Merge branch 'main' into zedwick/subset_inverse_indices

.github/workflows/ci.yml

@@ -75,7 +75,7 @@ jobs:
 
       - name: Upload code coverage to Codecov
         if: github.repository == 'UXARRAY/uxarray'
-        uses: codecov/codecov-action@v5.1.1
+        uses: codecov/codecov-action@v5.1.2
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.8.3
+  rev: v0.8.4
   hooks:
     # Run the linter.
     - id: ruff

benchmarks/mpas_ocean.py

@@ -138,7 +138,7 @@ def time_inverse_distance_weighted_remapping(self):
 
 class HoleEdgeIndices(DatasetBenchmark):
     def time_construct_hole_edge_indices(self, resolution):
-        ux.grid.geometry._construct_hole_edge_indices(self.uxds.uxgrid.edge_face_connectivity)
+        ux.grid.geometry._construct_boundary_edge_indices(self.uxds.uxgrid.edge_face_connectivity)
 
 
 class DualMesh(DatasetBenchmark):
@@ -167,10 +167,19 @@ def time_check_norm(self, resolution):
         from uxarray.grid.validation import _check_normalization
         _check_normalization(self.uxgrid)
 
+class CrossSection:
+    param_names = DatasetBenchmark.param_names + ['lat_step']
+    params = DatasetBenchmark.params + [[1, 2, 4]]
 
-class CrossSections(DatasetBenchmark):
-    param_names = DatasetBenchmark.param_names + ['n_lat']
-    params = DatasetBenchmark.params + [[1, 2, 4, 8]]
-    def time_constant_lat_fast(self, resolution, n_lat):
-        for lat in np.linspace(-89, 89, n_lat):
-            self.uxds.uxgrid.constant_latitude_cross_section(lat, method='fast')
+    def setup(self, resolution, lat_step):
+        self.uxgrid = ux.open_grid(file_path_dict[resolution][0])
+        self.uxgrid.normalize_cartesian_coordinates()
+        self.lats = np.arange(-45, 45, lat_step)
+        _ = self.uxgrid.bounds
+
+    def teardown(self, resolution, lat_step):
+        del self.uxgrid
+
+    def time_const_lat(self, resolution, lat_step):
+        for lat in self.lats:
+            self.uxgrid.cross_section.constant_latitude(lat)

test/test_api.py

@@ -1,11 +1,9 @@
 import os
-from unittest import TestCase
 from pathlib import Path
 import numpy.testing as nt
-
 import uxarray as ux
-import xarray as xr
 import numpy as np
+import pytest
 
 try:
     import constants
@@ -14,126 +12,111 @@
 
 current_path = Path(os.path.dirname(os.path.realpath(__file__)))
 
+geoflow_data_path = current_path / "meshfiles" / "ugrid" / "geoflow-small"
+gridfile_geoflow = current_path / "meshfiles" / "ugrid" / "geoflow-small" / "grid.nc"
+geoflow_data_v1 = geoflow_data_path / "v1.nc"
+geoflow_data_v2 = geoflow_data_path / "v2.nc"
+geoflow_data_v3 = geoflow_data_path / "v3.nc"
 
-class TestAPI(TestCase):
-    geoflow_data_path = current_path / "meshfiles" / "ugrid" / "geoflow-small"
-    gridfile_geoflow = current_path / "meshfiles" / "ugrid" / "geoflow-small" / "grid.nc"
-    geoflow_data_v1 = geoflow_data_path / "v1.nc"
-    geoflow_data_v2 = geoflow_data_path / "v2.nc"
-    geoflow_data_v3 = geoflow_data_path / "v3.nc"
-
-    gridfile_ne30 = current_path / "meshfiles" / "ugrid" / "outCSne30" / "outCSne30.ug"
-    dsfile_var2_ne30 = current_path / "meshfiles" / "ugrid" / "outCSne30" / "outCSne30_var2.nc"
-    dsfiles_mf_ne30 = str(
-        current_path) + "/meshfiles/ugrid/outCSne30/outCSne30_*.nc"
-
-    def test_open_geoflow_dataset(self):
-        """Loads a single dataset with its grid topology file using uxarray's
-        open_dataset call."""
+gridfile_ne30 = current_path / "meshfiles" / "ugrid" / "outCSne30" / "outCSne30.ug"
+dsfile_var2_ne30 = current_path / "meshfiles" / "ugrid" / "outCSne30" / "outCSne30_var2.nc"
+dsfiles_mf_ne30 = str(current_path) + "/meshfiles/ugrid/outCSne30/outCSne30_*.nc"
 
-        # Paths to Data Variable files
-        data_paths = [
-            self.geoflow_data_v1, self.geoflow_data_v2, self.geoflow_data_v3
-        ]
+def test_open_geoflow_dataset():
+    """Loads a single dataset with its grid topology file using uxarray's
+    open_dataset call."""
 
-        uxds_v1 = ux.open_dataset(self.gridfile_geoflow, data_paths[0])
+    # Paths to Data Variable files
+    data_paths = [
+        geoflow_data_v1, geoflow_data_v2, geoflow_data_v3
+    ]
 
-        # Ideally uxds_v1.uxgrid should NOT be None
-        with self.assertRaises(AssertionError):
-            nt.assert_equal(uxds_v1.uxgrid, None)
+    uxds_v1 = ux.open_dataset(gridfile_geoflow, data_paths[0])
 
-    def test_open_dataset(self):
-        """Loads a single dataset with its grid topology file using uxarray's
-        open_dataset call."""
+    # Ideally uxds_v1.uxgrid should NOT be None
+    nt.assert_equal(uxds_v1.uxgrid is not None, True)
 
-        uxds_var2_ne30 = ux.open_dataset(self.gridfile_ne30,
-                                         self.dsfile_var2_ne30)
+def test_open_dataset():
+    """Loads a single dataset with its grid topology file using uxarray's
+    open_dataset call."""
 
-        nt.assert_equal(uxds_var2_ne30.uxgrid.node_lon.size,
-                        constants.NNODES_outCSne30)
-        nt.assert_equal(len(uxds_var2_ne30.uxgrid._ds.data_vars),
-                        constants.DATAVARS_outCSne30)
-        nt.assert_equal(uxds_var2_ne30.source_datasets,
-                        str(self.dsfile_var2_ne30))
+    uxds_var2_ne30 = ux.open_dataset(gridfile_ne30, dsfile_var2_ne30)
 
-    def test_open_mf_dataset(self):
-        """Loads multiple datasets with their grid topology file using
-        uxarray's open_dataset call."""
+    nt.assert_equal(uxds_var2_ne30.uxgrid.node_lon.size, constants.NNODES_outCSne30)
+    nt.assert_equal(len(uxds_var2_ne30.uxgrid._ds.data_vars), constants.DATAVARS_outCSne30)
+    nt.assert_equal(uxds_var2_ne30.source_datasets, str(dsfile_var2_ne30))
 
-        uxds_mf_ne30 = ux.open_mfdataset(self.gridfile_ne30,
-                                         self.dsfiles_mf_ne30)
+def test_open_mf_dataset():
+    """Loads multiple datasets with their grid topology file using
+    uxarray's open_dataset call."""
 
-        nt.assert_equal(uxds_mf_ne30.uxgrid.node_lon.size,
-                        constants.NNODES_outCSne30)
-        nt.assert_equal(len(uxds_mf_ne30.uxgrid._ds.data_vars),
-                        constants.DATAVARS_outCSne30)
+    uxds_mf_ne30 = ux.open_mfdataset(gridfile_ne30, dsfiles_mf_ne30)
 
-        nt.assert_equal(uxds_mf_ne30.source_datasets, self.dsfiles_mf_ne30)
+    nt.assert_equal(uxds_mf_ne30.uxgrid.node_lon.size, constants.NNODES_outCSne30)
+    nt.assert_equal(len(uxds_mf_ne30.uxgrid._ds.data_vars), constants.DATAVARS_outCSne30)
+    nt.assert_equal(uxds_mf_ne30.source_datasets, dsfiles_mf_ne30)
 
-    def test_open_grid(self):
-        """Loads only a grid topology file using uxarray's open_grid call."""
-        uxgrid = ux.open_grid(self.gridfile_geoflow)
+def test_open_grid():
+    """Loads only a grid topology file using uxarray's open_grid call."""
+    uxgrid = ux.open_grid(gridfile_geoflow)
 
-        nt.assert_almost_equal(uxgrid.calculate_total_face_area(),
-                               constants.MESH30_AREA,
-                               decimal=3)
+    nt.assert_almost_equal(uxgrid.calculate_total_face_area(), constants.MESH30_AREA, decimal=3)
 
-    def test_copy_dataset(self):
-        """Loads a single dataset with its grid topology file using uxarray's
-        open_dataset call and make a copy of the object."""
+def test_copy_dataset():
+    """Loads a single dataset with its grid topology file using uxarray's
+    open_dataset call and make a copy of the object."""
 
-        uxds_var2_ne30 = ux.open_dataset(self.gridfile_ne30,
-                                         self.dsfile_var2_ne30)
+    uxds_var2_ne30 = ux.open_dataset(gridfile_ne30, dsfile_var2_ne30)
 
-        # make a shallow and deep copy of the dataset object
-        uxds_var2_ne30_copy_deep = uxds_var2_ne30.copy(deep=True)
-        uxds_var2_ne30_copy = uxds_var2_ne30.copy(deep=False)
+    # make a shallow and deep copy of the dataset object
+    uxds_var2_ne30_copy_deep = uxds_var2_ne30.copy(deep=True)
+    uxds_var2_ne30_copy = uxds_var2_ne30.copy(deep=False)
 
-        # Ideally uxds_var2_ne30_copy.uxgrid should NOT be None
-        with self.assertRaises(AssertionError):
-            nt.assert_equal(uxds_var2_ne30_copy.uxgrid, None)
+    # Ideally uxds_var2_ne30_copy.uxgrid should NOT be None
+    nt.assert_equal(uxds_var2_ne30_copy.uxgrid is not None, True)
 
-        # Check that the copy is a shallow copy
-        assert (uxds_var2_ne30_copy.uxgrid is uxds_var2_ne30.uxgrid)
-        assert (uxds_var2_ne30_copy.uxgrid == uxds_var2_ne30.uxgrid)
+    # Check that the copy is a shallow copy
+    assert uxds_var2_ne30_copy.uxgrid is uxds_var2_ne30.uxgrid
+    assert uxds_var2_ne30_copy.uxgrid == uxds_var2_ne30.uxgrid
 
-        # Check that the deep copy is a deep copy
-        assert (uxds_var2_ne30_copy_deep.uxgrid == uxds_var2_ne30.uxgrid)
-        assert (uxds_var2_ne30_copy_deep.uxgrid is not uxds_var2_ne30.uxgrid)
+    # Check that the deep copy is a deep copy
+    assert uxds_var2_ne30_copy_deep.uxgrid == uxds_var2_ne30.uxgrid
+    assert uxds_var2_ne30_copy_deep.uxgrid is not uxds_var2_ne30.uxgrid
 
-    def test_copy_dataarray(self):
-        """Loads an unstructured grid and data using uxarray's open_dataset
-        call and make a copy of the dataarray object."""
+def test_copy_dataarray():
+    """Loads an unstructured grid and data using uxarray's open_dataset
+    call and make a copy of the dataarray object."""
 
-        # Paths to Data Variable files
-        data_paths = [
-            self.geoflow_data_v1, self.geoflow_data_v2, self.geoflow_data_v3
-        ]
+    # Paths to Data Variable files
+    data_paths = [
+        geoflow_data_v1, geoflow_data_v2, geoflow_data_v3
+    ]
 
-        uxds_v1 = ux.open_dataset(self.gridfile_geoflow, data_paths[0])
+    uxds_v1 = ux.open_dataset(gridfile_geoflow, data_paths[0])
 
-        # get the uxdataarray object
-        v1_uxdata_array = uxds_v1['v1']
+    # get the uxdataarray object
+    v1_uxdata_array = uxds_v1['v1']
 
-        # make a shallow and deep copy of the dataarray object
-        v1_uxdata_array_copy_deep = v1_uxdata_array.copy(deep=True)
-        v1_uxdata_array_copy = v1_uxdata_array.copy(deep=False)
+    # make a shallow and deep copy of the dataarray object
+    v1_uxdata_array_copy_deep = v1_uxdata_array.copy(deep=True)
+    v1_uxdata_array_copy = v1_uxdata_array.copy(deep=False)
 
-        # Check that the copy is a shallow copy
-        assert (v1_uxdata_array_copy.uxgrid is v1_uxdata_array.uxgrid)
-        assert (v1_uxdata_array_copy.uxgrid == v1_uxdata_array.uxgrid)
+    # Check that the copy is a shallow copy
+    assert v1_uxdata_array_copy.uxgrid is v1_uxdata_array.uxgrid
+    assert v1_uxdata_array_copy.uxgrid == v1_uxdata_array.uxgrid
 
-        # Check that the deep copy is a deep copy
-        assert (v1_uxdata_array_copy_deep.uxgrid == v1_uxdata_array.uxgrid)
-        assert (v1_uxdata_array_copy_deep.uxgrid is not v1_uxdata_array.uxgrid)
+    # Check that the deep copy is a deep copy
+    assert v1_uxdata_array_copy_deep.uxgrid == v1_uxdata_array.uxgrid
+    assert v1_uxdata_array_copy_deep.uxgrid is not v1_uxdata_array.uxgrid
 
-    def test_open_dataset_grid_kwargs(self):
-        """Drops ``Mesh2_face_nodes`` from the inputted grid file using
-        ``grid_kwargs``"""
+def test_open_dataset_grid_kwargs():
+    """Drops ``Mesh2_face_nodes`` from the inputted grid file using
+    ``grid_kwargs``"""
 
-        with self.assertRaises(ValueError):
-            # attempt to open a dataset after dropping face nodes should raise a KeyError
-            uxds = ux.open_dataset(
-                self.gridfile_ne30,
-                self.dsfile_var2_ne30,
-                grid_kwargs={"drop_variables": "Mesh2_face_nodes"})
+    with pytest.raises(ValueError):
+        # attempt to open a dataset after dropping face nodes should raise a KeyError
+        uxds = ux.open_dataset(
+            gridfile_ne30,
+            dsfile_var2_ne30,
+            grid_kwargs={"drop_variables": "Mesh2_face_nodes"}
+        )