fix deprecation warnings/errors on pytest of schimpy

Author: lily-tomkovic-DWR

schimpy/param.py

@@ -100,10 +100,10 @@ def set_interval(self, name, freq):
         dt = int(self["dt"])
         if type(freq) in (str, pd.Timedelta):
             freq = pd.tseries.frequencies.to_offset(freq)
-            dt = pd.tseries.frequencies.to_offset(f"{dt}S")
+            dt = pd.tseries.frequencies.to_offset(f"{dt}s")
             nspool = freq / dt
         elif isinstance(freq, pd.offsets.DateOffset):
-            dt = pd.tseries.frequencies.to_offset(f"{dt}S")
+            dt = pd.tseries.frequencies.to_offset(f"{dt}s")
             nspool = freq / dt
             if abs(nspool - round(nspool)) > 0.01:
                 raise ValueError("Output interval not divisible by dt")
@@ -326,7 +326,7 @@ def test_param():
     print(parms.run_start)
     print("Stack")
     print(parms.nc_stack)
-    parms.nc_stack = "8H"
+    parms.nc_stack = "8h"
     print(parms.nc_stack)
     print("IHFSKIP")
     print(parms["ihfskip"])
@@ -335,7 +335,7 @@ def test_param():
     parms.station_out = None
     print(parms.station_out_freq)
     print(parms["iout_sta"])
-    parms.station_out_freq = "15T"
+    parms.station_out_freq = "15min"
     print(parms.station_out_freq)
     print(parms["iout_sta"])
 

schimpy/schism_linestring.py

@@ -12,10 +12,13 @@
     wkbLineString,
     Feature,
     CreateGeometryFromWkb,
+    UseExceptions,
 )
 import os
 import copy
 
+UseExceptions()  # Enable exceptions (recommended)
+
 
 class LineString(shapely.geometry.LineString):
     """ """
@@ -182,7 +185,7 @@ def write(self, fpath, lines, spatial_reference=None, driver_name=None, **kwargs
                 if val is not None:
                     feature.SetField(j, val)
             layer.CreateFeature(feature)
-        datasource.Destroy()
+        datasource.Close()
 
 
 class LineStringIoFactory(object):

schimpy/schism_polygon.py

@@ -14,10 +14,13 @@
     wkbPolygon,
     FieldDefn,
     Feature,
+    UseExceptions,
 )
 import numpy as np
 import os
 
+UseExceptions()  # Enable exceptions (recommended)
+
 
 class SchismPolygon(Polygon):
     """
@@ -291,7 +294,7 @@ def write(self, fpath, polygons, spatial_reference=None, driver_name=None):
             feature.SetField(1, polygon.type)
             feature.SetField(2, polygon.attribute)
             layer.CreateFeature(feature)
-        datasource.Destroy()
+        datasource.Close()
 
 
 class SchismPolygonIoFactory(object):

schimpy/vgrid_opt2.py

@@ -2,7 +2,7 @@
 """
 Package for optimising vgrid smoothness, shape and completeness
 """
-from scipy.ndimage.filters import gaussian_filter1d
+from scipy.ndimage import gaussian_filter1d
 from schimpy.lsc2 import *
 
 

tests/test_params.py

@@ -34,8 +34,8 @@ def test_param_special(datadir):
     assert parms["rnday"] == 3000
     parms.run_start = "2010-02-04"
     assert parms.run_start == pd.Timestamp(2010, 2, 4)
-    parms.nc_stack = "8H"
-    assert parms.nc_stack == pd.tseries.frequencies.to_offset("8H")
+    parms.nc_stack = "8h"
+    assert parms.nc_stack == pd.tseries.frequencies.to_offset("8h")
     parms.nc_stack = pd.tseries.frequencies.to_offset("1D")
     assert parms["ihfskip"] == 86400 / 90
     parms.hotstart_freq = None
@@ -44,12 +44,12 @@ def test_param_special(datadir):
     assert parms["nhot"] == 1
     assert parms["nhot_write"] == (5 * 86400 / parms["dt"])
 
-    parms.station_out_freq = "30T"
+    parms.station_out_freq = "30min"
     assert parms["iout_sta"] == 1
     assert parms["nspool_sta"] == 20
     parms.station_out_freq = None
     assert parms["iout_sta"] == 0
-    parms.station_out_freq = "15T"
+    parms.station_out_freq = "15min"
 
     print(parms.hotstart_freq)
     print(parms["nhot"])

tests/testdata/prepare_schism/simple_triquad/main_good.yaml

@@ -1,4 +1,5 @@
 # Main input file of SELFE pre-processor
+prepro_output_dir: ./
 mesh:
   mesh_inputfile:       testmesh.2dm
   # mesh input file:       baydelta73.gr3

tests/testdata/prepare_schism/simple_triquad/main_good_echo.yaml

@@ -1,3 +1,4 @@
+prepro_output_dir: ./
 mesh:
   mesh_inputfile: testmesh.2dm
   open_boundaries: