Actually remove it; don't just comment it out

doc/config.rst

@@ -134,8 +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.
 
@@ -199,4 +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:

stglib/core/utils.py

@@ -673,31 +673,6 @@ def create_epic_times(ds, waves=False):
     return ds
 
 
-# def create_2d_time(ds):
-#     print("Creating 2D time variable")
-#     # time increment in milliseconds
-#     td = ds.attrs["sample_interval"] * np.arange(ds.attrs["samples_per_burst"]) * 1000
-#
-#     # time_2d is a CF representation of a 2d time
-#     ds["time_2d"] = xr.DataArray(
-#         np.expand_dims(ds["time"], 1) + [np.timedelta64(int(x), "ms") for x in td],
-#         dims=("time", "sample"),
-#     )
-#
-#     raveljd = make_jd(pd.DatetimeIndex(np.ravel(ds["time_2d"])))
-#     jd_2d = np.reshape(raveljd, ds["time_2d"].shape)
-#
-#     ds["epic_time_2d"] = xr.DataArray(make_epic_time(jd_2d), dims=("time", "sample"))
-#     ds["epic_time_2d"].encoding["_FillValue"] = None
-#
-#     ds["epic_time2_2d"] = xr.DataArray(make_epic_time2(jd_2d), dims=("time", "sample"))
-#     ds["epic_time2_2d"].encoding["_FillValue"] = None
-#
-#     ds = ds.drop("time_2d")  # don't need it anymore
-#
-#     return ds
-
-
 def check_update_attrs(ds, key, value):
     """Update attr and raise warning if attr already exists and is different from replacement value"""
     if key in ds.attrs and ds.attrs[key] != value:

stglib/troll.py

@@ -152,15 +152,6 @@ def read_aquatroll(filnam, skiprows=69, encoding="utf-8", skipfooter=0):
     return df
 
 
-# def read_aquatroll_header(filnam, encoding="utf-8"):
-#     with open(filnam, encoding=encoding) as f:
-#         for line in f.readlines():
-#             if "Time Zone:" in line:
-#                 # remove commas and only return the value,
-#                 # not the 'Time Zone: ' part
-#                 return line.replace(",", "").strip()[11:]
-
-
 def ds_rename_vars(ds):
     varnames = {
         "pressure": "P_1ac",

stglib/wxt.py

@@ -178,14 +178,6 @@ def ds_rename_vars(ds):
     return ds.rename(newvars)
 
 
-# Convert data from float 64 to float32
-# def ds_convertfloat(ds):
-#     for var in ds.variables:
-#         if ds[var].name != "time":
-#             ds[var] = ds[var].astype("float32")
-#     return ds
-
-
 # Add attributes: units, standard name from CF website, epic code
 def ds_add_attrs(ds):
     ds = utils.ds_coord_no_fillvalue(ds)