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import numpy as np
import pandas as pd
import pytest
import xarray as xr
# Don't run cupy in CI because it requires a GPU
NAMESPACE_ARRAYS = {
"cupy": {
"attrs": {
"array": "ndarray",
"constructor": "asarray",
},
"xfails": {"quantile": "no nanquantile"},
},
"dask.array": {
"attrs": {
"array": "Array",
"constructor": "from_array",
},
"xfails": {
"argsort": "no argsort",
"conjugate": "conj but no conjugate",
"searchsorted": "dask.array.searchsorted but no Array.searchsorted",
},
},
"jax.numpy": {
"attrs": {
"array": "ndarray",
"constructor": "asarray",
},
"xfails": {
"rolling_construct": "no sliding_window_view",
"rolling_reduce": "no sliding_window_view",
"cumulative_construct": "no sliding_window_view",
"cumulative_reduce": "no sliding_window_view",
},
},
"pint": {
"attrs": {
"array": "Quantity",
"constructor": "Quantity",
},
"xfails": {
"all": "returns a bool",
"any": "returns a bool",
"argmax": "returns an int",
"argmin": "returns an int",
"argsort": "returns an int",
"count": "returns an int",
"dot": "no tensordot",
"full_like": "should work, see: https://github.com/hgrecco/pint/pull/1669",
"idxmax": "returns the coordinate",
"idxmin": "returns the coordinate",
"isin": "returns a bool",
"isnull": "returns a bool",
"notnull": "returns a bool",
"rolling_reduce": "no dispatch for numbagg/bottleneck",
"cumulative_reduce": "no dispatch for numbagg/bottleneck",
"searchsorted": "returns an int",
"weighted": "no tensordot",
},
},
"sparse": {
"attrs": {
"array": "COO",
"constructor": "COO",
},
"xfails": {
"cov": "dense output",
"corr": "no nanstd",
"cross": "no cross",
"count": "dense output",
"dot": "fails on some platforms/versions",
"isin": "no isin",
"rolling_construct": "no sliding_window_view",
"rolling_reduce": "no sliding_window_view",
"cumulative_construct": "no sliding_window_view",
"cumulative_reduce": "no sliding_window_view",
"coarsen_construct": "pad constant_values must be fill_value",
"coarsen_reduce": "pad constant_values must be fill_value",
"weighted": "fill_value error",
"coarsen": "pad constant_values must be fill_value",
"quantile": "no non skipping version",
"differentiate": "no gradient",
"argmax": "no nan skipping version",
"argmin": "no nan skipping version",
"idxmax": "no nan skipping version",
"idxmin": "no nan skipping version",
"median": "no nan skipping version",
"std": "no nan skipping version",
"var": "no nan skipping version",
"cumsum": "no cumsum",
"cumprod": "no cumprod",
"argsort": "no argsort",
"conjugate": "no conjugate",
"searchsorted": "no searchsorted",
"shift": "pad constant_values must be fill_value",
"pad": "pad constant_values must be fill_value",
},
},
}
try:
import jax
# enable double-precision
jax.config.update("jax_enable_x64", True)
except ImportError:
pass
class _BaseTest:
def setup_for_test(self, request, namespace):
self.namespace = namespace
self.xp = pytest.importorskip(namespace)
self.Array = getattr(self.xp, NAMESPACE_ARRAYS[namespace]["attrs"]["array"])
self.constructor = getattr(
self.xp, NAMESPACE_ARRAYS[namespace]["attrs"]["constructor"]
)
xarray_method = request.node.name.split("test_")[1].split("[")[0]
if xarray_method in NAMESPACE_ARRAYS[namespace]["xfails"]:
reason = NAMESPACE_ARRAYS[namespace]["xfails"][xarray_method]
pytest.xfail(f"xfail for {self.namespace}: {reason}")
def get_test_dataarray(self):
data = np.asarray([[1, 2, 3, np.nan, 5]])
x = np.arange(5)
data = self.constructor(data)
return xr.DataArray(
data,
dims=["y", "x"],
coords={"y": [1], "x": x},
name="foo",
)
@pytest.mark.parametrize("namespace", NAMESPACE_ARRAYS)
class TestTopLevelMethods(_BaseTest):
@pytest.fixture(autouse=True)
def setUp(self, request, namespace):
self.setup_for_test(request, namespace)
self.x1 = self.get_test_dataarray()
self.x2 = self.get_test_dataarray().assign_coords(x=np.arange(2, 7))
def test_apply_ufunc(self):
func = lambda x: x + 1
result = xr.apply_ufunc(func, self.x1, dask="parallelized")
assert isinstance(result.data, self.Array)
def test_align(self):
result = xr.align(self.x1, self.x2)
assert isinstance(result[0].data, self.Array)
assert isinstance(result[1].data, self.Array)
def test_broadcast(self):
result = xr.broadcast(self.x1, self.x2)
assert isinstance(result[0].data, self.Array)
assert isinstance(result[1].data, self.Array)
def test_concat(self):
result = xr.concat([self.x1, self.x2], dim="x")
assert isinstance(result.data, self.Array)
def test_merge(self):
result = xr.merge([self.x1, self.x2], compat="override", join="outer")
assert isinstance(result.foo.data, self.Array)
def test_where(self):
x1, x2 = xr.align(self.x1, self.x2, join="inner")
result = xr.where(x1 > 2, x1, x2)
assert isinstance(result.data, self.Array)
def test_full_like(self):
result = xr.full_like(self.x1, 0)
assert isinstance(result.data, self.Array)
def test_cov(self):
result = xr.cov(self.x1, self.x2)
assert isinstance(result.data, self.Array)
def test_corr(self):
result = xr.corr(self.x1, self.x2)
assert isinstance(result.data, self.Array)
def test_cross(self):
x1, x2 = xr.align(self.x1.squeeze(), self.x2.squeeze(), join="inner")
result = xr.cross(x1, x2, dim="x")
assert isinstance(result.data, self.Array)
def test_dot(self):
result = xr.dot(self.x1, self.x2)
assert isinstance(result.data, self.Array)
def test_map_blocks(self):
result = xr.map_blocks(lambda x: x + 1, self.x1)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("namespace", NAMESPACE_ARRAYS)
class TestDataArrayMethods(_BaseTest):
@pytest.fixture(autouse=True)
def setUp(self, request, namespace):
self.setup_for_test(request, namespace)
self.x = self.get_test_dataarray()
def test_loc(self):
result = self.x.loc[{"x": slice(1, 3)}]
assert isinstance(result.data, self.Array)
def test_isel(self):
result = self.x.isel(x=slice(1, 3))
assert isinstance(result.data, self.Array)
def test_sel(self):
result = self.x.sel(x=slice(1, 3))
assert isinstance(result.data, self.Array)
def test_squeeze(self):
result = self.x.squeeze("y")
assert isinstance(result.data, self.Array)
@pytest.mark.xfail(reason="interp uses numpy and scipy")
def test_interp(self):
# TODO: some cases could be made to work
result = self.x.interp(x=2.5)
assert isinstance(result.data, self.Array)
def test_isnull(self):
result = self.x.isnull()
assert isinstance(result.data, self.Array)
def test_notnull(self):
result = self.x.notnull()
assert isinstance(result.data, self.Array)
def test_count(self):
result = self.x.count()
assert isinstance(result.data, self.Array)
def test_dropna(self):
result = self.x.dropna(dim="x")
assert isinstance(result.data, self.Array)
def test_fillna(self):
result = self.x.fillna(0)
assert isinstance(result.data, self.Array)
@pytest.mark.xfail(reason="ffill uses bottleneck or numbagg")
def test_ffill(self):
result = self.x.ffill()
assert isinstance(result.data, self.Array)
@pytest.mark.xfail(reason="bfill uses bottleneck or numbagg")
def test_bfill(self):
result = self.x.bfill()
assert isinstance(result.data, self.Array)
@pytest.mark.xfail(reason="interpolate_na uses numpy and scipy")
def test_interpolate_na(self):
result = self.x.interpolate_na()
assert isinstance(result.data, self.Array)
def test_where(self):
result = self.x.where(self.x > 2)
assert isinstance(result.data, self.Array)
def test_isin(self):
test_elements = self.constructor(np.asarray([1]))
result = self.x.isin(test_elements)
assert isinstance(result.data, self.Array)
def test_groupby(self):
result = self.x.groupby("x").mean()
assert isinstance(result.data, self.Array)
def test_groupby_bins(self):
result = self.x.groupby_bins("x", bins=[0, 2, 4, 6]).mean()
assert isinstance(result.data, self.Array)
def test_rolling_iter(self):
result = self.x.rolling(x=3)
elem = next(iter(result))[1]
assert isinstance(elem.data, self.Array)
def test_rolling_construct(self):
result = self.x.rolling(x=3).construct(x="window")
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_rolling_reduce(self, skipna):
result = self.x.rolling(x=3).mean(skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.xfail(reason="rolling_exp uses numbagg")
def test_rolling_exp_reduce(self):
result = self.x.rolling_exp(x=3).mean()
assert isinstance(result.data, self.Array)
def test_cumulative_iter(self):
result = self.x.cumulative("x")
elem = next(iter(result))[1]
assert isinstance(elem.data, self.Array)
def test_cumulative_construct(self):
result = self.x.cumulative("x").construct(x="window")
assert isinstance(result.data, self.Array)
def test_cumulative_reduce(self):
result = self.x.cumulative("x").sum()
assert isinstance(result.data, self.Array)
def test_weighted(self):
result = self.x.weighted(self.x.fillna(0)).mean()
assert isinstance(result.data, self.Array)
def test_coarsen_construct(self):
result = self.x.coarsen(x=2, boundary="pad").construct(x=["a", "b"])
assert isinstance(result.data, self.Array)
def test_coarsen_reduce(self):
result = self.x.coarsen(x=2, boundary="pad").mean()
assert isinstance(result.data, self.Array)
def test_resample(self):
time_coord = pd.date_range("2000-01-01", periods=5)
result = self.x.assign_coords(x=time_coord).resample(x="D").mean()
assert isinstance(result.data, self.Array)
def test_diff(self):
result = self.x.diff("x")
assert isinstance(result.data, self.Array)
def test_dot(self):
result = self.x.dot(self.x)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_quantile(self, skipna):
result = self.x.quantile(0.5, skipna=skipna)
assert isinstance(result.data, self.Array)
def test_differentiate(self):
# edge_order is not implemented in jax, and only supports passing None
edge_order = None if self.namespace == "jax.numpy" else 1
result = self.x.differentiate("x", edge_order=edge_order)
assert isinstance(result.data, self.Array)
def test_integrate(self):
result = self.x.integrate("x")
assert isinstance(result.data, self.Array)
@pytest.mark.xfail(reason="polyfit uses numpy linalg")
def test_polyfit(self):
# TODO: this could work, there are just a lot of different linalg calls
result = self.x.polyfit("x", 1)
assert isinstance(result.polyfit_coefficients.data, self.Array)
def test_map_blocks(self):
result = self.x.map_blocks(lambda x: x + 1)
assert isinstance(result.data, self.Array)
def test_all(self):
result = self.x.all(dim="x")
assert isinstance(result.data, self.Array)
def test_any(self):
result = self.x.any(dim="x")
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_argmax(self, skipna):
result = self.x.argmax(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_argmin(self, skipna):
result = self.x.argmin(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_idxmax(self, skipna):
result = self.x.idxmax(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_idxmin(self, skipna):
result = self.x.idxmin(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_max(self, skipna):
result = self.x.max(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_min(self, skipna):
result = self.x.min(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_mean(self, skipna):
result = self.x.mean(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_median(self, skipna):
result = self.x.median(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_prod(self, skipna):
result = self.x.prod(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_sum(self, skipna):
result = self.x.sum(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_std(self, skipna):
result = self.x.std(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_var(self, skipna):
result = self.x.var(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_cumsum(self, skipna):
result = self.x.cumsum(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
@pytest.mark.parametrize("skipna", [True, False])
def test_cumprod(self, skipna):
result = self.x.cumprod(dim="x", skipna=skipna)
assert isinstance(result.data, self.Array)
def test_argsort(self):
result = self.x.argsort()
assert isinstance(result.data, self.Array)
def test_astype(self):
result = self.x.astype(int)
assert isinstance(result.data, self.Array)
def test_clip(self):
result = self.x.clip(min=2.0, max=4.0)
assert isinstance(result.data, self.Array)
def test_conj(self):
result = self.x.conj()
assert isinstance(result.data, self.Array)
def test_conjugate(self):
result = self.x.conjugate()
assert isinstance(result.data, self.Array)
def test_imag(self):
result = self.x.imag
assert isinstance(result.data, self.Array)
def test_searchsorted(self):
v = self.constructor(np.asarray([3]))
result = self.x.squeeze().searchsorted(v)
assert isinstance(result, self.Array)
def test_round(self):
result = self.x.round()
assert isinstance(result.data, self.Array)
def test_real(self):
result = self.x.real
assert isinstance(result.data, self.Array)
def test_T(self):
result = self.x.T
assert isinstance(result.data, self.Array)
@pytest.mark.xfail(reason="rank uses bottleneck")
def test_rank(self):
# TODO: scipy has rankdata, as does jax, so this can work
result = self.x.rank()
assert isinstance(result.data, self.Array)
def test_transpose(self):
result = self.x.transpose()
assert isinstance(result.data, self.Array)
def test_stack(self):
result = self.x.stack(z=("x", "y"))
assert isinstance(result.data, self.Array)
def test_unstack(self):
result = self.x.stack(z=("x", "y")).unstack("z")
assert isinstance(result.data, self.Array)
def test_shift(self):
result = self.x.shift(x=1)
assert isinstance(result.data, self.Array)
def test_roll(self):
result = self.x.roll(x=1)
assert isinstance(result.data, self.Array)
def test_pad(self):
result = self.x.pad(x=1)
assert isinstance(result.data, self.Array)
def test_sortby(self):
result = self.x.sortby("x")
assert isinstance(result.data, self.Array)
def test_broadcast_like(self):
result = self.x.broadcast_like(self.x)
assert isinstance(result.data, self.Array)
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