Use Path objects instead of string manipulation

Importantly, reduces number of subprocess/os calls, in favour of using
Python-native operations.

regional_mom6/regional_mom6.py

@@ -1,6 +1,6 @@
 import numpy as np
 from itertools import cycle
-import os
+from pathlib import Path
 import dask.array as da
 import dask.bag as db
 import numpy as np
@@ -475,15 +475,12 @@ def __init__(
         toolpath,
         gridtype="even_spacing",
     ):
-        try:
-            os.mkdir(mom_run_dir)
-        except:
-            pass
+        self.mom_run_dir = Path(mom_run_dir)
+        self.mom_input_dir = Path(mom_input_dir)
+
+        self.mom_run_dir.mkdir(exist_ok=True)
+        self.mom_input_dir.mkdir(exist_ok=True)
 
-        try:
-            os.mkdir(mom_input_dir)
-        except:
-            pass
         self.xextent = xextent
         self.yextent = yextent
         self.daterange = [
@@ -494,29 +491,17 @@ def __init__(
         self.vlayers = vlayers
         self.dz_ratio = dz_ratio
         self.depth = depth
-        self.mom_run_dir = mom_run_dir
-        self.mom_input_dir = mom_input_dir
         self.toolpath = toolpath
         self.hgrid = self._make_hgrid(gridtype)
         self.vgrid = self._make_vgrid()
         self.gridtype = gridtype
-        # if "temp" not in os.listdir(inputdir):
-        #     os.mkdir(inputdir + "temp")
-
-        if "weights" not in os.listdir(self.mom_input_dir):
-            os.mkdir(mom_input_dir + "weights")
-        if "forcing" not in os.listdir(self.mom_input_dir):
-            os.mkdir(self.mom_input_dir + "forcing")
 
-        # create a simlink from input directory to run directory and vv
-        subprocess.run(
-            f"ln -s {self.mom_input_dir} {self.mom_run_dir}/inputdir", shell=True
-        )
-        subprocess.run(
-            f"ln -s {self.mom_run_dir} {self.mom_input_dir}/rundir", shell=True
-        )
+        # create additional directories and links
+        (self.mom_input_dir / "weights").mkdir(exist_ok=True)
+        (self.mom_input_dir / "forcing").mkdir(exist_ok=True)
 
-        return
+        (self.mom_run_dir / "inputdir").link_to(self.mom_input_dir.resolve())
+        (self.mom_input_dir / "rundir").link_to(self.mom_run_dir.resolve())
 
     def _make_hgrid(self, gridtype):
         """Sets up hgrid based on users specification of
@@ -548,7 +533,7 @@ def _make_hgrid(self, gridtype):
 
             y = np.linspace(self.yextent[0], self.yextent[1], ny)
             hgrid = rectangular_hgrid(x, y)
-            hgrid.to_netcdf(self.mom_input_dir + "/hgrid.nc")
+            hgrid.to_netcdf(self.mom_input_dir / "hgrid.nc")
 
             return hgrid
 
@@ -566,7 +551,7 @@ def _make_vgrid(self):
             }  ## THIS MIGHT BE WRONG REVISIT
         )
         vcoord["zi"].attrs = {"units": "meters"}
-        vcoord.to_netcdf(self.mom_input_dir + "/vcoord.nc")
+        vcoord.to_netcdf(self.mom_input_dir / "vcoord.nc")
 
         return vcoord
 
@@ -806,7 +791,7 @@ def ocean_forcing(
             eta_out = eta_out.isel(time=0).drop("time")
 
         vel_out.fillna(0).to_netcdf(
-            self.mom_input_dir + "forcing/init_vel.nc",
+            self.mom_input_dir / "forcing/init_vel.nc",
             mode="w",
             encoding={
                 "u": {"_FillValue": netCDF4.default_fillvals["f4"]},
@@ -815,7 +800,7 @@ def ocean_forcing(
         )
 
         tracers_out.to_netcdf(
-            self.mom_input_dir + "forcing/init_tracers.nc",
+            self.mom_input_dir / "forcing/init_tracers.nc",
             mode="w",
             encoding={
                 "xh": {"_FillValue": None},
@@ -826,7 +811,7 @@ def ocean_forcing(
             },
         )
         eta_out.to_netcdf(
-            self.mom_input_dir + "forcing/init_eta.nc",
+            self.mom_input_dir / "forcing/init_eta.nc",
             mode="w",
             encoding={
                 "xh": {"_FillValue": None},
@@ -840,12 +825,14 @@ def ocean_forcing(
         self.ic_tracers = tracers_out
         self.ic_vels = vel_out
 
-        if boundaries == None:
+        if boundaries is None:
             return
 
         print("BRUSHCUT BOUNDARIES")
 
-        ## Generate a rectangular OBC domain. This is the default configuration. For fancier domains, need to use the segment class manually
+        ## Generate a rectangular OBC domain. This is the default
+        ## configuration. For fancier domains, need to use the segment
+        ## class manually
         for i, o in enumerate(boundaries):
             print(f"Processing {o}...", end="")
             seg = segment(
@@ -956,7 +943,7 @@ def bathymetry(
             bathyout.elevation.attrs["long_name"] = "Elevation relative to sea level"
             bathyout.elevation.attrs["coordinates"] = "lon lat"
             bathyout.to_netcdf(
-                f"{self.mom_input_dir}bathy_original.nc", mode="w", engine="netcdf4"
+                self.mom_input_dir / "bathy_original.nc", mode="w", engine="netcdf4"
             )
 
             tgrid = xr.Dataset(
@@ -1003,7 +990,7 @@ def bathymetry(
             tgrid.lon.attrs["_FillValue"] = 1e20
             tgrid.lat.attrs["units"] = "degrees_north"
             tgrid.to_netcdf(
-                f"{self.mom_input_dir}topog_raw.nc", mode="w", engine="netcdf4"
+                self.mom_input_dir / "topog_raw.nc", mode="w", engine="netcdf4"
             )
             tgrid.close()
 
@@ -1020,12 +1007,12 @@ def bathymetry(
 
             topog = regridder(bathyout)
             topog.to_netcdf(
-                f"{self.mom_input_dir}topog_raw.nc", mode="w", engine="netcdf4"
+                self.mom_input_dir / "topog_raw.nc", mode="w", engine="netcdf4"
             )
 
         ## reopen topography to modify
         print("Reading in regridded bathymetry to fix up metadata...", end="")
-        topog = xr.open_dataset(self.mom_input_dir + "topog_raw.nc", engine="netcdf4")
+        topog = xr.open_dataset(self.mom_input_dir / "topog_raw.nc", engine="netcdf4")
 
         ## Ensure correct encoding
         topog = xr.Dataset(
@@ -1181,32 +1168,26 @@ def bathymetry(
         topog["depth"] = topog["depth"].where(topog["depth"] != 0, np.nan)
 
         topog.expand_dims({"ntiles": 1}).to_netcdf(
-            self.mom_input_dir + "topog_deseas.nc",
+            self.mom_input_dir / "topog_deseas.nc",
             mode="w",
             encoding={"depth": {"_FillValue": None}},
         )
 
-        subprocess.run(
-            "mv topog_deseas.nc topog.nc", shell=True, cwd=self.mom_input_dir
-        )
+        (self.mom_input_dir / "topog_deseas.nc").rename(self.mom_input_dir / "topog.nc")
         print("done.")
         self.topog = topog
-        return
 
     def FRE_tools(self, layout):
         """
         Just a wrapper for FRE Tools check_mask, make_solo_mosaic and make_quick_mosaic. User provides processor layout tuple of processing units.
         """
 
-        if "topog.nc" not in os.listdir(self.mom_input_dir):
+        if not (self.mom_input_dir / "topog.nc").exists():
             print("No topography file! Need to run make_bathymetry first")
             return
-        try:
-            os.remove(
-                "mask_table*"
-            )  ## Removes old mask table so as not to clog up inputdir
-        except:
-            pass
+
+        for p in self.mom_input_dir.glob("mask_table*"):
+            p.unlink()
 
         print(
             "MAKE SOLO MOSAIC",
@@ -1240,7 +1221,6 @@ def FRE_tools(self, layout):
             ),
         )
         self.layout = layout
-        return
 
 
 class segment: