Merge pull request #683 from metno/dummy_cube_latlon_fix

Dummy cube latlon fix

.github/workflows/CI.yml

@@ -74,8 +74,9 @@ jobs:
       with:
         path: |
           ~/.cache/pip
+          ~/.cache/srtm
           .tox
-        key: ${{ runner.os }}-tox-${{ matrix.python-version }}-${{ hashFiles('setup.cfg') }}
+        key: ${{ runner.os }}-tox-${{ matrix.python-version }}-${{ hashFiles('setup.cfg', 'pyproject.toml') }}
     - name: Install Tox
       run: |
         python -m pip install --upgrade pip

pyaerocom/helpers.py

@@ -1,6 +1,7 @@
 """
 General helper methods for the pyaerocom library.
 """
+from __future__ import annotations
 
 import logging
 import math as ma
@@ -204,7 +205,12 @@ def tuple_list_to_lists(tuple_list):
     return list(map(list, zip(tuple_list)))
 
 
-def make_dummy_cube_latlon(lat_res_deg=2, lon_res_deg=3, lat_range=None, lon_range=None):
+def make_dummy_cube_latlon(
+    lat_res_deg: float = 2,
+    lon_res_deg: float = 3,
+    lat_range: list[float] | tuple[float, float] = (-90, 90),
+    lon_range: list[float] | tuple[float, float] = (-180, 180),
+):
     """Make an empty Cube with given latitude and longitude resolution
 
     Dimensions will be lat, lon
@@ -227,13 +233,16 @@ def make_dummy_cube_latlon(lat_res_deg=2, lon_res_deg=3, lat_range=None, lon_ran
     Cube
         dummy cube in input resolution
     """
-    if lat_range is None:
-        lat_range = (-90, 90)
-    if lon_range is None:
-        lon_range = (-180, 180)
 
-    lons = np.arange(lon_range[0] + lon_res_deg / 2, lon_range[1] + lon_res_deg / 2, lon_res_deg)
-    lats = np.arange(lat_range[0] + lat_res_deg / 2, lat_range[1] + lat_res_deg / 2, lat_res_deg)
+    # Accept lists for lat_range and lon_range, but make sure correct length
+    assert len(lat_range) == len(lon_range) == 2
+
+    lons = np.arange(
+        lon_range[0] + (lon_res_deg / 2), lon_range[1] + (lon_res_deg / 2), lon_res_deg
+    )
+    lats = np.arange(
+        lat_range[0] + (lat_res_deg / 2), lat_range[1] + (lat_res_deg / 2), lat_res_deg
+    )
 
     lon_circ = check_coord_circular(lons, modulus=360)
     latdim = iris.coords.DimCoord(
@@ -1710,14 +1719,18 @@ def make_dummy_cube(
     days_since_start = np.arange(len(times))
     unit = get_variable(var_name).units
 
-    lat_range = (-180, 180)
-    lon_range = (-90, 90)
-    lat_res_deg = 90
-    lon_res_deg = 45
+    lat_range = (-90, 90)
+    lon_range = (-180, 180)
+    lat_res_deg = 45
+    lon_res_deg = 90
     time_unit = Unit(startstr, calendar="gregorian")
 
-    lons = np.arange(lon_range[0] + lon_res_deg / 2, lon_range[1] + lon_res_deg / 2, lon_res_deg)
-    lats = np.arange(lat_range[0] + lat_res_deg / 2, lat_range[1] + lat_res_deg / 2, lat_res_deg)
+    lons = np.arange(
+        lon_range[0] + (lon_res_deg / 2), lon_range[1] + (lon_res_deg / 2), lon_res_deg
+    )
+    lats = np.arange(
+        lat_range[0] + (lat_res_deg / 2), lat_range[1] + (lat_res_deg / 2), lat_res_deg
+    )
 
     latdim = iris.coords.DimCoord(
         lats,

pyaerocom/mathutils.py

@@ -187,7 +187,7 @@ def _nanmean_and_std(data):
 
 
 @ignore_warnings(
-    RuntimeWarning, "An input array is constant", "invalid value encountered in true_divide"
+    RuntimeWarning, "An input array is constant", "invalid value encountered in .*divide"
 )
 def calc_statistics(data, ref_data, lowlim=None, highlim=None, min_num_valid=1, weights=None):
     """Calc statistical properties from two data arrays

tests/test_geodesy.py

@@ -26,6 +26,11 @@ def test_is_within_radius_km():
     assert geodesy.is_within_radius_km(0, 15, 0, 16, 1000, 111.2)
 
 
+@pytest.mark.xfail(
+    reason="fails in CI when geonum can not download 'srtm' data",
+    raises=FileNotFoundError,
+    strict=False,
+)
 def test_srtm_altitude():
     assert geodesy.get_topo_altitude(TEST_LAT, TEST_LON) == pytest.approx(207)
 

tests/test_helpers.py

@@ -209,7 +209,8 @@ def test_extract_latlon_dataarray():
     lon = [1, 15, 18]
     subset = helpers.extract_latlon_dataarray(data, lat, lon, check_domain=True)
     assert isinstance(subset, xr.DataArray)
-    assert len(subset.lat) == len(lat) - 1 and len(subset.lon) == len(lon) - 1
+    assert len(subset.lat) == len(lat) - 1
+    assert len(subset.lon) == len(lon) - 1
 
 
 def test_extract_latlon_dataarray_no_matches():
@@ -250,3 +251,16 @@ def test_extract_latlon_dataarray_no_matches_error(lat, lon):
 def test_seconds_in_periods(date, ts_type, days):
     seconds = timedelta(days=days) / timedelta(seconds=1)
     assert helpers.seconds_in_periods(np.datetime64(date), ts_type) == seconds
+
+
+def test_make_dummy_cube():
+    # make a dummy cube of an arbitrary variable name over one year
+    cube = helpers.make_dummy_cube("concpm10", start_yr=2020, stop_yr=2021)
+    data = xr.DataArray.from_iris(cube)
+    # First coordinate does not exist in the dataarray.
+    lat = [90, -67.5, 22.2]
+    lon = [180, -135.0, 45.0]
+    subset = helpers.extract_latlon_dataarray(data, lat, lon, check_domain=True)
+    assert isinstance(subset, xr.DataArray)
+    assert len(subset.lat) == len(lat) - 1
+    assert len(subset.lon) == len(lon) - 1

tests/test_ungriddeddata.py

@@ -212,7 +212,7 @@ def test_check_unit(data_scat_jungfraujoch):
         data_scat_jungfraujoch.check_unit("sc550aer", unit="m-1")
 
 
-@pytest.mark.filterwarnings("ignore:invalid value encountered in true_divide:RuntimeWarning")
+@pytest.mark.filterwarnings("ignore:invalid value encountered in .*divide:RuntimeWarning")
 def test_check_convert_var_units(data_scat_jungfraujoch):
 
     out = data_scat_jungfraujoch.check_convert_var_units("sc550aer", "m-1", inplace=False)