refactor: move resolve_exe to utils.flopy_io, various fixes

autotest/test_modflow.py

@@ -814,20 +814,23 @@ def test_bcs_check(function_tmpdir):
     assert np.array_equal(chk.summary_array["j"], np.array([0, 1, 1, 1, 1]))
 
 
-def test_path_arguments(function_tmpdir, module_tmpdir):
+def test_path_params_and_props(function_tmpdir, module_tmpdir):
+    # properties should be set to string abspaths regardless of
+    # pathlib.Path or str arguments
+
     mf = Modflow(
         version="mf2005", model_ws=function_tmpdir, external_path=module_tmpdir
     )
-    assert mf.model_ws == function_tmpdir
-    assert mf.external_path == module_tmpdir
+    assert mf.model_ws == str(function_tmpdir)
+    assert mf.external_path == str(module_tmpdir)
 
     mf = Modflow(
         version="mf2005",
         model_ws=str(function_tmpdir),
         external_path=str(module_tmpdir),
     )
-    assert mf.model_ws == function_tmpdir
-    assert mf.external_path == module_tmpdir
+    assert mf.model_ws == str(function_tmpdir)
+    assert mf.external_path == str(module_tmpdir)
 
 
 def test_properties_check(function_tmpdir):

autotest/test_uzf.py

@@ -643,8 +643,7 @@ def test_uzf_negative_iuzfopt(function_tmpdir):
 
     ml.write_input()
     success, buff = ml.run_model()
-    if not success:
-        raise AssertionError("UZF model with -1 iuzfopt failed to run")
+    assert success, "UZF model with -1 iuzfopt failed to run"
 
     ml2 = Modflow.load(
         "uzf_neg.nam", version="mfnwt", model_ws=function_tmpdir
@@ -653,8 +652,9 @@ def test_uzf_negative_iuzfopt(function_tmpdir):
     pet = ml2.uzf.pet.array
     extpd = ml2.uzf.pet.array
 
-    if not np.max(pet) == np.min(pet) and np.max(pet) != 0.1:
-        raise AssertionError("Read error for iuzfopt less than 0")
-
-    if not np.max(extpd) == np.min(extpd) and np.max(extpd) != 0.2:
-        raise AssertionError("Read error for iuzfopt less than 0")
+    assert (
+        np.max(pet) == np.min(pet) and np.max(pet) != 0.1
+    ), "Read error for iuzfopt less than 0"
+    assert (
+        np.max(extpd) == np.min(extpd) and np.max(extpd) != 0.2
+    ), "Read error for iuzfopt less than 0"

flopy/export/shapefile_utils.py

@@ -534,7 +534,7 @@ def recarray2shp(
     shpname: Union[str, os.PathLike] = "recarray.shp",
     mg=None,
     epsg=None,
-    prj: Union[str, os.PathLike] = None,
+    prj: Optional[Union[str, os.PathLike]] = None,
     verbose=False,
     **kwargs,
 ):
@@ -558,7 +558,7 @@ def recarray2shp(
         Path for the output shapefile
     epsg : int
         EPSG code. See https://www.epsg-registry.org/ or spatialreference.org
-    prj : str or PathLike, default None
+    prj : str or PathLike, optional, default None
         Existing projection file to be used with new shapefile.
     verbose : bool
         Whether to print verbose output

flopy/mbase.py

@@ -41,6 +41,37 @@
 iprn = -1
 
 
+def resolve_exe(exe_name: Union[str, os.PathLike]) -> str:
+    """
+    Resolves the absolute path of the executable.
+
+    Parameters
+    ----------
+    exe_name : str or PathLike
+        The executable's name or path. If only the name is provided,
+        the executable must be on the system path.
+
+    Returns
+    -------
+        str: absolute path to the executable
+    """
+
+    exe_name = str(exe_name)
+    exe = which(exe_name)
+    if exe is None:
+        if exe_name.lower().endswith(".exe"):
+            # try removing .exe suffix
+            exe = which(exe_name[:-4])
+    if exe is None:
+        # try tilde-expanded abspath
+        exe = which(Path(exe_name).expanduser().absolute())
+    if exe is None:
+        raise FileNotFoundError(
+            f"The program {exe_name} does not exist or is not executable."
+        )
+    return exe
+
+
 # external exceptions for users
 class PackageLoadException(Exception):
     """
@@ -336,7 +367,7 @@ def __init__(
         self._namefile = self.__name + "." + self.namefile_ext
         self._packagelist = []
         self.heading = ""
-        self.exe_name = resolve_exe(exe_name)
+        self.exe_name = resolve_exe(exe_name) if exe_name else "mf2005"
         self._verbose = verbose
         self.external_path = None
         self.external_extension = "ref"
@@ -1364,7 +1395,7 @@ def run_model(
         pause=False,
         report=False,
         normal_msg="normal termination",
-    ):
+    ) -> Tuple[bool, List[str]]:
         """
         This method will run the model using subprocess.Popen.
 
@@ -1383,7 +1414,6 @@ def run_model(
 
         Returns
         -------
-        (success, buff)
         success : boolean
         buff : list of lines of stdout
 
@@ -1656,37 +1686,6 @@ def to_shapefile(
         self.export(filename, package_names=package_names)
 
 
-def resolve_exe(exe_name: Union[str, os.PathLike]) -> str:
-    """
-    Resolves the absolute path of the executable.
-
-    Parameters
-    ----------
-    exe_name : str or PathLike
-        The executable's name or path. If only the name is provided,
-        the executable must be on the system path.
-
-    Returns
-    -------
-        str: absolute path to the executable
-    """
-
-    exe_name = str(exe_name)
-    exe = which(exe_name)
-    if exe is None:
-        if exe_name.lower().endswith(".exe"):
-            # try removing .exe suffix
-            exe = which(exe_name[:-4])
-    if exe is None:
-        # try tilde-expanded abspath
-        exe = which(Path(exe_name).expanduser().absolute())
-    if exe is None:
-        raise FileNotFoundError(
-            f"The program {exe_name} does not exist or is not executable."
-        )
-    return exe
-
-
 def run_model(
     exe_name: Union[str, os.PathLike],
     namefile: Optional[str],
@@ -1734,7 +1733,6 @@ def run_model(
         (Default is None)
     Returns
     -------
-    (success, buff)
     success : boolean
     buff : list of lines of stdout (empty if report is False)
 

flopy/mf6/mfmodel.py

@@ -1,6 +1,7 @@
 import inspect
 import os
 import sys
+from typing import Union
 
 import numpy as np
 
@@ -691,9 +692,9 @@ def load_base(
         model_nam_file="modflowtest.nam",
         mtype="gwf",
         version="mf6",
-        exe_name="mf6",
+        exe_name: Union[str, os.PathLike] = "mf6",
         strict=True,
-        model_rel_path=".",
+        model_rel_path=os.curdir,
         load_only=None,
     ):
         """
@@ -713,10 +714,8 @@ def load_base(
             relative path to the model name file from model working folder
         version : str
             version of modflow
-        exe_name : str
-            model executable name
-        model_ws : str
-            model working folder relative to simulation working folder
+        exe_name : str or PathLike
+            model executable name or path
         strict : bool
             strict mode when loading files
         model_rel_path : str

flopy/mf6/modflow/mfgwf.py

@@ -1,6 +1,9 @@
 # DO NOT MODIFY THIS FILE DIRECTLY.  THIS FILE MUST BE CREATED BY
 # mf6/utils/createpackages.py
 # FILE created on January 27, 2023 18:36:16 UTC
+import os
+from typing import Union
+
 from .. import mfmodel
 from ..data.mfdatautil import ArrayTemplateGenerator, ListTemplateGenerator
 
@@ -119,9 +122,9 @@ def load(
         modelname="NewModel",
         model_nam_file="modflowtest.nam",
         version="mf6",
-        exe_name="mf6",
+        exe_name: Union[str, os.PathLike] = "mf6",
         strict=True,
-        model_rel_path=".",
+        model_rel_path=os.curdir,
         load_only=None,
     ):
         return mfmodel.MFModel.load_base(

flopy/mfusg/mfusg.py

@@ -146,9 +146,9 @@ def __repr__(self):
     @classmethod
     def load(
         cls,
-        f,
+        f: str,
         version="mfusg",
-        exe_name="mfusg",
+        exe_name: Union[str, os.PathLike] = "mfusg",
         verbose=False,
         model_ws: Union[str, os.PathLike] = os.curdir,
         load_only=None,
@@ -159,23 +159,23 @@ def load(
 
         Parameters
         ----------
-        f : str or PathLike
-            Path to MODFLOW name file to load.
+        f : str
+            Name of MODFLOW name file to load.
         version : str, default "mfusg"
             MODFLOW version. Must be "mfusg".
         exe_name : str, default "mfusg"
             MODFLOW executable name.
         verbose : bool, default False
             Show messages that can be useful for debugging.
-        model_ws : str, default "."
+        model_ws : str or PathLike, default "."
             Model workspace path. Default is the current directory.
         load_only : list, str or None
             List of case insensitive packages to load, e.g. ["bas6", "lpf"].
             One package can also be specified, e.g. "rch". Default is None,
             which attempts to load all files. An empty list [] will not load
             any additional packages than is necessary. At a minimum, "dis" or
             "disu" is always loaded.
-        forgive : bool, optional
+        forgive : bool, optional, default False
             Option to raise exceptions on package load failure, which can be
             useful for debugging. Default False.
         check : boolean, optional

flopy/modflow/mf.py

@@ -71,8 +71,8 @@ class Modflow(BaseModel):
     version : str, default "mf2005"
         MODFLOW version. Choose one of: "mf2k", "mf2005" (default),
         "mfnwt", or "mfusg".
-    exe_name : str, default "mf2005"
-        The name of the executable to use.
+    exe_name : str or PathLike, default "mf2005"
+        The name or path of the executable to use.
     structured : bool, default True
         Specify if model grid is structured (default) or unstructured.
     listunit : int, default 2
@@ -162,7 +162,9 @@ def __init__(
                 print(f"Note: external_path {external_path} already exists")
             else:
                 os.makedirs(os.path.join(model_ws, external_path))
-        self.external_path = str(external_path)
+            self.external_path = str(external_path)
+        else:
+            self.external_path = None
         self.verbose = verbose
         self.mfpar = ModflowPar()
 
@@ -649,9 +651,9 @@ def load_results(self, **kwargs):
     @classmethod
     def load(
         cls,
-        f: Union[str, os.PathLike],
+        f: str,
         version="mf2005",
-        exe_name="mf2005",
+        exe_name: Union[str, os.PathLike] = "mf2005",
         verbose=False,
         model_ws: Union[str, os.PathLike] = os.curdir,
         load_only=None,
@@ -663,14 +665,14 @@ def load(
 
         Parameters
         ----------
-        f : str or PathLike
+        f : str
             Path to MODFLOW name file to load.
         version : str, default "mf2005"
             MODFLOW version. Choose one of: "mf2k", "mf2005" (default),
             or "mfnwt". Note that this can be modified on loading
             packages unique to different MODFLOW versions.
-        exe_name : str, default "mf2005"
-            MODFLOW executable name.
+        exe_name : str or PathLike, default "mf2005"
+            MODFLOW executable name or path.
         verbose : bool, default False
             Show messages that can be useful for debugging.
         model_ws : str or PathLike, default "."

flopy/pakbase.py

@@ -7,6 +7,7 @@
 import abc
 import os
 import webbrowser as wb
+from typing import Union
 
 import numpy as np
 from numpy.lib.recfunctions import stack_arrays
@@ -881,7 +882,13 @@ def write_file(self, f=None, check=False):
         return
 
     @staticmethod
-    def load(f, model, pak_type, ext_unit_dict=None, **kwargs):
+    def load(
+        f: Union[str, bytes, os.PathLike],
+        model,
+        pak_type,
+        ext_unit_dict=None,
+        **kwargs,
+    ):
         """
         Default load method for standard boundary packages.
 

flopy/seawat/swt.py

@@ -1,4 +1,5 @@
 import os
+from typing import Union
 
 from ..discretization.modeltime import ModelTime
 from ..discretization.structuredgrid import StructuredGrid
@@ -425,11 +426,11 @@ def write_name_file(self):
     @classmethod
     def load(
         cls,
-        f,
+        f: str,
         version="seawat",
-        exe_name="swtv4",
+        exe_name: Union[str, os.PathLike] = "swtv4",
         verbose=False,
-        model_ws=".",
+        model_ws: Union[str, os.PathLike] = os.curdir,
         load_only=None,
     ):
         """
@@ -438,15 +439,15 @@ def load(
         Parameters
         ----------
         f : str
-            Path to SEAWAT name file to load.
+            Name of SEAWAT name file to load.
         version : str, default "seawat"
             Version of SEAWAT to use. Valid versions are "seawat" (default).
         exe_name : str, default "swtv4"
             The name of the executable to use.
         verbose : bool, default False
             Print additional information to the screen.
-        model_ws : str, default "."
-            Model workspace.  Directory name to create model data sets.
+        model_ws : str or PathLike, default "."
+            Model workspace.  Directory to create model data sets.
             Default is the present working directory.
         load_only : list of str, optional
             Packages to load (e.g. ["lpf", "adv"]). Default None

flopy/utils/binaryfile.py

@@ -485,7 +485,6 @@ def _build_index(self):
         self.recordarray = np.array(self.recordarray, dtype=self.header_dtype)
         self.iposarray = np.array(self.iposarray)
         self.nlay = np.max(self.recordarray["ilay"])
-        return
 
     def get_databytes(self, header):
         """