Begin testing

Author: dcherian

flox/aggregate_flox.py

@@ -14,7 +14,9 @@ def _prepare_for_flox(group_idx, array):
     if issorted:
         ordered_array = array
     else:
-        perm = group_idx.argsort(kind="stable")
+        kind = "stable" if isinstance(group_idx, np.ndarray) else None
+
+        perm = np.argsort(group_idx, kind=kind)
         group_idx = group_idx[..., perm]
         ordered_array = array[..., perm]
     return group_idx, ordered_array

flox/core.py

@@ -570,6 +570,8 @@ def factorize_(
                 else:
                     assert sort
                     groups, idx = np.unique(flat, return_inverse=True)
+                    idx[np.isnan(flat)] = -1
+                    groups = groups[~np.isnan(groups)]
 
             found_groups.append(groups)
         factorized.append(idx.reshape(groupvar.shape))

flox/xrutils.py

@@ -294,7 +294,6 @@ def _select_along_axis(values, idx, axis):
 def nanfirst(values, axis, keepdims=False):
     if isinstance(axis, tuple):
         (axis,) = axis
-    values = np.asarray(values)
     axis = normalize_axis_index(axis, values.ndim)
     idx_first = np.argmax(~pd.isnull(values), axis=axis)
     result = _select_along_axis(values, idx_first, axis)
@@ -307,7 +306,6 @@ def nanfirst(values, axis, keepdims=False):
 def nanlast(values, axis, keepdims=False):
     if isinstance(axis, tuple):
         (axis,) = axis
-    values = np.asarray(values)
     axis = normalize_axis_index(axis, values.ndim)
     rev = (slice(None),) * axis + (slice(None, None, -1),)
     idx_last = -1 - np.argmax(~pd.isnull(values)[rev], axis=axis)

tests/__init__.py

@@ -24,6 +24,13 @@
 except ImportError:
     xr_types = ()  # type: ignore
 
+try:
+    import cupy as cp
+
+    cp_types = (cp.ndarray,)
+except ImportError:
+    cp_types = ()  # type: ignore
+
 
 def _importorskip(modname, minversion=None):
     try:
@@ -88,6 +95,12 @@ def assert_equal(a, b, tolerance=None):
     if isinstance(b, list):
         b = np.array(b)
 
+    if isinstance(a, cp_types):
+        a = a.get()
+
+    if isinstance(b, cp_types):
+        b = b.get()
+
     if isinstance(a, pd_types) or isinstance(b, pd_types):
         pd.testing.assert_index_equal(a, b)
         return

tests/conftest.py

@@ -9,3 +9,18 @@ def engine(request):
         except ImportError:
             pytest.xfail()
     return request.param
+
+
+@pytest.fixture(scope="module", params=["numpy", "cupy"])
+def array_module(request):
+    if request.param == "cupy":
+        try:
+            import cupy  # noqa
+
+            return cupy
+        except ImportError:
+            pytest.xfail()
+    elif request.param == "numpy":
+        import numpy
+
+        return numpy

tests/test_core.py

@@ -178,31 +178,53 @@ def test_groupby_reduce(
     assert_equal(expected_result, result)
 
 
-def gen_array_by(size, func):
-    by = np.ones(size[-1])
-    rng = np.random.default_rng(12345)
+def maybe_skip_cupy(array_module, func, engine):
+    if array_module is np:
+        return
+
+    import cupy
+
+    assert array_module is cupy
+
+    if engine == "numba":
+        pytest.skip()
+
+    if engine == "numpy" and ("prod" in func or "first" in func or "last" in func):
+        pytest.xfail()
+    elif engine == "flox" and not (
+        "sum" in func or "mean" in func or "std" in func or "var" in func
+    ):
+        pytest.xfail()
+
+
+def gen_array_by(size, func, array_module):
+    xp = array_module
+    by = xp.ones(size[-1])
+    rng = xp.random.default_rng(12345)
     array = rng.random(size)
     if "nan" in func and "nanarg" not in func:
-        array[[1, 4, 5], ...] = np.nan
+        array[[1, 4, 5], ...] = xp.nan
     elif "nanarg" in func and len(size) > 1:
-        array[[1, 4, 5], 1] = np.nan
+        array[[1, 4, 5], 1] = xp.nan
     if func in ["any", "all"]:
         array = array > 0.5
     return array, by
 
 
-@pytest.mark.parametrize("chunks", [None, -1, 3, 4])
 @pytest.mark.parametrize("nby", [1, 2, 3])
 @pytest.mark.parametrize("size", ((12,), (12, 9)))
-@pytest.mark.parametrize("add_nan_by", [True, False])
+@pytest.mark.parametrize("chunks", [None, -1, 3, 4])
 @pytest.mark.parametrize("func", ALL_FUNCS)
-def test_groupby_reduce_all(nby, size, chunks, func, add_nan_by, engine):
+@pytest.mark.parametrize("add_nan_by", [True, False])
+def test_groupby_reduce_all(nby, size, chunks, func, add_nan_by, engine, array_module):
     if chunks is not None and not has_dask:
         pytest.skip()
     if "arg" in func and engine == "flox":
         pytest.skip()
 
-    array, by = gen_array_by(size, func)
+    maybe_skip_cupy(array_module, func, engine)
+
+    array, by = gen_array_by(size, func, array_module)
     if chunks:
         array = dask.array.from_array(array, chunks=chunks)
     by = (by,) * nby