roms-tools 1.4.1__py3-none-any.whl → 1.5.0__py3-none-any.whl

roms_tools/tests/test_setup/test_surface_forcing.py

@@ -1,5 +1,6 @@
 import pytest
 from datetime import datetime
+import xarray as xr
 from roms_tools import Grid, SurfaceForcing
 from roms_tools.setup.download import download_test_data
 import textwrap
@@ -9,9 +10,8 @@ from conftest import calculate_file_hash
 
 @pytest.fixture
 def grid_that_straddles_dateline():
-    """
-    Fixture for creating a domain that straddles the dateline and lies within the bounds of the regional ERA5 data.
-    """
+    """Fixture for creating a domain that straddles the dateline and lies within the
+    bounds of the regional ERA5 data."""
     grid = Grid(
         nx=20,
         ny=20,
@@ -27,8 +27,9 @@ def grid_that_straddles_dateline():
 
 @pytest.fixture
 def grid_that_straddles_dateline_but_is_too_big_for_regional_test_data():
-    """
-    Fixture for creating a domain that straddles the dateline but exceeds the bounds of the regional ERA5 data.
+    """Fixture for creating a domain that straddles the dateline but exceeds the bounds
+    of the regional ERA5 data.
+
     Centered east of dateline.
     """
     grid = Grid(
@@ -46,9 +47,11 @@ def grid_that_straddles_dateline_but_is_too_big_for_regional_test_data():
 
 @pytest.fixture
 def another_grid_that_straddles_dateline_but_is_too_big_for_regional_test_data():
-    """
-    Fixture for creating a domain that straddles the dateline but exceeds the bounds of the regional ERA5 data.
-    Centered west of dateline. This one was hard to catch for the nan_check for a long time, but should work now.
+    """Fixture for creating a domain that straddles the dateline but exceeds the bounds
+    of the regional ERA5 data.
+
+    Centered west of dateline. This one was hard to catch for the nan_check for a long
+    time, but should work now.
     """
     grid = Grid(
         nx=5,
@@ -65,9 +68,11 @@ def another_grid_that_straddles_dateline_but_is_too_big_for_regional_test_data()
 
 @pytest.fixture
 def grid_that_lies_east_of_dateline_less_than_five_degrees_away():
-    """
-    Fixture for creating a domain that lies east of Greenwich meridian, but less than 5 degrees away.
-    We care about the 5 degree mark because it decides whether the code handles the longitudes as straddling the dateline or not.
+    """Fixture for creating a domain that lies east of Greenwich meridian, but less than
+    5 degrees away.
+
+    We care about the 5 degree mark because it decides whether the code handles the
+    longitudes as straddling the dateline or not.
     """
 
     grid = Grid(
@@ -85,9 +90,11 @@ def grid_that_lies_east_of_dateline_less_than_five_degrees_away():
 
 @pytest.fixture
 def grid_that_lies_east_of_dateline_more_than_five_degrees_away():
-    """
-    Fixture for creating a domain that lies east of Greenwich meridian, more than 5 degrees away.
-    We care about the 5 degree mark because it decides whether the code handles the longitudes as straddling the dateline or not.
+    """Fixture for creating a domain that lies east of Greenwich meridian, more than 5
+    degrees away.
+
+    We care about the 5 degree mark because it decides whether the code handles the
+    longitudes as straddling the dateline or not.
     """
     grid = Grid(
         nx=5,
@@ -104,9 +111,11 @@ def grid_that_lies_east_of_dateline_more_than_five_degrees_away():
 
 @pytest.fixture
 def grid_that_lies_west_of_dateline_less_than_five_degrees_away():
-    """
-    Fixture for creating a domain that lies west of Greenwich meridian, less than 5 degrees away.
-    We care about the 5 degree mark because it decides whether the code handles the longitudes as straddling the dateline or not.
+    """Fixture for creating a domain that lies west of Greenwich meridian, less than 5
+    degrees away.
+
+    We care about the 5 degree mark because it decides whether the code handles the
+    longitudes as straddling the dateline or not.
     """
 
     grid = Grid(
@@ -124,9 +133,11 @@ def grid_that_lies_west_of_dateline_less_than_five_degrees_away():
 
 @pytest.fixture
 def grid_that_lies_west_of_dateline_more_than_five_degrees_away():
-    """
-    Fixture for creating a domain that lies west of Greenwich meridian, more than 5 degrees away.
-    We care about the 5 degree mark because it decides whether the code handles the longitudes as straddling the dateline or not.
+    """Fixture for creating a domain that lies west of Greenwich meridian, more than 5
+    degrees away.
+
+    We care about the 5 degree mark because it decides whether the code handles the
+    longitudes as straddling the dateline or not.
     """
 
     grid = Grid(
@@ -144,8 +155,10 @@ def grid_that_lies_west_of_dateline_more_than_five_degrees_away():
 
 @pytest.fixture
 def grid_that_straddles_180_degree_meridian():
-    """
-    Fixture for creating a domain that straddles 180 degree meridian. This is a good test grid for the global ERA5 data, which comes on an [-180, 180] longitude grid.
+    """Fixture for creating a domain that straddles 180 degree meridian.
+
+    This is a good test grid for the global ERA5 data, which comes on an [-180, 180]
+    longitude grid.
     """
 
     grid = Grid(
@@ -172,8 +185,7 @@ def grid_that_straddles_180_degree_meridian():
     ],
 )
 def test_successful_initialization_with_regional_data(grid_fixture, request, use_dask):
-    """
-    Test the initialization of SurfaceForcing with regional ERA5 data.
+    """Test the initialization of SurfaceForcing with regional ERA5 data.
 
     This test checks the following:
     1. SurfaceForcing object initializes successfully with provided regional data.
@@ -242,8 +254,7 @@ def test_successful_initialization_with_regional_data(grid_fixture, request, use
 def test_nan_detection_initialization_with_regional_data(
     grid_fixture, request, use_dask
 ):
-    """
-    Test handling of NaN values during initialization with regional data.
+    """Test handling of NaN values during initialization with regional data.
 
     Ensures ValueError is raised if NaN values are detected in the dataset.
     """
@@ -270,10 +281,11 @@ def test_nan_detection_initialization_with_regional_data(
 def test_no_longitude_intersection_initialization_with_regional_data(
     grid_that_straddles_180_degree_meridian, use_dask
 ):
-    """
-    Test initialization of SurfaceForcing with a grid that straddles the 180° meridian.
+    """Test initialization of SurfaceForcing with a grid that straddles the 180°
+    meridian.
 
-    Ensures ValueError is raised when the longitude range does not intersect with the dataset.
+    Ensures ValueError is raised when the longitude range does not intersect with the
+    dataset.
     """
     start_time = datetime(2020, 1, 31)
     end_time = datetime(2020, 2, 2)
@@ -309,11 +321,11 @@ def test_no_longitude_intersection_initialization_with_regional_data(
     ],
 )
 def test_successful_initialization_with_global_data(grid_fixture, request, use_dask):
-    """
-    Test initialization of SurfaceForcing with global data.
+    """Test initialization of SurfaceForcing with global data.
 
     Verifies that the SurfaceForcing object is correctly initialized with global data,
-    including the correct handling of the grid and physics data. Checks both coarse and fine grid initialization.
+    including the correct handling of the grid and physics data. Checks both coarse and
+    fine grid initialization.
     """
     start_time = datetime(2020, 1, 31)
     end_time = datetime(2020, 2, 2)
@@ -357,8 +369,7 @@ def test_successful_initialization_with_global_data(grid_fixture, request, use_d
 
 
 def test_nans_filled_in(grid_that_straddles_dateline, use_dask):
-    """
-    Test that the surface forcing fields contain no NaNs.
+    """Test that the surface forcing fields contain no NaNs.
 
     The test is performed twice:
     - First with the default fine grid.
@@ -405,10 +416,8 @@ def test_nans_filled_in(grid_that_straddles_dateline, use_dask):
 
 
 def test_time_attr_climatology(bgc_surface_forcing_from_climatology):
-    """
-    Test that the 'cycle_length' attribute is present in the time coordinate of the BGC dataset
-    when using climatology data.
-    """
+    """Test that the 'cycle_length' attribute is present in the time coordinate of the
+    BGC dataset when using climatology data."""
     for time_coord in ["pco2_time", "iron_time", "dust_time", "nox_time", "nhy_time"]:
         assert hasattr(
             bgc_surface_forcing_from_climatology.ds[time_coord],
@@ -418,10 +427,8 @@ def test_time_attr_climatology(bgc_surface_forcing_from_climatology):
 
 
 def test_time_attr(bgc_surface_forcing):
-    """
-    Test that the 'cycle_length' attribute is not present in the time coordinate of the BGC dataset
-    when not using climatology data.
-    """
+    """Test that the 'cycle_length' attribute is not present in the time coordinate of
+    the BGC dataset when not using climatology data."""
     for time_coord in ["pco2_time", "iron_time", "dust_time", "nox_time", "nhy_time"]:
         assert not hasattr(
             bgc_surface_forcing.ds[time_coord],
@@ -448,12 +455,11 @@ def test_time_attr(bgc_surface_forcing):
 def test_surface_forcing_creation(
     sfc_forcing_fixture, expected_climatology, expected_fname, request
 ):
-    """
-    Test the creation and initialization of the SurfaceForcing object with BGC.
+    """Test the creation and initialization of the SurfaceForcing object with BGC.
 
     Verifies that the SurfaceForcing object is properly created with correct attributes.
-    Ensures that expected variables are present in the dataset
-    and that attributes match the given configurations.
+    Ensures that expected variables are present in the dataset and that attributes match
+    the given configurations.
     """
 
     sfc_forcing = request.getfixturevalue(sfc_forcing_fixture)
@@ -482,6 +488,23 @@ def test_surface_forcing_creation(
     sfc_forcing.plot("pco2_air", time=0)
 
 
+@pytest.mark.parametrize(
+    "sfc_forcing_fixture",
+    [
+        "bgc_surface_forcing",
+        "bgc_surface_forcing_from_climatology",
+    ],
+)
+def test_surface_forcing_pco2_replication(sfc_forcing_fixture, request):
+    """Test whether pco2_air and pco2_air_alt is the same after processing."""
+
+    sfc_forcing = request.getfixturevalue(sfc_forcing_fixture)
+
+    xr.testing.assert_allclose(
+        sfc_forcing.ds.pco2_air, sfc_forcing.ds.pco2_air_alt, rtol=1.0e-5
+    )
+
+
 @pytest.mark.parametrize(
     "sfc_forcing_fixture",
     [
@@ -491,9 +514,7 @@ def test_surface_forcing_creation(
     ],
 )
 def test_surface_forcing_plot_save(sfc_forcing_fixture, request, tmp_path):
-    """
-    Test plot and save methods.
-    """
+    """Test plot and save methods."""
     sfc_forcing = request.getfixturevalue(sfc_forcing_fixture)
     sfc_forcing.plot(varname="uwnd", time=0)
 
@@ -525,9 +546,7 @@ def test_surface_forcing_plot_save(sfc_forcing_fixture, request, tmp_path):
 
 
 def test_surface_forcing_bgc_plot_save(bgc_surface_forcing, tmp_path):
-    """
-    Test plot and save methods.
-    """
+    """Test plot and save methods."""
 
     # Check the values in the dataset
     bgc_surface_forcing.plot(varname="pco2_air", time=0)
@@ -562,9 +581,7 @@ def test_surface_forcing_bgc_plot_save(bgc_surface_forcing, tmp_path):
 def test_surface_forcing_bgc_from_clim_plot_save(
     bgc_surface_forcing_from_climatology, tmp_path
 ):
-    """
-    Test plot and save methods.
-    """
+    """Test plot and save methods."""
 
     # Check the values in the dataset
     bgc_surface_forcing_from_climatology.plot(varname="pco2_air", time=0)
@@ -609,7 +626,8 @@ def test_surface_forcing_bgc_from_clim_plot_save(
     ],
 )
 def test_roundtrip_yaml(sfc_forcing_fixture, request, tmp_path, use_dask):
-    """Test that creating an SurfaceForcing object, saving its parameters to yaml file, and re-opening yaml file creates the same object."""
+    """Test that creating an SurfaceForcing object, saving its parameters to yaml file,
+    and re-opening yaml file creates the same object."""
 
     sfc_forcing = request.getfixturevalue(sfc_forcing_fixture)
 

roms_tools/tests/test_setup/test_tides.py

@@ -25,9 +25,7 @@ def grid_that_is_out_of_bounds_of_regional_tpxo_data():
 
 @pytest.fixture
 def grid_that_straddles_dateline():
-    """
-    Fixture for creating a domain that straddles the dateline.
-    """
+    """Fixture for creating a domain that straddles the dateline."""
     grid = Grid(
         nx=5,
         ny=5,
@@ -43,9 +41,7 @@ def grid_that_straddles_dateline():
 
 @pytest.fixture
 def grid_that_straddles_180_degree_meridian():
-    """
-    Fixture for creating a domain that straddles 180 degree meridian.
-    """
+    """Fixture for creating a domain that straddles 180 degree meridian."""
 
     grid = Grid(
         nx=5,
@@ -174,9 +170,8 @@ def test_insufficient_number_of_consituents(grid_that_straddles_dateline, use_da
 
 
 def test_tidal_forcing_plot_save(tidal_forcing, tmp_path):
-    """
-    Test plot and save methods in the same test since we dask arrays are already computed.
-    """
+    """Test plot and save methods in the same test since we dask arrays are already
+    computed."""
     tidal_forcing.ds.load()
 
     tidal_forcing.plot(varname="ssh_Re", ntides=0)
@@ -211,7 +206,8 @@ def test_tidal_forcing_plot_save(tidal_forcing, tmp_path):
 
 
 def test_roundtrip_yaml(tidal_forcing, tmp_path, use_dask):
-    """Test that creating a TidalForcing object, saving its parameters to yaml file, and re-opening yaml file creates the same object."""
+    """Test that creating a TidalForcing object, saving its parameters to yaml file, and
+    re-opening yaml file creates the same object."""
 
     # Create a temporary filepath using the tmp_path fixture
     file_str = "test_yaml"

roms_tools/tests/test_setup/test_topography.py

@@ -59,10 +59,8 @@ def test_hmin_criterion():
 
 
 def test_mask_topography_boundary():
-    """
-    Test that the mask and topography along the grid boundaries (north, south, east, west)
-    are identical to the adjacent inland cells.
-    """
+    """Test that the mask and topography along the grid boundaries (north, south, east,
+    west) are identical to the adjacent inland cells."""
 
     # Create a grid with some land along the northern boundary
     grid = Grid(

roms_tools/tests/test_setup/test_vertical_coordinate.py

@@ -3,9 +3,7 @@ from roms_tools import Grid
 
 
 def test_invalid_theta_s_value():
-    """
-    Test the validation of the theta_s value.
-    """
+    """Test the validation of the theta_s value."""
     with pytest.raises(ValueError):
 
         Grid(
@@ -24,9 +22,7 @@ def test_invalid_theta_s_value():
 
 
 def test_invalid_theta_b_value():
-    """
-    Test the validation of the theta_b value.
-    """
+    """Test the validation of the theta_b value."""
     with pytest.raises(ValueError):
         Grid(
             nx=2,

roms_tools/tests/test_utils.py

@@ -23,8 +23,8 @@ class TestPartitionGrid:
             "xi_rho": 32,
             "xi_u": 31,
             "eta_v": 10,
-            "eta_psi": 11,
-            "xi_psi": 33,
+            # "eta_psi": 11,
+            # "xi_psi": 33,
             "eta_coarse": 6,
             "xi_coarse": 17,
             "s_rho": 100,
@@ -35,8 +35,8 @@ class TestPartitionGrid:
             "xi_rho": 32,
             "xi_u": 31,
             "eta_v": 10,
-            "eta_psi": 10,
-            "xi_psi": 33,
+            # "eta_psi": 10,
+            # "xi_psi": 33,
             "eta_coarse": 5,
             "xi_coarse": 17,
             "s_rho": 100,
@@ -47,8 +47,8 @@ class TestPartitionGrid:
             "xi_rho": 32,
             "xi_u": 31,
             "eta_v": 11,
-            "eta_psi": 12,
-            "xi_psi": 33,
+            # "eta_psi": 12,
+            # "xi_psi": 33,
             "eta_coarse": 6,
             "xi_coarse": 17,
             "s_rho": 100,
@@ -63,8 +63,8 @@ class TestPartitionGrid:
             "xi_rho": 11,
             "xi_u": 10,
             "eta_v": 31,
-            "eta_psi": 33,
-            "xi_psi": 11,
+            # "eta_psi": 33,
+            # "xi_psi": 11,
             "eta_coarse": 17,
             "xi_coarse": 6,
             "s_rho": 100,
@@ -75,8 +75,8 @@ class TestPartitionGrid:
             "xi_rho": 10,
             "xi_u": 10,
             "eta_v": 31,
-            "eta_psi": 33,
-            "xi_psi": 10,
+            # "eta_psi": 33,
+            # "xi_psi": 10,
             "eta_coarse": 17,
             "xi_coarse": 5,
             "s_rho": 100,
@@ -87,8 +87,8 @@ class TestPartitionGrid:
             "xi_rho": 11,
             "xi_u": 11,
             "eta_v": 31,
-            "eta_psi": 33,
-            "xi_psi": 12,
+            # "eta_psi": 33,
+            # "xi_psi": 12,
             "eta_coarse": 17,
             "xi_coarse": 6,
             "s_rho": 100,
@@ -108,8 +108,8 @@ class TestPartitionGrid:
             "xi_rho": 11,
             "xi_u": 10,
             "eta_v": 10,
-            "eta_psi": 11,
-            "xi_psi": 11,
+            # "eta_psi": 11,
+            # "xi_psi": 11,
             "eta_coarse": 6,
             "xi_coarse": 6,
             "s_rho": 100,
@@ -121,8 +121,8 @@ class TestPartitionGrid:
             "xi_u": 10,
             "eta_v": 10,
             "eta_coarse": 5,
-            "eta_psi": 10,
-            "xi_psi": 11,
+            # "eta_psi": 10,
+            # "xi_psi": 11,
             "xi_coarse": 6,
             "s_rho": 100,
             "s_w": 101,
@@ -132,8 +132,8 @@ class TestPartitionGrid:
             "xi_rho": 11,
             "xi_u": 10,
             "eta_v": 11,
-            "eta_psi": 12,
-            "xi_psi": 11,
+            # "eta_psi": 12,
+            # "xi_psi": 11,
             "eta_coarse": 6,
             "xi_coarse": 6,
             "s_rho": 100,
@@ -144,8 +144,8 @@ class TestPartitionGrid:
             "xi_rho": 10,
             "xi_u": 10,
             "eta_v": 10,
-            "eta_psi": 11,
-            "xi_psi": 10,
+            # "eta_psi": 11,
+            # "xi_psi": 10,
             "eta_coarse": 6,
             "xi_coarse": 5,
             "s_rho": 100,
@@ -156,8 +156,8 @@ class TestPartitionGrid:
             "xi_rho": 10,
             "xi_u": 10,
             "eta_v": 10,
-            "eta_psi": 10,
-            "xi_psi": 10,
+            # "eta_psi": 10,
+            # "xi_psi": 10,
             "eta_coarse": 5,
             "xi_coarse": 5,
             "s_rho": 100,
@@ -168,8 +168,8 @@ class TestPartitionGrid:
             "xi_rho": 10,
             "xi_u": 10,
             "eta_v": 11,
-            "eta_psi": 12,
-            "xi_psi": 10,
+            # "eta_psi": 12,
+            # "xi_psi": 10,
             "eta_coarse": 6,
             "xi_coarse": 5,
             "s_rho": 100,
@@ -180,8 +180,8 @@ class TestPartitionGrid:
             "xi_rho": 11,
             "xi_u": 11,
             "eta_v": 10,
-            "eta_psi": 11,
-            "xi_psi": 12,
+            # "eta_psi": 11,
+            # "xi_psi": 12,
             "eta_coarse": 6,
             "xi_coarse": 6,
             "s_rho": 100,
@@ -192,8 +192,8 @@ class TestPartitionGrid:
             "xi_rho": 11,
             "xi_u": 11,
             "eta_v": 10,
-            "eta_psi": 10,
-            "xi_psi": 12,
+            # "eta_psi": 10,
+            # "xi_psi": 12,
             "eta_coarse": 5,
             "xi_coarse": 6,
             "s_rho": 100,
@@ -204,8 +204,8 @@ class TestPartitionGrid:
             "xi_rho": 11,
             "xi_u": 11,
             "eta_v": 11,
-            "eta_psi": 12,
-            "xi_psi": 12,
+            # "eta_psi": 12,
+            # "xi_psi": 12,
             "eta_coarse": 6,
             "xi_coarse": 6,
             "s_rho": 100,

roms_tools/utils.py

@@ -9,8 +9,8 @@ from pathlib import Path
 def partition(
     ds: xr.Dataset, np_eta: int = 1, np_xi: int = 1
 ) -> tuple[list[int], list[xr.Dataset]]:
-    """
-    Partition a ROMS (Regional Ocean Modeling System) dataset into smaller spatial tiles.
+    """Partition a ROMS (Regional Ocean Modeling System) dataset into smaller spatial
+    tiles.
 
     This function divides the input dataset into `np_eta` by `np_xi` tiles, where each tile
     represents a subdomain of the original dataset. The partitioning is performed along
@@ -32,6 +32,7 @@ def partition(
     -------
     tuple[list[int], list[xr.Dataset]]
         A tuple containing two elements:
+
         - A list of integers representing the file numbers associated with each partition.
         - A list of `xarray.Dataset` objects, each representing a partitioned subdomain of the original dataset.
 
@@ -90,8 +91,7 @@ def partition(
         n_xi_ghost_cells = 1
 
     def integer_division_or_raise(a: int, b: int, dimension: str) -> int:
-        """
-        Perform integer division and ensure that the division is exact.
+        """Perform integer division and ensure that the division is exact.
 
         Parameters
         ----------
@@ -214,7 +214,7 @@ def partition(
             )
 
     def cumsum(pmf):
-        """Implementation of cumsum which ensures the result starts with zero"""
+        """Implementation of cumsum which ensures the result starts with zero."""
         cdf = np.empty(len(pmf) + 1, dtype=int)
         cdf[0] = 0
         np.cumsum(pmf, out=cdf[1:])
@@ -290,8 +290,7 @@ def partition(
 def partition_netcdf(
     filepath: Union[str, Path], np_eta: int = 1, np_xi: int = 1
 ) -> None:
-    """
-    Partition a ROMS NetCDF file into smaller spatial tiles and save them to disk.
+    """Partition a ROMS NetCDF file into smaller spatial tiles and save them to disk.
 
     This function divides the dataset in the specified NetCDF file into `np_eta` by `np_xi` tiles.
     Each tile is saved as a separate NetCDF file.

{roms_tools-1.4.1.dist-info → roms_tools-1.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: roms-tools
-Version: 1.4.1
+Version: 1.5.0
 Summary: Tools for running and analysing UCLA-ROMS simulations
 Author-email: Nora Loose <nora.loose@gmail.com>, Thomas Nicholas <tom@cworthy.org>
 License: Apache-2
@@ -47,7 +47,7 @@ A suite of python tools for setting up a [ROMS](https://github.com/CESR-lab/ucla
 
 <mark>**DISCLAIMER**: This project is **ALPHA** and will be **EXPERIMENTAL** at least throughout Fall 2024. We do not recommend to use this software before this ALPHA development and test phase is completed.</mark>
 
-## Installation instructions
+## Installation
 
 ### Installation from pip