refactor: various cleanup/fixes

autotest/test_flopy_io.py

@@ -27,7 +27,9 @@ def test_relpath_safe(function_tmpdir, scrub):
         platform.system() == "Windows"
         and splitdrive(function_tmpdir)[0] != splitdrive(getcwd())[0]
     ):
-        assert Path(relpath_safe(function_tmpdir)) == function_tmpdir.absolute()
+        assert (
+            Path(relpath_safe(function_tmpdir)) == function_tmpdir.absolute()
+        )
         assert relpath_safe(which("mf6")) == str(Path(which("mf6")).absolute())
     else:
         assert Path(

flopy/export/shapefile_utils.py

@@ -64,7 +64,7 @@ def write_grid_shapefile(
     nan_val=np.nan,
     epsg=None,
     prj: Union[str, os.PathLike] = None,
-    verbose=False
+    verbose=False,
 ):
     """
     Method to write a shapefile of gridded input data

flopy/export/utils.py

@@ -295,7 +295,7 @@ def output_helper(
     ml,
     oudic,
     verbose=False,
-    **kwargs
+    **kwargs,
 ):
     """
     Export model outputs using the model spatial reference info.
@@ -663,7 +663,7 @@ def package_export(
     pak,
     fmt=None,
     verbose=False,
-    **kwargs
+    **kwargs,
 ):
     """
     Method to export a package to shapefile or netcdf
@@ -1336,7 +1336,9 @@ def array3d_export(f: Union[str, os.PathLike], u3d, fmt=None, **kwargs):
         raise NotImplementedError(f"unrecognized export argument:{f}")
 
 
-def array2d_export(f: Union[str, os.PathLike], u2d, fmt=None, verbose=False, **kwargs):
+def array2d_export(
+    f: Union[str, os.PathLike], u2d, fmt=None, verbose=False, **kwargs
+):
     """
     export helper for Util2d instances
 
@@ -1377,7 +1379,9 @@ def array2d_export(f: Union[str, os.PathLike], u2d, fmt=None, verbose=False, **k
 
     if isinstance(f, str) and f.lower().endswith(".shp"):
         name = shapefile_utils.shape_attr_name(u2d.name, keep_layer=True)
-        shapefile_utils.write_grid_shapefile(f, modelgrid, {name: u2d.array}, verbose=verbose)
+        shapefile_utils.write_grid_shapefile(
+            f, modelgrid, {name: u2d.array}, verbose=verbose
+        )
         return
 
     elif isinstance(f, str) and f.lower().endswith(".asc"):

flopy/utils/compare.py

@@ -1,6 +1,6 @@
 import os
 import textwrap
-from typing import List, Union
+from typing import List, Union, Optional
 
 import numpy as np
 
@@ -79,13 +79,13 @@ def _difftol(v1, v2, tol):
 
 
 def compare_budget(
-    namefile1,
-    namefile2,
+    namefile1: Optional[Union[str, os.PathLike]],
+    namefile2: Optional[Union[str, os.PathLike]],
     max_cumpd=0.01,
     max_incpd=0.01,
-    outfile=None,
-    files1=None,
-    files2=None,
+    outfile: Optional[Union[str, os.PathLike]] = None,
+    files1: Optional[Union[str, os.PathLike, List[Union[str, os.PathLike]]]] = None,
+    files2: Optional[Union[str, os.PathLike, List[Union[str, os.PathLike]]]] = None,
 ):
     """Compare the budget results from two simulations.
 
@@ -282,13 +282,13 @@ def compare_budget(
 
 
 def compare_swrbudget(
-    namefile1,
-    namefile2,
+    namefile1: Optional[Union[str, os.PathLike]],
+    namefile2: Optional[Union[str, os.PathLike]],
     max_cumpd=0.01,
     max_incpd=0.01,
-    outfile=None,
-    files1=None,
-    files2=None,
+    outfile: Optional[Union[str, os.PathLike]] = None,
+    files1: Optional[Union[str, os.PathLike, List[Union[str, os.PathLike]]]] = None,
+    files2: Optional[Union[str, os.PathLike, List[Union[str, os.PathLike]]]] = None,
 ):
     """Compare the SWR budget results from two simulations.
 
@@ -477,18 +477,18 @@ def compare_swrbudget(
 
 
 def compare_heads(
-    namefile1: Union[str, os.PathLike, None],
-    namefile2: Union[str, os.PathLike, None],
+    namefile1: Optional[Union[str, os.PathLike]],
+    namefile2: Optional[Union[str, os.PathLike]],
     precision="auto",
     text="head",
     text2=None,
     htol=0.001,
-    outfile: Union[str, os.PathLike, None] = None,
-    files1: Union[str, os.PathLike, List[Union[str, os.PathLike]]] = None,
-    files2: Union[str, os.PathLike, List[Union[str, os.PathLike]]] = None,
+    outfile: Optional[Union[str, os.PathLike]] = None,
+    files1: Optional[Union[str, os.PathLike, List[Union[str, os.PathLike]]]] = None,
+    files2: Optional[Union[str, os.PathLike, List[Union[str, os.PathLike]]]] = None,
     difftol=False,
     verbose=False,
-    exfile: Union[str, os.PathLike, None] = None,
+    exfile: Optional[Union[str, os.PathLike]] = None,
     exarr=None,
     maxerr=None,
 ):
@@ -868,13 +868,13 @@ def compare_heads(
 
 
 def compare_concentrations(
-    namefile1,
-    namefile2,
+    namefile1: Union[str, os.PathLike],
+    namefile2: Union[str, os.PathLike],
     precision="auto",
     ctol=0.001,
-    outfile=None,
-    files1=None,
-    files2=None,
+    outfile: Optional[Union[str, os.PathLike]] = None,
+    files1: Optional[Union[str, os.PathLike, List[Union[str, os.PathLike]]]] = None,
+    files2: Optional[Union[str, os.PathLike, List[Union[str, os.PathLike]]]] = None,
     difftol=False,
     verbose=False,
 ):
@@ -1098,12 +1098,12 @@ def compare_concentrations(
 
 
 def compare_stages(
-    namefile1=None,
-    namefile2=None,
-    files1=None,
-    files2=None,
+    namefile1: Union[str, os.PathLike] = None,
+    namefile2: Union[str, os.PathLike] = None,
+    files1: Optional[Union[str, os.PathLike, List[Union[str, os.PathLike]]]] = None,
+    files2: Optional[Union[str, os.PathLike, List[Union[str, os.PathLike]]]] = None,
     htol=0.001,
-    outfile=None,
+    outfile: Optional[Union[str, os.PathLike]] = None,
     difftol=False,
     verbose=False,
 ):
@@ -1310,16 +1310,16 @@ def compare_stages(
 
 
 def compare(
-    namefile1,
-    namefile2,
+    namefile1: Union[str, os.PathLike] = None,
+    namefile2: Union[str, os.PathLike] = None,
     precision="auto",
     max_cumpd=0.01,
     max_incpd=0.01,
     htol=0.001,
-    outfile1=None,
-    outfile2=None,
-    files1=None,
-    files2=None,
+    outfile1: Optional[Union[str, os.PathLike]] = None,
+    outfile2: Optional[Union[str, os.PathLike]] = None,
+    files1: Optional[Union[str, os.PathLike, List[Union[str, os.PathLike]]]] = None,
+    files2: Optional[Union[str, os.PathLike, List[Union[str, os.PathLike]]]] = None,
 ):
     """Compare the budget and head results for two MODFLOW-based model
     simulations.
@@ -1389,7 +1389,7 @@ def compare(
     return success
 
 
-def eval_bud_diff(fpth, b0, b1, ia=None, dtol=1e-6):
+def eval_bud_diff(fpth: Union[str, os.PathLike], b0, b1, ia=None, dtol=1e-6):
     # To use this eval_bud_diff function on a gwf or gwt budget file,
     # the function may need ia, in order to exclude comparison of the residual
     # term, which is stored in the diagonal position of the flowja array.

flopy/utils/datafile.py

@@ -221,7 +221,7 @@ def to_shapefile(
         totim=None,
         mflay=None,
         attrib_name="lf_data",
-        verbose=False
+        verbose=False,
     ):
         """
         Export model output data to a shapefile at a specific location