Always context managers when handling netCDF4.Dataset objects (#2734)

Author: schlunma

esmvalcore/cmor/_fixes/cmip6/cesm2.py

@@ -31,12 +31,11 @@ def _fix_formula_terms(
             output_dir, filepath, add_unique_suffix=add_unique_suffix
         )
         copyfile(filepath, new_path)
-        dataset = Dataset(new_path, mode="a")
-        dataset.variables["lev"].formula_terms = "p0: p0 a: a b: b ps: ps"
-        dataset.variables[
-            "lev"
-        ].standard_name = "atmosphere_hybrid_sigma_pressure_coordinate"
-        dataset.close()
+        with Dataset(new_path, mode="a") as dataset:
+            dataset.variables["lev"].formula_terms = "p0: p0 a: a b: b ps: ps"
+            dataset.variables[
+                "lev"
+            ].standard_name = "atmosphere_hybrid_sigma_pressure_coordinate"
         return new_path
 
     def fix_file(self, filepath, output_dir, add_unique_suffix=False):
@@ -69,10 +68,13 @@ def fix_file(self, filepath, output_dir, add_unique_suffix=False):
         new_path = self._fix_formula_terms(
             filepath, output_dir, add_unique_suffix=add_unique_suffix
         )
-        dataset = Dataset(new_path, mode="a")
-        dataset.variables["a_bnds"][:] = dataset.variables["a_bnds"][::-1, :]
-        dataset.variables["b_bnds"][:] = dataset.variables["b_bnds"][::-1, :]
-        dataset.close()
+        with Dataset(new_path, mode="a") as dataset:
+            dataset.variables["a_bnds"][:] = dataset.variables["a_bnds"][
+                ::-1, :
+            ]
+            dataset.variables["b_bnds"][:] = dataset.variables["b_bnds"][
+                ::-1, :
+            ]
         return new_path
 
     def fix_metadata(self, cubes):

esmvalcore/cmor/_fixes/cmip6/cesm2_waccm.py

@@ -45,10 +45,13 @@ def fix_file(self, filepath, output_dir, add_unique_suffix=False):
         new_path = self._fix_formula_terms(
             filepath, output_dir, add_unique_suffix=add_unique_suffix
         )
-        dataset = Dataset(new_path, mode="a")
-        dataset.variables["a_bnds"][:] = dataset.variables["a_bnds"][:, ::-1]
-        dataset.variables["b_bnds"][:] = dataset.variables["b_bnds"][:, ::-1]
-        dataset.close()
+        with Dataset(new_path, mode="a") as dataset:
+            dataset.variables["a_bnds"][:] = dataset.variables["a_bnds"][
+                :, ::-1
+            ]
+            dataset.variables["b_bnds"][:] = dataset.variables["b_bnds"][
+                :, ::-1
+            ]
         return new_path
 
 

esmvalcore/local.py

@@ -145,20 +145,20 @@ def _get_start_end_date(
         and Path(file).exists()
     ):
         logger.debug("Must load file %s for daterange ", file)
-        dataset = Dataset(file)
-        for variable in dataset.variables.values():
-            var_name = _get_var_name(variable)
-            if var_name == "time" and "units" in variable.ncattrs():
-                time_units = Unit(variable.getncattr("units"))
-                start_date = isodate.date_isoformat(
-                    time_units.num2date(variable[0]),
-                    format=isodate.isostrf.DATE_BAS_COMPLETE,
-                )
-                end_date = isodate.date_isoformat(
-                    time_units.num2date(variable[-1]),
-                    format=isodate.isostrf.DATE_BAS_COMPLETE,
-                )
-                break
+        with Dataset(file) as dataset:
+            for variable in dataset.variables.values():
+                var_name = _get_var_name(variable)
+                if var_name == "time" and "units" in variable.ncattrs():
+                    time_units = Unit(variable.getncattr("units"))
+                    start_date = isodate.date_isoformat(
+                        time_units.num2date(variable[0]),
+                        format=isodate.isostrf.DATE_BAS_COMPLETE,
+                    )
+                    end_date = isodate.date_isoformat(
+                        time_units.num2date(variable[-1]),
+                        format=isodate.isostrf.DATE_BAS_COMPLETE,
+                    )
+                    break
 
     if start_date is None or end_date is None:
         raise ValueError(