Merge pull request pyoceans#228 from ocefpaf/fix_failures_227

Fix failures 227

Author: ocefpaf

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
       files: requirements-dev.txt
 
 - repo: https://github.com/keewis/blackdoc
-  rev: v0.3.9
+  rev: v0.4.1
   hooks:
     - id: blackdoc
 
@@ -39,7 +39,7 @@ repos:
     - id: add-trailing-comma
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.11.12
+  rev: v0.12.2
   hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]

README.md

@@ -33,34 +33,31 @@ and then,
 from pathlib import Path
 import ctd
 
-path = Path('tests', 'data', 'CTD')
-fname = path.joinpath('g01l06s01.cnv.gz')
+path = Path("tests", "data", "CTD")
+fname = path.joinpath("g01l06s01.cnv.gz")
 
 down, up = ctd.from_cnv(fname).split()
-ax = down['t090C'].plot_cast()
+ax = down["t090C"].plot_cast()
 ```
 
 ![Bad Processing](https://raw.githubusercontent.com/pyoceans/python-ctd/main/docs/readme_01.png)
 
 We can do [better](https://www.go-ship.org/Manual/McTaggart_et_al_CTD.pdf):
 
 ```python
-temperature = down['t090C']
+temperature = down["t090C"]
 
 fig, ax = plt.subplots(figsize=(5.5, 6))
 temperature.plot_cast(ax=ax)
-temperature.remove_above_water()\
-           .despike()\
-           .lp_filter()\
-           .press_check()\
-           .interpolate(method='index',
-                        limit_direction='both',
-                        limit_area='inside')\
-           .bindata(delta=1, method='interpolate')\
-           .smooth(window_len=21, window='hanning') \
-           .plot_cast(ax=ax)
-ax.set_ylabel('Pressure (dbar)')
-ax.set_xlabel('Temperature (°C)')
+temperature.remove_above_water().despike().lp_filter().press_check().interpolate(
+    method="index", limit_direction="both", limit_area="inside"
+).bindata(delta=1, method="interpolate").smooth(
+    window_len=21, window="hanning"
+).plot_cast(
+    ax=ax
+)
+ax.set_ylabel("Pressure (dbar)")
+ax.set_xlabel("Temperature (°C)")
 ```
 
 ![Good Processing](https://raw.githubusercontent.com/pyoceans/python-ctd/main/docs/readme_02.png)

ctd/extras.py

@@ -68,7 +68,7 @@ def extrap_sec(
                  Extrapolated variable
 
     """
-    from scipy.interpolate import interp1d
+    from scipy.interpolate import interp1d  # noqa: PLC0415
 
     new_data1 = []
     for row in data:
@@ -138,8 +138,8 @@ def gen_topomask(
     André Palóczy Filho ([email protected]) --  October/2012
 
     """
-    import gsw
-    from scipy.interpolate import interp1d
+    import gsw  # noqa: PLC0415
+    from scipy.interpolate import interp1d  # noqa: PLC0415
 
     h, lon, lat = list(map(np.asanyarray, (h, lon, lat)))
     # Distance in km.
@@ -160,7 +160,7 @@ def plot_section(  # noqa: PLR0915
     **kw: dict,
 ) -> tuple:
     """Plot a sequence of CTD casts as a section."""
-    import gsw
+    import gsw  # noqa: PLC0415
 
     lon, lat, data = list(
         map(np.asanyarray, (self.lon, self.lat, self.to_numpy())),
@@ -298,7 +298,7 @@ def barrier_layer_thickness(sa: pd.Series, ct: pd.Series) -> pd.Series:
     using density.
 
     """
-    import gsw
+    import gsw  # noqa: PLC0415
 
     sigma_theta = gsw.sigma0(sa, ct)
     mask = mixed_layer_depth(ct)

ctd/processing.py

@@ -13,7 +13,7 @@ def _rolling_window(data: np.ndarray, block: int) -> np.ndarray:
     Using strides for an efficient moving average filter.
 
     """
-    shape = data.shape[:-1] + (data.shape[-1] - block + 1, block)
+    shape = *data.shape[:-1], *(data.shape[-1] - block + 1, block)
     strides = (*data.strides, data.strides[-1])
     return np.lib.stride_tricks.as_strided(data, shape=shape, strides=strides)
 
@@ -80,7 +80,7 @@ def lp_filter(
     https://scipy-cookbook.readthedocs.io/items/FIRFilter.html
 
     """
-    from scipy import signal
+    from scipy import signal  # noqa: PLC0415
 
     # Butter is closer to what SBE is doing with their cosine filter.
     wn = (1.0 / time_constant) / (sample_rate * 2.0)