Simulation {self.name}: {exe} failed to run with returncode "  # type: ignore
-                    f"{retcode}, and error message:\n\n{stdout + stderr} "
+                    f"Simulation {self.name}: {exe} failed with "  # type: ignore
+                    f"return code {ret}, output:\n\n{out + err} "
                 )
 
     def load(self, format="ascii"):
         """Load the simulation in the specified format."""
-        super().load(format)
+        with cd(self.workspace):
+            super().load(format)
 
     def write(self, format="ascii"):
         """Write the simulation in the specified format."""
-        super().write(format)
+        with cd(self.workspace):
+            super().write(format)

test/test_examples.py

@@ -4,7 +4,7 @@
 
 import pytest
 from modflow_devtools.markers import requires_exe
-from modflow_devtools.misc import run_cmd
+from modflow_devtools.misc import cd, run_cmd
 
 
 @pytest.mark.slow
@@ -16,7 +16,7 @@ def test_scripts(example_script):
 
 @pytest.mark.slow
 @requires_exe("jupytext")
-def test_notebooks(example_script):
+def test_notebooks(example_script, tmp_path):
     args = [
         "jupytext",
         "--from",
@@ -26,5 +26,6 @@ def test_notebooks(example_script):
         "--execute",
         example_script,
     ]
-    stdout, stderr, retcode = run_cmd(*args, verbose=True)
-    assert not retcode, stdout + stderr
+    with cd(tmp_path):
+        out, err, ret = run_cmd(*args, verbose=True)
+    assert not ret, out + err

test/test_interface.py

@@ -37,7 +37,7 @@ def quickstart_model():
     return gwf
 
 
-def test_flopy3_model():
+def test_flopy3_model(tmp_path):
     from flopy.mbase import ModelInterface
     from flopy.pakbase import PackageInterface
 
@@ -114,12 +114,12 @@ def test_flopy3_model():
             print(f"data_type: {d.data_type}")
             print(f"array: {d.array}\n")
 
-    bpth = Path("output/flopy3_model/flopy3_model")
-    Path("output/flopy3_model").mkdir(parents=True, exist_ok=True)
+    bpth = Path(tmp_path) / "flopy3_model" / "flopy3_model"
+    (Path(tmp_path) / "flopy3_model").mkdir(parents=True, exist_ok=True)
     gwf3.plot(filename_base=bpth)
 
 
-def test_flopy3_package():
+def test_flopy3_package(tmp_path):
     from flopy.mbase import ModelInterface
     from flopy.pakbase import PackageInterface
 
@@ -236,12 +236,12 @@ def test_flopy3_package():
             if di.name == k:
                 assert np.all(np.equal(di.array, v))
 
-    bpth = Path("output/flopy3_package/flopy3_package")
-    Path("output/flopy3_package").mkdir(parents=True, exist_ok=True)
+    bpth = Path(tmp_path) / "flopy3_package" / "flopy3_package"
+    (Path(tmp_path) / "flopy3_package").mkdir(parents=True, exist_ok=True)
     dis3.plot(filename_base=bpth)
 
 
-def norun_test_flopy3_cbd_small():
+def norun_test_flopy3_cbd_small(tmp_path):
     import sys
 
     sys.path.append("/home/mjreno/.clone/usgs/flopy/autotest")
@@ -262,13 +262,13 @@ def norun_test_flopy3_cbd_small():
         dis=dis,
         dims=dims,
     )
-    bpth = Path("output/flopy3_cbd_small/flopy3_cbd_small")
-    Path("output/flopy3_cbd_small").mkdir(parents=True, exist_ok=True)
+    bpth = Path(tmp_path) / "flopy3_cbd_small" / "flopy3_cbd_small"
+    (Path(tmp_path) / "flopy3_cbd_small").mkdir(parents=True, exist_ok=True)
     gwf3 = Flopy3Model(model=gwf, modelgrid=cbd_small, modeltime=time)
     gwf3.plot(filename_base=bpth)
 
 
-def test_flopy3_grid2():
+def test_flopy3_grid2(tmp_path):
     lx = 5.0
     lz = 1.0
     nlay = 1
@@ -303,18 +303,18 @@ def test_flopy3_grid2():
         dis=dis,
         dims=dims,
     )
-    bpth = Path("output/flopy3_grid2/flopy3_grid2")
-    Path("output/flopy3_grid2").mkdir(parents=True, exist_ok=True)
+    bpth = Path(tmp_path) / "flopy3_grid2" / "flopy3_grid2"
+    (Path(tmp_path) / "flopy3_grid2").mkdir(parents=True, exist_ok=True)
     gwf3 = Flopy3Model(model=gwf, modeltime=time)
     gwf3.plot(filename_base=bpth)
 
 
-def test_flopy3_export():
+def test_flopy3_export(tmp_path):
     # see flopy test_export.py test_export_output()
-    Path("output/flopy3_model/shape").mkdir(parents=True, exist_ok=True)
-    Path("output/flopy3_package/shape").mkdir(parents=True, exist_ok=True)
-    Path("output/flopy3_model/netcdf").mkdir(parents=True, exist_ok=True)
-    Path("output/flopy3_package/netcdf").mkdir(parents=True, exist_ok=True)
+    (Path(tmp_path) / "flopy3_model" / "shape").mkdir(parents=True, exist_ok=True)
+    (Path(tmp_path) / "flopy3_package/shape").mkdir(parents=True, exist_ok=True)
+    (Path(tmp_path) / "flopy3_model/netcdf").mkdir(parents=True, exist_ok=True)
+    (Path(tmp_path) / "flopy3_package/netcdf").mkdir(parents=True, exist_ok=True)
 
     time = ModelTime(perlen=[1.0], nstp=[1], tsmult=[1.0])
 
@@ -323,20 +323,20 @@ def test_flopy3_export():
     dis3 = Flopy3Package(gwf.dis, model=gwf3)
 
     # model shapefile export
-    shp_mpth = Path("output/flopy3_model/shape/flopy3_model.shp")
+    shp_mpth = Path(tmp_path / "flopy3_model" / "shape" / "flopy3_model.shp")
     gwf3.export(f=shp_mpth)
 
     # package shapefile export
-    shp_ppth = Path("output/flopy3_package/shape/flopy3_package.shp")
+    shp_ppth = Path(tmp_path / "flopy3_package" / "shape" / "flopy3_package.shp")
     dis3.export(f=shp_ppth)
 
     # model netcdf export
-    nc_mpth = Path("output/flopy3_model/netcdf/flopy3_model.nc")
+    nc_mpth = Path(tmp_path / "flopy3_model" / "netcdf" / "flopy3_model.nc")
     # TODO: needs flopy3 fix
     # gwf3.export(f=nc_mpth)
 
     # package netcdf export
-    nc_ppth = Path("output/flopy3_package/netcdf/flopy3_package.nc")
+    nc_ppth = Path(tmp_path / "flopy3_package" / "netcdf" / "flopy3_package.nc")
     # TODO: needs flopy3 fix
     # dis3.export(f=nc_ppth)