refactor: use PathLike and curdir concisely and consistently (#2589)

This refactor is mostly related to PathLike and curdir from the os module.

- Import these items to use as (e.g.) PathLike or os.PathLike
- Try to make docstrings related to these more consistent
- Replace typing Optional[Union[...]] with Union[..., None]

Author: mwtoews

.docs/Notebooks/groundwater2023_watershed_example.py

@@ -22,8 +22,8 @@
 #
 
 import os
-import pathlib as pl
 import sys
+from pathlib import Path
 
 import git
 import matplotlib as mpl
@@ -111,11 +111,11 @@ def set_idomain(grid, boundary):
 # Check if we are in the repository and define the data path.
 
 try:
-    root = pl.Path(git.Repo(".", search_parent_directories=True).working_dir)
+    root = Path(git.Repo(".", search_parent_directories=True).working_dir)
 except:
     root = None
 
-data_path = root / "examples" / "data" if root else pl.Path.cwd()
+data_path = root / "examples" / "data" if root else Path.cwd()
 folder_name = "groundwater2023"
 fname = "geometries.yml"
 pooch.retrieve(

.docs/Notebooks/mf6_support_example.py

@@ -46,7 +46,7 @@
 # - `sim_ws`: `os.curdir` ('.')
 # - `sim_tdis_file`: 'modflow6.tdis'
 #
-# The `sim_ws` parameter accepts `str` or `os.PathLike` arguments.
+# The `sim_ws` parameter accepts `str` or `PathLike` arguments.
 
 # +
 import os
@@ -495,7 +495,7 @@
 model.dis.export(pth / "dis.nc")
 
 # export the botm array to a shapefile
-model.dis.botm.export(str(pth / "botm.shp"))  # supports os.PathLike or str
+model.dis.botm.export(pth / "botm.shp")  # supports PathLike or str
 # -
 
 # ## Loading an Existing MF6 Simulation

flopy/discretization/grid.py

@@ -3,6 +3,7 @@
 import re
 import warnings
 from collections import defaultdict
+from os import PathLike
 
 import numpy as np
 
@@ -70,7 +71,7 @@ class Grid:
         The value can be anything accepted by
         :meth:`pyproj.CRS.from_user_input() <pyproj.crs.CRS.from_user_input>`,
         such as an authority string (eg "EPSG:26916") or a WKT string.
-    prjfile : str or pathlike, optional if `crs` is specified
+    prjfile : str or PathLike, optional if `crs` is specified
         ESRI-style projection file with well-known text defining the CRS
         for the model grid (must be projected; geographic CRS are not supported).
     xoff : float
@@ -87,7 +88,7 @@ class Grid:
         .. deprecated:: 3.5
            The following keyword options will be removed for FloPy 3.6:
 
-             - ``prj`` (str or pathlike): use ``prjfile`` instead.
+             - ``prj`` (str or PathLike): use ``prjfile`` instead.
              - ``epsg`` (int): use ``crs`` instead.
              - ``proj4`` (str): use ``crs`` instead.
 
@@ -381,7 +382,7 @@ def prjfile(self, prjfile):
         if prjfile is None:
             self._prjfile = None
             return
-        if not isinstance(prjfile, (str, os.PathLike)):
+        if not isinstance(prjfile, (str, PathLike)):
             raise ValueError("prjfile property must be str, PathLike or None")
         self._prjfile = prjfile
         # If crs was previously unset, use .prj file input
@@ -997,7 +998,7 @@ def set_coord_info(
             The value can be anything accepted by
             :meth:`pyproj.CRS.from_user_input() <pyproj.crs.CRS.from_user_input>`,
             such as an authority string (eg "EPSG:26916") or a WKT string.
-        prjfile : str or pathlike, optional
+        prjfile : str or PathLike, optional
             ESRI-style projection file with well-known text defining the CRS
             for the model grid (must be projected; geographic CRS are not
             supported).

flopy/discretization/structuredgrid.py

@@ -1,5 +1,6 @@
 import copy
 import os.path
+from os import PathLike
 from typing import Union
 
 import numpy as np
@@ -102,7 +103,7 @@ class for a structured model grid
         The value can be anything accepted by
         :meth:`pyproj.CRS.from_user_input() <pyproj.crs.CRS.from_user_input>`,
         such as an authority string (eg "EPSG:26916") or a WKT string.
-    prjfile : str or pathlike, optional if `crs` is specified
+    prjfile : str or PathLike, optional if `crs` is specified
         ESRI-style projection file with well-known text defining the CRS
         for the model grid (must be projected; geographic CRS are not supported).
     xoff : float
@@ -119,7 +120,7 @@ class for a structured model grid
         .. deprecated:: 3.5
            The following keyword options will be removed for FloPy 3.6:
 
-             - ``prj`` (str or pathlike): use ``prjfile`` instead.
+             - ``prj`` (str or PathLike): use ``prjfile`` instead.
              - ``epsg`` (int): use ``crs`` instead.
              - ``proj4`` (str): use ``crs`` instead.
 
@@ -1779,7 +1780,7 @@ def from_binary_grid_file(cls, file_path, verbose=False):
         )
 
     @classmethod
-    def from_gridspec(cls, file_path: Union[str, os.PathLike], lenuni=0):
+    def from_gridspec(cls, file_path: Union[str, PathLike], lenuni=0):
         """
         Instantiate a StructuredGrid from grid specification file.
 

flopy/discretization/unstructuredgrid.py

@@ -1,5 +1,6 @@
 import copy
 import os
+from os import PathLike
 from typing import Union
 
 import numpy as np
@@ -56,7 +57,7 @@ class UnstructuredGrid(Grid):
         The value can be anything accepted by
         :meth:`pyproj.CRS.from_user_input() <pyproj.crs.CRS.from_user_input>`,
         such as an authority string (eg "EPSG:26916") or a WKT string.
-    prjfile : str or pathlike, optional if `crs` is specified
+    prjfile : str or PathLike, optional if `crs` is specified
         ESRI-style projection file with well-known text defining the CRS
         for the model grid (must be projected; geographic CRS are not supported).
         beneath the top layer.
@@ -78,7 +79,7 @@ class UnstructuredGrid(Grid):
         .. deprecated:: 3.5
            The following keyword options will be removed for FloPy 3.6:
 
-             - ``prj`` (str or pathlike): use ``prjfile`` instead.
+             - ``prj`` (str or PathLike): use ``prjfile`` instead.
              - ``epsg`` (int): use ``crs`` instead.
              - ``proj4`` (str): use ``crs`` instead.
 
@@ -1118,7 +1119,7 @@ def from_binary_grid_file(cls, file_path, verbose=False):
             )
 
     @classmethod
-    def from_gridspec(cls, file_path: Union[str, os.PathLike]):
+    def from_gridspec(cls, file_path: Union[str, PathLike]):
         """
         Create an UnstructuredGrid from a grid specification file.
 

flopy/discretization/vertexgrid.py

@@ -32,7 +32,7 @@ class for a vertex model grid
         The value can be anything accepted by
         :meth:`pyproj.CRS.from_user_input() <pyproj.crs.CRS.from_user_input>`,
         such as an authority string (eg "EPSG:26916") or a WKT string.
-    prjfile : str or pathlike, optional if `crs` is specified
+    prjfile : str or PathLike, optional if `crs` is specified
         ESRI-style projection file with well-known text defining the CRS
         for the model grid (must be projected; geographic CRS are not supported).
     xoff : float
@@ -49,7 +49,7 @@ class for a vertex model grid
         .. deprecated:: 3.5
            The following keyword options will be removed for FloPy 3.6:
 
-             - ``prj`` (str or pathlike): use ``prjfile`` instead.
+             - ``prj`` (str or PathLike): use ``prjfile`` instead.
              - ``epsg`` (int): use ``crs`` instead.
              - ``proj4`` (str): use ``crs`` instead.
 

flopy/export/netcdf.py

@@ -5,6 +5,7 @@
 import socket
 import time
 from datetime import datetime
+from os import PathLike
 from pathlib import Path
 from typing import Optional, Union
 
@@ -150,7 +151,7 @@ class NetCdf:
 
     def __init__(
         self,
-        output_filename: Union[str, os.PathLike],
+        output_filename: Union[str, PathLike],
         model,
         time_values=None,
         z_positive="up",
@@ -170,9 +171,9 @@ def __init__(
             self.logger = Logger(verbose)
         self.var_attr_dict = {}
         self.log = self.logger.log
-        if os.path.exists(output_filename):
+        if output_filename.exists():
             self.logger.warn(f"removing existing nc file: {output_filename}")
-            os.remove(output_filename)
+            output_filename.unlink()
         self.output_filename = output_filename
 
         self.forgive = bool(forgive)

flopy/export/shapefile_utils.py

@@ -9,6 +9,7 @@
 import shutil
 import sys
 import warnings
+from os import PathLike
 from pathlib import Path
 from typing import Optional, Union
 from warnings import warn
@@ -21,7 +22,7 @@
 from ..utils.crs import get_crs
 
 
-def write_gridlines_shapefile(filename: Union[str, os.PathLike], mg):
+def write_gridlines_shapefile(filename: Union[str, PathLike], mg):
     """
     Write a polyline shapefile of the grid lines - a lightweight alternative
     to polygons.
@@ -59,12 +60,12 @@ def write_gridlines_shapefile(filename: Union[str, os.PathLike], mg):
 
 
 def write_grid_shapefile(
-    path: Union[str, os.PathLike],
+    path: Union[str, PathLike],
     mg,
     array_dict,
     nan_val=np.nan,
     crs=None,
-    prjfile: Optional[Union[str, os.PathLike]] = None,
+    prjfile: Union[str, PathLike, None] = None,
     verbose=False,
     **kwargs,
 ):
@@ -87,7 +88,7 @@ def write_grid_shapefile(
         The value can be anything accepted by
         :meth:`pyproj.CRS.from_user_input() <pyproj.crs.CRS.from_user_input>`,
         such as an authority string (eg "EPSG:26916") or a WKT string.
-    prjfile : str or pathlike, optional if `crs` is specified
+    prjfile : str or PathLike, optional if `crs` is specified
         ESRI-style projection file with well-known text defining the CRS
         for the model grid (must be projected; geographic CRS are not supported).
     **kwargs : dict, optional
@@ -224,7 +225,7 @@ def write_grid_shapefile(
 
 
 def model_attributes_to_shapefile(
-    path: Union[str, os.PathLike],
+    path: Union[str, PathLike],
     ml,
     package_names=None,
     array_dict=None,
@@ -259,7 +260,7 @@ def model_attributes_to_shapefile(
             The value can be anything accepted by
             :meth:`pyproj.CRS.from_user_input() <pyproj.crs.CRS.from_user_input>`,
             such as an authority string (eg "EPSG:26916") or a WKT string.
-        prjfile : str or pathlike, optional if `crs` is specified
+        prjfile : str or PathLike, optional if `crs` is specified
             ESRI-style projection file with well-known text defining the CRS
             for the model grid (must be projected; geographic CRS are not supported).
 
@@ -535,7 +536,7 @@ def get_pyshp_field_dtypes(code):
     return dtypes.get(code, object)
 
 
-def shp2recarray(shpname: Union[str, os.PathLike]):
+def shp2recarray(shpname: Union[str, PathLike]):
     """Read a shapefile into a numpy recarray.
 
     Parameters
@@ -566,10 +567,10 @@ def shp2recarray(shpname: Union[str, os.PathLike]):
 def recarray2shp(
     recarray,
     geoms,
-    shpname: Union[str, os.PathLike] = "recarray.shp",
+    shpname: Union[str, PathLike] = "recarray.shp",
     mg=None,
     crs=None,
-    prjfile: Optional[Union[str, os.PathLike]] = None,
+    prjfile: Union[str, PathLike, None] = None,
     verbose=False,
     **kwargs,
 ):
@@ -599,7 +600,7 @@ def recarray2shp(
         The value can be anything accepted by
         :meth:`pyproj.CRS.from_user_input() <pyproj.crs.CRS.from_user_input>`,
         such as an authority string (eg "EPSG:26916") or a WKT string.
-    prjfile : str or pathlike, optional if `crs` is specified
+    prjfile : str or PathLike, optional if `crs` is specified
         ESRI-style projection file with well-known text defining the CRS
         for the model grid (must be projected; geographic CRS are not supported).
     **kwargs : dict, optional