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import pytest
import fsspec
import numpy as np
import zarr
import kerchunk.combine
import kerchunk.zarr
import kerchunk.df
from kerchunk.utils import fs_as_store, refs_as_store
@pytest.mark.parametrize(
"arrays,chunks,axis",
[
(
[np.arange(10), np.arange(10, 20)],
(2,),
0,
),
(
[np.arange(12), np.arange(12, 36), np.arange(36, 42)],
(6,),
0,
),
(
# Terminal chunk does not need to be filled
[np.arange(5), np.arange(5, 10), np.arange(10, 17)],
(5,),
0,
),
(
[
np.broadcast_to(np.arange(6), (10, 6)),
np.broadcast_to(np.arange(7, 10), (10, 3)),
],
(10, 3),
1,
),
(
[
np.broadcast_to(np.arange(6), (10, 6)).T,
np.broadcast_to(np.arange(7, 10), (10, 3)).T,
],
(3, 10),
0,
),
],
)
def test_success(tmpdir, arrays, chunks, axis, m):
fns = []
refs = []
for i, x in enumerate(arrays):
fn = f"{tmpdir}/out{i}.zarr"
g = zarr.open(fn, zarr_format=2)
arr = g.create_array("x", shape=x.shape, dtype=x.dtype, chunks=chunks)
arr[:] = x
fns.append(fn)
ref = kerchunk.zarr.single_zarr(fn, inline=0)
refs.append(ref)
out = kerchunk.combine.concatenate_arrays(
refs, axis=axis, path="x", check_arrays=True
)
store = refs_as_store(out)
g = zarr.open(store, zarr_format=2)
assert (g["x"][:] == np.concatenate(arrays, axis=axis)).all()
try:
import fastparquet
except ImportError:
return
kerchunk.df.refs_to_dataframe(out, "memory://out.parq")
storage_options = dict(
fo="memory://out.parq",
remote_protocol="file",
skip_instance_cache=True,
)
g = zarr.open("reference://", zarr_format=2, storage_options=storage_options)
assert (g["x"][:] == np.concatenate(arrays, axis=axis)).all()
kerchunk.df.refs_to_dataframe(out, "memory://out.parq", record_size=1)
storage_options = dict(
fo="memory://out.parq",
remote_protocol="file",
skip_instance_cache=True,
)
g = zarr.open("reference://", zarr_format=2, storage_options=storage_options)
assert (g["x"][:] == np.concatenate(arrays, axis=axis)).all()
def test_fail_chunks(tmpdir):
fn1 = f"{tmpdir}/out1.zarr"
fn2 = f"{tmpdir}/out2.zarr"
x1 = np.arange(10)
x2 = np.arange(10, 20)
g = zarr.open(fn1, zarr_format=2)
arr = g.create_array("x", shape=x1.shape, dtype=x1.dtype, chunks=(2,))
arr[:] = x1
g = zarr.open(fn2, zarr_format=2)
arr = g.create_array("x", shape=x2.shape, dtype=x2.dtype, chunks=(3,))
arr[:] = x2
ref1 = kerchunk.zarr.single_zarr(fn1, inline=0)
ref2 = kerchunk.zarr.single_zarr(fn2, inline=0)
with pytest.raises(ValueError, match=r"Incompatible array chunks at index 1.*"):
kerchunk.combine.concatenate_arrays([ref1, ref2], path="x", check_arrays=True)
def test_fail_shape(tmpdir):
fn1 = f"{tmpdir}/out1.zarr"
fn2 = f"{tmpdir}/out2.zarr"
x1 = np.arange(12).reshape(6, 2)
x2 = np.arange(12, 24)
g = zarr.open(fn1, zarr_format=2)
arr = g.create_array("x", shape=x1.shape, dtype=x1.dtype)
arr[:] = x1
g = zarr.open(fn2, zarr_format=2)
arr = g.create_array("x", shape=x2.shape, dtype=x2.dtype)
arr[:] = x2
ref1 = kerchunk.zarr.single_zarr(fn1, inline=0)
ref2 = kerchunk.zarr.single_zarr(fn2, inline=0)
with pytest.raises(ValueError, match=r"Incompatible array shape at index 1.*"):
kerchunk.combine.concatenate_arrays([ref1, ref2], path="x", check_arrays=True)
def test_fail_irregular_chunk_boundaries(tmpdir):
fn1 = f"{tmpdir}/out1.zarr"
fn2 = f"{tmpdir}/out2.zarr"
x1 = np.arange(10)
x2 = np.arange(10, 24)
g = zarr.open(fn1, zarr_format=2)
arr = g.create_array("x", shape=x1.shape, dtype=x1.dtype, chunks=(4,))
arr[:] = x1
g = zarr.open(fn2, zarr_format=2)
arr = g.create_array("x", shape=x2.shape, dtype=x2.dtype, chunks=(4,))
arr[:] = x2
ref1 = kerchunk.zarr.single_zarr(fn1, inline=0)
ref2 = kerchunk.zarr.single_zarr(fn2, inline=0)
with pytest.raises(ValueError, match=r"Array at index 0 has irregular chunking.*"):
kerchunk.combine.concatenate_arrays([ref1, ref2], path="x", check_arrays=True)
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