Apply unsafe fixes

fixes were checked and tests passed

Author: DocOtak

src/cchdo/hydro/accessors.py

@@ -264,7 +264,7 @@ def to_matdate(dt):
         def dt_list_to_str_list(dtl):
             return list(map(to_matdate, dtl))
 
-        for _, value in mat_dict.items():
+        for value in mat_dict.values():
             if value.get("attrs", {}).get("standard_name") == "time":
                 # the case of list of lists is bottle closure times, which is a sparse array
                 if any(isinstance(v, list) for v in value["data"]):
@@ -392,13 +392,13 @@ def sum_lon(deg_float):
 
             sect_id = ""
             sect_ids = prof.filter_by_attrs(whp_name="SECT_ID")
-            for _, ids in sect_ids.items():
+            for ids in sect_ids.values():
                 sect_id = str(ids.values)
                 break
 
             depth = ""
             depths = prof.filter_by_attrs(whp_name="DEPTH")
-            for _, meters in depths.items():
+            for meters in depths.values():
                 depth = f"{meters.values:.0f}"
                 if depth == "nan":
                     depth = ""

src/cchdo/hydro/dt.py

@@ -46,7 +46,7 @@ def _parse_datetime(date_val: str) -> np.datetime64:
 
     if time_pad:
         if np.any(np.char.str_len(time_arr[time_arr != ""]) < 4):
-            warn("Time values are being padded with zeros")
+            warn("Time values are being padded with zeros", stacklevel=2)
         if not np.all(time_arr == ""):
             time_arr[time_arr != ""] = np.char.zfill(time_arr[time_arr != ""], 4)
 

src/cchdo/hydro/exchange/__init__.py

@@ -323,7 +323,7 @@ def __post_init__(self):
                 self.error_cols.values(),
             )
         ]
-        if not all([shape == shapes[0] for shape in shapes]):
+        if not all(shape == shapes[0] for shape in shapes):
             # TODO Error handling
             raise ValueError("shape error")
 
@@ -634,7 +634,7 @@ def whp_errors(self):
     @property
     def _np_data_block(self):
         _raw_data = tuple(
-            tuple((*self.ctd_headers.values(), *line.replace(" ", "").split(",")))
+            (*self.ctd_headers.values(), *line.replace(" ", "").split(","))
             for line in self.data
         )
         return np.array(_raw_data, dtype="U")
@@ -931,7 +931,7 @@ def read_csv(
         0,
         0,
     )
-    new_data = tuple((",".join(params_units_list), *splitdata[1:]))
+    new_data = (",".join(params_units_list), *splitdata[1:])
     exchange_data = _ExchangeInfo(
         stamp_slice=NONE_SLICE,
         comments_slice=NONE_SLICE,

src/cchdo/hydro/exchange/helpers.py

@@ -58,8 +58,7 @@ def gen_template(
 
     ftype = FileType(ftype)
 
-    exclude = set(
-        [
+    exclude = {
             "EXPOCODE",
             "STNNBR",
             "CASTNO",
@@ -71,8 +70,7 @@ def gen_template(
             "CTDPRS",
             "BTL_TIME",
             "BTL_DATE",
-        ]
-    )
+        }
 
     params = [
         "EXPOCODE",

src/cchdo/hydro/legacy/coards/__init__.py

@@ -162,7 +162,7 @@ def get_filename(expocode, station, cast, extension):
     station = _pad_station_cast(station)
     cast = _pad_station_cast(cast)
 
-    stem = "_".join((expocode, station, cast, extension))
+    stem = f"{expocode}_{station}_{cast}_{extension}"
     return f"{stem}.{FILE_EXTENSION}"
 
 

src/cchdo/hydro/legacy/woce/__init__.py

@@ -126,7 +126,7 @@ def get_filename(expocode, station, cast, file_ext):
     station = _pad_station_cast(station)
     cast = _pad_station_cast(cast)
     return "{}.{}".format(
-        "_".join((expocode, station, cast)),
+        f"{expocode}_{station}_{cast}",
         file_ext,
     )
 
@@ -281,9 +281,7 @@ def quality_flags_of(column):
     flags = []
     for column in columns:
         format_str = column.attrs.get("cchdo.hydro._format", "%s")
-        str_column = list(
-            map(lambda x: format_str % x, column.fillna(FILL_VALUE).to_numpy())
-        )
+        str_column = [format_str % x for x in column.fillna(FILL_VALUE).to_numpy()]
         for i, d in enumerate(str_column):
             if len(d) > COLUMN_WIDTH:
                 extra = len(d) - COLUMN_WIDTH
@@ -298,12 +296,7 @@ def quality_flags_of(column):
 
         if acc.FLAG_NAME in column.attrs:
             flags.append(
-                list(
-                    map(
-                        lambda x: f"{x:1d}",
-                        column.attrs[acc.FLAG_NAME].fillna(9).to_numpy().astype(int),
-                    )
-                )
+                [f"{x:1d}" for x in column.attrs[acc.FLAG_NAME].fillna(9).to_numpy().astype(int)]
             )
 
     for row_d, row_f in zip_longest(zip(*data, strict=True), zip(*flags, strict=True), fillvalue=""):
@@ -336,7 +329,7 @@ def write_bottle(ds: xr.Dataset):
     record_1 += "\n"
 
     data = write_data(ds, columns, base_format)
-    return "".join([record_1, data]).encode("ascii", "replace")
+    return f"{record_1}{data}".encode("ascii", "replace")
 
 
 def write_ctd(ds: xr.Dataset):
@@ -367,9 +360,9 @@ def write_ctd(ds: xr.Dataset):
         f"INSTRUMENT NO. {instrument_no: >5s} SAMPLING RATE {sampling_rate:>6.2f} HZ"
     )
 
-    headers = "\n".join([record1, record2, record3])
+    headers = f"{record1}\n{record2}\n{record3}"
     data = write_data(ds, columns, base_format)
-    return "\n".join([headers, data]).encode("ascii", "replace")
+    return f"{headers}\n{data}".encode("ascii", "replace")
 
 
 def to_woce(ds: xr.Dataset) -> bytes:

src/cchdo/hydro/tests/test_core_ops.py

@@ -270,9 +270,9 @@ def test_remove_param(param, flag, error, empty, require_empty):
             *filter(lambda x: not x[0], zip(bools, params, units, data, strict=True)), strict=True
         )
     else:
-        _params = tuple()
-        _units = tuple()
-        _data = tuple()
+        _params = ()
+        _units = ()
+        _data = ()
 
     expected_ds = read_exchange(
         io.BytesIO(simple_bottle_exchange(params=_params, units=_units, data=_data)),

src/cchdo/hydro/tests/test_rename.py

@@ -24,7 +24,7 @@ def test_rename():
     name_dict = {"var1": "new_var1"}
     result = rename_with_bookkeeping(example, name_dict, attrs=["ancillary_variables"])
     assert "new_var1" in result.data_vars.keys()
-    for var, da in result.filter_by_attrs(ancillary_variables=is_not_none).items():
+    for da in result.filter_by_attrs(ancillary_variables=is_not_none).values():
         assert "new_var1" in da.attrs["ancillary_variables"]
         assert "var2" in da.attrs["ancillary_variables"]
 

src/cchdo/hydro/utils.py

@@ -67,9 +67,7 @@ def add_geometry_var(dataset: xr.Dataset) -> xr.Dataset:
 def add_cdom_coordinate(dataset: xr.Dataset) -> xr.Dataset:
     """Find all the paraters in the cdom group and add their wavelength in a new coordinate"""
 
-    cdom_names = [
-        name for name in filter(lambda x: x.nc_group == "cdom", WHPNames.values())
-    ]
+    cdom_names = list(filter(lambda x: x.nc_group == "cdom", WHPNames.values()))
 
     cdom_names = sorted(cdom_names, key=lambda x: x.radiation_wavelength or 0)