roms-tools 1.4.1__py3-none-any.whl → 1.4.2__py3-none-any.whl

roms_tools/setup/surface_forcing.py

@@ -28,8 +28,7 @@ from pathlib import Path
 
 @dataclass(frozen=True, kw_only=True)
 class SurfaceForcing(ROMSToolsMixins):
-    """
-    Represents surface forcing input data for ROMS.
+    """Represents surface forcing input data for ROMS.
 
     Parameters
     ----------
@@ -40,14 +39,22 @@ class SurfaceForcing(ROMSToolsMixins):
     end_time : datetime
         End time of the desired surface forcing data.
     source : Dict[str, Union[str, Path, List[Union[str, Path]]], bool]
-        Dictionary specifying the source of the surface forcing data:
-        - "name" (str): Name of the data source (e.g., "ERA5").
-        - "path" (Union[str, Path, List[Union[str, Path]]]): The path to the raw data file(s). Can be a single string (with or without wildcards),
-          a single Path object, or a list of strings or Path objects containing multiple files.
-        - "climatology" (bool): Indicates if the data is climatology data. Defaults to False.
+        Dictionary specifying the source of the surface forcing data. Keys include:
+
+          - "name" (str): Name of the data source (e.g., "ERA5").
+          - "path" (Union[str, Path, List[Union[str, Path]]]): The path to the raw data file(s). This can be:
+
+            - A single string (with or without wildcards).
+            - A single Path object.
+            - A list of strings or Path objects containing multiple files.
+          - "climatology" (bool): Indicates if the data is climatology data. Defaults to False.
+
     type : str
-        Specifies the type of forcing data, either "physics" for physical
-        atmospheric forcing or "bgc" for biogeochemical forcing.
+        Specifies the type of forcing data. Options are:
+
+          - "physics": for physical atmospheric forcing.
+          - "bgc": for biogeochemical forcing.
+
     correct_radiation : bool
         Whether to correct shortwave radiation. Default is False.
     use_coarse_grid: bool
@@ -57,12 +64,6 @@ class SurfaceForcing(ROMSToolsMixins):
     use_dask: bool, optional
         Indicates whether to use dask for processing. If True, data is processed with dask; if False, data is processed eagerly. Defaults to False.
 
-    Attributes
-    ----------
-    ds : xr.Dataset
-        Xarray Dataset containing the surface forcing data.
-
-
     Examples
     --------
     >>> surface_forcing = SurfaceForcing(
@@ -90,7 +91,7 @@ class SurfaceForcing(ROMSToolsMixins):
     def __post_init__(self):
 
         self._input_checks()
-        lon, lat, angle, straddle = super().get_target_lon_lat(self.use_coarse_grid)
+        lon, lat, angle, straddle = super()._get_target_lon_lat(self.use_coarse_grid)
         object.__setattr__(self, "target_lon", lon)
         object.__setattr__(self, "target_lat", lat)
 
@@ -107,10 +108,10 @@ class SurfaceForcing(ROMSToolsMixins):
             vars_2d = data.var_names.keys()
         vars_3d = []
 
-        data_vars = super().regrid_data(data, vars_2d, vars_3d, lon, lat)
+        data_vars = super()._regrid_data(data, vars_2d, vars_3d, lon, lat)
 
         if self.type == "physics":
-            data_vars = super().process_velocities(
+            data_vars = super()._process_velocities(
                 data_vars, angle, "uwnd", "vwnd", interpolate=False
             )
             if self.correct_radiation:
@@ -136,7 +137,7 @@ class SurfaceForcing(ROMSToolsMixins):
                 vars_2d = ["swr_corr"]
                 vars_3d = []
                 # spatial interpolation
-                data_vars_corr = super().regrid_data(
+                data_vars_corr = super()._regrid_data(
                     correction_data, vars_2d, vars_3d, lon, lat
                 )
                 # temporal interpolation
@@ -333,13 +334,13 @@ class SurfaceForcing(ROMSToolsMixins):
         return ds
 
     def plot(self, varname, time=0) -> None:
-        """
-        Plot the specified surface forcing field for a given time slice.
+        """Plot the specified surface forcing field for a given time slice.
 
         Parameters
         ----------
         varname : str
             The name of the surface forcing field to plot. Options include:
+
             - "uwnd": 10 meter wind in x-direction.
             - "vwnd": 10 meter wind in y-direction.
             - "swrad": Downward short-wave (solar) radiation.
@@ -353,6 +354,7 @@ class SurfaceForcing(ROMSToolsMixins):
             - "dust": Dust decomposition.
             - "nox": NOx decomposition.
             - "nhy": NHy decomposition.
+
         time : int, optional
             The time index to plot. Default is 0, which corresponds to the first
             time slice.
@@ -416,21 +418,22 @@ class SurfaceForcing(ROMSToolsMixins):
     def save(
         self, filepath: Union[str, Path], np_eta: int = None, np_xi: int = None
     ) -> None:
-        """
-        Save the surface forcing fields to netCDF4 files.
+        """Save the surface forcing fields to netCDF4 files.
 
         This method saves the dataset by grouping it into subsets based on the data frequency. The subsets are then written
         to one or more netCDF4 files. The filenames of the output files reflect the temporal coverage of the data.
 
         There are two modes of saving the dataset:
 
-        1. **Single File Mode (default)**:
-           - If both `np_eta` and `np_xi` are `None`, the entire dataset, divided by temporal subsets, is saved as a single netCDF4 file
-             with the base filename specified by `filepath.nc`.
+          1. **Single File Mode (default)**:
 
-        2. **Partitioned Mode**:
-           - If either `np_eta` or `np_xi` is specified, the dataset is divided into spatial tiles along the eta-axis and xi-axis.
-           - Each spatial tile is saved as a separate netCDF4 file.
+            If both `np_eta` and `np_xi` are `None`, the entire dataset, divided by temporal subsets, is saved as a single netCDF4 file
+            with the base filename specified by `filepath.nc`.
+
+          2. **Partitioned Mode**:
+
+            - If either `np_eta` or `np_xi` is specified, the dataset is divided into spatial tiles along the eta-axis and xi-axis.
+            - Each spatial tile is saved as a separate netCDF4 file.
 
         Parameters
         ----------
@@ -464,8 +467,8 @@ class SurfaceForcing(ROMSToolsMixins):
         return saved_filenames
 
     def to_yaml(self, filepath: Union[str, Path]) -> None:
-        """
-        Export the parameters of the class to a YAML file, including the version of roms-tools.
+        """Export the parameters of the class to a YAML file, including the version of
+        roms-tools.
 
         Parameters
         ----------
@@ -520,8 +523,7 @@ class SurfaceForcing(ROMSToolsMixins):
     def from_yaml(
         cls, filepath: Union[str, Path], use_dask: bool = False
     ) -> "SurfaceForcing":
-        """
-        Create an instance of the SurfaceForcing class from a YAML file.
+        """Create an instance of the SurfaceForcing class from a YAML file.
 
         Parameters
         ----------

roms_tools/setup/tides.py

@@ -24,18 +24,22 @@ from pathlib import Path
 
 @dataclass(frozen=True, kw_only=True)
 class TidalForcing(ROMSToolsMixins):
-    """
-    Represents tidal forcing data used in ocean modeling.
+    """Represents tidal forcing data used in ocean modeling.
 
     Parameters
     ----------
     grid : Grid
         The grid object representing the ROMS grid associated with the tidal forcing data.
     source : Dict[str, Union[str, Path, List[Union[str, Path]]]]
-        Dictionary specifying the source of the tidal data:
-        - "name" (str): Name of the data source (e.g., "TPXO").
-        - "path" (Union[str, Path, List[Union[str, Path]]]): The path to the raw data file(s). Can be a single string (with or without wildcards),
-          a single Path object, or a list of strings or Path objects containing multiple files.
+        Dictionary specifying the source of the tidal data. Keys include:
+
+          - "name" (str): Name of the data source (e.g., "TPXO").
+          - "path" (Union[str, Path, List[Union[str, Path]]]): The path to the raw data file(s). This can be:
+
+            - A single string (with or without wildcards).
+            - A single Path object.
+            - A list of strings or Path objects containing multiple files.
+
     ntides : int, optional
         Number of constituents to consider. Maximum number is 14. Default is 10.
     allan_factor : float, optional
@@ -45,11 +49,6 @@ class TidalForcing(ROMSToolsMixins):
     use_dask: bool, optional
         Indicates whether to use dask for processing. If True, data is processed with dask; if False, data is processed eagerly. Defaults to False.
 
-    Attributes
-    ----------
-    ds : xr.Dataset
-        The xarray Dataset containing the tidal forcing data.
-
     Examples
     --------
     >>> tidal_forcing = TidalForcing(
@@ -69,7 +68,7 @@ class TidalForcing(ROMSToolsMixins):
     def __post_init__(self):
 
         self._input_checks()
-        lon, lat, angle, straddle = super().get_target_lon_lat()
+        lon, lat, angle, straddle = super()._get_target_lon_lat()
 
         data = self._get_data()
 
@@ -98,12 +97,12 @@ class TidalForcing(ROMSToolsMixins):
         ]
         vars_3d = []
 
-        data_vars = super().regrid_data(data, vars_2d, vars_3d, lon, lat)
+        data_vars = super()._regrid_data(data, vars_2d, vars_3d, lon, lat)
 
-        data_vars = super().process_velocities(
+        data_vars = super()._process_velocities(
             data_vars, angle, "u_Re", "v_Re", interpolate=False
         )
-        data_vars = super().process_velocities(
+        data_vars = super()._process_velocities(
             data_vars, angle, "u_Im", "v_Im", interpolate=False
         )
 
@@ -180,13 +179,13 @@ class TidalForcing(ROMSToolsMixins):
         return ds
 
     def plot(self, varname, ntides=0) -> None:
-        """
-        Plot the specified tidal forcing variable for a given tidal constituent.
+        """Plot the specified tidal forcing variable for a given tidal constituent.
 
         Parameters
         ----------
         varname : str
             The tidal forcing variable to plot. Options include:
+
             - "ssh_Re": Real part of tidal elevation.
             - "ssh_Im": Imaginary part of tidal elevation.
             - "pot_Re": Real part of tidal potential.
@@ -195,6 +194,7 @@ class TidalForcing(ROMSToolsMixins):
             - "u_Im": Imaginary part of tidal velocity in the x-direction.
             - "v_Re": Real part of tidal velocity in the y-direction.
             - "v_Im": Imaginary part of tidal velocity in the y-direction.
+
         ntides : int, optional
             The index of the tidal constituent to plot. Default is 0, which corresponds
             to the first constituent.
@@ -258,17 +258,19 @@ class TidalForcing(ROMSToolsMixins):
     def save(
         self, filepath: Union[str, Path], np_eta: int = None, np_xi: int = None
     ) -> None:
-        """
-        Save the tidal forcing information to a netCDF4 file.
+        """Save the tidal forcing information to a netCDF4 file.
 
         This method supports saving the dataset in two modes:
 
-        1. **Single File Mode (default)**:
-           - If both `np_eta` and `np_xi` are `None`, the entire dataset is saved as a single file at the specified `filepath.nc`.
+          1. **Single File Mode (default)**:
+
+            If both `np_eta` and `np_xi` are `None`, the entire dataset is saved as a single netCDF4 file
+            with the base filename specified by `filepath.nc`.
 
-        2. **Partitioned Mode**:
-           - If either `np_eta` or `np_xi` is specified, the dataset is divided into spatial tiles along the eta-axis and xi-axis.
-           - The files are saved as `filepath.0.nc`, `filepath.1.nc`, ..., where the numbering corresponds to the partition index.
+          2. **Partitioned Mode**:
+
+            - If either `np_eta` or `np_xi` is specified, the dataset is divided into spatial tiles along the eta-axis and xi-axis.
+            - Each spatial tile is saved as a separate netCDF4 file.
 
         Parameters
         ----------
@@ -302,8 +304,8 @@ class TidalForcing(ROMSToolsMixins):
         return saved_filenames
 
     def to_yaml(self, filepath: Union[str, Path]) -> None:
-        """
-        Export the parameters of the class to a YAML file, including the version of roms-tools.
+        """Export the parameters of the class to a YAML file, including the version of
+        roms-tools.
 
         Parameters
         ----------
@@ -351,8 +353,7 @@ class TidalForcing(ROMSToolsMixins):
     def from_yaml(
         cls, filepath: Union[str, Path], use_dask: bool = False
     ) -> "TidalForcing":
-        """
-        Create an instance of the TidalForcing class from a YAML file.
+        """Create an instance of the TidalForcing class from a YAML file.
 
         Parameters
         ----------
@@ -400,10 +401,10 @@ class TidalForcing(ROMSToolsMixins):
         return cls(grid=grid, **tidal_forcing_params, use_dask=use_dask)
 
     def _correct_tides(self, data):
-        """
-        Apply tidal corrections to the dataset.
-        This method corrects the dataset for equilibrium tides, self-attraction and loading (SAL) effects, and
-        adjusts phases and amplitudes of tidal elevations and transports using Egbert's correction.
+        """Apply tidal corrections to the dataset. This method corrects the dataset for
+        equilibrium tides, self-attraction and loading (SAL) effects, and adjusts phases
+        and amplitudes of tidal elevations and transports using Egbert's correction.
+
         Parameters
         ----------
         data : Dataset
@@ -460,8 +461,7 @@ class TidalForcing(ROMSToolsMixins):
 
 
 def modified_julian_days(year, month, day, hour=0):
-    """
-    Calculate the Modified Julian Day (MJD) for a given date and time.
+    """Calculate the Modified Julian Day (MJD) for a given date and time.
 
     The Modified Julian Day (MJD) is a modified Julian day count starting from
     November 17, 1858 AD. It is commonly used in astronomy and geodesy.
@@ -519,9 +519,8 @@ def modified_julian_days(year, month, day, hour=0):
 
 
 def egbert_correction(date):
-    """
-    Correct phases and amplitudes for real-time runs using parts of the
-    post-processing code from Egbert's & Erofeeva's (OSU) TPXO model.
+    """Correct phases and amplitudes for real-time runs using parts of the post-
+    processing code from Egbert's & Erofeeva's (OSU) TPXO model.
 
     Parameters
     ----------
@@ -541,7 +540,6 @@ def egbert_correction(date):
     ----------
     - Egbert, G.D., and S.Y. Erofeeva. "Efficient inverse modeling of barotropic ocean
       tides." Journal of Atmospheric and Oceanic Technology 19, no. 2 (2002): 183-204.
-
     """
 
     year = date.year
@@ -676,8 +674,7 @@ def egbert_correction(date):
 
 
 def compute_equilibrium_tide(lon, lat):
-    """
-    Compute equilibrium tide for given longitudes and latitudes.
+    """Compute equilibrium tide for given longitudes and latitudes.
 
     Parameters
     ----------
@@ -699,7 +696,6 @@ def compute_equilibrium_tide(lon, lat):
         - 2: semidiurnal
         - 1: diurnal
         - 0: long-term
-
     """
 
     # Amplitudes and elasticity factors for 15 tidal constituents

roms_tools/setup/topography.py

@@ -12,8 +12,8 @@ from itertools import count
 def _add_topography_and_mask(
     ds, topography_source, hmin, smooth_factor=8.0, rmax=0.2
 ) -> xr.Dataset:
-    """
-    Adds topography and a land/water mask to the dataset based on the provided topography source.
+    """Adds topography and a land/water mask to the dataset based on the provided
+    topography source.
 
     This function performs the following operations:
     1. Interpolates topography data onto the desired grid.
@@ -86,9 +86,8 @@ def _add_topography_and_mask(
 
 
 def _make_raw_topography(lon, lat, topography_source) -> np.ndarray:
-    """
-    Given a grid of (lon, lat) points, fetch the topography file and interpolate height values onto the desired grid.
-    """
+    """Given a grid of (lon, lat) points, fetch the topography file and interpolate
+    height values onto the desired grid."""
 
     topo_ds = fetch_topo(topography_source)
 
@@ -150,9 +149,7 @@ def _smooth_topography_globally(hraw, factor) -> xr.DataArray:
 
 
 def _fill_enclosed_basins(mask) -> np.ndarray:
-    """
-    Fills in enclosed basins with land
-    """
+    """Fills in enclosed basins with land."""
 
     # Label connected regions in the mask
     reg, nreg = label(mask)
@@ -174,9 +171,7 @@ def _fill_enclosed_basins(mask) -> np.ndarray:
 
 
 def _smooth_topography_locally(h, hmin=5, rmax=0.2):
-    """
-    Smoothes topography locally to satisfy r < rmax
-    """
+    """Smoothes topography locally to satisfy r < rmax."""
     # Compute rmax_log
     if rmax > 0.0:
         rmax_log = np.log((1.0 + rmax * 0.9) / (1.0 - rmax * 0.9))
@@ -254,8 +249,7 @@ def _smooth_topography_locally(h, hmin=5, rmax=0.2):
 
 
 def _handle_boundaries(field):
-    """
-    Adjust the boundaries of a 2D field by copying values from adjacent cells.
+    """Adjust the boundaries of a 2D field by copying values from adjacent cells.
 
     Parameters
     ----------
@@ -267,7 +261,6 @@ def _handle_boundaries(field):
     -------
     field : numpy.ndarray or xarray.DataArray
         The input field with adjusted boundary values.
-
     """
 
     field[0, :] = field[1, :]
@@ -279,9 +272,8 @@ def _handle_boundaries(field):
 
 
 def _compute_rfactor(h):
-    """
-    Computes slope parameter (or r-factor) r = |Delta h| / 2h in both horizontal grid directions.
-    """
+    """Computes slope parameter (or r-factor) r = |Delta h| / 2h in both horizontal grid
+    directions."""
     # compute r_{i-1/2} = |h_i - h_{i-1}| / (h_i + h_{i+1})
     r_eta = np.abs(h.diff("eta_rho")) / (h + h.shift(eta_rho=1)).isel(
         eta_rho=slice(1, None)

roms_tools/setup/utils.py

@@ -8,8 +8,7 @@ from pathlib import Path
 
 
 def nan_check(field, mask) -> None:
-    """
-    Checks for NaN values at wet points in the field.
+    """Checks for NaN values at wet points in the field.
 
     This function examines the interpolated input field for NaN values at positions indicated as wet points by the mask.
     If any NaN values are found at these wet points, a ValueError is raised.
@@ -28,7 +27,6 @@ def nan_check(field, mask) -> None:
     ValueError
         If the field contains NaN values at any of the wet points indicated by the mask.
         The error message will explain the potential cause and suggest ensuring the dataset's coverage.
-
     """
 
     # Replace values in field with 0 where mask is not 1
@@ -44,8 +42,7 @@ def nan_check(field, mask) -> None:
 
 
 def substitute_nans_by_fillvalue(field, fill_value=0.0) -> xr.DataArray:
-    """
-    Replace NaN values in the field with a specified fill value.
+    """Replace NaN values in the field with a specified fill value.
 
     This function replaces any NaN values in the input field with the provided fill value.
 
@@ -66,9 +63,7 @@ def substitute_nans_by_fillvalue(field, fill_value=0.0) -> xr.DataArray:
 
 
 def interpolate_from_rho_to_u(field, method="additive"):
-
-    """
-    Interpolates the given field from rho points to u points.
+    """Interpolates the given field from rho points to u points.
 
     This function performs an interpolation from the rho grid (cell centers) to the u grid
     (cell edges in the xi direction). Depending on the chosen method, it either averages
@@ -114,9 +109,7 @@ def interpolate_from_rho_to_u(field, method="additive"):
 
 
 def interpolate_from_rho_to_v(field, method="additive"):
-
-    """
-    Interpolates the given field from rho points to v points.
+    """Interpolates the given field from rho points to v points.
 
     This function performs an interpolation from the rho grid (cell centers) to the v grid
     (cell edges in the eta direction). Depending on the chosen method, it either averages
@@ -164,8 +157,8 @@ def interpolate_from_rho_to_v(field, method="additive"):
 
 
 def extrapolate_deepest_to_bottom(field: xr.DataArray, dim: str) -> xr.DataArray:
-    """
-    Extrapolates the deepest non-NaN values to the bottom along the specified dimension using forward fill.
+    """Extrapolates the deepest non-NaN values to the bottom along the specified
+    dimension using forward fill.
 
     This function assumes that the specified dimension is ordered from top to bottom (e.g., a vertical dimension like 'depth').
     It fills `NaN` values below the deepest valid (non-NaN) entry along the given dimension by carrying forward the last valid value.
@@ -187,7 +180,6 @@ def extrapolate_deepest_to_bottom(field: xr.DataArray, dim: str) -> xr.DataArray
         A new `xarray.DataArray` with the `NaN` values along the specified dimension
         filled by forward filling the deepest valid values down to the bottom.
         The original input data remains unmodified.
-
     """
     field_interpolated = field.ffill(dim=dim)
 
@@ -195,8 +187,7 @@ def extrapolate_deepest_to_bottom(field: xr.DataArray, dim: str) -> xr.DataArray
 
 
 def assign_dates_to_climatology(ds: xr.Dataset, time_dim: str) -> xr.Dataset:
-    """
-    Assigns climatology dates to the dataset's time dimension.
+    """Assigns climatology dates to the dataset's time dimension.
 
     This function updates the dataset's time coordinates to reflect climatological dates.
     It defines fixed day increments for each month and assigns these to the specified time dimension.
@@ -213,7 +204,6 @@ def assign_dates_to_climatology(ds: xr.Dataset, time_dim: str) -> xr.Dataset:
     -------
     xr.Dataset
         The updated xarray Dataset with climatological dates assigned to the specified time dimension.
-
     """
     # Define the days in each month and convert to timedelta
     increments = [15, 30, 29, 31, 30, 31, 30, 31, 31, 30, 31, 30]
@@ -229,8 +219,7 @@ def interpolate_from_climatology(
     time_dim_name: str,
     time: Union[xr.DataArray, pd.DatetimeIndex],
 ) -> Union[xr.DataArray, xr.Dataset]:
-    """
-    Interpolates the given field temporally based on the specified time points.
+    """Interpolates the given field temporally based on the specified time points.
 
     If `field` is an xarray.Dataset, this function applies the interpolation to all data variables in the dataset.
 
@@ -305,8 +294,7 @@ def interpolate_from_climatology(
 
 
 def get_time_type(data_array: xr.DataArray) -> str:
-    """
-    Determines the type of time values in the xarray DataArray.
+    """Determines the type of time values in the xarray DataArray.
 
     Parameters
     ----------
@@ -354,8 +342,7 @@ def get_time_type(data_array: xr.DataArray) -> str:
 
 
 def convert_cftime_to_datetime(data_array: np.ndarray) -> np.ndarray:
-    """
-    Converts cftime datetime objects to numpy datetime64 objects in a numpy ndarray.
+    """Converts cftime datetime objects to numpy datetime64 objects in a numpy ndarray.
 
     Parameters
     ----------
@@ -391,8 +378,7 @@ def convert_cftime_to_datetime(data_array: np.ndarray) -> np.ndarray:
 
 
 def get_variable_metadata():
-    """
-    Retrieves metadata for commonly used variables in the dataset.
+    """Retrieves metadata for commonly used variables in the dataset.
 
     This function returns a dictionary containing the metadata for various variables, including long names
     and units for each variable.
@@ -401,7 +387,6 @@ def get_variable_metadata():
     -------
     dict of str: dict
         Dictionary where keys are variable names and values are dictionaries with "long_name" and "units" keys.
-
     """
 
     d = {
@@ -519,10 +504,8 @@ def get_variable_metadata():
 
 
 def get_boundary_info():
-
-    """
-    This function provides information about the boundary points for the rho, u, and v
-    variables on the grid, specifying the indices for the south, east, north, and west
+    """This function provides information about the boundary points for the rho, u, and
+    v variables on the grid, specifying the indices for the south, east, north, and west
     boundaries.
 
     Returns
@@ -559,8 +542,7 @@ def get_boundary_info():
 
 
 def extract_single_value(data):
-    """
-    Extracts a single value from an xarray.DataArray or numpy array.
+    """Extracts a single value from an xarray.DataArray or numpy array.
 
     Parameters
     ----------
@@ -589,8 +571,8 @@ def extract_single_value(data):
 
 
 def group_dataset(ds, filepath):
-    """
-    Group the dataset into monthly or yearly subsets based on the frequency of the data.
+    """Group the dataset into monthly or yearly subsets based on the frequency of the
+    data.
 
     Parameters
     ----------
@@ -643,8 +625,7 @@ def group_dataset(ds, filepath):
 
 
 def group_by_month(ds, filepath):
-    """
-    Group the dataset by month and generate filenames with 'YYYYMM' format.
+    """Group the dataset by month and generate filenames with 'YYYYMM' format.
 
     Parameters
     ----------
@@ -681,8 +662,7 @@ def group_by_month(ds, filepath):
 
 
 def group_by_year(ds, filepath):
-    """
-    Group the dataset by year and generate filenames with 'YYYY' format.
+    """Group the dataset by year and generate filenames with 'YYYY' format.
 
     Parameters
     ----------
@@ -715,8 +695,7 @@ def group_by_year(ds, filepath):
 
 
 def save_datasets(dataset_list, output_filenames, np_eta=None, np_xi=None):
-    """
-    Save the list of datasets to netCDF4 files, with optional spatial partitioning.
+    """Save the list of datasets to netCDF4 files, with optional spatial partitioning.
 
     Parameters
     ----------

roms_tools/setup/vertical_coordinate.py

@@ -3,8 +3,8 @@ import xarray as xr
 
 
 def compute_cs(sigma, theta_s, theta_b):
-    """
-    Compute the S-coordinate stretching curves according to Shchepetkin and McWilliams (2009).
+    """Compute the S-coordinate stretching curves according to Shchepetkin and
+    McWilliams (2009).
 
     Parameters
     ----------
@@ -37,8 +37,7 @@ def compute_cs(sigma, theta_s, theta_b):
 
 
 def sigma_stretch(theta_s, theta_b, N, type):
-    """
-    Compute sigma and stretching curves based on the type and parameters.
+    """Compute sigma and stretching curves based on the type and parameters.
 
     Parameters
     ----------
@@ -80,8 +79,7 @@ def sigma_stretch(theta_s, theta_b, N, type):
 
 
 def compute_depth(zeta, h, hc, cs, sigma):
-    """
-    Compute the depth at different sigma levels.
+    """Compute the depth at different sigma levels.
 
     Parameters
     ----------