cattrs converter with hook factory using xattree.asdict (#151)

Set up the boilerplace needed to use cattrs. Send the component to jinja as a dictionary instead of the instance itself, so the filter for value lookup can just use dict access instead of getattr().

Still need to set up conversion for list input, etc.

Also some tests weren't cleaning up after themselves, fix it.

Author: wpbonelli

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)