Delete the temporary NETCDF4 file if converting to CDF5

Test to make sure it's been deleted.

Author: xylar

conda_package/mpas_tools/io.py

@@ -2,6 +2,7 @@
 import subprocess
 import sys
 from datetime import datetime
+from pathlib import Path
 
 import netCDF4
 import numpy
@@ -121,8 +122,10 @@ def write_netcdf(
     convert = format == 'NETCDF3_64BIT_DATA'
 
     if convert:
-        basename, extension = os.path.splitext(fileName)
-        out_filename = f'{basename}.netcdf4{extension}'
+        out_path = Path(fileName)
+        out_filename = (
+            out_path.parent / f'_tmp_{out_path.stem}.netcdf4{out_path.suffix}'
+        )
         format = 'NETCDF4'
         if engine == 'scipy':
             # that's not going to work
@@ -151,6 +154,8 @@ def write_netcdf(
             )
         else:
             check_call(args, logger=logger)
+        # delete the temporary NETCDF4 file
+        os.remove(out_filename)
 
 
 def update_history(ds):

conda_package/tests/test_io.py

@@ -43,6 +43,11 @@ def test_write_netcdf_cdf5_format(tmp_path):
     )
     # Should be cdf5 for NETCDF3_64BIT_DATA
     assert result.stdout.strip() == 'cdf5'
+    # Check that the temporary file was deleted
+    tmp_file = (
+        out_file.parent / f'_tmp_{out_file.stem}.netcdf4{out_file.suffix}'
+    )
+    assert not os.path.exists(tmp_file)
 
 
 def test_write_netcdf_int64_conversion_and_attr(tmp_path):
@@ -58,3 +63,40 @@ def test_write_netcdf_int64_conversion_and_attr(tmp_path):
     # Attribute should be preserved
     assert ds2['foo'].attrs['myattr'] == 'testattr'
     ds2.close()
+
+
+def test_write_netcdf_fill_value(tmp_path):
+    # Test that NaN values are written with correct fill value
+    arr = np.array([1.0, np.nan, 3.0], dtype=np.float32)
+    ds = xr.Dataset({'bar': (('x',), arr)})
+    out_file = tmp_path / 'test_fill.nc'
+    write_netcdf(ds, str(out_file))
+    ds2 = xr.open_dataset(out_file)
+    # The second value should be the default fill value for float32
+    fill_value = ds2['bar'].encoding.get('_FillValue', None)
+    assert fill_value is not None
+    assert np.isnan(ds2['bar'].values[1])
+    ds2.close()
+
+
+def test_write_netcdf_string_dim_name(tmp_path):
+    # Test that custom char_dim_name is used in encoding
+    arr = np.array([b'abc', b'def'])
+    ds = xr.Dataset({'baz': (('x',), arr)})
+    out_file = tmp_path / 'test_strdim.nc'
+    write_netcdf(ds, str(out_file), char_dim_name='CustomStrLen')
+    ds2 = xr.open_dataset(out_file)
+    # Should have the variable and correct shape
+    assert 'baz' in ds2.variables
+    ds2.close()
+    arr = np.array([1, 2, 3], dtype=np.int64)
+    ds = xr.Dataset({'foo': (('x',), arr)})
+    ds['foo'].attrs['myattr'] = 'testattr'
+    out_file = tmp_path / 'test_int64.nc'
+    write_netcdf(ds, str(out_file))
+    ds2 = xr.open_dataset(out_file)
+    # Should be int32, not int64
+    assert ds2['foo'].dtype == np.int32
+    # Attribute should be preserved
+    assert ds2['foo'].attrs['myattr'] == 'testattr'
+    ds2.close()