Merge pull request #20 from hgloeckner/minor_l3_changes

Minor l3 changes

pydropsonde/helper/__init__.py

@@ -80,6 +80,15 @@
             "positive": "up",
         }
     },
+    "alt": {
+        "attributes": {
+            "standard_name": "altitude",
+            "long_name": "altitude above MSL",
+            "units": "m",
+            "axis": "Z",
+            "positive": "up",
+        }
+    },
 }
 
 encoding_variables = {
@@ -176,7 +185,7 @@ def calc_q_from_rh(ds):
     )
     q = mpcalc.specific_humidity_from_mixing_ratio(vmr)
 
-    ds["q"] = (ds.rh.dims, q.magnitude)
+    ds = ds.assign(q=(ds.rh.dims, q.magnitude))
     ds["q"].attrs = dict(
         standard_name="specific humidity",
         long_name="specific humidity",
@@ -201,7 +210,7 @@ def calc_theta_from_T(ds):
     theta = mpcalc.potential_temperature(
         ds.p.values * units.Pa, ds.ta.values * units.kelvin
     )
-    ds["theta"] = (ds.ta.dims, theta.magnitude)
+    ds = ds.assign(theta=(ds.ta.dims, theta.magnitude))
     ds["theta"].attrs = dict(
         standard_name="potential temperature",
         long_name="potential temperature",

pydropsonde/pipeline.py

@@ -280,15 +280,14 @@ def iterate_Sonde_method_over_dict_of_Sondes_objects(
             result = function(value, **get_args_for_function(config, function))
             if result is not None:
                 new_dict[key] = result
-        my_dict = new_dict
+
+            my_dict = new_dict
 
     return my_dict
 
 
 def sondes_to_gridded(sondes: dict, config: configparser.ConfigParser):
-    flight_id = list(sondes.values())[0].flight_id
-    platform_id = list(sondes.values())[0].platform_id
-    gridded = Gridded(sondes, flight_id, platform_id)
+    gridded = Gridded(sondes)
     gridded.concat_sondes()
     return gridded
 
@@ -449,7 +448,7 @@ def run_pipeline(pipeline: dict, config: configparser.ConfigParser):
             "add_q_and_theta_to_l2_ds",
             "remove_non_mono_incr_alt",
             "interpolate_alt",
-            "prepare_l2_for_gridded",
+            "add_attributes_as_var",
         ],
         "output": "sondes",
         "comment": "This step reads from the saved L2 files and prepares individual sonde datasets before they can be concatenated to create L3.",

pydropsonde/processor.py

@@ -1008,7 +1008,7 @@ def add_q_and_theta_to_l2_ds(self):
         ds = hh.calc_q_from_rh(ds)
         ds = hh.calc_theta_from_T(ds)
 
-        object.__setattr__(self, "_interim_l3_ds", ds)
+        object.__setattr__(self, "_prep_l3_ds", ds)
 
         return self
 
@@ -1096,7 +1096,7 @@ def interpolate_alt(
 
         return self
 
-    def prepare_l2_for_gridded(self):
+    def add_attributes_as_var(self):
         """
         Prepares l2 datasets to be concatenated to gridded.
         adds all attributes as variables to avoid conflicts when concatenating because attributes are different
@@ -1114,8 +1114,6 @@ def prepare_l2_for_gridded(self):
 @dataclass(order=True)
 class Gridded:
     sondes: dict
-    flight_id: str
-    platform_id: str
 
     def concat_sondes(self):
         """

tests/test_gridded.py

@@ -0,0 +1,27 @@
+import pytest
+import os
+import xarray as xr
+from pydropsonde.processor import Gridded
+
+sondes = None
+l3_default = f"Level_3.nc"
+
+
+@pytest.fixture
+def gridded():
+    return Gridded(sondes)
+
+
+def test_l3_dir(gridded):
+    with pytest.raises(ValueError):
+        gridded.get_l3_dir()
+
+
+def test_l3_dir_name(gridded):
+    gridded.get_l3_dir(l3_dir="test")
+    assert gridded.l3_dir == "test"
+
+
+def test_l3_default(gridded):
+    gridded.get_l3_filename()
+    assert gridded.l3_filename == l3_default