File: __init__.py

package info (click to toggle)
python-xarray 2025.08.0-1
  • links: PTS, VCS
  • area: main
  • in suites: sid
  • size: 11,796 kB
  • sloc: python: 115,416; makefile: 258; sh: 47
file content (440 lines) | stat: -rw-r--r-- 14,404 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
from __future__ import annotations

import importlib
import platform
import string
import warnings
from contextlib import contextmanager, nullcontext
from unittest import mock  # noqa: F401

import numpy as np
import pandas as pd
import pytest
from numpy.testing import assert_array_equal  # noqa: F401
from packaging.version import Version
from pandas.testing import assert_frame_equal  # noqa: F401

import xarray.testing
from xarray import Dataset
from xarray.coding.times import _STANDARD_CALENDARS as _STANDARD_CALENDARS_UNSORTED
from xarray.core.duck_array_ops import allclose_or_equiv  # noqa: F401
from xarray.core.extension_array import PandasExtensionArray
from xarray.core.options import set_options
from xarray.core.variable import IndexVariable
from xarray.testing import (  # noqa: F401
    assert_chunks_equal,
    assert_duckarray_allclose,
    assert_duckarray_equal,
)
from xarray.tests.arrays import (  # noqa: F401
    ConcatenatableArray,
    DuckArrayWrapper,
    FirstElementAccessibleArray,
    InaccessibleArray,
    UnexpectedDataAccess,
)

# import mpl and change the backend before other mpl imports
try:
    import matplotlib as mpl

    # Order of imports is important here.
    # Using a different backend makes Travis CI work
    mpl.use("Agg")
except ImportError:
    pass

# https://github.com/pydata/xarray/issues/7322
warnings.filterwarnings("ignore", "'urllib3.contrib.pyopenssl' module is deprecated")
warnings.filterwarnings("ignore", "Deprecated call to `pkg_resources.declare_namespace")
warnings.filterwarnings("ignore", "pkg_resources is deprecated as an API")
warnings.filterwarnings("ignore", message="numpy.ndarray size changed")

arm_xfail = pytest.mark.xfail(
    platform.machine() == "aarch64" or "arm" in platform.machine(),
    reason="expected failure on ARM",
)


def assert_writeable(ds):
    readonly = [
        name
        for name, var in ds.variables.items()
        if not isinstance(var, IndexVariable)
        and not isinstance(
            var.data, PandasExtensionArray | pd.api.extensions.ExtensionArray
        )
        and not var.data.flags.writeable
    ]
    assert not readonly, readonly


def _importorskip(
    modname: str, minversion: str | None = None
) -> tuple[bool, pytest.MarkDecorator]:
    try:
        mod = importlib.import_module(modname)
        has = True
        if minversion is not None:
            v = getattr(mod, "__version__", "999")
            if Version(v) < Version(minversion):
                raise ImportError("Minimum version not satisfied")
    except ImportError:
        has = False

    reason = f"requires {modname}"
    if minversion is not None:
        reason += f">={minversion}"
    func = pytest.mark.skipif(not has, reason=reason)
    return has, func


has_matplotlib, requires_matplotlib = _importorskip("matplotlib")
has_scipy, requires_scipy = _importorskip("scipy")
has_scipy_ge_1_13, requires_scipy_ge_1_13 = _importorskip("scipy", "1.13")
with warnings.catch_warnings():
    warnings.filterwarnings(
        "ignore",
        message="'cgi' is deprecated and slated for removal in Python 3.13",
        category=DeprecationWarning,
    )
    has_pydap, requires_pydap = _importorskip("pydap.client")
has_netCDF4, requires_netCDF4 = _importorskip("netCDF4")
with warnings.catch_warnings():
    # see https://github.com/pydata/xarray/issues/8537
    warnings.filterwarnings(
        "ignore",
        message="h5py is running against HDF5 1.14.3",
        category=UserWarning,
    )

    has_h5netcdf, requires_h5netcdf = _importorskip("h5netcdf")
has_cftime, requires_cftime = _importorskip("cftime")
has_dask, requires_dask = _importorskip("dask")
has_dask_ge_2024_08_1, requires_dask_ge_2024_08_1 = _importorskip(
    "dask", minversion="2024.08.1"
)
has_dask_ge_2024_11_0, requires_dask_ge_2024_11_0 = _importorskip("dask", "2024.11.0")
has_dask_ge_2025_1_0, requires_dask_ge_2025_1_0 = _importorskip("dask", "2025.1.0")
if has_dask_ge_2025_1_0:
    has_dask_expr = True
    requires_dask_expr = pytest.mark.skipif(not has_dask_expr, reason="should not skip")
else:
    with warnings.catch_warnings():
        warnings.filterwarnings(
            "ignore",
            message="The current Dask DataFrame implementation is deprecated.",
            category=DeprecationWarning,
        )
        has_dask_expr, requires_dask_expr = _importorskip("dask_expr")
has_bottleneck, requires_bottleneck = _importorskip("bottleneck")
has_rasterio, requires_rasterio = _importorskip("rasterio")
has_zarr, requires_zarr = _importorskip("zarr")
has_zarr_v3, requires_zarr_v3 = _importorskip("zarr", "3.0.0")
has_zarr_v3_dtypes, requires_zarr_v3_dtypes = _importorskip("zarr", "3.1.0")
has_zarr_v3_async_oindex, requires_zarr_v3_async_oindex = _importorskip("zarr", "3.1.2")
if has_zarr_v3:
    import zarr

    # manual update by checking attrs for now
    # TODO: use version specifier
    # installing from git main is giving me a lower version than the
    # most recently released zarr
    has_zarr_v3_dtypes = hasattr(zarr.core, "dtype")
    has_zarr_v3_async_oindex = hasattr(zarr.AsyncArray, "oindex")

    requires_zarr_v3_dtypes = pytest.mark.skipif(
        not has_zarr_v3_dtypes, reason="requires zarr>3.1.0"
    )
    requires_zarr_v3_async_oindex = pytest.mark.skipif(
        not has_zarr_v3_async_oindex, reason="requires zarr>3.1.1"
    )


has_fsspec, requires_fsspec = _importorskip("fsspec")
has_iris, requires_iris = _importorskip("iris")
has_numbagg, requires_numbagg = _importorskip("numbagg")
has_pyarrow, requires_pyarrow = _importorskip("pyarrow")
with warnings.catch_warnings():
    warnings.filterwarnings(
        "ignore",
        message="is_categorical_dtype is deprecated and will be removed in a future version.",
        category=DeprecationWarning,
    )
    # seaborn uses the deprecated `pandas.is_categorical_dtype`
    has_seaborn, requires_seaborn = _importorskip("seaborn")
has_sparse, requires_sparse = _importorskip("sparse")
has_cupy, requires_cupy = _importorskip("cupy")
has_cartopy, requires_cartopy = _importorskip("cartopy")
has_pint, requires_pint = _importorskip("pint")
has_numexpr, requires_numexpr = _importorskip("numexpr")
has_flox, requires_flox = _importorskip("flox")
has_netcdf, requires_netcdf = _importorskip("netcdf")
has_pandas_ge_2_2, requires_pandas_ge_2_2 = _importorskip("pandas", "2.2")
has_pandas_3, requires_pandas_3 = _importorskip("pandas", "3.0.0.dev0")


# some special cases
has_scipy_or_netCDF4 = has_scipy or has_netCDF4
requires_scipy_or_netCDF4 = pytest.mark.skipif(
    not has_scipy_or_netCDF4, reason="requires scipy or netCDF4"
)
has_numbagg_or_bottleneck = has_numbagg or has_bottleneck
requires_numbagg_or_bottleneck = pytest.mark.skipif(
    not has_numbagg_or_bottleneck, reason="requires numbagg or bottleneck"
)
has_numpy_2, requires_numpy_2 = _importorskip("numpy", "2.0.0")
has_flox_0_9_12, requires_flox_0_9_12 = _importorskip("flox", "0.9.12")

has_array_api_strict, requires_array_api_strict = _importorskip("array_api_strict")

parametrize_zarr_format = pytest.mark.parametrize(
    "zarr_format",
    [
        pytest.param(2, id="zarr_format=2"),
        pytest.param(
            3,
            marks=pytest.mark.skipif(
                not has_zarr_v3,
                reason="zarr-python v2 cannot understand the zarr v3 format",
            ),
            id="zarr_format=3",
        ),
    ],
)


def _importorskip_h5netcdf_ros3(has_h5netcdf: bool):
    if not has_h5netcdf:
        return has_h5netcdf, pytest.mark.skipif(
            not has_h5netcdf, reason="requires h5netcdf"
        )

    import h5py

    h5py_with_ros3 = h5py.get_config().ros3

    return h5py_with_ros3, pytest.mark.skipif(
        not h5py_with_ros3,
        reason="requires h5netcdf>=1.3.0 and h5py with ros3 support",
    )


has_h5netcdf_ros3, requires_h5netcdf_ros3 = _importorskip_h5netcdf_ros3(has_h5netcdf)
has_netCDF4_1_6_2_or_above, requires_netCDF4_1_6_2_or_above = _importorskip(
    "netCDF4", "1.6.2"
)

has_h5netcdf_1_4_0_or_above, requires_h5netcdf_1_4_0_or_above = _importorskip(
    "h5netcdf", "1.4.0.dev"
)

has_netCDF4_1_7_0_or_above, requires_netCDF4_1_7_0_or_above = _importorskip(
    "netCDF4", "1.7.0"
)

# change some global options for tests
set_options(warn_for_unclosed_files=True)

if has_dask:
    import dask


class CountingScheduler:
    """Simple dask scheduler counting the number of computes.

    Reference: https://stackoverflow.com/questions/53289286/"""

    def __init__(self, max_computes=0):
        self.total_computes = 0
        self.max_computes = max_computes

    def __call__(self, dsk, keys, **kwargs):
        self.total_computes += 1
        if self.total_computes > self.max_computes:
            raise RuntimeError(
                f"Too many computes. Total: {self.total_computes} > max: {self.max_computes}."
            )
        return dask.get(dsk, keys, **kwargs)


def raise_if_dask_computes(max_computes=0):
    # return a dummy context manager so that this can be used for non-dask objects
    if not has_dask:
        return nullcontext()
    scheduler = CountingScheduler(max_computes)
    return dask.config.set(scheduler=scheduler)


flaky = pytest.mark.flaky
network = pytest.mark.network


class ReturnItem:
    def __getitem__(self, key):
        return key


class IndexerMaker:
    def __init__(self, indexer_cls):
        self._indexer_cls = indexer_cls

    def __getitem__(self, key):
        if not isinstance(key, tuple):
            key = (key,)
        return self._indexer_cls(key)


def source_ndarray(array):
    """Given an ndarray, return the base object which holds its memory, or the
    object itself.
    """
    with warnings.catch_warnings():
        warnings.filterwarnings("ignore", "DatetimeIndex.base")
        warnings.filterwarnings("ignore", "TimedeltaIndex.base")
        base = getattr(array, "base", np.asarray(array).base)
    if base is None:
        base = array
    return base


def format_record(record) -> str:
    """Format warning record like `FutureWarning('Function will be deprecated...')`"""
    return f"{str(record.category)[8:-2]}('{record.message}'))"


@contextmanager
def assert_no_warnings():
    with warnings.catch_warnings(record=True) as record:
        yield record
        assert len(record) == 0, (
            f"Got {len(record)} unexpected warning(s): {[format_record(r) for r in record]}"
        )


# Internal versions of xarray's test functions that validate additional
# invariants


def assert_equal(a, b, check_default_indexes=True):
    __tracebackhide__ = True
    xarray.testing.assert_equal(a, b)
    xarray.testing._assert_internal_invariants(a, check_default_indexes)
    xarray.testing._assert_internal_invariants(b, check_default_indexes)


def assert_identical(a, b, check_default_indexes=True):
    __tracebackhide__ = True
    xarray.testing.assert_identical(a, b)
    xarray.testing._assert_internal_invariants(a, check_default_indexes)
    xarray.testing._assert_internal_invariants(b, check_default_indexes)


def assert_allclose(a, b, check_default_indexes=True, **kwargs):
    __tracebackhide__ = True
    xarray.testing.assert_allclose(a, b, **kwargs)
    xarray.testing._assert_internal_invariants(a, check_default_indexes)
    xarray.testing._assert_internal_invariants(b, check_default_indexes)


_DEFAULT_TEST_DIM_SIZES = (8, 9, 10)


def create_test_data(
    seed: int = 12345,
    add_attrs: bool = True,
    dim_sizes: tuple[int, int, int] = _DEFAULT_TEST_DIM_SIZES,
    use_extension_array: bool = False,
) -> Dataset:
    rs = np.random.default_rng(seed)
    _vars = {
        "var1": ["dim1", "dim2"],
        "var2": ["dim1", "dim2"],
        "var3": ["dim3", "dim1"],
    }
    _dims = {"dim1": dim_sizes[0], "dim2": dim_sizes[1], "dim3": dim_sizes[2]}

    obj = Dataset()
    obj["dim2"] = ("dim2", 0.5 * np.arange(_dims["dim2"]))
    if _dims["dim3"] > 26:
        raise RuntimeError(
            f"Not enough letters for filling this dimension size ({_dims['dim3']})"
        )
    obj["dim3"] = ("dim3", list(string.ascii_lowercase[0 : _dims["dim3"]]))
    obj["time"] = (
        "time",
        pd.date_range(
            "2000-01-01",
            periods=20,
            unit="ns",
        ),
    )
    for v, dims in sorted(_vars.items()):
        data = rs.normal(size=tuple(_dims[d] for d in dims))
        obj[v] = (dims, data)
        if add_attrs:
            obj[v].attrs = {"foo": "variable"}
    if use_extension_array:
        obj["var4"] = (
            "dim1",
            pd.Categorical(
                rs.choice(
                    list(string.ascii_lowercase[: rs.integers(1, 5)]),
                    size=dim_sizes[0],
                )
            ),
        )
        if has_pyarrow:
            obj["var5"] = (
                "dim1",
                pd.array(
                    rs.integers(1, 10, size=dim_sizes[0]).tolist(),
                    dtype="int64[pyarrow]",
                ),
            )
    if dim_sizes == _DEFAULT_TEST_DIM_SIZES:
        numbers_values = np.array([0, 1, 2, 0, 0, 1, 1, 2, 2, 3], dtype="int64")
    else:
        numbers_values = rs.integers(0, 3, _dims["dim3"], dtype="int64")
    obj.coords["numbers"] = ("dim3", numbers_values)
    obj.encoding = {"foo": "bar"}
    assert_writeable(obj)
    return obj


_STANDARD_CALENDAR_NAMES = sorted(_STANDARD_CALENDARS_UNSORTED)
_NON_STANDARD_CALENDAR_NAMES = {
    "noleap",
    "365_day",
    "360_day",
    "julian",
    "all_leap",
    "366_day",
}
_NON_STANDARD_CALENDARS = [
    pytest.param(cal, marks=requires_cftime)
    for cal in sorted(_NON_STANDARD_CALENDAR_NAMES)
]
_STANDARD_CALENDARS = [
    pytest.param(cal, marks=requires_cftime if cal != "standard" else ())
    for cal in _STANDARD_CALENDAR_NAMES
]
_ALL_CALENDARS = sorted(_STANDARD_CALENDARS + _NON_STANDARD_CALENDARS)
_CFTIME_CALENDARS = [
    pytest.param(*p.values, marks=requires_cftime) for p in _ALL_CALENDARS
]


def _all_cftime_date_types():
    import cftime

    return {
        "noleap": cftime.DatetimeNoLeap,
        "365_day": cftime.DatetimeNoLeap,
        "360_day": cftime.Datetime360Day,
        "julian": cftime.DatetimeJulian,
        "all_leap": cftime.DatetimeAllLeap,
        "366_day": cftime.DatetimeAllLeap,
        "gregorian": cftime.DatetimeGregorian,
        "proleptic_gregorian": cftime.DatetimeProlepticGregorian,
    }