Linter fixes (#192)

* Linter stuff * More linter stuff * Haven't been calling add_attributes for a long time, so remove
USGS-CMG · Mar 12, 2024 · 75f125b · 75f125b
1 parent 2096894
commit 75f125b
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Showing 8 changed files with 30 additions and 65 deletions.
diff --git a/stglib/aqd/aqdutils.py b/stglib/aqd/aqdutils.py
@@ -983,24 +983,23 @@ def add_vel_attributes(vel, dsattrs):
                     "Velocity bins trimmed if out of water or if side lobes intersect sea surface."
                 )
 
-    def add_attributes(var, dsattrs):
-        if inst_type == "AQD":
-            sn = dsattrs["AQDSerial_Number"]
-        elif inst_type == "VEC":
-            sn = dsattrs["VECSerialNumber"]
-        elif inst_type == "SIG":
-            sn = dsattrs["SIGSerialNo"]
-        """
-        var.attrs.update(
-            {
-                # "serial_number": sn,
-                # "initial_instrument_height": dsattrs["initial_instrument_height"],
-                # "nominal_instrument_depth": dsattrs["nominal_instrument_depth"],
-                # "height_depth_units": "m",
-                # "sensor_type": dsattrs["INST_TYPE"],
-            }
-        )
-        """
+    # def add_attributes(var, dsattrs):
+    #     if inst_type == "AQD":
+    #         sn = dsattrs["AQDSerial_Number"]
+    #     elif inst_type == "VEC":
+    #         sn = dsattrs["VECSerialNumber"]
+    #     elif inst_type == "SIG":
+    #         sn = dsattrs["SIGSerialNo"]
+    #
+    #     var.attrs.update(
+    #         {
+    #             # "serial_number": sn,
+    #             # "initial_instrument_height": dsattrs["initial_instrument_height"],
+    #             # "nominal_instrument_depth": dsattrs["nominal_instrument_depth"],
+    #             # "height_depth_units": "m",
+    #             # "sensor_type": dsattrs["INST_TYPE"],
+    #         }
+    #     )
 
     # if utils.is_cf(ds):
     #    ds.attrs["featureType"] = "timeSeriesProfile"
@@ -1216,8 +1215,6 @@ def add_attributes(var, dsattrs):
         if "P_1ac_note" in ds.attrs:
             ds["P_1ac"].attrs.update({"note": ds.attrs["P_1ac_note"]})
 
-        add_attributes(ds["P_1ac"], ds.attrs)
-
     if "bin_depth" in ds:
         ds["bin_depth"].attrs.update({"units": "m", "long_name": "bin depth"})
 
@@ -1321,36 +1318,9 @@ def add_attributes(var, dsattrs):
         )
 
     if not waves:
-        for v in ["AGC_1202", "u_1205", "v_1206", "w_1204"]:
-            if v in ds:
-                add_attributes(ds[v], ds.attrs)
         for v in ["u_1205", "v_1206", "w_1204", "w2_1204"]:
             if v in ds:
                 add_vel_attributes(ds[v], ds.attrs)
-    elif waves:
-        for v in [
-            "vel1_1277",
-            "vel2_1278",
-            "vel3_1279",
-            "AGC1_1221",
-            "AGC2_1222",
-            "AGC3_1223",
-        ]:
-            if v in ds:
-                add_attributes(ds[v], ds.attrs)
-
-    for v in [
-        "P_1",
-        "Tx_1211",
-        "Hdg_1215",
-        "Ptch_1216",
-        "Roll_1217",
-        "Bat_106",
-        "bin_depth",
-        "bindist",
-    ]:
-        if v in ds:
-            add_attributes(ds[v], ds.attrs)
 
     return ds
 

diff --git a/stglib/core/utils.py b/stglib/core/utils.py
@@ -812,6 +812,7 @@ def create_water_depth_var(ds):
             ds[press].squeeze().mean(dim="sample")
             + ds.attrs["initial_instrument_height"]
         )
+
     else:
         ds["water_depth"] = xr.DataArray(
             ds[press].squeeze() + ds.attrs["initial_instrument_height"]
@@ -1267,14 +1268,7 @@ def salinity_from_spcon(spcon):
     K5 = -6.4788
     K6 = 2.5842
 
-    return (
-        K1
-        + K2 * R**0.5
-        + K3 * R
-        + K4 * R ** (3 / 2)
-        + K5 * R**2
-        + K6 * R ** (5 / 2)
-    )
+    return K1 + K2 * R**0.5 + K3 * R + K4 * R ** (3 / 2) + K5 * R**2 + K6 * R ** (5 / 2)
 
 
 def spcon_from_salinity(S):

diff --git a/stglib/hobo.py b/stglib/hobo.py
@@ -481,7 +481,6 @@ def cdf_to_nc(cdf_filename):
 
     if "vert_dim" in ds.attrs:
         vdim = ds.attrs["vert_dim"]
-        attrsbak = ds[vdim].attrs
         # axis attr set for z in utils.create_z so need to del if other than z
         if ds.attrs["vert_dim"] != "z":
             ds[vdim].attrs["axis"] = "Z"

diff --git a/stglib/rsk/cdf2nc.py b/stglib/rsk/cdf2nc.py
@@ -1,7 +1,4 @@
-import warnings
-
 import numpy as np
-import pandas as pd
 import xarray as xr
 
 from ..core import qaqc, utils

diff --git a/stglib/rsk/csv2cdf.py b/stglib/rsk/csv2cdf.py
@@ -176,7 +176,6 @@ def csv_to_cdf(metadata):
         if utils.check_fits_in_int32(ds, "obs"):
             ds["obs"].encoding["dtype"] = "i4"
 
-        dstime = ds["time"].values
         ds = ds.drop("time")
 
         ds = ds.rename({"obs": "time"}).set_coords("time").rename({"time": "obs"})
@@ -337,7 +336,7 @@ def get_metadata(ds, var, meta, field="dataheader"):
     thisname = np.where(metanames == var.replace("_", " "))[0][0]
     for v in ["units", "calibration", "ranging"]:
         if v in dh[thisname]:
-            if type(dh[thisname][v]) == dict:
+            if isinstance(dh[thisname][v], dict):
                 ds[var].attrs[v] = str(dh[thisname][v])
             else:
                 ds[var].attrs[v] = dh[thisname][v]

diff --git a/stglib/sig/dlfncdf2nc.py b/stglib/sig/dlfncdf2nc.py
@@ -1,8 +1,8 @@
 import pkgutil
 import time
+import warnings
 
 import dolfyn
-import xarray as xr
 import xmltodict
 
 from ..aqd import aqdutils
@@ -13,6 +13,13 @@ def cdf_to_nc(cdf_filename, atmpres=False):
     """
     Load a raw .cdf file and generate a processed .nc file
     """
+
+    warnings.warn(
+        "The use of Dolfyn to process Signature data is not currently supported. Use mat_to_cdf instead. Refer to the stglib documentation for more details.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+
     # TODO: Add atmospheric pressure offset
     print(f"Loading {cdf_filename}")
     start_time = time.time()

diff --git a/stglib/tcm.py b/stglib/tcm.py
@@ -367,7 +367,6 @@ def cdf_to_nc(cdf_filename):
 
     if "vert_dim" in ds.attrs:
         vdim = ds.attrs["vert_dim"]
-        attrsbak = ds[vdim].attrs
         # axis attr set for z in utils.create_z so need to del if other than z
         if ds.attrs["vert_dim"] != "z":
             ds[vdim].attrs["axis"] = "Z"

diff --git a/stglib/vec/cdf2nc.py b/stglib/vec/cdf2nc.py
@@ -201,10 +201,10 @@ def ds_drop(ds):
 def scale_analoginput(ds):
     """convert AnalogInput from counts to volts"""
     ds["AnalogInput1"] = ds["AnalogInput1"] * 5 / 65535
-    notetxt = f"Converted from counts to volts: volts=counts*5/65535."
+    notetxt = "Converted from counts to volts: volts=counts*5/65535."
     ds = utils.insert_note(ds, "AnalogInput1", notetxt)
     ds["AnalogInput2"] = ds["AnalogInput2"] * 5 / 65535
-    notetxt = f"Converted from counts to volts: volts=counts*5/65535."
+    notetxt = "Converted from counts to volts: volts=counts*5/65535."
     ds = utils.insert_note(ds, "AnalogInput2", notetxt)
 
     return ds