refactor(shapefile_utils): pathlib compatibility, other improvements

autotest/test_export.py

@@ -9,11 +9,12 @@
 import pytest
 from autotest.conftest import (
     SHAPEFILE_EXTENSIONS,
+    excludes_platform,
     get_example_data_path,
     has_pkg,
     requires_exe,
     requires_pkg,
-    requires_spatial_reference, excludes_platform,
+    requires_spatial_reference,
 )
 from flaky import flaky
 
@@ -197,13 +198,38 @@ def test_export_output(tmpdir, example_data_path):
     nc.nc.close()
 
 
+@requires_pkg("shapefile")
+def test_write_gridlines_shapefile(tmpdir):
+    import shapefile
+
+    from flopy.discretization import StructuredGrid
+    from flopy.export.shapefile_utils import write_gridlines_shapefile
+
+    sg = StructuredGrid(
+        delr=np.ones(10) * 1.1,
+        # cell spacing along model rows
+        delc=np.ones(10) * 1.1,
+        # cell spacing along model columns
+        epsg=26715,
+    )
+    outshp = tmpdir / "gridlines.shp"
+    write_gridlines_shapefile(outshp, sg)
+
+    for suffix in [".dbf", ".prj", ".shp", ".shx"]:
+        assert outshp.with_suffix(suffix).exists()
+
+    with shapefile.Reader(str(outshp)) as sf:
+        assert sf.shapeType == shapefile.POLYLINE
+        assert len(sf) == 22
+
+
 @flaky
 @requires_pkg("shapefile", "shapely")
 def test_write_grid_shapefile(tmpdir):
     from shapefile import Reader
 
     from flopy.discretization import StructuredGrid
-    from flopy.export.shapefile_utils import shp2recarray, write_grid_shapefile
+    from flopy.export.shapefile_utils import write_grid_shapefile
 
     sg = StructuredGrid(
         delr=np.ones(10) * 1.1,
@@ -212,14 +238,17 @@ def test_write_grid_shapefile(tmpdir):
         # cell spacing along model columns
         epsg=26715,
     )
-    outshp = os.path.join(tmpdir, "junk.shp")
+    outshp = tmpdir / "junk.shp"
     write_grid_shapefile(outshp, sg, array_dict={})
 
+    for suffix in [".dbf", ".prj", ".shp", ".shx"]:
+        assert outshp.with_suffix(suffix).exists()
+
     # test that vertices aren't getting altered by writing shapefile
     # check that pyshp reads integers
     # this only check that row/column were recorded as "N"
     # not how they will be cast by python or numpy
-    sfobj = Reader(outshp)
+    sfobj = Reader(str(outshp))
     for f in sfobj.fields:
         if f[0] == "row" or f[0] == "column":
             assert f[1] == "N"
@@ -240,7 +269,7 @@ def test_write_grid_shapefile(tmpdir):
             meta = src.meta
             assert "int" in meta["schema"]["properties"]["row"]
             assert "int" in meta["schema"]["properties"]["column"]
-    except:
+    except ImportError:
         pass
 
 

flopy/export/shapefile_utils.py

@@ -4,10 +4,10 @@
 """
 import copy
 import json
-import os
 import shutil
 import sys
 import warnings
+from os.path import expandvars
 from pathlib import Path
 
 import numpy as np
@@ -26,7 +26,7 @@ def write_gridlines_shapefile(filename, mg):
 
     Parameters
     ----------
-    filename : string
+    filename : Path or str
         name of the shapefile to write
     mg : model grid
 
@@ -36,7 +36,7 @@ def write_gridlines_shapefile(filename, mg):
 
     """
     shapefile = import_optional_dependency("shapefile")
-    wr = shapefile.Writer(filename, shapeType=shapefile.POLYLINE)
+    wr = shapefile.Writer(str(filename), shapeType=shapefile.POLYLINE)
     wr.field("number", "N", 18, 0)
     if mg.__class__.__name__ == "SpatialReference":
         grid_lines = mg.get_grid_lines()
@@ -52,6 +52,7 @@ def write_gridlines_shapefile(filename, mg):
         wr.record(i)
 
     wr.close()
+    write_prj(filename, mg=mg)
     return
 
 
@@ -68,7 +69,7 @@ def write_grid_shapefile(
 
     Parameters
     ----------
-    path : str
+    path : Path or str
         shapefile file path
     mg : flopy.discretization.Grid object
         flopy model grid
@@ -78,7 +79,7 @@ def write_grid_shapefile(
         value to fill nans
     epsg : str, int
         epsg code
-    prj : str
+    prj : Path or str
         projection file name path
 
     Returns
@@ -87,7 +88,7 @@ def write_grid_shapefile(
 
     """
     shapefile = import_optional_dependency("shapefile")
-    w = shapefile.Writer(path, shapeType=shapefile.POLYGON)
+    w = shapefile.Writer(str(path), shapeType=shapefile.POLYGON)
     w.autoBalance = 1
 
     if mg.__class__.__name__ == "SpatialReference":
@@ -214,7 +215,7 @@ def model_attributes_to_shapefile(
 
     Parameters
     ----------
-    path : string
+    path : Path or str
         path to write the shapefile to
     ml : flopy.mbase
         model instance
@@ -230,7 +231,7 @@ def model_attributes_to_shapefile(
             of the modelgrid attached to the modflow model object
         epsg : int
             epsg projection information
-        prj : str
+        prj : Path or str
             user supplied prj file
 
     Returns
@@ -388,7 +389,7 @@ def shape_attr_name(name, length=6, keep_layer=False):
 
     Parameters
     ----------
-    name : string
+    name : str
         data array name
     length : int
         maximum length of string to return. Value passed to function is
@@ -400,7 +401,7 @@ def shape_attr_name(name, length=6, keep_layer=False):
 
     Returns
     -------
-    String
+    str
 
     Examples
     --------
@@ -442,7 +443,8 @@ def enforce_10ch_limit(names):
 
     Returns
     -------
-    names : list of unique strings of len <= 10.
+    list
+        list of unique strings of len <= 10.
     """
     names = [n[:5] + n[-4:] + "_" if len(n) > 10 else n for n in names]
     dups = {x: names.count(x) for x in names}
@@ -488,19 +490,19 @@ def shp2recarray(shpname):
 
     Parameters
     ----------
-    shpname : str
+    shpname : Path or str
         ESRI Shapefile.
 
     Returns
     -------
-    recarray : np.recarray
+    np.recarray
 
     """
     from ..utils.geospatial_utils import GeoSpatialCollection
 
     sf = import_optional_dependency("shapefile")
 
-    sfobj = sf.Reader(shpname)
+    sfobj = sf.Reader(str(shpname))
     dtype = [
         (str(f[0]), get_pyshp_field_dtypes(f[1])) for f in sfobj.fields[1:]
     ]
@@ -540,11 +542,11 @@ def recarray2shp(
             list of shapefile.Shape objects, or geojson geometry collection
         The number of geometries in geoms must equal the number of records in
         recarray.
-    shpname : str
+    shpname : Path or str, default "recarray.shp"
         Path for the output shapefile
     epsg : int
         EPSG code. See https://www.epsg-registry.org/ or spatialreference.org
-    prj : str
+    prj : Path or str
         Existing projection file to be used with new shapefile.
 
     Notes
@@ -578,7 +580,7 @@ def recarray2shp(
 
     # set up for pyshp 2
     shapefile = import_optional_dependency("shapefile")
-    w = shapefile.Writer(shpname, shapeType=geomtype)
+    w = shapefile.Writer(str(shpname), shapeType=geomtype)
     w.autoBalance = 1
 
     # set up the attribute fields
@@ -615,7 +617,7 @@ def recarray2shp(
 
 def write_prj(shpname, mg=None, epsg=None, prj=None, wkt_string=None):
     # projection file name
-    prjname = shpname.replace(".shp", ".prj")
+    prjname = Path(shpname).with_suffix(".prj")
 
     # figure which CRS option to use
     # prioritize args over grid reference
@@ -626,10 +628,10 @@ def write_prj(shpname, mg=None, epsg=None, prj=None, wkt_string=None):
         prjtxt = CRS.getprj(epsg)
     # copy a supplied prj file
     elif prj is not None:
-        if os.path.exists(prjname):
-            print(".prj file {} already exists ".format(prjname))
+        if prjname.exists():
+            print(f".prj file {prjname} already exists")
         else:
-            shutil.copy(prj, prjname)
+            shutil.copy(str(prj), str(prjname))
 
     elif mg is not None:
         if mg.epsg is not None:
@@ -643,8 +645,7 @@ def write_prj(shpname, mg=None, epsg=None, prj=None, wkt_string=None):
             "(writing .prj files from proj4 strings not supported)"
         )
     if prjtxt is not None:
-        with open(prjname, "w") as output:
-            output.write(prjtxt)
+        prjname.write_text(prjtxt)
 
 
 class CRS:
@@ -868,9 +869,10 @@ def getprj(epsg, addlocalreference=True, text="esriwkt"):
         addlocalreference : boolean
             adds the projection file text associated with epsg to a local
             database, epsgref.json, located in the user's data directory.
+
         Returns
         -------
-        prj : str
+        str
             text for a projection (*.prj) file.
 
         """
@@ -896,9 +898,10 @@ def get_spatialreference(epsg, text="esriwkt"):
             epsg code for coordinate system
         text : str
             string added to url
+
         Returns
         -------
-        url : str
+        str
 
         """
         from ..utils.flopy_io import get_url_text
@@ -938,9 +941,10 @@ def getproj4(epsg):
         ----------
         epsg : int
             epsg code for coordinate system
+
         Returns
         -------
-        prj : str
+        str
             text for a projection (*.prj) file.
         """
         return CRS.get_spatialreference(epsg, text="proj4")
@@ -957,22 +961,21 @@ class EpsgReference:
 
     def __init__(self):
         if sys.platform.startswith("win"):
-            flopy_appdata = Path(os.path.expandvars(r"%LOCALAPPDATA%\flopy"))
+            flopy_appdata = Path(expandvars(r"%LOCALAPPDATA%\flopy"))
         else:
             flopy_appdata = Path.home() / ".local" / "share" / "flopy"
         if not flopy_appdata.exists():
             flopy_appdata.mkdir(parents=True, exist_ok=True)
         dbname = "epsgref.json"
-        self.location = str(flopy_appdata / dbname)
+        self.location = flopy_appdata / dbname
 
     def to_dict(self):
         """
         returns dict with EPSG code integer key, and WKT CRS text
         """
         data = {}
-        if os.path.exists(self.location):
-            with open(self.location, "r") as f:
-                loaded_data = json.load(f)
+        if self.location.exists():
+            loaded_data = json.loads(self.location.read_text())
             # convert JSON key from str to EPSG integer
             for key, value in loaded_data.items():
                 try:
@@ -982,15 +985,15 @@ def to_dict(self):
         return data
 
     def _write(self, data):
-        with open(self.location, "w") as f:
+        with self.location.open("w") as f:
             json.dump(data, f, indent=0)
             f.write("\n")
 
     def reset(self, verbose=True):
-        if os.path.exists(self.location):
+        if self.location.exists():
             if verbose:
                 print(f"Resetting {self.location}")
-            os.remove(self.location)
+            self.location.unlink()
         elif verbose:
             print(f"{self.location} does not exist, no reset required")
 

flopy/mt3d/mt.py

@@ -61,7 +61,7 @@ class Mt3dms(BaseModel):
         (False, default).
     version : str, default "mt3dms"
         Mt3d version. Choose one of: "mt3dms" (default) or "mt3d-usgs".
-    exe_name : str, default "mt3dms.exe"
+    exe_name : str, default "mt3dms"
         The name of the executable to use.
     structured : bool, default True
         Specify if model grid is structured (default) or unstructured.
@@ -109,7 +109,7 @@ def __init__(
         ftlfilename="mt3d_link.ftl",
         ftlfree=False,
         version="mt3dms",
-        exe_name="mt3dms.exe",
+        exe_name="mt3dms",
         structured=True,
         listunit=16,
         ftlunit=10,
@@ -444,7 +444,7 @@ def load(
         cls,
         f,
         version="mt3dms",
-        exe_name="mt3dms.exe",
+        exe_name="mt3dms",
         verbose=False,
         model_ws=".",
         load_only=None,
@@ -460,7 +460,7 @@ def load(
             Path to MT3D name file to load.
         version : str, default "mt3dms"
             Mt3d version. Choose one of: "mt3dms" (default) or "mt3d-usgs".
-        exe_name : str, default "mt3dms.exe"
+        exe_name : str, default "mt3dms"
             The name of the executable to use.
         verbose : bool, default False
             Print information on the load process if True.