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cioos-siooc · Nov 16, 2023 · 5fa4c13 · 5fa4c13
1 parent 2ad9ab7
commit 5fa4c13
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Showing 5 changed files with 24 additions and 26 deletions.
diff --git a/ocean_data_parser/parsers/amundsen.py b/ocean_data_parser/parsers/amundsen.py
@@ -109,15 +109,17 @@ def int_format(
                 key, value = line.strip()[1:].split(":", 1)
                 metadata[key.strip()] = value.strip()
             elif line == "% Fluorescence [ug/L]":
-                metadata['Fluo'] = "Fluorescence [ug/L]"
+                metadata["Fluo"] = "Fluorescence [ug/L]"
             elif line == "% Conservative Temperature (TEOS-10) [deg C]":
-                metadata['CONT'] = "Conservative Temperature (TEOS-10) [deg C]"
+                metadata["CONT"] = "Conservative Temperature (TEOS-10) [deg C]"
             elif line == "% In situ density TEOS10 ((s, t, p) - 1000) [kg/m^3]":
-                metadata['D_CT'] = "In situ density TEOS10 ((s, t, p) - 1000) [kg/m^3]"
+                metadata["D_CT"] = "In situ density TEOS10 ((s, t, p) - 1000) [kg/m^3]"
             elif line == "% Potential density TEOS10 ((s, t, 0) - 1000) [kg/m^3]":
-                metadata['D0CT'] = "Potential density TEOS10 ((s, t, 0) - 1000) [kg/m^3]"
+                metadata[
+                    "D0CT"
+                ] = "Potential density TEOS10 ((s, t, 0) - 1000) [kg/m^3]"
             elif line == "% Potential density TEOS10 (s, t, 0) [kg/m^3]":
-                metadata['D0CT'] = "Potential density TEOS10 (s, t, 0) [kg/m^3]"
+                metadata["D0CT"] = "Potential density TEOS10 (s, t, 0) [kg/m^3]"
             elif re.match(r"% .* \[.+\]", line):
                 logger.warning(
                     "Unknown variable name will be saved to unknown_variables_information: %s",

diff --git a/ocean_data_parser/parsers/nmea.py b/ocean_data_parser/parsers/nmea.py
@@ -179,7 +179,11 @@ def _generate_extra_terms(nmea):
             f"{nmea['year']}-{nmea['month']}-{nmea['day']}T{nmea['timestamp']} UTC",
             f"%Y-%m-%dT%H%M%S{'.%f' if len(nmea['timestamp'])>6 else''} %Z",
         )
-    if nmea["sentence_type"] == "RMC" and nmea.get('timestamp') and nmea.get('datestamp'):
+    if (
+        nmea["sentence_type"] == "RMC"
+        and nmea.get("timestamp")
+        and nmea.get("datestamp")
+    ):
         extra[("GPS Time", "gps_datetime")] = datetime.strptime(
             f"{nmea['datestamp']}T{nmea['timestamp']} UTC",
             f"%d%m%yT%H%M%S{'.%f' if len(nmea['timestamp'])>6 else''} %Z",
@@ -297,9 +301,7 @@ def rename_variable(name):
     for col in df:
         if nmea_dtype_mapping.get(col) != datetime:
             continue
-        df[col] = (
-            pd.to_datetime(df[col], utc=True).dt.tz_convert(None)
-        )
+        df[col] = pd.to_datetime(df[col], utc=True).dt.tz_convert(None)
 
     df = df.replace({np.nan: None, "": None, "None": None})
 

diff --git a/ocean_data_parser/parsers/sunburst.py b/ocean_data_parser/parsers/sunburst.py
@@ -95,23 +95,17 @@ def superCO2(path: str, output: str = None) -> xarray.Dataset:
     df.columns = [_format_variables(var) for var in df.columns]
 
     # Generate time variable from Date and Time columns
-    df["time"] = (
-        pd.to_datetime(
-            (df["Date"] + " " + df["Time"]), format="%Y%m%d %H%M%S", utc=True
-        )
-        .dt.tz_convert(None)
-    )
+    df["time"] = pd.to_datetime(
+        (df["Date"] + " " + df["Time"]), format="%Y%m%d %H%M%S", utc=True
+    ).dt.tz_convert(None)
 
     # Review day of the year variable
-    df["time_doy_utc"] = (
-        pd.to_datetime(
-            df["DOY_UTC"] - 1,
-            unit="D",
-            origin=pd.Timestamp(collected_beginning_date.year, 1, 1),
-            utc=True,
-        )
-        .dt.tz_convert(None)
-    )
+    df["time_doy_utc"] = pd.to_datetime(
+        df["DOY_UTC"] - 1,
+        unit="D",
+        origin=pd.Timestamp(collected_beginning_date.year, 1, 1),
+        utc=True,
+    ).dt.tz_convert(None)
 
     # Compare DOY_UTC vs Date + Time
     dt = (df["time"] - df["time_doy_utc"]).mean().total_seconds()

diff --git a/ocean_data_parser/process/process.py b/ocean_data_parser/process/process.py
@@ -38,7 +38,7 @@ def load_cnv(file: str):
     ds = seabird.cnv(file)
     ds["time"] = (
         ds["timeK"].dims,
-        pd.to_datetime(ds["timeK"], origin="2000-01-01", unit="s")
+        pd.to_datetime(ds["timeK"], origin="2000-01-01", unit="s"),
     )
     return ds.swap_dims({"index": "time"}).drop("index")
 

diff --git a/tests/test_process.py b/tests/test_process.py
@@ -56,7 +56,7 @@ def load_test_dataset():
     ds = seabird.cnv(TEST_SEABIRD_FILE)
     ds["time"] = (
         ds["timeK"].dims,
-        pd.to_datetime(ds["timeK"], origin="2000-01-01", unit="s")
+        pd.to_datetime(ds["timeK"], origin="2000-01-01", unit="s"),
     )
     ds.process.time = "time"
     ds.process.lat = "latitude"