roms-tools 1.5.0__py3-none-any.whl → 1.6.0__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

@@ -181,37 +181,37 @@ def test_initial_conditions_plot_save(
 ):
     """Test plot and save methods."""
 
-    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)
 
     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

@@ -516,7 +516,7 @@ def test_surface_forcing_pco2_replication(sfc_forcing_fixture, request):
 def test_surface_forcing_plot_save(sfc_forcing_fixture, request, tmp_path):
     """Test plot and save methods."""
     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
@@ -549,7 +549,7 @@ def test_surface_forcing_bgc_plot_save(bgc_surface_forcing, tmp_path):
     """Test plot and save methods."""
 
     # 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)
 
     for file_str in ["test_sf", "test_sf.nc"]:
         # Create a temporary filepath using the tmp_path fixture
@@ -584,7 +584,7 @@ def test_surface_forcing_bgc_from_clim_plot_save(
     """Test plot and save methods."""
 
     # Check the values in the dataset
-    bgc_surface_forcing_from_climatology.plot(varname="pco2_air", time=0)
+    bgc_surface_forcing_from_climatology.plot(var_name="pco2_air", time=0)
 
     for file_str in ["test_sf", "test_sf.nc"]:
         # Create a temporary filepath using the tmp_path fixture

roms_tools/tests/test_setup/test_tides.py

@@ -174,7 +174,7 @@ def test_tidal_forcing_plot_save(tidal_forcing, tmp_path):
     computed."""
     tidal_forcing.ds.load()
 
-    tidal_forcing.plot(varname="ssh_Re", ntides=0)
+    tidal_forcing.plot(var_name="ssh_Re", ntides=0)
 
     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-1.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: roms-tools
-Version: 1.5.0
+Version: 1.6.0
 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
@@ -34,6 +34,7 @@ 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 +50,14 @@ 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 +84,7 @@ 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 +106,7 @@ 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