roms-tools 1.5.0__py3-none-any.whl → 1.6.1__py3-none-any.whl

roms_tools/tests/test_setup/test_fill.py

@@ -1,110 +1,18 @@
 import pytest
-from roms_tools.setup.datasets import (
-    GLORYSDataset,
-    ERA5Dataset,
-    CESMBGCDataset,
-    CESMBGCSurfaceForcingDataset,
-    TPXODataset,
-)
-from roms_tools.setup.download import download_test_data
 from roms_tools.setup.fill import LateralFill
-from roms_tools.setup.utils import extrapolate_deepest_to_bottom
-from datetime import datetime
 import numpy as np
 import xarray as xr
 
 
-@pytest.fixture()
-def era5_data(request, use_dask):
-    fname = download_test_data("ERA5_regional_test_data.nc")
-    data = ERA5Dataset(
-        filename=fname,
-        start_time=datetime(2020, 1, 31),
-        end_time=datetime(2020, 2, 2),
-        use_dask=use_dask,
-    )
-
-    return data
-
-
-@pytest.fixture()
-def glorys_data(request, use_dask):
-    # the following GLORYS data has a wide enough domain
-    # to have different masks for tracers vs. velocities
-    fname = download_test_data("GLORYS_test_data.nc")
-
-    data = GLORYSDataset(
-        filename=fname,
-        start_time=datetime(2012, 1, 1),
-        end_time=datetime(2013, 1, 1),
-        use_dask=use_dask,
-    )
-
-    ds = data.ds.isel(depth=[0, 10, 30])
-    object.__setattr__(data, "ds", ds)
-
-    # extrapolate deepest value to bottom so all levels can use the same surface mask
-    for var in data.var_names:
-        if var != "zeta":
-            data.ds[data.var_names[var]] = extrapolate_deepest_to_bottom(
-                data.ds[data.var_names[var]], data.dim_names["depth"]
-            )
-
-    return data
-
-
-@pytest.fixture()
-def tpxo_data(request, use_dask):
-    fname = download_test_data("TPXO_regional_test_data.nc")
-
-    data = TPXODataset(
-        filename=fname,
-        use_dask=use_dask,
-    )
-
-    return data
-
-
-@pytest.fixture()
-def cesm_bgc_data(request, use_dask):
-    fname = download_test_data("CESM_BGC_2012.nc")
-
-    data = CESMBGCDataset(
-        filename=fname,
-        start_time=datetime(2012, 1, 1),
-        end_time=datetime(2013, 1, 1),
-        climatology=False,
-        use_dask=use_dask,
-    )
-
-    # extrapolate deepest value to bottom so all levels can use the same surface mask
-    for var in data.var_names:
-        data.ds[data.var_names[var]] = extrapolate_deepest_to_bottom(
-            data.ds[data.var_names[var]], data.dim_names["depth"]
-        )
-
-    return data
-
-
-@pytest.fixture()
-def cesm_surface_bgc_data(request, use_dask):
-    fname = download_test_data("CESM_BGC_SURFACE_2012.nc")
-
-    data = CESMBGCSurfaceForcingDataset(
-        filename=fname,
-        start_time=datetime(2012, 1, 1),
-        end_time=datetime(2013, 1, 1),
-        climatology=False,
-        use_dask=use_dask,
-    )
-    data.post_process()
-
-    return data
-
-
 @pytest.mark.parametrize(
     "data_fixture",
-    ["era5_data", "glorys_data", "tpxo_data", "cesm_bgc_data", "cesm_surface_bgc_data"],
+    [
+        "era5_data",
+        "glorys_data",
+        "tpxo_data",
+        "coarsened_cesm_bgc_data",
+        "cesm_surface_bgc_data",
+    ],
 )
 def test_lateral_fill_no_nans(data_fixture, request):
     data = request.getfixturevalue(data_fixture)
@@ -128,18 +36,23 @@ def test_lateral_fill_no_nans(data_fixture, request):
         assert not filled.isnull().any()
 
 
-def test_lateral_fill_correct_order_of_magnitude(cesm_bgc_data):
+def test_lateral_fill_correct_order_of_magnitude(coarsened_cesm_bgc_data):
 
     lateral_fill = LateralFill(
-        cesm_bgc_data.ds["mask"],
-        [cesm_bgc_data.dim_names["latitude"], cesm_bgc_data.dim_names["longitude"]],
+        coarsened_cesm_bgc_data.ds["mask"],
+        [
+            coarsened_cesm_bgc_data.dim_names["latitude"],
+            coarsened_cesm_bgc_data.dim_names["longitude"],
+        ],
     )
 
-    ALK = cesm_bgc_data.ds["ALK"]
+    ALK = coarsened_cesm_bgc_data.ds["ALK"]
 
     # zero out alkalinity field in all depth levels but the uppermost
-    ALK = xr.where(cesm_bgc_data.ds.ALK.depth > 25, 0, cesm_bgc_data.ds.ALK)
-    ALK = ALK.where(cesm_bgc_data.ds.mask)
+    ALK = xr.where(
+        coarsened_cesm_bgc_data.ds.ALK.depth > 25, 0, coarsened_cesm_bgc_data.ds.ALK
+    )
+    ALK = ALK.where(coarsened_cesm_bgc_data.ds.mask)
 
     filled = lateral_fill.apply(ALK.astype(np.float64))
 

roms_tools/tests/test_setup/test_initial_conditions.py

@@ -176,42 +176,46 @@ def test_interpolation_from_climatology(
     )
 
 
-def test_initial_conditions_plot_save(
-    initial_conditions_with_bgc_from_climatology, tmp_path
-):
-    """Test plot and save methods."""
+def test_initial_conditions_plot(initial_conditions_with_bgc_from_climatology):
+    """Test plot method."""
 
-    initial_conditions_with_bgc_from_climatology.plot(varname="temp", s=0)
+    initial_conditions_with_bgc_from_climatology.plot(var_name="temp", s=0)
     initial_conditions_with_bgc_from_climatology.plot(
-        varname="temp", s=0, depth_contours=True
+        var_name="temp", s=0, depth_contours=True
     )
     initial_conditions_with_bgc_from_climatology.plot(
-        varname="temp", eta=0, layer_contours=True
+        var_name="temp", eta=0, layer_contours=True
     )
     initial_conditions_with_bgc_from_climatology.plot(
-        varname="temp", xi=0, layer_contours=True
+        var_name="temp", xi=0, layer_contours=True
     )
-    initial_conditions_with_bgc_from_climatology.plot(varname="temp", eta=0)
-    initial_conditions_with_bgc_from_climatology.plot(varname="temp", xi=0)
-    initial_conditions_with_bgc_from_climatology.plot(varname="temp", s=0, xi=0)
-    initial_conditions_with_bgc_from_climatology.plot(varname="temp", eta=0, xi=0)
+    initial_conditions_with_bgc_from_climatology.plot(var_name="temp", eta=0)
+    initial_conditions_with_bgc_from_climatology.plot(var_name="temp", xi=0)
+    initial_conditions_with_bgc_from_climatology.plot(var_name="temp", s=0, xi=0)
+    initial_conditions_with_bgc_from_climatology.plot(var_name="temp", eta=0, xi=0)
     initial_conditions_with_bgc_from_climatology.plot(
-        varname="u", s=0, layer_contours=True
+        var_name="u", s=0, layer_contours=True
     )
-    initial_conditions_with_bgc_from_climatology.plot(varname="u", s=0)
-    initial_conditions_with_bgc_from_climatology.plot(varname="u", eta=0)
-    initial_conditions_with_bgc_from_climatology.plot(varname="u", xi=0)
+    initial_conditions_with_bgc_from_climatology.plot(var_name="u", s=0)
+    initial_conditions_with_bgc_from_climatology.plot(var_name="u", eta=0)
+    initial_conditions_with_bgc_from_climatology.plot(var_name="u", xi=0)
     initial_conditions_with_bgc_from_climatology.plot(
-        varname="v", s=0, layer_contours=True
+        var_name="v", s=0, layer_contours=True
     )
-    initial_conditions_with_bgc_from_climatology.plot(varname="v", s=0)
-    initial_conditions_with_bgc_from_climatology.plot(varname="v", eta=0)
-    initial_conditions_with_bgc_from_climatology.plot(varname="v", xi=0)
-    initial_conditions_with_bgc_from_climatology.plot(varname="zeta")
-    initial_conditions_with_bgc_from_climatology.plot(varname="ubar")
-    initial_conditions_with_bgc_from_climatology.plot(varname="vbar")
-    initial_conditions_with_bgc_from_climatology.plot(varname="ALK", s=0, xi=0)
-    initial_conditions_with_bgc_from_climatology.plot(varname="ALK", eta=0, xi=0)
+    initial_conditions_with_bgc_from_climatology.plot(var_name="v", s=0)
+    initial_conditions_with_bgc_from_climatology.plot(var_name="v", eta=0)
+    initial_conditions_with_bgc_from_climatology.plot(var_name="v", xi=0)
+    initial_conditions_with_bgc_from_climatology.plot(var_name="zeta")
+    initial_conditions_with_bgc_from_climatology.plot(var_name="ubar")
+    initial_conditions_with_bgc_from_climatology.plot(var_name="vbar")
+    initial_conditions_with_bgc_from_climatology.plot(var_name="ALK", s=0, xi=0)
+    initial_conditions_with_bgc_from_climatology.plot(var_name="ALK", eta=0, xi=0)
+
+
+def test_initial_conditions_save(
+    initial_conditions_with_bgc_from_climatology, tmp_path
+):
+    """Test save method."""
 
     for file_str in ["test_ic", "test_ic.nc"]:
         # Create a temporary filepath using the tmp_path fixture

roms_tools/tests/test_setup/test_regrid.py

@@ -18,16 +18,10 @@ def vertical_regridder(depth_values, layer_depth_rho_values):
         def __init__(self, ds):
             self.ds = ds
 
-    # Creating minimal mock data for testing
-    # Depth levels in meters
-
-    # Create mock datasets for DataContainer and Grid
-    data_ds = xr.Dataset({"depth": (["depth"], depth_values)})
     target_depth = xr.DataArray(data=layer_depth_rho_values, dims=["s_rho"])
-    # Instantiate DataContainer and Grid objects with mock datasets
-    mock_data = DataContainer(data_ds)
+    source_depth = xr.DataArray(data=depth_values, dims=["depth"])
 
-    return VerticalRegrid(mock_data, target_depth)
+    return VerticalRegrid(target_depth, source_depth)
 
 
 @pytest.mark.parametrize(

roms_tools/tests/test_setup/test_surface_forcing.py

@@ -187,12 +187,6 @@ 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.
 
-    This test checks the following:
-    1. SurfaceForcing object initializes successfully with provided regional data.
-    2. Attributes such as `start_time`, `end_time`, and `source` are set correctly.
-    3. The dataset contains expected variables, including "uwnd", "vwnd", "swrad", "lwrad", "Tair", "qair", and "rain".
-    4. Surface forcing plots for "uwnd", "vwnd", and "rain" are generated without errors.
-
     The test is performed twice:
     - First with the default fine grid.
     - Then with the coarse grid enabled.
@@ -513,10 +507,10 @@ def test_surface_forcing_pco2_replication(sfc_forcing_fixture, request):
         "coarse_surface_forcing",
     ],
 )
-def test_surface_forcing_plot_save(sfc_forcing_fixture, request, tmp_path):
-    """Test plot and save methods."""
+def test_surface_forcing_save(sfc_forcing_fixture, request, tmp_path):
+    """Test save method."""
     sfc_forcing = request.getfixturevalue(sfc_forcing_fixture)
-    sfc_forcing.plot(varname="uwnd", time=0)
+    sfc_forcing.plot(var_name="uwnd", time=0)
 
     for file_str in ["test_sf", "test_sf.nc"]:
         # Create a temporary filepath using the tmp_path fixture
@@ -525,16 +519,24 @@ def test_surface_forcing_plot_save(sfc_forcing_fixture, request, tmp_path):
             str(tmp_path / file_str),
         ]:  # test for Path object and str
 
-            # Test saving without partitioning
+            # Test saving without partitioning and grouping
             saved_filenames = sfc_forcing.save(filepath)
             filepath_str = str(Path(filepath).with_suffix(""))
+            expected_filepath = Path(f"{filepath_str}.nc")
+            assert saved_filenames == [expected_filepath]
+            assert expected_filepath.exists()
+            expected_filepath.unlink()
+
+            # Test saving without partitioning but with grouping
+            saved_filenames = sfc_forcing.save(filepath, group=True)
+            filepath_str = str(Path(filepath).with_suffix(""))
             expected_filepath = Path(f"{filepath_str}_202002.nc")
             assert saved_filenames == [expected_filepath]
             assert expected_filepath.exists()
             expected_filepath.unlink()
 
             # Test saving with partitioning
-            saved_filenames = sfc_forcing.save(filepath, np_eta=1)
+            saved_filenames = sfc_forcing.save(filepath, np_eta=1, group=True)
 
             expected_filepath_list = [
                 Path(filepath_str + f"_202002.{index}.nc") for index in range(1)
@@ -545,11 +547,14 @@ def test_surface_forcing_plot_save(sfc_forcing_fixture, request, tmp_path):
                 expected_filepath.unlink()
 
 
-def test_surface_forcing_bgc_plot_save(bgc_surface_forcing, tmp_path):
-    """Test plot and save methods."""
+def test_surface_forcing_bgc_plot(bgc_surface_forcing):
+    """Test plot method."""
 
-    # Check the values in the dataset
-    bgc_surface_forcing.plot(varname="pco2_air", time=0)
+    bgc_surface_forcing.plot(var_name="pco2_air", time=0)
+
+
+def test_surface_forcing_bgc_save(bgc_surface_forcing, tmp_path):
+    """Test save method."""
 
     for file_str in ["test_sf", "test_sf.nc"]:
         # Create a temporary filepath using the tmp_path fixture
@@ -558,16 +563,24 @@ def test_surface_forcing_bgc_plot_save(bgc_surface_forcing, tmp_path):
             str(tmp_path / file_str),
         ]:  # test for Path object and str
 
-            # Test saving without partitioning
+            # Test saving without partitioning and grouping
             saved_filenames = bgc_surface_forcing.save(filepath)
             filepath_str = str(Path(filepath).with_suffix(""))
+            expected_filepath = Path(f"{filepath_str}.nc")
+            assert saved_filenames == [expected_filepath]
+            assert expected_filepath.exists()
+            expected_filepath.unlink()
+
+            # Test saving without partitioning but with grouping
+            saved_filenames = bgc_surface_forcing.save(filepath, group=True)
+            filepath_str = str(Path(filepath).with_suffix(""))
             expected_filepath = Path(f"{filepath_str}_202002.nc")
             assert saved_filenames == [expected_filepath]
             assert expected_filepath.exists()
             expected_filepath.unlink()
 
             # Test saving with partitioning
-            saved_filenames = bgc_surface_forcing.save(filepath, np_xi=5)
+            saved_filenames = bgc_surface_forcing.save(filepath, np_xi=5, group=True)
 
             expected_filepath_list = [
                 Path(filepath_str + f"_202002.{index}.nc") for index in range(5)
@@ -578,13 +591,10 @@ def test_surface_forcing_bgc_plot_save(bgc_surface_forcing, tmp_path):
                 expected_filepath.unlink()
 
 
-def test_surface_forcing_bgc_from_clim_plot_save(
+def test_surface_forcing_bgc_from_clim_save(
     bgc_surface_forcing_from_climatology, tmp_path
 ):
-    """Test plot and save methods."""
-
-    # Check the values in the dataset
-    bgc_surface_forcing_from_climatology.plot(varname="pco2_air", time=0)
+    """Test save method."""
 
     for file_str in ["test_sf", "test_sf.nc"]:
         # Create a temporary filepath using the tmp_path fixture
@@ -593,17 +603,27 @@ def test_surface_forcing_bgc_from_clim_plot_save(
             str(tmp_path / file_str),
         ]:  # test for Path object and str
 
-            # Test saving without partitioning
+            # Test saving without partitioning and grouping
             saved_filenames = bgc_surface_forcing_from_climatology.save(filepath)
             filepath_str = str(Path(filepath).with_suffix(""))
+            expected_filepath = Path(f"{filepath_str}.nc")
+            assert saved_filenames == [expected_filepath]
+            assert expected_filepath.exists()
+            expected_filepath.unlink()
+
+            # Test saving without partitioning but with grouping
+            saved_filenames = bgc_surface_forcing_from_climatology.save(
+                filepath, group=True
+            )
+            filepath_str = str(Path(filepath).with_suffix(""))
             expected_filepath = Path(f"{filepath_str}_clim.nc")
             assert saved_filenames == [expected_filepath]
             assert expected_filepath.exists()
             expected_filepath.unlink()
 
-            # Test saving with partitioning
+            # Test saving with partitioning and grouping
             saved_filenames = bgc_surface_forcing_from_climatology.save(
-                filepath, np_eta=5
+                filepath, np_eta=5, group=True
             )
 
             expected_filepath_list = [
@@ -666,9 +686,9 @@ def test_files_have_same_hash(sfc_forcing_fixture, request, tmp_path, use_dask):
     filepath2 = tmp_path / "test2.nc"
 
     sfc_forcing.to_yaml(yaml_filepath)
-    sfc_forcing.save(filepath1)
+    sfc_forcing.save(filepath1, group=True)
     sfc_forcing_from_file = SurfaceForcing.from_yaml(yaml_filepath, use_dask=use_dask)
-    sfc_forcing_from_file.save(filepath2)
+    sfc_forcing_from_file.save(filepath2, group=True)
 
     filepath_str1 = str(Path(filepath1).with_suffix(""))
     filepath_str2 = str(Path(filepath2).with_suffix(""))
@@ -694,9 +714,9 @@ def test_files_have_same_hash_clim(
     filepath2 = tmp_path / "test2.nc"
 
     bgc_surface_forcing_from_climatology.to_yaml(yaml_filepath)
-    bgc_surface_forcing_from_climatology.save(filepath1)
+    bgc_surface_forcing_from_climatology.save(filepath1, group=True)
     sfc_forcing_from_file = SurfaceForcing.from_yaml(yaml_filepath, use_dask=use_dask)
-    sfc_forcing_from_file.save(filepath2)
+    sfc_forcing_from_file.save(filepath2, group=True)
 
     filepath_str1 = str(Path(filepath1).with_suffix(""))
     filepath_str2 = str(Path(filepath2).with_suffix(""))

roms_tools/tests/test_setup/test_tides.py

@@ -169,12 +169,14 @@ 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."""
-    tidal_forcing.ds.load()
+def test_tidal_forcing_plot(tidal_forcing):
+    """Test plot method."""
 
-    tidal_forcing.plot(varname="ssh_Re", ntides=0)
+    tidal_forcing.plot(var_name="ssh_Re", ntides=0)
+
+
+def test_tidal_forcing_save(tidal_forcing, tmp_path):
+    """Test save method."""
 
     for file_str in ["test_tides", "test_tides.nc"]:
         # Create a temporary filepath using the tmp_path fixture

{roms_tools-1.5.0.dist-info → roms_tools-1.6.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: roms-tools
-Version: 1.5.0
+Version: 1.6.1
 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
@@ -15,6 +15,7 @@ Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
@@ -34,6 +35,7 @@ Provides-Extra: dask
 Requires-Dist: dask; extra == "dask"
 
 # ROMS-Tools
+[![Conda version](https://img.shields.io/conda/vn/conda-forge/roms-tools.svg)](https://anaconda.org/conda-forge/roms-tools)
 [![PyPI version](https://img.shields.io/pypi/v/roms-tools.svg)](https://pypi.org/project/roms-tools/)
 [![codecov](https://codecov.io/gh/CWorthy-ocean/roms-tools/graph/badge.svg?token=5S1oNu39xE)](https://codecov.io/gh/CWorthy-ocean/roms-tools)
 [![Documentation Status](https://readthedocs.org/projects/roms-tools/badge/?version=latest)](https://roms-tools.readthedocs.io/en/latest/?badge=latest)
@@ -49,6 +51,14 @@ A suite of python tools for setting up a [ROMS](https://github.com/CESR-lab/ucla
 
 ## Installation
 
+### Installation from conda forge
+
+```bash
+conda install -c conda-forge roms-tools
+```
+
+This command installs `ROMS-Tools` along with its `dask` dependency.
+
 ### Installation from pip
 
 ```bash
@@ -75,7 +85,7 @@ Next, install and activate the following conda environment:
 
 ```bash
 conda env create -f ci/environment.yml
-conda activate romstools
+conda activate romstools-test
 ```
 
 Finally, install `ROMS-Tools` in the same environment:
@@ -97,7 +107,7 @@ pip install -e .[dask]
 Before running the tests, you can activate the conda environment created in the previous section:
 
 ```bash
-conda activate romstools
+conda activate romstools-test
 ```
 
 Check the installation of `ROMS-Tools` has worked by running the test suite