Merge pull request #76 from EcoExtreML/fix_issue_74

Add time units and calendar when writing netcdf

Author: SarahAlidoost

PyStemmusScope/save.py

@@ -284,7 +284,7 @@ def to_netcdf(config_file: str, cf_filename: str) -> str:
         )
 
     # get time info
-    time = forcing_dict["time"].values
+    time = forcing_dict["time"]
 
     # read convention file
     conventions = pd.read_csv(cf_filename)
@@ -327,11 +327,18 @@ def to_netcdf(config_file: str, cf_filename: str) -> str:
     # update dimensions
     dataset = _update_dataset_attrs_dims(dataset, forcing_dict)
 
-    # # save to nc file
+    # for writing to netcdf, time attrs should be added
+    # time attrs should be the same as plumber 2 forcing data
+    # otherwise it cannot be uploaded to modelevaluation portal
+    start_time = time.dt.strftime("%Y-%m-%d").values[0]
+    time_encode = {
+        "time": {"units": f"seconds since {start_time}", "calendar": "standard"}
+    }
+    # save to nc file
     nc_filename = (
         Path(config["OutputPath"])
         / f"{Path(config['OutputPath']).stem}_STEMMUS_SCOPE.nc"
     )
-    dataset.to_netcdf(path=nc_filename)
+    dataset.to_netcdf(path=nc_filename, encoding=time_encode)
 
     return str(nc_filename)

tests/test_save.py

@@ -372,3 +372,9 @@ def test_save_to_netcdf(self, cf_convention, _make_csv_file, model_with_setup):
         assert "z" in dataset
         # check z attributes
         assert "layer_1: 0.0 - 1.0 cm" in dataset["z"].attrs["definition"]
+
+        # test time attrs
+        start_time = forcing_data["time"].dt.strftime("%Y-%m-%d").values[0]
+        dataset = xr.open_dataset(saved_nc_file, decode_times=False)
+        assert dataset.time.attrs["units"] == f"seconds since {start_time}"
+        assert dataset.time.attrs["calendar"] == "standard"