File: test_v3.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 (463 lines) | stat: -rw-r--r-- 16,239 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
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
from __future__ import annotations

import json
import re
from typing import TYPE_CHECKING, Literal

import numpy as np
import pytest

from zarr import consolidate_metadata, create_group
from zarr.codecs.bytes import BytesCodec
from zarr.core.buffer import default_buffer_prototype
from zarr.core.chunk_key_encodings import DefaultChunkKeyEncoding, V2ChunkKeyEncoding
from zarr.core.config import config
from zarr.core.dtype import UInt8, get_data_type_from_native_dtype
from zarr.core.dtype.npy.string import _NUMPY_SUPPORTS_VLEN_STRING
from zarr.core.dtype.npy.time import DateTime64
from zarr.core.group import GroupMetadata, parse_node_type
from zarr.core.metadata.v3 import (
    ArrayMetadataJSON_V3,
    ArrayV3Metadata,
    parse_codecs,
    parse_dimension_names,
    parse_zarr_format,
)
from zarr.errors import (
    MetadataValidationError,
    NodeTypeValidationError,
    UnknownCodecError,
    ZarrUserWarning,
)

if TYPE_CHECKING:
    from collections.abc import Sequence
    from typing import Any

    from zarr.core.types import JSON

    from zarr.abc.codec import Codec


from zarr.core.metadata.v3 import (
    parse_node_type_array,
)

bool_dtypes = ("bool",)

int_dtypes = (
    "int8",
    "int16",
    "int32",
    "int64",
    "uint8",
    "uint16",
    "uint32",
    "uint64",
)

float_dtypes = (
    "float16",
    "float32",
    "float64",
)

complex_dtypes = ("complex64", "complex128")
flexible_dtypes = ("str", "bytes", "void")
if _NUMPY_SUPPORTS_VLEN_STRING:
    vlen_string_dtypes = ("T",)
else:
    vlen_string_dtypes = ("O",)

dtypes = (
    *bool_dtypes,
    *int_dtypes,
    *float_dtypes,
    *complex_dtypes,
    *flexible_dtypes,
    *vlen_string_dtypes,
)


@pytest.mark.parametrize("data", [None, 1, 2, 4, 5, "3"])
def test_parse_zarr_format_invalid(data: Any) -> None:
    with pytest.raises(
        MetadataValidationError,
        match=f"Invalid value for 'zarr_format'. Expected '3'. Got '{data}'.",
    ):
        parse_zarr_format(data)


def test_parse_zarr_format_valid() -> None:
    assert parse_zarr_format(3) == 3


def test_parse_node_type_valid() -> None:
    assert parse_node_type("array") == "array"
    assert parse_node_type("group") == "group"


@pytest.mark.parametrize("node_type", [None, 2, "other"])
def test_parse_node_type_invalid(node_type: Any) -> None:
    with pytest.raises(
        MetadataValidationError,
        match=f"Invalid value for 'node_type'. Expected 'array' or 'group'. Got '{node_type}'.",
    ):
        parse_node_type(node_type)


@pytest.mark.parametrize("data", [None, "group"])
def test_parse_node_type_array_invalid(data: Any) -> None:
    with pytest.raises(
        NodeTypeValidationError,
        match=f"Invalid value for 'node_type'. Expected 'array'. Got '{data}'.",
    ):
        parse_node_type_array(data)


def test_parse_node_typev_array_alid() -> None:
    assert parse_node_type_array("array") == "array"


@pytest.mark.parametrize("data", [(), [1, 2, "a"], {"foo": 10}])
def parse_dimension_names_invalid(data: Any) -> None:
    with pytest.raises(TypeError, match="Expected either None or iterable of str,"):
        parse_dimension_names(data)


@pytest.mark.parametrize("data", [None, ("a", "b", "c"), ["a", "a", "a"]])
def parse_dimension_names_valid(data: Sequence[str] | None) -> None:
    assert parse_dimension_names(data) == data


@pytest.mark.parametrize("fill_value", [[1.0, 0.0], [0, 1]])
@pytest.mark.parametrize("dtype_str", [*complex_dtypes])
def test_jsonify_fill_value_complex(fill_value: Any, dtype_str: str) -> None:
    """
    Test that parse_fill_value(fill_value, dtype) correctly handles complex values represented
    as length-2 sequences
    """
    zarr_format: Literal[3] = 3
    dtype = get_data_type_from_native_dtype(dtype_str)
    expected = dtype.to_native_dtype().type(complex(*fill_value))
    observed = dtype.from_json_scalar(fill_value, zarr_format=zarr_format)
    assert observed == expected
    assert dtype.to_json_scalar(observed, zarr_format=zarr_format) == tuple(fill_value)


@pytest.mark.parametrize("fill_value", [{"foo": 10}])
@pytest.mark.parametrize("dtype_str", [*int_dtypes, *float_dtypes, *complex_dtypes])
def test_parse_fill_value_invalid_type(fill_value: Any, dtype_str: str) -> None:
    """
    Test that parse_fill_value(fill_value, dtype) raises TypeError for invalid non-sequential types.
    This test excludes bool because the bool constructor takes anything.
    """
    dtype_instance = get_data_type_from_native_dtype(dtype_str)
    with pytest.raises(TypeError, match=f"Invalid type: {fill_value}"):
        dtype_instance.from_json_scalar(fill_value, zarr_format=3)


@pytest.mark.parametrize(
    "fill_value",
    [
        [
            1,
        ],
        (1, 23, 4),
    ],
)
@pytest.mark.parametrize("dtype_str", [*int_dtypes, *float_dtypes])
def test_parse_fill_value_invalid_type_sequence(fill_value: Any, dtype_str: str) -> None:
    """
    Test that parse_fill_value(fill_value, dtype) raises TypeError for invalid sequential types.
    This test excludes bool because the bool constructor takes anything, and complex because
    complex values can be created from length-2 sequences.
    """
    dtype_instance = get_data_type_from_native_dtype(dtype_str)
    with pytest.raises(TypeError, match=re.escape(f"Invalid type: {fill_value}")):
        dtype_instance.from_json_scalar(fill_value, zarr_format=3)


@pytest.mark.parametrize("chunk_grid", ["regular"])
@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}])
@pytest.mark.parametrize("codecs", [[BytesCodec(endian=None)]])
@pytest.mark.parametrize("fill_value", [0, 1])
@pytest.mark.parametrize("chunk_key_encoding", ["v2", "default"])
@pytest.mark.parametrize("dimension_separator", [".", "/", None])
@pytest.mark.parametrize("dimension_names", ["nones", "strings", "missing"])
@pytest.mark.parametrize("storage_transformers", [None, ()])
def test_metadata_to_dict(
    chunk_grid: str,
    codecs: list[Codec],
    fill_value: Any,
    chunk_key_encoding: Literal["v2", "default"],
    dimension_separator: Literal[".", "/"] | None,
    dimension_names: Literal["nones", "strings", "missing"],
    attributes: dict[str, Any] | None,
    storage_transformers: tuple[dict[str, JSON]] | None,
) -> None:
    shape = (1, 2, 3)
    data_type_str = "uint8"
    if chunk_grid == "regular":
        cgrid = {"name": "regular", "configuration": {"chunk_shape": (1, 1, 1)}}

    cke: dict[str, Any]
    cke_name_dict = {"name": chunk_key_encoding}
    if dimension_separator is not None:
        cke = cke_name_dict | {"configuration": {"separator": dimension_separator}}
    else:
        cke = cke_name_dict
    dnames: tuple[str | None, ...] | None

    if dimension_names == "strings":
        dnames = tuple(map(str, range(len(shape))))
    elif dimension_names == "missing":
        dnames = None
    elif dimension_names == "nones":
        dnames = (None,) * len(shape)

    metadata_dict = {
        "zarr_format": 3,
        "node_type": "array",
        "shape": shape,
        "chunk_grid": cgrid,
        "data_type": data_type_str,
        "chunk_key_encoding": cke,
        "codecs": tuple(c.to_dict() for c in codecs),
        "fill_value": fill_value,
        "storage_transformers": storage_transformers,
    }

    if attributes is not None:
        metadata_dict["attributes"] = attributes
    if dnames is not None:
        metadata_dict["dimension_names"] = dnames

    metadata = ArrayV3Metadata.from_dict(metadata_dict)
    observed = metadata.to_dict()
    expected = metadata_dict.copy()

    # if unset or None or (), storage_transformers gets normalized to ()
    assert observed["storage_transformers"] == ()
    observed.pop("storage_transformers")
    expected.pop("storage_transformers")

    if attributes is None:
        assert observed["attributes"] == {}
        observed.pop("attributes")

    if dimension_separator is None:
        if chunk_key_encoding == "default":
            expected_cke_dict = DefaultChunkKeyEncoding(separator="/").to_dict()
        else:
            expected_cke_dict = V2ChunkKeyEncoding(separator=".").to_dict()
        assert observed["chunk_key_encoding"] == expected_cke_dict
        observed.pop("chunk_key_encoding")
        expected.pop("chunk_key_encoding")
    assert observed == expected


@pytest.mark.parametrize("indent", [2, 4, None])
def test_json_indent(indent: int) -> None:
    with config.set({"json_indent": indent}):
        m = GroupMetadata()
        d = m.to_buffer_dict(default_buffer_prototype())["zarr.json"].to_bytes()
        assert d == json.dumps(json.loads(d), indent=indent).encode()


@pytest.mark.parametrize("fill_value", [-1, 0, 1, 2932897])
@pytest.mark.parametrize("precision", ["ns", "D"])
async def test_datetime_metadata(fill_value: int, precision: Literal["ns", "D"]) -> None:
    dtype = DateTime64(unit=precision)
    metadata_dict: dict[str, Any] = {
        "zarr_format": 3,
        "node_type": "array",
        "shape": (1,),
        "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": (1,)}},
        "data_type": dtype.to_json(zarr_format=3),
        "chunk_key_encoding": {"name": "default", "separator": "."},
        "codecs": (BytesCodec(),),
        "fill_value": dtype.to_json_scalar(
            dtype.to_native_dtype().type(fill_value, dtype.unit), zarr_format=3
        ),
    }
    metadata = ArrayV3Metadata.from_dict(metadata_dict)
    # ensure there isn't a TypeError here.
    d = metadata.to_buffer_dict(default_buffer_prototype())

    result = json.loads(d["zarr.json"].to_bytes())
    assert result["fill_value"] == fill_value


@pytest.mark.parametrize(
    ("data_type", "fill_value"), [("uint8", {}), ("int32", [0, 1]), ("float32", "foo")]
)
async def test_invalid_fill_value_raises(data_type: str, fill_value: float) -> None:
    metadata_dict: dict[str, Any] = {
        "zarr_format": 3,
        "node_type": "array",
        "shape": (1,),
        "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": (1,)}},
        "data_type": data_type,
        "chunk_key_encoding": {"name": "default", "separator": "."},
        "codecs": ({"name": "bytes"},),
        "fill_value": fill_value,  # this is not a valid fill value for uint8
    }
    # multiple things can go wrong here, so we don't match on the error message.
    with pytest.raises(TypeError):
        ArrayV3Metadata.from_dict(metadata_dict)


@pytest.mark.parametrize("fill_value", [("NaN"), "Infinity", "-Infinity"])
async def test_special_float_fill_values(fill_value: str) -> None:
    metadata_dict: dict[str, Any] = {
        "zarr_format": 3,
        "node_type": "array",
        "shape": (1,),
        "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": (1,)}},
        "data_type": "float64",
        "chunk_key_encoding": {"name": "default", "separator": "."},
        "codecs": [{"name": "bytes"}],
        "fill_value": fill_value,  # this is not a valid fill value for uint8
    }
    m = ArrayV3Metadata.from_dict(metadata_dict)
    d = json.loads(m.to_buffer_dict(default_buffer_prototype())["zarr.json"].to_bytes())
    assert m.fill_value is not None
    if fill_value == "NaN":
        assert np.isnan(m.fill_value)
        assert d["fill_value"] == "NaN"
    elif fill_value == "Infinity":
        assert np.isposinf(m.fill_value)
        assert d["fill_value"] == "Infinity"
    elif fill_value == "-Infinity":
        assert np.isneginf(m.fill_value)
        assert d["fill_value"] == "-Infinity"


def test_parse_codecs_unknown_codec_raises(monkeypatch: pytest.MonkeyPatch) -> None:
    from collections import defaultdict

    import zarr.registry
    from zarr.registry import Registry

    # to make sure the codec is always unknown (not sure if that's necessary)
    monkeypatch.setattr(zarr.registry, "__codec_registries", defaultdict(Registry))

    codecs = [{"name": "unknown"}]
    with pytest.raises(UnknownCodecError):
        parse_codecs(codecs)


@pytest.mark.parametrize(
    "extra_value",
    [
        {"must_understand": False, "param": 10},
        {"must_understand": True},
        10,
    ],
)
def test_from_dict_extra_fields(extra_value: dict[str, object] | int) -> None:
    """
    Test that from_dict accepts extra fields if they have are a JSON object with
    "must_understand": false, and raises an exception otherwise.
    """
    metadata_dict: ArrayMetadataJSON_V3 = {  # type: ignore[typeddict-unknown-key]
        "zarr_format": 3,
        "node_type": "array",
        "shape": (1,),
        "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": (1,)}},
        "data_type": "uint8",
        "chunk_key_encoding": {"name": "default", "configuration": {"separator": "."}},
        "codecs": ({"name": "bytes"},),
        "fill_value": 0,
        "storage_transformers": (),
        "attributes": {},
        "foo": extra_value,
    }

    if isinstance(extra_value, dict) and extra_value.get("must_understand") is False:
        # should be accepted
        metadata = ArrayV3Metadata.from_dict(metadata_dict)  # type: ignore[arg-type]
        assert isinstance(metadata, ArrayV3Metadata)
        assert metadata.to_dict() == metadata_dict
    else:
        # should raise an exception
        with pytest.raises(MetadataValidationError, match="Got a Zarr V3 metadata document"):
            metadata = ArrayV3Metadata.from_dict(metadata_dict)  # type: ignore[arg-type]


def test_init_invalid_extra_fields() -> None:
    """
    Test that initializing ArrayV3Metadata with extra fields fails when those fields
    shadow the array metadata fields.
    """
    extra_fields: dict[str, object] = {"shape": (10,), "data_type": "uint8"}
    conflict_keys = set(extra_fields.keys())
    msg = (
        "Invalid extra fields. "
        "The following keys: "
        f"{sorted(conflict_keys)} "
        "are invalid because they collide with keys reserved for use by the "
        "array metadata document."
    )
    with pytest.raises(ValueError, match=re.escape(msg)):
        ArrayV3Metadata(
            shape=(10,),
            data_type=UInt8(),
            chunk_grid={"name": "regular", "configuration": {"chunk_shape": (10,)}},
            chunk_key_encoding={"name": "default", "configuration": {"separator": "/"}},
            fill_value=0,
            codecs=({"name": "bytes", "configuration": {"endian": "little"}},),
            attributes={},
            dimension_names=None,
            extra_fields=extra_fields,  # type: ignore[arg-type]
        )


@pytest.mark.parametrize("use_consolidated", [True, False])
@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}])
def test_group_to_dict(use_consolidated: bool, attributes: None | dict[str, Any]) -> None:
    """
    Test that the output of GroupMetadata.to_dict() is what we expect
    """
    store: dict[str, object] = {}
    if attributes is None:
        expect_attributes = {}
    else:
        expect_attributes = attributes

    group = create_group(store, attributes=attributes, zarr_format=3)
    group.create_group("foo")
    if use_consolidated:
        with pytest.warns(
            ZarrUserWarning,
            match="Consolidated metadata is currently not part in the Zarr format 3 specification.",
        ):
            group = consolidate_metadata(store)
        meta = group.metadata
        expect = {
            "node_type": "group",
            "zarr_format": 3,
            "consolidated_metadata": {
                "kind": "inline",
                "must_understand": False,
                "metadata": {
                    "foo": {
                        "attributes": {},
                        "zarr_format": 3,
                        "node_type": "group",
                        "consolidated_metadata": {
                            "kind": "inline",
                            "metadata": {},
                            "must_understand": False,
                        },
                    }
                },
            },
            "attributes": expect_attributes,
        }
    else:
        meta = group.metadata
        expect = {"node_type": "group", "zarr_format": 3, "attributes": expect_attributes}

    assert meta.to_dict() == expect