Merge pull request #99 from ocefpaf/coverage

implement coverage tests

Author: ocefpaf

.github/workflows/codecov.yml

@@ -0,0 +1,26 @@
+name: Code coverage report
+
+# no permissions by default
+permissions: {}
+
+on:
+  pull_request:
+  push:
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8  # v6.0.1
+      with:
+        persist-credentials: false
+
+    - name: Setup pixi
+      uses: prefix-dev/setup-pixi@82d477f15f3a381dbcc8adc1206ce643fe110fb7  # v0.9.3
+      with:
+        cache: true
+
+    - name: Run tests with coverage
+      run: >
+        pixi run --environment testcov test_cov

.pre-commit-config.yaml

@@ -27,19 +27,14 @@ repos:
         - --ignore-words-list=astroid,fo
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.14.10
+  rev: v0.15.0
   hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
     - id: ruff-format
 
-- repo: https://github.com/tox-dev/pyproject-fmt
-  rev: v2.11.1
-  hooks:
-    - id: pyproject-fmt
-
 - repo: https://github.com/woodruffw/zizmor-pre-commit
-  rev: v1.19.0
+  rev: v1.22.0
   hooks:
     - id: zizmor
 

pixi.lock

@@ -36,7 +36,6 @@ dependencies = [
   "cf-xarray",
   "cftime",
   "dask",
-  # "dask[complete]", # getting errors from pixi with the "complete"
   "netcdf4",
   "numpy",
   "xarray>=2024.6",
@@ -51,7 +50,7 @@ optional-dependencies.dev = [
   "sphinx-rtd-theme",
 ]
 optional-dependencies.examples = [ "fsspec", "h5netcdf", "matplotlib", "s3fs", "zarr<3" ]
-urls."Homepage" = "https://github.com/asascience-open/xarray-subset-grid"
+urls."Homepage" = "https://github.com/ioos/xarray-subset-grid/"
 
 [tool.setuptools]
 packages = [ "xarray_subset_grid" ]
@@ -108,6 +107,7 @@ test311 = [ "dev", "py311" ]
 test312 = [ "dev", "py312" ]
 test313 = [ "dev", "py313" ]
 test314 = [ "dev", "py314" ]
+testcov = [ "dev", "py314" ]
 
 [tool.pixi.system-requirements]
 macos = "11.0"
@@ -146,6 +146,7 @@ myst-nb = "*"
 lint = "ruff check tests xarray_subset_grid"
 test = "pytest tests/"
 test_all = "pytest --online tests/"
+test_cov = "pytest --cov=xarray_subset_grid tests"
 
 [tool.pixi.feature.examples.dependencies]
 matplotlib = "*"

pyproject.toml

@@ -38,17 +38,20 @@ def pytest_collection_modifyitems(config, items):
 #         if item.config.getoption("-E") not in envnames:
 #             pytest.skip(f"test requires env in {envnames!r}")
 
-EXAMPLE_DATA = Path(__file__).parent / 'example_data'
-
-UGRID_FILES = [EXAMPLE_DATA / 'SFBOFS_subset1.nc',
-               EXAMPLE_DATA / 'small_ugrid_zero_based.nc',
-               EXAMPLE_DATA / 'tris_and_bounds.nc',
-               ]
-
-SGRID_FILES = [EXAMPLE_DATA / 'arakawa_c_test_grid.nc',
-               ]
-
-RGRID_FILES = [EXAMPLE_DATA / '2D-rectangular_grid_wind.nc',
-               EXAMPLE_DATA / 'rectangular_grid_decreasing.nc',
-               EXAMPLE_DATA / 'AMSEAS-subset.nc',
-               ]
+EXAMPLE_DATA = Path(__file__).parent / "example_data"
+
+UGRID_FILES = [
+    EXAMPLE_DATA / "SFBOFS_subset1.nc",
+    EXAMPLE_DATA / "small_ugrid_zero_based.nc",
+    EXAMPLE_DATA / "tris_and_bounds.nc",
+]
+
+SGRID_FILES = [
+    EXAMPLE_DATA / "arakawa_c_test_grid.nc",
+]
+
+RGRID_FILES = [
+    EXAMPLE_DATA / "2D-rectangular_grid_wind.nc",
+    EXAMPLE_DATA / "rectangular_grid_decreasing.nc",
+    EXAMPLE_DATA / "AMSEAS-subset.nc",
+]

tests/conftest.py

@@ -24,6 +24,7 @@
 
 # It was created by the "OFS subsetter"
 
+
 @pytest.mark.parametrize("test_file", RGRID_FILES)
 def test_recognize(test_file):
     """
@@ -77,8 +78,6 @@ def create_synthetic_rectangular_grid_dataset(decreasing=False):
     return ds
 
 
-
-
 def test_grid_vars():
     """
     Check if the grid vars are defined properly
@@ -88,7 +87,7 @@ def test_grid_vars():
     grid_vars = ds.xsg.grid_vars
 
     # ['mesh', 'nv', 'lon', 'lat', 'lonc', 'latc']
-    assert grid_vars == {'lat', 'lon'}
+    assert grid_vars == {"lat", "lon"}
 
 
 def test_data_vars():
@@ -106,27 +105,28 @@ def test_data_vars():
     # the extra "time" variables are not using the grid
     # so they should not be listed as data_vars
     assert data_vars == {
-        'water_w',
-        'salinity',
-        'surf_roughness',
-        'surf_temp_flux',
-        'water_v',
+        "water_w",
+        "salinity",
+        "surf_roughness",
+        "surf_temp_flux",
+        "water_v",
         # 'time_offset',
-        'water_temp',
-        'water_baro_v',
-        'surf_atm_press',
-        'surf_el',
-        'surf_salt_flux',
-        'water_u',
-        'surf_wnd_stress_gridy',
-        'water_baro_u',
-        'watdep',
-        'surf_solar_flux',
+        "water_temp",
+        "water_baro_v",
+        "surf_atm_press",
+        "surf_el",
+        "surf_salt_flux",
+        "water_u",
+        "surf_wnd_stress_gridy",
+        "water_baro_u",
+        "watdep",
+        "surf_solar_flux",
         # 'time1_run',
-        'surf_wnd_stress_gridx',
+        "surf_wnd_stress_gridx",
         # 'time1_offset'
     }
 
+
 # might not be needed if tested elsewhere.
 def test_data_vars2():
     """
@@ -141,7 +141,7 @@ def test_data_vars2():
     data_vars = ds.xsg.data_vars
     print(f"data_vars: {data_vars}")
 
-    assert data_vars == {'salt', 'temp'}
+    assert data_vars == {"salt", "temp"}
 
 
 def test_extra_vars():
@@ -154,42 +154,43 @@ def test_extra_vars():
 
     # the extra "time" variables are not using the grid
     # so they should be listed as extra_vars
-    assert extra_vars == {
-        'time_offset',
-        'time1_run',
-        'time1_offset'
-    }
+    assert extra_vars == {"time_offset", "time1_run", "time1_offset"}
+
 
 def test_subset_to_bb():
     """
     Not a complete test by any means, but the basics are there.
 
-    NOTE: it doesn't test if the variables got subset corectly ...
+    NOTE: it doesn't test if the variables got subset correctly ...
 
     """
     ds = xr.open_dataset(EXAMPLE_DATA / "2D-rectangular_grid_wind.nc")
 
-    print("initial bounds:", ds['lon'].data.min(),
-                             ds['lat'].data.min(),
-                             ds['lon'].data.max(),
-                             ds['lat'].data.max(),
-                            )
+    print(
+        "initial bounds:",
+        ds["lon"].data.min(),
+        ds["lat"].data.min(),
+        ds["lon"].data.max(),
+        ds["lat"].data.max(),
+    )
 
     bbox = (-0.5, 0, 0.5, 0.5)
 
     ds2 = ds.xsg.subset_bbox(bbox)
 
-    assert ds2['lat'].size == 15
-    assert ds2['lon'].size == 29
+    assert ds2["lat"].size == 15
+    assert ds2["lon"].size == 29
 
-    new_bounds = (ds2['lon'].data.min(),
-                  ds2['lat'].data.min(),
-                  ds2['lon'].data.max(),
-                  ds2['lat'].data.max(),
-                  )
+    new_bounds = (
+        ds2["lon"].data.min(),
+        ds2["lat"].data.min(),
+        ds2["lon"].data.max(),
+        ds2["lat"].data.max(),
+    )
     print("new bounds:", new_bounds)
     assert new_bounds == bbox
 
+
 def test_decreasing_latitude():
     """
     Some datasets have the latitude or longitude decreasing: 10, 9, 8 etc.
@@ -200,27 +201,31 @@ def test_decreasing_latitude():
     """
     ds = xr.open_dataset(EXAMPLE_DATA / "rectangular_grid_decreasing.nc")
 
-    print("initial bounds:", ds['lon'].data.min(),
-                             ds['lat'].data.min(),
-                             ds['lon'].data.max(),
-                             ds['lat'].data.max(),
-                            )
+    print(
+        "initial bounds:",
+        ds["lon"].data.min(),
+        ds["lat"].data.min(),
+        ds["lon"].data.max(),
+        ds["lat"].data.max(),
+    )
 
     bbox = (-0.5, 0, 0.5, 0.5)
 
     ds2 = ds.xsg.subset_bbox(bbox)
 
-    assert ds2['lat'].size == 15
-    assert ds2['lon'].size == 29
+    assert ds2["lat"].size == 15
+    assert ds2["lon"].size == 29
 
-    new_bounds = (ds2['lon'].data.min(),
-                  ds2['lat'].data.min(),
-                  ds2['lon'].data.max(),
-                  ds2['lat'].data.max(),
-                  )
+    new_bounds = (
+        ds2["lon"].data.min(),
+        ds2["lat"].data.min(),
+        ds2["lon"].data.max(),
+        ds2["lat"].data.max(),
+    )
     print("new bounds:", new_bounds)
     assert new_bounds == bbox
 
+
 def test_decreasing_coords():
     """
     Redundant with above, but already written ...
@@ -239,20 +244,23 @@ def test_decreasing_coords():
     assert subset.sizes["lat"] > 0
     assert subset.sizes["lon"] > 0
 
+
 def test_subset_polygon():
     """
     Not a complete test by any means, but the basics are there.
 
-    NOTE: it doesn't test if the variables got subset corectly ...
+    NOTE: it doesn't test if the variables got subset correctly ...
 
     """
     ds = xr.open_dataset(EXAMPLE_DATA / "2D-rectangular_grid_wind.nc")
 
-    print("initial bounds:", ds['lon'].data.min(),
-                             ds['lat'].data.min(),
-                             ds['lon'].data.max(),
-                             ds['lat'].data.max(),
-                            )
+    print(
+        "initial bounds:",
+        ds["lon"].data.min(),
+        ds["lat"].data.min(),
+        ds["lon"].data.max(),
+        ds["lat"].data.max(),
+    )
 
     poly = [(-0.5, 0.0), (0.0, 0.5), (0.5, 0.5), (0.5, 0.0), (0, 0.0)]
     # this poly has this bounding box:
@@ -261,19 +269,19 @@ def test_subset_polygon():
 
     ds2 = ds.xsg.subset_polygon(poly)
 
-    assert ds2['lat'].size == 15
-    assert ds2['lon'].size == 29
+    assert ds2["lat"].size == 15
+    assert ds2["lon"].size == 29
 
-    new_bounds = (ds2['lon'].data.min(),
-                  ds2['lat'].data.min(),
-                  ds2['lon'].data.max(),
-                  ds2['lat'].data.max(),
-                  )
+    new_bounds = (
+        ds2["lon"].data.min(),
+        ds2["lat"].data.min(),
+        ds2["lon"].data.max(),
+        ds2["lat"].data.max(),
+    )
     print("new bounds:", new_bounds)
     assert new_bounds == (-0.5, 0, 0.5, 0.5)
 
 
-
 # def test_vertical_levels():
 #     ds = xr.open_dataset(EXAMPLE_DATA / "SFBOFS_subset1.nc")
 #     ds = ugrid.assign_ugrid_topology(ds, **grid_topology)

tests/test_grids/test_regular_grid.py

@@ -19,6 +19,7 @@
 
 EXAMPLE_DATA = Path(__file__).parent.parent / "example_data"
 
+
 @pytest.mark.parametrize("test_file", UGRID_FILES[:3])
 def test_recognize(test_file):
     """
@@ -31,14 +32,10 @@ def test_recognize(test_file):
     except KeyError:  # no mesh variable
         # Hacky way to deal with non-conforming examples
         # This should be in a config somewhere, or ??
-        if 'tris' in ds:
-            grid_top = {'face_node_connectivity': 'tris',
-             'node_coordinates': ('lon', 'lat')
-             }
-        elif 'nv' in ds:
-            grid_top = {'face_node_connectivity': 'nv',
-             'node_coordinates': ('lon', 'lat')
-             }
+        if "tris" in ds:
+            grid_top = {"face_node_connectivity": "tris", "node_coordinates": ("lon", "lat")}
+        elif "nv" in ds:
+            grid_top = {"face_node_connectivity": "nv", "node_coordinates": ("lon", "lat")}
         ds = ugrid.assign_ugrid_topology(ds, **grid_top)
 
     assert UGrid.recognize(ds)