Merge branch 'master' into vecwaves

doc/config.rst

@@ -134,7 +134,6 @@ EXO
 EXO-specific options include:
 
 - ``skiprows``: number of lines to skip in the CSV before the real data begins
-- ``trim_by_salinity``: if ``'true'``, use salinity (``S_41``) as a master variable. Wherever salinity is ``_FillValue``, all other variables will be filled as well. Useful for when the instrument comes out of the water.
 
 Note that negative numeric values in the YAML config file must be treated with care so as not to be interpreted as strings. If you want the minimum value to be, say, -0.2 units for a particular parameter, you must write this as ``-0.2`` and not ``-.2`` in the config file. The latter format will be interpreted as a string and will cause an error.
 
@@ -198,4 +197,4 @@ Lowell TCM Hobo
 - All the _min, _max, _bad_ens, etc. options available to the EXO.
 - ``skipfooter``: number of lines to skip in the CSV file at the end of the file
 - ``ncols``: number of columns of data to read, starting at first
-- ``names``: option for user specified column names (only recommended when code will not read names using automated/default method)
+- ``names``: option for user specified column names (only recommended when code will not read names using automated/default method)

stglib/aqd/aqdutils.py

@@ -218,10 +218,6 @@ def coord_transform(vel1, vel2, vel3, heading, pitch, roll, T, T_orig, cs, out="
     return u, v, w
 
 
-def swap_bindist_to_depth(ds):
-    return ds.swap_dims({"bindist": "depth"})
-
-
 def set_orientation(VEL, T):
     """
     Create Z variable depending on instrument orientation

stglib/aqd/wvscdf2nc.py

@@ -25,8 +25,6 @@ def cdf_to_nc(cdf_filename, atmpres=False, writefile=True):
     # Make bin_depth variable
     ds = aqdutils.make_bin_depth(ds, waves=True)
 
-    # Swap dimensions from bindist to depth
-    # ds = aqdutils.swap_bindist_to_depth(ds)
     ds = cdf2nc.ds_swap_dims(ds)
     # Rename DataArrays within Dataset for EPIC compliance
     # and append depth coord to velocities and amplitudes

stglib/core/qaqc.py

@@ -186,29 +186,6 @@ def trim_bad_ens_indiv(ds, var):
     return ds
 
 
-def trim_by_salinity(ds, var):
-    if (
-        "trim_by_salinity" in ds.attrs
-        and ds.attrs["trim_by_salinity"].lower() == "true"
-        and var in ds
-    ):  # xarray doesn't support writing attributes as booleans
-        if (
-            "trim_by_salinity_exclude" in ds.attrs
-            and var in ds.attrs["trim_by_salinity_exclude"]
-        ):
-            pass
-        else:
-            print("%s: Trimming using valid salinity threshold" % var)
-            ds[var][ds["S_41"].isnull()] = np.nan
-
-            if var != "S_41":
-                notetxt = "Values filled using valid salinity threshold. "
-
-                ds = utils.insert_note(ds, var, notetxt)
-
-    return ds
-
-
 def trim_by_any(ds, var):
     attrlist = []
     for a in ds.attrs:
@@ -406,8 +383,8 @@ def trim_std_ratio(ds, var):
             ds = utils.insert_note(ds, var, notetxt)
 
         else:
-            print(
-                f"{var}_std does not exist was NOT able to trim using standard deviation ratio method"
+            raise ValueError(
+                f"User specified {ds.attrs[var + '_std_ratio']=} but {var}_std does not exist. Was not able to trim using standard deviation ratio method"
             )
 
     return ds
@@ -416,9 +393,7 @@ def trim_std_ratio(ds, var):
 def trim_warmup(ds, var):
     if var + "_warmup_samples" in ds.attrs:
         if "sample" in ds[var].coords:
-            print(ds[var])
             ds[var] = ds[var].where(ds["sample"] > ds.attrs[var + "_warmup_samples"])
-            print(ds[var])
             notetxt = f"Removed {ds.attrs[var + '_warmup_samples']} samples at the beginning of each burst. "
 
             ds = utils.insert_note(ds, var, notetxt)

stglib/core/runcmd.py

@@ -13,12 +13,15 @@ def get_metadata(args):
     with open(args.config) as f:
         config = yaml.safe_load(f)
 
-    for k in config:
-        if k in metadata:
-            warnings.warn(
-                f"attrs collision. Replacing '{k}={metadata[k]}' from global attributes file with '{k}={config[k]}' from YAML config file."
-            )
-        metadata[k] = config[k]
+    try:
+        for k in config:
+            if k in metadata:
+                warnings.warn(
+                    f"attrs collision. Replacing '{k}={metadata[k]}' from global attributes file with '{k}={config[k]}' from YAML config file."
+                )
+            metadata[k] = config[k]
+    except TypeError:
+        raise TypeError(f"Could not load metadata from {args.config}")
 
     return metadata