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

roms_tools/_version.py

@@ -1,2 +1,2 @@
 # Do not change! Do not track in version control!
-__version__ = "1.4.1"
+__version__ = "1.4.2"

roms_tools/setup/boundary_forcing.py

@@ -24,8 +24,7 @@ from pathlib import Path
 
 @dataclass(frozen=True, kw_only=True)
 class BoundaryForcing(ROMSToolsMixins):
-    """
-    Represents boundary forcing input data for ROMS.
+    """Represents boundary forcing input data for ROMS.
 
     Parameters
     ----------
@@ -38,21 +37,27 @@ class BoundaryForcing(ROMSToolsMixins):
     boundaries : Dict[str, bool], optional
         Dictionary specifying which boundaries are forced (south, east, north, west). Default is all True.
     source : Dict[str, Union[str, Path, List[Union[str, Path]]], bool]
-        Dictionary specifying the source of the boundary forcing data:
-        - "name" (str): Name of the data source (e.g., "GLORYS").
-        - "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 boundary forcing data. Keys include:
+
+          - "name" (str): Name of the data source (e.g., "GLORYS").
+          - "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. Options are:
+
+          - "physics": for physical atmospheric forcing.
+          - "bgc": for biogeochemical forcing.
+
     model_reference_date : datetime, optional
         Reference date for the model. Default is January 1, 2000.
     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 boundary forcing data.
-
     Examples
     --------
     >>> boundary_forcing = BoundaryForcing(
@@ -86,7 +91,7 @@ class BoundaryForcing(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()
         data.choose_subdomain(
@@ -103,10 +108,10 @@ class BoundaryForcing(ROMSToolsMixins):
             vars_2d = []
             vars_3d = data.var_names.keys()
 
-        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, angle, "u", "v")
+            data_vars = super()._process_velocities(data_vars, angle, "u", "v")
         object.__setattr__(data, "data_vars", data_vars)
 
         d_meta = get_variable_metadata()
@@ -286,8 +291,7 @@ class BoundaryForcing(ROMSToolsMixins):
         return ds
 
     def _get_coordinates(self, direction, point):
-        """
-        Retrieve layer and interface depth coordinates for a specified grid boundary.
+        """Retrieve layer and interface depth coordinates for a specified grid boundary.
 
         This method extracts the layer depth and interface depth coordinates along
         a specified boundary (north, south, east, or west) and for a specified point
@@ -349,52 +353,55 @@ class BoundaryForcing(ROMSToolsMixins):
         time=0,
         layer_contours=False,
     ) -> None:
-        """
-        Plot the boundary forcing field for a given time-slice.
+        """Plot the boundary forcing field for a given time-slice.
 
         Parameters
         ----------
         varname : str
             The name of the boundary forcing field to plot. Options include:
-            - "temp_{direction}": Potential temperature, where {direction} can be one of ["south", "east", "north", "west"].
-            - "salt_{direction}": Salinity, where {direction} can be one of ["south", "east", "north", "west"].
-            - "zeta_{direction}": Sea surface height, where {direction} can be one of ["south", "east", "north", "west"].
-            - "u_{direction}": u-flux component, where {direction} can be one of ["south", "east", "north", "west"].
-            - "v_{direction}": v-flux component, where {direction} can be one of ["south", "east", "north", "west"].
-            - "ubar_{direction}": Vertically integrated u-flux component, where {direction} can be one of ["south", "east", "north", "west"].
-            - "vbar_{direction}": Vertically integrated v-flux component, where {direction} can be one of ["south", "east", "north", "west"].
-            - "PO4_{direction}": Dissolved Inorganic Phosphate (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "NO3_{direction}": Dissolved Inorganic Nitrate (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "SiO3_{direction}": Dissolved Inorganic Silicate (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "NH4_{direction}": Dissolved Ammonia (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "Fe_{direction}": Dissolved Inorganic Iron (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "Lig_{direction}": Iron Binding Ligand (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "O2_{direction}": Dissolved Oxygen (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "DIC_{direction}": Dissolved Inorganic Carbon (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "DIC_ALT_CO2_{direction}": Dissolved Inorganic Carbon, Alternative CO2 (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "ALK_{direction}": Alkalinity (meq/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "ALK_ALT_CO2_{direction}": Alkalinity, Alternative CO2 (meq/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "DOC_{direction}": Dissolved Organic Carbon (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "DON_{direction}": Dissolved Organic Nitrogen (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "DOP_{direction}": Dissolved Organic Phosphorus (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "DOPr_{direction}": Refractory Dissolved Organic Phosphorus (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "DONr_{direction}": Refractory Dissolved Organic Nitrogen (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "DOCr_{direction}": Refractory Dissolved Organic Carbon (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "zooC_{direction}": Zooplankton Carbon (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "spChl_{direction}": Small Phytoplankton Chlorophyll (mg/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "spC_{direction}": Small Phytoplankton Carbon (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "spP_{direction}": Small Phytoplankton Phosphorous (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "spFe_{direction}": Small Phytoplankton Iron (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "spCaCO3_{direction}": Small Phytoplankton CaCO3 (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "diatChl_{direction}": Diatom Chlorophyll (mg/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "diatC_{direction}": Diatom Carbon (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "diatP_{direction}": Diatom Phosphorus (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "diatFe_{direction}": Diatom Iron (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "diatSi_{direction}": Diatom Silicate (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "diazChl_{direction}": Diazotroph Chlorophyll (mg/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "diazC_{direction}": Diazotroph Carbon (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "diazP_{direction}": Diazotroph Phosphorus (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
-            - "diazFe_{direction}": Diazotroph Iron (mmol/m³), where {direction} can be one of ["south", "east", "north", "west"].
+
+            - "temp_{direction}": Potential temperature,
+            - "salt_{direction}": Salinity,
+            - "zeta_{direction}": Sea surface height,
+            - "u_{direction}": u-flux component,
+            - "v_{direction}": v-flux component,
+            - "ubar_{direction}": Vertically integrated u-flux component,
+            - "vbar_{direction}": Vertically integrated v-flux component,
+            - "PO4_{direction}": Dissolved Inorganic Phosphate (mmol/m³),
+            - "NO3_{direction}": Dissolved Inorganic Nitrate (mmol/m³),
+            - "SiO3_{direction}": Dissolved Inorganic Silicate (mmol/m³),
+            - "NH4_{direction}": Dissolved Ammonia (mmol/m³),
+            - "Fe_{direction}": Dissolved Inorganic Iron (mmol/m³),
+            - "Lig_{direction}": Iron Binding Ligand (mmol/m³),
+            - "O2_{direction}": Dissolved Oxygen (mmol/m³),
+            - "DIC_{direction}": Dissolved Inorganic Carbon (mmol/m³),
+            - "DIC_ALT_CO2_{direction}": Dissolved Inorganic Carbon, Alternative CO2 (mmol/m³),
+            - "ALK_{direction}": Alkalinity (meq/m³),
+            - "ALK_ALT_CO2_{direction}": Alkalinity, Alternative CO2 (meq/m³),
+            - "DOC_{direction}": Dissolved Organic Carbon (mmol/m³),
+            - "DON_{direction}": Dissolved Organic Nitrogen (mmol/m³),
+            - "DOP_{direction}": Dissolved Organic Phosphorus (mmol/m³),
+            - "DOPr_{direction}": Refractory Dissolved Organic Phosphorus (mmol/m³),
+            - "DONr_{direction}": Refractory Dissolved Organic Nitrogen (mmol/m³),
+            - "DOCr_{direction}": Refractory Dissolved Organic Carbon (mmol/m³),
+            - "zooC_{direction}": Zooplankton Carbon (mmol/m³),
+            - "spChl_{direction}": Small Phytoplankton Chlorophyll (mg/m³),
+            - "spC_{direction}": Small Phytoplankton Carbon (mmol/m³),
+            - "spP_{direction}": Small Phytoplankton Phosphorous (mmol/m³),
+            - "spFe_{direction}": Small Phytoplankton Iron (mmol/m³),
+            - "spCaCO3_{direction}": Small Phytoplankton CaCO3 (mmol/m³),
+            - "diatChl_{direction}": Diatom Chlorophyll (mg/m³),
+            - "diatC_{direction}": Diatom Carbon (mmol/m³),
+            - "diatP_{direction}": Diatom Phosphorus (mmol/m³),
+            - "diatFe_{direction}": Diatom Iron (mmol/m³),
+            - "diatSi_{direction}": Diatom Silicate (mmol/m³),
+            - "diazChl_{direction}": Diazotroph Chlorophyll (mg/m³),
+            - "diazC_{direction}": Diazotroph Carbon (mmol/m³),
+            - "diazP_{direction}": Diazotroph Phosphorus (mmol/m³),
+            - "diazFe_{direction}": Diazotroph Iron (mmol/m³),
+
+            where {direction} can be one of ["south", "east", "north", "west"].
+
         time : int, optional
             The time index to plot. Default is 0.
         layer_contours : bool, optional
@@ -468,21 +475,22 @@ class BoundaryForcing(ROMSToolsMixins):
     def save(
         self, filepath: Union[str, Path], np_eta: int = None, np_xi: int = None
     ) -> None:
-        """
-        Save the boundary forcing fields to netCDF4 files.
+        """Save the boundary 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
         ----------
@@ -516,8 +524,8 @@ class BoundaryForcing(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
         ----------
@@ -568,8 +576,7 @@ class BoundaryForcing(ROMSToolsMixins):
     def from_yaml(
         cls, filepath: Union[str, Path], use_dask: bool = False
     ) -> "BoundaryForcing":
-        """
-        Create an instance of the BoundaryForcing class from a YAML file.
+        """Create an instance of the BoundaryForcing class from a YAML file.
 
         Parameters
         ----------

roms_tools/setup/datasets.py

@@ -18,8 +18,7 @@ from roms_tools.setup.download import download_correction_data
 
 @dataclass(frozen=True, kw_only=True)
 class Dataset:
-    """
-    Represents forcing data on original grid.
+    """Represents forcing data on original grid.
 
     Parameters
     ----------
@@ -131,8 +130,7 @@ class Dataset:
             self.post_process()
 
     def load_data(self) -> xr.Dataset:
-        """
-        Load dataset from the specified file.
+        """Load dataset from the specified file.
 
         Returns
         -------
@@ -246,8 +244,7 @@ class Dataset:
         return ds
 
     def clean_up(self, ds: xr.Dataset) -> xr.Dataset:
-        """
-        Dummy method to be overridden by child classes to clean up the dataset.
+        """Dummy method to be overridden by child classes to clean up the dataset.
 
         This method is intended as a placeholder and should be implemented in subclasses
         to provide specific functionality.
@@ -265,8 +262,7 @@ class Dataset:
         return ds
 
     def check_dataset(self, ds: xr.Dataset) -> None:
-        """
-        Check if the dataset contains the specified variables and dimensions.
+        """Check if the dataset contains the specified variables and dimensions.
 
         Parameters
         ----------
@@ -293,8 +289,8 @@ class Dataset:
             )
 
     def select_relevant_fields(self, ds) -> xr.Dataset:
-        """
-        Selects and returns a subset of the dataset containing only the variables specified in `self.var_names`.
+        """Selects and returns a subset of the dataset containing only the variables
+        specified in `self.var_names`.
 
         Parameters
         ----------
@@ -305,7 +301,6 @@ class Dataset:
         -------
         xr.Dataset
             A dataset containing only the variables specified in `self.var_names`.
-
         """
 
         for var in ds.data_vars:
@@ -315,8 +310,8 @@ class Dataset:
         return ds
 
     def add_time_info(self, ds: xr.Dataset) -> xr.Dataset:
-        """
-        Dummy method to be overridden by child classes to add time information to the dataset.
+        """Dummy method to be overridden by child classes to add time information to the
+        dataset.
 
         This method is intended as a placeholder and should be implemented in subclasses
         to provide specific functionality for adding time-related information to the dataset.
@@ -334,8 +329,7 @@ class Dataset:
         return ds
 
     def select_relevant_times(self, ds) -> xr.Dataset:
-        """
-        Select a subset of the dataset based on the specified time range.
+        """Select a subset of the dataset based on the specified time range.
 
         This method filters the dataset to include all records between `start_time` and `end_time`.
         Additionally, it ensures that one record at or before `start_time` and one record at or
@@ -467,8 +461,7 @@ class Dataset:
     def ensure_dimension_is_ascending(
         self, ds: xr.Dataset, dim="latitude"
     ) -> xr.Dataset:
-        """
-        Ensure that the specified dimension in the dataset is in ascending order.
+        """Ensure that the specified dimension in the dataset is in ascending order.
 
         If the values along the specified dimension are in descending order, this function reverses the order of the dimension to make it ascending.
 
@@ -486,7 +479,6 @@ class Dataset:
             A new `xarray.Dataset` with the specified dimension in ascending order.
             If the dimension was already in ascending order, the original dataset is returned unchanged.
             If the dimension was in descending order, the dataset is returned with the dimension reversed.
-
         """
         # Make sure that latitude is ascending
         diff = np.diff(ds[self.dim_names[dim]])
@@ -496,8 +488,7 @@ class Dataset:
         return ds
 
     def check_if_global(self, ds) -> bool:
-        """
-        Checks if the dataset covers the entire globe in the longitude dimension.
+        """Checks if the dataset covers the entire globe in the longitude dimension.
 
         This function calculates the mean difference between consecutive longitude values.
         It then checks if the difference between the first and last longitude values (plus 360 degrees)
@@ -508,7 +499,6 @@ class Dataset:
         -------
         bool
             True if the dataset covers the entire globe in the longitude dimension, False otherwise.
-
         """
         dlon_mean = (
             ds[self.dim_names["longitude"]].diff(dim=self.dim_names["longitude"]).mean()
@@ -569,8 +559,8 @@ class Dataset:
         return ds_concatenated
 
     def post_process(self):
-        """
-        Placeholder method to be overridden by subclasses for dataset post-processing.
+        """Placeholder method to be overridden by subclasses for dataset post-
+        processing.
 
         Returns
         -------
@@ -582,10 +572,9 @@ class Dataset:
     def choose_subdomain(
         self, latitude_range, longitude_range, margin, straddle, return_subdomain=False
     ):
-        """
-        Selects a subdomain from the xarray Dataset based on specified latitude and longitude ranges,
-        extending the selection by a specified margin. Handles longitude conversions to accommodate different
-        longitude ranges.
+        """Selects a subdomain from the xarray Dataset based on specified latitude and
+        longitude ranges, extending the selection by a specified margin. Handles
+        longitude conversions to accommodate different longitude ranges.
 
         Parameters
         ----------
@@ -679,8 +668,7 @@ class Dataset:
 
 @dataclass(frozen=True, kw_only=True)
 class TPXODataset(Dataset):
-    """
-    Represents tidal data on the original grid from the TPXO dataset.
+    """Represents tidal data on the original grid from the TPXO dataset.
 
     Parameters
     ----------
@@ -732,8 +720,8 @@ class TPXODataset(Dataset):
     reference_date: datetime = datetime(1992, 1, 1)
 
     def clean_up(self, ds: xr.Dataset) -> xr.Dataset:
-        """
-        Clean up and standardize the dimensions and coordinates of the dataset for further processing.
+        """Clean up and standardize the dimensions and coordinates of the dataset for
+        further processing.
 
         This method performs the following operations:
         - Assigns new coordinate variables for 'omega', 'longitude', and 'latitude' based on existing dataset variables.
@@ -782,8 +770,7 @@ class TPXODataset(Dataset):
         return ds
 
     def check_number_constituents(self, ntides: int):
-        """
-        Checks if the number of constituents in the dataset is at least `ntides`.
+        """Checks if the number of constituents in the dataset is at least `ntides`.
 
         Parameters
         ----------
@@ -801,8 +788,8 @@ class TPXODataset(Dataset):
             )
 
     def post_process(self):
-        """
-        Apply a depth-based mask to the dataset, ensuring only positive depths are retained.
+        """Apply a depth-based mask to the dataset, ensuring only positive depths are
+        retained.
 
         This method checks if the 'depth' variable is present in the dataset. If found, a mask is created where
         depths greater than 0 are considered valid (mask value of 1). This mask is applied to all data variables
@@ -826,8 +813,7 @@ class TPXODataset(Dataset):
 
 @dataclass(frozen=True, kw_only=True)
 class GLORYSDataset(Dataset):
-    """
-    Represents GLORYS data on original grid.
+    """Represents GLORYS data on original grid.
 
     Parameters
     ----------
@@ -873,8 +859,8 @@ class GLORYSDataset(Dataset):
     climatology: Optional[bool] = False
 
     def post_process(self):
-        """
-        Apply a mask to the dataset based on the 'zeta' variable, with 0 where 'zeta' is NaN.
+        """Apply a mask to the dataset based on the 'zeta' variable, with 0 where 'zeta'
+        is NaN.
 
         This method creates a mask based on the
         first time step (time=0) of 'zeta'. The mask has 1 for valid data and 0 where 'zeta' is NaN. This mask is applied
@@ -885,7 +871,6 @@ class GLORYSDataset(Dataset):
         -------
         None
             The dataset is modified in-place by applying the mask to each variable.
-
         """
 
         mask = xr.where(
@@ -902,8 +887,7 @@ class GLORYSDataset(Dataset):
 
 @dataclass(frozen=True, kw_only=True)
 class CESMDataset(Dataset):
-    """
-    Represents CESM data on original grid.
+    """Represents CESM data on original grid.
 
     Parameters
     ----------
@@ -929,8 +913,7 @@ class CESMDataset(Dataset):
 
     # overwrite clean_up method from parent class
     def clean_up(self, ds: xr.Dataset) -> xr.Dataset:
-        """
-        Ensure the dataset's time dimension is correctly defined and standardized.
+        """Ensure the dataset's time dimension is correctly defined and standardized.
 
         This method verifies that the time dimension exists in the dataset and assigns it appropriately. If the "time" dimension is missing, the method attempts to assign an existing "time" or "month" dimension. If neither exists, it expands the dataset to include a "time" dimension with a size of one.
 
@@ -938,7 +921,6 @@ class CESMDataset(Dataset):
         -------
         ds : xr.Dataset
             The xarray Dataset with the correct time dimension assigned or added.
-
         """
 
         if "time" not in self.dim_names:
@@ -954,8 +936,8 @@ class CESMDataset(Dataset):
         return ds
 
     def add_time_info(self, ds: xr.Dataset) -> xr.Dataset:
-        """
-        Adds time information to the dataset based on the climatology flag and dimension names.
+        """Adds time information to the dataset based on the climatology flag and
+        dimension names.
 
         This method processes the dataset to include time information according to the climatology
         setting. If the dataset represents climatology data and the time dimension is labeled as
@@ -991,8 +973,7 @@ class CESMDataset(Dataset):
 
 @dataclass(frozen=True, kw_only=True)
 class CESMBGCDataset(CESMDataset):
-    """
-    Represents CESM BGC data on original grid.
+    """Represents CESM BGC data on original grid.
 
     Parameters
     ----------
@@ -1115,8 +1096,7 @@ class CESMBGCDataset(CESMDataset):
 
 @dataclass(frozen=True, kw_only=True)
 class CESMBGCSurfaceForcingDataset(CESMDataset):
-    """
-    Represents CESM BGC surface forcing data on original grid.
+    """Represents CESM BGC surface forcing data on original grid.
 
     Parameters
     ----------
@@ -1161,8 +1141,7 @@ class CESMBGCSurfaceForcingDataset(CESMDataset):
     climatology: Optional[bool] = False
 
     def post_process(self):
-        """
-        Perform post-processing on the dataset to remove specific variables.
+        """Perform post-processing on the dataset to remove specific variables.
 
         This method checks if the variable "z_t" exists in the dataset. If it does,
         the variable is removed from the dataset. The modified dataset is then
@@ -1189,8 +1168,7 @@ class CESMBGCSurfaceForcingDataset(CESMDataset):
 
 @dataclass(frozen=True, kw_only=True)
 class ERA5Dataset(Dataset):
-    """
-    Represents ERA5 data on original grid.
+    """Represents ERA5 data on original grid.
 
     Parameters
     ----------
@@ -1301,8 +1279,9 @@ class ERA5Dataset(Dataset):
 
 @dataclass(frozen=True, kw_only=True)
 class ERA5Correction(Dataset):
-    """
-    Global dataset to correct ERA5 radiation. The dataset contains multiplicative correction factors for the ERA5 shortwave radiation, obtained by comparing the COREv2 climatology to the ERA5 climatology.
+    """Global dataset to correct ERA5 radiation. The dataset contains multiplicative
+    correction factors for the ERA5 shortwave radiation, obtained by comparing the
+    COREv2 climatology to the ERA5 climatology.
 
     Parameters
     ----------
@@ -1352,8 +1331,8 @@ class ERA5Correction(Dataset):
         super().__post_init__()
 
     def choose_subdomain(self, coords, straddle: bool):
-        """
-        Converts longitude values in the dataset if necessary and selects a subdomain based on the specified coordinates.
+        """Converts longitude values in the dataset if necessary and selects a subdomain
+        based on the specified coordinates.
 
         This method converts longitude values between different ranges if required and then extracts a subset of the
         dataset according to the given coordinates. It updates the dataset in place to reflect the selected subdomain.

roms_tools/setup/download.py

@@ -53,8 +53,7 @@ pup_test_data = pooch.create(
 
 
 def fetch_topo(topography_source: str) -> xr.Dataset:
-    """
-    Load the global topography data as an xarray Dataset.
+    """Load the global topography data as an xarray Dataset.
 
     Parameters
     ----------
@@ -79,8 +78,7 @@ def fetch_topo(topography_source: str) -> xr.Dataset:
 
 
 def download_correction_data(filename: str) -> str:
-    """
-    Download the correction data file.
+    """Download the correction data file.
 
     Parameters
     ----------
@@ -100,8 +98,7 @@ def download_correction_data(filename: str) -> str:
 
 
 def download_test_data(filename: str) -> str:
-    """
-    Download the test data file.
+    """Download the test data file.
 
     Parameters
     ----------

roms_tools/setup/fill.py

@@ -6,9 +6,8 @@ from scipy import sparse
 
 class LateralFill:
     def __init__(self, mask, dims, tol=1.0e-4):
-        """
-        Initializes the LateralFill class, which fills NaN values in a DataArray
-        by iteratively solving a Poisson equation using a lateral diffusion approach.
+        """Initializes the LateralFill class, which fills NaN values in a DataArray by
+        iteratively solving a Poisson equation using a lateral diffusion approach.
 
         Parameters
         ----------
@@ -51,8 +50,7 @@ class LateralFill:
         self.tol = tol
 
     def apply(self, var):
-        """
-        Fills NaN values in an xarray DataArray using iterative lateral diffusion.
+        """Fills NaN values in an xarray DataArray using iterative lateral diffusion.
 
         Parameters
         ----------
@@ -65,7 +63,6 @@ class LateralFill:
         var_filled : xarray.DataArray
             A DataArray with NaN values filled by iterative smoothing, while preserving
             non-NaN values.
-
         """
         # Apply fill to anomaly field
         mean = var.mean(dim=self.dims, skipna=True)
@@ -96,11 +93,9 @@ class LateralFill:
 
 
 def _lateral_fill_np_array(x0, b, ml, tol=1.0e-4):
-    """
-    Fills all NaN values in a 2D NumPy array using an iterative solver,
-    while preserving the existing non-NaN values.
-    The filling process uses an AMG solver to efficiently perform smoothing
-    based on the Laplace operator.
+    """Fills all NaN values in a 2D NumPy array using an iterative solver, while
+    preserving the existing non-NaN values. The filling process uses an AMG solver to
+    efficiently perform smoothing based on the Laplace operator.
 
     Parameters
     ----------
@@ -136,8 +131,7 @@ def _lateral_fill_np_array(x0, b, ml, tol=1.0e-4):
 
 
 def laplacian(grid, mask, dtype=float, format=None):
-    """
-    Return a sparse matrix for solving a 2-dimensional Poisson problem.
+    """Return a sparse matrix for solving a 2-dimensional Poisson problem.
 
     This function generates a finite difference approximation of the Laplacian operator
     on a 2-dimensional grid with unit grid spacing and Dirichlet boundary conditions.
@@ -164,7 +158,6 @@ def laplacian(grid, mask, dtype=float, format=None):
     sparse matrix
         A sparse matrix representing the finite difference Laplacian operator for
         the given grid.
-
     """
     grid = tuple(grid)
 
@@ -180,8 +173,7 @@ def laplacian(grid, mask, dtype=float, format=None):
 
 
 def stencil_grid_mod(S, grid, msk, dtype=None, format=None):
-    """
-    Construct a sparse matrix from a local matrix stencil.
+    """Construct a sparse matrix from a local matrix stencil.
 
     This function generates a sparse matrix that represents an operator
     by applying the given stencil `S` at each vertex of a regular grid with