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Merged
merged 3 commits into from
Dec 12, 2024
Merged

Un-pin numpy #2552

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29f2335
Un-pin numpy
dstansby Dec 11, 2024
b311a4e
Fix doctests
dstansby Dec 12, 2024
6c455ed
Merge branch 'support/v2' into unpin-numpy
d-v-b Dec 12, 2024
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ maintainers = [{ name = "Alistair Miles", email = "[email protected]" }]
requires-python = ">=3.11"
dependencies = [
'asciitree',
'numpy>=1.24,<2.2',
'numpy>=1.24',
'fasteners; sys_platform != "emscripten"',
'numcodecs>=0.10.0,!=0.14.0,!=0.14.1',
]
Expand Down
34 changes: 18 additions & 16 deletions zarr/convenience.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,8 @@

_builtin_open = open # builtin open is later shadowed by a local open function

__doctest_requires__ = {("*"): ["numpy>=2.2"]}


def _check_and_update_path(store: BaseStore, path):
if getattr(store, "_store_version", 2) > 2 and not path:
Expand Down Expand Up @@ -174,13 +176,13 @@ def save_array(store: StoreLike, arr, *, zarr_version=None, path=None, **kwargs)
>>> arr = np.arange(10000)
>>> zarr.save_array('data/example.zarr', arr)
>>> zarr.load('data/example.zarr')
array([ 0, 1, 2, ..., 9997, 9998, 9999])
array([ 0, 1, 2, ..., 9997, 9998, 9999], shape=(10000,))

Save an array to a single file (uses a :class:`ZipStore`)::

>>> zarr.save_array('data/example.zip', arr)
>>> zarr.load('data/example.zip')
array([ 0, 1, 2, ..., 9997, 9998, 9999])
array([ 0, 1, 2, ..., 9997, 9998, 9999], shape=(10000,))

"""
may_need_closing = _might_close(store)
Expand Down Expand Up @@ -234,9 +236,9 @@ def save_group(store: StoreLike, *args, zarr_version=None, path=None, **kwargs):
>>> loader
<LazyLoader: arr_0, arr_1>
>>> loader['arr_0']
array([ 0, 1, 2, ..., 9997, 9998, 9999])
array([ 0, 1, 2, ..., 9997, 9998, 9999], shape=(10000,))
>>> loader['arr_1']
array([10000, 9999, 9998, ..., 3, 2, 1])
array([10000, 9999, 9998, ..., 3, 2, 1], shape=(10000,))

Save several arrays using named keyword arguments::

Expand All @@ -245,9 +247,9 @@ def save_group(store: StoreLike, *args, zarr_version=None, path=None, **kwargs):
>>> loader
<LazyLoader: bar, foo>
>>> loader['foo']
array([ 0, 1, 2, ..., 9997, 9998, 9999])
array([ 0, 1, 2, ..., 9997, 9998, 9999], shape=(10000,))
>>> loader['bar']
array([10000, 9999, 9998, ..., 3, 2, 1])
array([10000, 9999, 9998, ..., 3, 2, 1], shape=(10000,))

Store several arrays in a single zip file (uses a :class:`ZipStore`)::

Expand All @@ -256,9 +258,9 @@ def save_group(store: StoreLike, *args, zarr_version=None, path=None, **kwargs):
>>> loader
<LazyLoader: bar, foo>
>>> loader['foo']
array([ 0, 1, 2, ..., 9997, 9998, 9999])
array([ 0, 1, 2, ..., 9997, 9998, 9999], shape=(10000,))
>>> loader['bar']
array([10000, 9999, 9998, ..., 3, 2, 1])
array([10000, 9999, 9998, ..., 3, 2, 1], shape=(10000,))

Notes
-----
Expand Down Expand Up @@ -316,13 +318,13 @@ def save(store: StoreLike, *args, zarr_version=None, path=None, **kwargs):
>>> arr = np.arange(10000)
>>> zarr.save('data/example.zarr', arr)
>>> zarr.load('data/example.zarr')
array([ 0, 1, 2, ..., 9997, 9998, 9999])
array([ 0, 1, 2, ..., 9997, 9998, 9999], shape=(10000,))

Save an array to a Zip file (uses a :class:`ZipStore`)::

>>> zarr.save('data/example.zip', arr)
>>> zarr.load('data/example.zip')
array([ 0, 1, 2, ..., 9997, 9998, 9999])
array([ 0, 1, 2, ..., 9997, 9998, 9999], shape=(10000,))

Save several arrays to a directory on the file system (uses a
:class:`DirectoryStore` and stores arrays in a group)::
Expand All @@ -336,9 +338,9 @@ def save(store: StoreLike, *args, zarr_version=None, path=None, **kwargs):
>>> loader
<LazyLoader: arr_0, arr_1>
>>> loader['arr_0']
array([ 0, 1, 2, ..., 9997, 9998, 9999])
array([ 0, 1, 2, ..., 9997, 9998, 9999], shape=(10000,))
>>> loader['arr_1']
array([10000, 9999, 9998, ..., 3, 2, 1])
array([10000, 9999, 9998, ..., 3, 2, 1], shape=(10000,))

Save several arrays using named keyword arguments::

Expand All @@ -347,9 +349,9 @@ def save(store: StoreLike, *args, zarr_version=None, path=None, **kwargs):
>>> loader
<LazyLoader: bar, foo>
>>> loader['foo']
array([ 0, 1, 2, ..., 9997, 9998, 9999])
array([ 0, 1, 2, ..., 9997, 9998, 9999], shape=(10000,))
>>> loader['bar']
array([10000, 9999, 9998, ..., 3, 2, 1])
array([10000, 9999, 9998, ..., 3, 2, 1], shape=(10000,))

Store several arrays in a single zip file (uses a :class:`ZipStore`)::

Expand All @@ -358,9 +360,9 @@ def save(store: StoreLike, *args, zarr_version=None, path=None, **kwargs):
>>> loader
<LazyLoader: bar, foo>
>>> loader['foo']
array([ 0, 1, 2, ..., 9997, 9998, 9999])
array([ 0, 1, 2, ..., 9997, 9998, 9999], shape=(10000,))
>>> loader['bar']
array([10000, 9999, 9998, ..., 3, 2, 1])
array([10000, 9999, 9998, ..., 3, 2, 1], shape=(10000,))

See Also
--------
Expand Down
17 changes: 9 additions & 8 deletions zarr/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,7 @@
)

__all__ = ["Array"]
__doctest_requires__ = {("*"): ["numpy>=2.2"]}


# noinspection PyUnresolvedReferences
Expand Down Expand Up @@ -2793,33 +2794,33 @@ def view(
>>> a = zarr.array(data, chunks=1000, filters=filters)
>>> a[:]
array(['female', 'male', 'female', ..., 'male', 'male', 'female'],
dtype='<U6')
shape=(10000,), dtype='<U6')
>>> v = a.view(dtype='u1', filters=[])
>>> v.is_view
True
>>> v[:]
array([1, 2, 1, ..., 2, 2, 1], dtype=uint8)
array([1, 2, 1, ..., 2, 2, 1], shape=(10000,), dtype=uint8)

Views can be used to modify data:

>>> x = v[:]
>>> x.sort()
>>> v[:] = x
>>> v[:]
array([1, 1, 1, ..., 2, 2, 2], dtype=uint8)
array([1, 1, 1, ..., 2, 2, 2], shape=(10000,), dtype=uint8)
>>> a[:]
array(['female', 'female', 'female', ..., 'male', 'male', 'male'],
dtype='<U6')
shape=(10000,), dtype='<U6')

View as a different dtype with the same item size:

>>> data = np.random.randint(0, 2, size=10000, dtype='u1')
>>> a = zarr.array(data, chunks=1000)
>>> a[:]
array([0, 0, 1, ..., 1, 0, 0], dtype=uint8)
array([0, 0, 1, ..., 1, 0, 0], shape=(10000,), dtype=uint8)
>>> v = a.view(dtype=bool)
>>> v[:]
array([False, False, True, ..., True, False, False])
array([False, False, True, ..., True, False, False], shape=(10000,))
>>> np.all(a[:].view(dtype=bool) == v[:])
np.True_

Expand All @@ -2841,10 +2842,10 @@ def view(

>>> a = zarr.full(10000, chunks=1000, fill_value=-1, dtype='i1')
>>> a[:]
array([-1, -1, -1, ..., -1, -1, -1], dtype=int8)
array([-1, -1, -1, ..., -1, -1, -1], shape=(10000,), dtype=int8)
>>> v = a.view(fill_value=42)
>>> v[:]
array([42, 42, 42, ..., 42, 42, 42], dtype=int8)
array([42, 42, 42, ..., 42, 42, 42], shape=(10000,), dtype=int8)

Note that resizing or appending to views is not permitted:

Expand Down
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