updates per reviewer suggestions

Author: dgergel

dodola/cli.py

@@ -55,21 +55,21 @@ def dodola_cli(debug):
 @click.argument("x", required=True)
 @click.argument("out", required=True)
 @click.option(
-    "--drop_leapdays/--no-drop_leapdays",
+    "--drop-leapdays/--no-drop-leapdays",
     default=True,
     help="Whether to remove leap days",
 )
 def cleancmip6(x, out, drop_leapdays):
     """Clean and standardize CMIP6 GCM to 'out'. If drop-leapdays option is set, remove leap days"""
-    services.clean_cmip6(x, out, drop_leapdays)
+    services.clean_cmip6(x, out, drop_leapdays, storage=_authenticate_storage())
 
 
 @dodola_cli.command(help="Remove leap days and update calendar")
 @click.argument("x", required=True)
 @click.argument("out", required=True)
 def removeleapdays(x, out):
     """ Remove leap days and update calendar attribute"""
-    services.remove_leapdays(x, out)
+    services.remove_leapdays(x, out, storage=_authenticate_storage())
 
 
 @dodola_cli.command(help="Bias-correct GCM on observations")

dodola/core.py

@@ -120,13 +120,13 @@ def xesmf_regrid(x, domain, method, weights_path=None):
     return regridder(x)
 
 
-def standardize_gcm(ds, leapday_removal):
+def standardize_gcm(ds, leapday_removal=True):
     """
 
     Parameters
     ----------
     x : xr.Dataset
-    leapday_removal : bool
+    leapday_removal : bool, optional
 
     Returns
     -------

dodola/services.py

@@ -165,19 +165,19 @@ def regrid(x, out, method, storage, domain_file, weights_path=None):
 
 
 @log_service
-def clean_cmip6(x, out, storage, leapday_removal=True):
+def clean_cmip6(x, out, leapday_removal, storage):
     """Cleans and standardizes CMIP6 GCM
 
     Parameters
     ----------
     x : str
-        Storage URL to input xr.Dataset that will be regridded.
+        Storage URL to input xr.Dataset that will be cleaned.
     out : str
-        Storage URL to write regridded output to.
-    storage : dodola.repository._ZarrRepo
-        Storage abstraction for data IO.
+        Storage URL to write cleaned GCM output to.
     leapday_removal : bool
         Whether or not to remove leap days.
+    storage : dodola.repository._ZarrRepo
+        Storage abstraction for data IO.
     """
     ds = storage.read(x)
     cleaned_ds = standardize_gcm(ds, leapday_removal)

dodola/tests/test_services.py

@@ -39,8 +39,11 @@ def _datafactory(x, start_time="1950-01-01"):
     )
     return out
 
+
 def _gcmfactory(x, start_time="1950-01-01"):
-    """Populate xr.Dataset with synthetic data for testing"""
+    """Populate xr.Dataset with synthetic GCM data for testing
+    that includes extra dimensions and leap days to be removed.
+    """
     start_time = str(start_time)
     if x.ndim != 1:
         raise ValueError("'x' needs dim of one")
@@ -69,6 +72,7 @@ def _gcmfactory(x, start_time="1950-01-01"):
     # out['time'] = out['time'].assign_attrs({'calendar': 'standard'})
     return out
 
+
 @pytest.fixture
 def domain_file(request):
     """ Creates a fake domain Dataset for testing"""