File: test_v2.py

package info (click to toggle)
zarr 3.1.5-2
  • links: PTS, VCS
  • area: main
  • in suites: forky, sid
  • size: 3,068 kB
  • sloc: python: 31,589; makefile: 10
file content (311 lines) | stat: -rw-r--r-- 9,954 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
import json
from pathlib import Path
from typing import Any, Literal

import numpy as np
import pytest
from numcodecs import Delta, Zlib
from numcodecs.blosc import Blosc
from numcodecs.zstd import Zstd

import zarr
import zarr.core.buffer
import zarr.storage
from zarr import config
from zarr.abc.store import Store
from zarr.core.buffer.core import default_buffer_prototype
from zarr.core.dtype import FixedLengthUTF32, Structured, VariableLengthUTF8
from zarr.core.dtype.npy.bytes import NullTerminatedBytes
from zarr.core.dtype.wrapper import ZDType
from zarr.core.group import Group
from zarr.core.sync import sync
from zarr.errors import ZarrDeprecationWarning
from zarr.storage import MemoryStore, StorePath


@pytest.fixture
async def store() -> StorePath:
    return StorePath(await MemoryStore.open())


def test_simple(store: StorePath) -> None:
    data = np.arange(0, 256, dtype="uint16").reshape((16, 16))

    a = zarr.create_array(
        store / "simple_v2",
        zarr_format=2,
        shape=data.shape,
        chunks=(16, 16),
        dtype=data.dtype,
        fill_value=0,
    )

    a[:, :] = data
    assert np.array_equal(data, a[:, :])


def test_codec_pipeline() -> None:
    # https://github.com/zarr-developers/zarr-python/issues/2243
    store = MemoryStore()
    array = zarr.create(
        store=store,
        shape=(1,),
        dtype="i4",
        zarr_format=2,
        filters=[Delta(dtype="i4").get_config()],
        compressor=Blosc().get_config(),
    )
    array[:] = 1
    result = array[:]
    expected = np.ones(1)
    np.testing.assert_array_equal(result, expected)


@pytest.mark.parametrize(
    ("dtype", "expected_dtype", "fill_value", "fill_value_json"),
    [
        ("|S1", "|S1", b"X", "WA=="),
        ("|V1", "|V1", b"X", "WA=="),
        ("|V10", "|V10", b"X", "WAAAAAAAAAAAAA=="),
    ],
)
async def test_v2_encode_decode(
    dtype: str, expected_dtype: str, fill_value: bytes, fill_value_json: str
) -> None:
    store = zarr.storage.MemoryStore()
    g = zarr.group(store=store, zarr_format=2)
    g.create_array(
        name="foo", shape=(3,), chunks=(3,), dtype=dtype, fill_value=fill_value, compressor=None
    )

    result = await store.get("foo/.zarray", zarr.core.buffer.default_buffer_prototype())
    assert result is not None

    serialized = json.loads(result.to_bytes())
    expected = {
        "chunks": [3],
        "compressor": None,
        "dtype": expected_dtype,
        "fill_value": fill_value_json,
        "filters": None,
        "order": "C",
        "shape": [3],
        "zarr_format": 2,
        "dimension_separator": ".",
    }
    assert serialized == expected

    data = zarr.open_array(store=store, path="foo")[:]
    np.testing.assert_equal(data, np.full((3,), b"X", dtype=dtype))

    data = zarr.open_array(store=store, path="foo")[:]
    np.testing.assert_equal(data, np.full((3,), b"X", dtype=dtype))


@pytest.mark.parametrize(
    ("dtype", "value"),
    [
        (NullTerminatedBytes(length=1), b"Y"),
        (FixedLengthUTF32(length=1), "Y"),
        (VariableLengthUTF8(), "Y"),
    ],
)
def test_v2_encode_decode_with_data(dtype: ZDType[Any, Any], value: str) -> None:
    expected = np.full((3,), value, dtype=dtype.to_native_dtype())
    a = zarr.create(
        shape=(3,),
        zarr_format=2,
        dtype=dtype,
    )
    a[:] = expected
    data = a[:]
    np.testing.assert_equal(data, expected)


@pytest.mark.parametrize("filters", [[], [Delta(dtype="<i4")], [Zlib(level=2)]])
@pytest.mark.parametrize("order", ["C", "F"])
def test_v2_filters_codecs(filters: Any, order: Literal["C", "F"]) -> None:
    array_fixture = [42]
    with config.set({"array.order": order}):
        arr = zarr.create(shape=1, dtype="<i4", zarr_format=2, filters=filters)
    arr[:] = array_fixture
    result = arr[:]
    np.testing.assert_array_equal(result, array_fixture)


@pytest.mark.filterwarnings("ignore")
@pytest.mark.parametrize("store", ["memory"], indirect=True)
def test_create_array_defaults(store: Store) -> None:
    """
    Test that passing compressor=None results in no compressor. Also test that the default value of the compressor
    parameter does produce a compressor.
    """
    g = zarr.open(store, mode="w", zarr_format=2)
    assert isinstance(g, Group)
    arr = g.create_array("one", dtype="i8", shape=(1,), chunks=(1,), compressor=None)
    assert arr.async_array.compressor is None
    assert not (arr.filters)
    arr = g.create_array("two", dtype="i8", shape=(1,), chunks=(1,))
    assert arr.async_array.compressor is not None
    assert not (arr.filters)
    arr = g.create_array("three", dtype="i8", shape=(1,), chunks=(1,), compressor=Zstd())
    assert arr.async_array.compressor is not None
    assert not (arr.filters)
    with pytest.raises(ValueError):
        g.create_array(
            "four", dtype="i8", shape=(1,), chunks=(1,), compressor=None, compressors=None
        )


@pytest.mark.parametrize("numpy_order", ["C", "F"])
@pytest.mark.parametrize("zarr_order", ["C", "F"])
def test_v2_non_contiguous(numpy_order: Literal["C", "F"], zarr_order: Literal["C", "F"]) -> None:
    """
    Make sure zarr v2 arrays save data using the memory order given to the zarr array,
    not the memory order of the original numpy array.
    """
    store = MemoryStore()
    arr = zarr.create_array(
        store,
        shape=(10, 8),
        chunks=(3, 3),
        fill_value=np.nan,
        dtype="float64",
        zarr_format=2,
        filters=None,
        compressors=None,
        overwrite=True,
        order=zarr_order,
    )

    # Non-contiguous write, using numpy memory order
    a = np.arange(arr.shape[0] * arr.shape[1]).reshape(arr.shape, order=numpy_order)
    arr[6:9, 3:6] = a[6:9, 3:6]  # The slice on the RHS is important
    np.testing.assert_array_equal(arr[6:9, 3:6], a[6:9, 3:6])

    buf = sync(store.get("2.1", default_buffer_prototype()))
    assert buf is not None
    np.testing.assert_array_equal(
        a[6:9, 3:6],
        np.frombuffer(buf.to_bytes(), dtype="float64").reshape((3, 3), order=zarr_order),
    )
    # After writing and reading from zarr array, order should be same as zarr order
    sub_arr = arr[6:9, 3:6]
    assert isinstance(sub_arr, np.ndarray)
    if zarr_order == "F":
        assert (sub_arr).flags.f_contiguous
    else:
        assert (sub_arr).flags.c_contiguous

    # Contiguous write
    store = MemoryStore()
    arr = zarr.create_array(
        store,
        shape=(10, 8),
        chunks=(3, 3),
        fill_value=np.nan,
        dtype="float64",
        zarr_format=2,
        compressors=None,
        filters=None,
        overwrite=True,
        order=zarr_order,
    )

    a = np.arange(9).reshape((3, 3), order=numpy_order)
    arr[6:9, 3:6] = a
    np.testing.assert_array_equal(arr[6:9, 3:6], a)
    # After writing and reading from zarr array, order should be same as zarr order
    sub_arr = arr[6:9, 3:6]
    assert isinstance(sub_arr, np.ndarray)
    if zarr_order == "F":
        assert (sub_arr).flags.f_contiguous
    else:
        assert (sub_arr).flags.c_contiguous


def test_default_compressor_deprecation_warning() -> None:
    with pytest.warns(ZarrDeprecationWarning, match="default_compressor is deprecated"):
        zarr.storage.default_compressor = "zarr.codecs.zstd.ZstdCodec()"  # type: ignore[attr-defined]


@pytest.mark.parametrize("fill_value", [None, (b"", 0, 0.0)], ids=["no_fill", "fill"])
def test_structured_dtype_roundtrip(fill_value: float | bytes, tmp_path: Path) -> None:
    a = np.array(
        [(b"aaa", 1, 4.2), (b"bbb", 2, 8.4), (b"ccc", 3, 12.6)],
        dtype=[("foo", "S3"), ("bar", "i4"), ("baz", "f8")],
    )
    array_path = tmp_path / "data.zarr"
    za = zarr.create(
        shape=(3,),
        store=array_path,
        chunks=(2,),
        fill_value=fill_value,
        zarr_format=2,
        dtype=a.dtype,
    )
    if fill_value is not None:
        assert (np.array([fill_value] * a.shape[0], dtype=a.dtype) == za[:]).all()
    za[...] = a
    za = zarr.open_array(store=array_path)
    assert (a == za[:]).all()


@pytest.mark.parametrize(
    (
        "fill_value",
        "dtype",
        "expected_result",
    ),
    [
        (
            ("Alice", 30),
            np.dtype([("name", "U10"), ("age", "i4")]),
            np.array([("Alice", 30)], dtype=[("name", "U10"), ("age", "i4")])[0],
        ),
        (
            ["Bob", 25],
            np.dtype([("name", "U10"), ("age", "i4")]),
            np.array([("Bob", 25)], dtype=[("name", "U10"), ("age", "i4")])[0],
        ),
        (
            b"\x01\x00\x00\x00\x02\x00\x00\x00",
            np.dtype([("x", "i4"), ("y", "i4")]),
            np.array([(1, 2)], dtype=[("x", "i4"), ("y", "i4")])[0],
        ),
    ],
    ids=[
        "tuple_input",
        "list_input",
        "bytes_input",
    ],
)
def test_parse_structured_fill_value_valid(
    fill_value: Any, dtype: np.dtype[Any], expected_result: Any
) -> None:
    zdtype = Structured.from_native_dtype(dtype)
    result = zdtype.cast_scalar(fill_value)
    assert result.dtype == expected_result.dtype
    assert result == expected_result
    if isinstance(expected_result, np.void):
        for name in expected_result.dtype.names or []:
            assert result[name] == expected_result[name]


@pytest.mark.parametrize("fill_value", [None, b"x"], ids=["no_fill", "fill"])
def test_other_dtype_roundtrip(fill_value: None | bytes, tmp_path: Path) -> None:
    a = np.array([b"a\0\0", b"bb", b"ccc"], dtype="V7")
    array_path = tmp_path / "data.zarr"
    za = zarr.create(
        shape=(3,),
        store=array_path,
        chunks=(2,),
        fill_value=fill_value,
        zarr_format=2,
        dtype=a.dtype,
    )
    if fill_value is not None:
        assert (np.array([fill_value] * a.shape[0], dtype=a.dtype) == za[:]).all()
    za[...] = a
    za = zarr.open_array(store=array_path)
    assert (a == za[:]).all()