Fix a bug when setting complete chunks (#2851)

* Fix a bug when setting complete chunks

Closes #2849

* much simpler test

* add release note

* Update strategy priorities:

1. Emphasize arrays of side > 1,
2. Emphasize indexing the last chunk for both setitem & getitem

* Use short node names

* bug fix

* Add scalar tests

* [revert]

* Add unit test

* one more test

* Add xfails

* switch to skip, XPASS is not allwoed

* Fix test

* cleaniup

---------

Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>

changes/2851.bugfix.rst

@@ -0,0 +1 @@
+Fix a bug when setting values of a smaller last chunk.

src/zarr/core/codec_pipeline.py

@@ -296,17 +296,6 @@ def _merge_chunk_array(
         is_complete_chunk: bool,
         drop_axes: tuple[int, ...],
     ) -> NDBuffer:
-        if is_complete_chunk and value.shape == chunk_spec.shape:
-            return value
-        if existing_chunk_array is None:
-            chunk_array = chunk_spec.prototype.nd_buffer.create(
-                shape=chunk_spec.shape,
-                dtype=chunk_spec.dtype,
-                order=chunk_spec.order,
-                fill_value=fill_value_or_default(chunk_spec),
-            )
-        else:
-            chunk_array = existing_chunk_array.copy()  # make a writable copy
         if chunk_selection == () or is_scalar(value.as_ndarray_like(), chunk_spec.dtype):
             chunk_value = value
         else:
@@ -320,6 +309,20 @@ def _merge_chunk_array(
                     for idx in range(chunk_spec.ndim)
                 )
                 chunk_value = chunk_value[item]
+        if is_complete_chunk and chunk_value.shape == chunk_spec.shape:
+            # TODO: For the last chunk, we could have is_complete_chunk=True
+            #       that is smaller than the chunk_spec.shape but this throws
+            #       an error in the _decode_single
+            return chunk_value
+        if existing_chunk_array is None:
+            chunk_array = chunk_spec.prototype.nd_buffer.create(
+                shape=chunk_spec.shape,
+                dtype=chunk_spec.dtype,
+                order=chunk_spec.order,
+                fill_value=fill_value_or_default(chunk_spec),
+            )
+        else:
+            chunk_array = existing_chunk_array.copy()  # make a writable copy
         chunk_array[chunk_selection] = chunk_value
         return chunk_array
 

src/zarr/storage/_fsspec.py

@@ -178,7 +178,7 @@ def from_url(
             try:
                 from fsspec.implementations.asyn_wrapper import AsyncFileSystemWrapper
 
-                fs = AsyncFileSystemWrapper(fs)
+                fs = AsyncFileSystemWrapper(fs, asynchronous=True)
             except ImportError as e:
                 raise ImportError(
                     f"The filesystem for URL '{url}' is synchronous, and the required "

src/zarr/testing/stateful.py

@@ -325,7 +325,7 @@ def __init__(self, store: Store) -> None:
     def init_store(self) -> None:
         self.store.clear()
 
-    @rule(key=zarr_keys, data=st.binary(min_size=0, max_size=MAX_BINARY_SIZE))
+    @rule(key=zarr_keys(), data=st.binary(min_size=0, max_size=MAX_BINARY_SIZE))
     def set(self, key: str, data: DataObject) -> None:
         note(f"(set) Setting {key!r} with {data}")
         assert not self.store.read_only
@@ -334,7 +334,7 @@ def set(self, key: str, data: DataObject) -> None:
         self.model[key] = data_buf
 
     @precondition(lambda self: len(self.model.keys()) > 0)
-    @rule(key=zarr_keys, data=st.data())
+    @rule(key=zarr_keys(), data=st.data())
     def get(self, key: str, data: DataObject) -> None:
         key = data.draw(
             st.sampled_from(sorted(self.model.keys()))
@@ -344,7 +344,7 @@ def get(self, key: str, data: DataObject) -> None:
         # to bytes here necessary because data_buf set to model in set()
         assert self.model[key] == store_value
 
-    @rule(key=zarr_keys, data=st.data())
+    @rule(key=zarr_keys(), data=st.data())
     def get_invalid_zarr_keys(self, key: str, data: DataObject) -> None:
         note("(get_invalid)")
         assume(key not in self.model)
@@ -408,7 +408,7 @@ def is_empty(self) -> None:
         # make sure they either both are or both aren't empty (same state)
         assert self.store.is_empty("") == (not self.model)
 
-    @rule(key=zarr_keys)
+    @rule(key=zarr_keys())
     def exists(self, key: str) -> None:
         note("(exists)")
 

src/zarr/testing/strategies.py

@@ -1,10 +1,11 @@
+import math
 import sys
 from typing import Any, Literal
 
 import hypothesis.extra.numpy as npst
 import hypothesis.strategies as st
 import numpy as np
-from hypothesis import given, settings  # noqa: F401
+from hypothesis import event, given, settings  # noqa: F401
 from hypothesis.strategies import SearchStrategy
 
 import zarr
@@ -28,6 +29,16 @@
 )
 
 
+@st.composite  # type: ignore[misc]
+def keys(draw: st.DrawFn, *, max_num_nodes: int | None = None) -> Any:
+    return draw(st.lists(node_names, min_size=1, max_size=max_num_nodes).map("/".join))
+
+
+@st.composite  # type: ignore[misc]
+def paths(draw: st.DrawFn, *, max_num_nodes: int | None = None) -> Any:
+    return draw(st.just("/") | keys(max_num_nodes=max_num_nodes))
+
+
 def v3_dtypes() -> st.SearchStrategy[np.dtype]:
     return (
         npst.boolean_dtypes()
@@ -87,17 +98,19 @@ def clear_store(x: Store) -> Store:
 node_names = st.text(zarr_key_chars, min_size=1).filter(
     lambda t: t not in (".", "..") and not t.startswith("__")
 )
+short_node_names = st.text(zarr_key_chars, max_size=3, min_size=1).filter(
+    lambda t: t not in (".", "..") and not t.startswith("__")
+)
 array_names = node_names
 attrs = st.none() | st.dictionaries(_attr_keys, _attr_values)
-keys = st.lists(node_names, min_size=1).map("/".join)
-paths = st.just("/") | keys
 # st.builds will only call a new store constructor for different keyword arguments
 # i.e. stores.examples() will always return the same object per Store class.
 # So we map a clear to reset the store.
 stores = st.builds(MemoryStore, st.just({})).map(clear_store)
 compressors = st.sampled_from([None, "default"])
 zarr_formats: st.SearchStrategy[ZarrFormat] = st.sampled_from([3, 2])
-array_shapes = npst.array_shapes(max_dims=4, min_side=0)
+# We de-prioritize arrays having dim sizes 0, 1, 2
+array_shapes = npst.array_shapes(max_dims=4, min_side=3) | npst.array_shapes(max_dims=4, min_side=0)
 
 
 @st.composite  # type: ignore[misc]
@@ -152,13 +165,15 @@ def numpy_arrays(
     draw: st.DrawFn,
     *,
     shapes: st.SearchStrategy[tuple[int, ...]] = array_shapes,
-    zarr_formats: st.SearchStrategy[ZarrFormat] = zarr_formats,
+    dtype: np.dtype[Any] | None = None,
+    zarr_formats: st.SearchStrategy[ZarrFormat] | None = zarr_formats,
 ) -> Any:
     """
     Generate numpy arrays that can be saved in the provided Zarr format.
     """
     zarr_format = draw(zarr_formats)
-    dtype = draw(v3_dtypes() if zarr_format == 3 else v2_dtypes())
+    if dtype is None:
+        dtype = draw(v3_dtypes() if zarr_format == 3 else v2_dtypes())
     if np.issubdtype(dtype, np.str_):
         safe_unicode_strings = safe_unicode_for_dtype(dtype)
         return draw(npst.arrays(dtype=dtype, shape=shapes, elements=safe_unicode_strings))
@@ -174,11 +189,19 @@ def chunk_shapes(draw: st.DrawFn, *, shape: tuple[int, ...]) -> tuple[int, ...]:
         st.tuples(*[st.integers(min_value=0 if size == 0 else 1, max_value=size) for size in shape])
     )
     # 2. and now generate the chunks tuple
-    return tuple(
+    chunks = tuple(
         size // nchunks if nchunks > 0 else 0
         for size, nchunks in zip(shape, numchunks, strict=True)
     )
 
+    for c in chunks:
+        event("chunk size", c)
+
+    if any((c != 0 and s % c != 0) for s, c in zip(shape, chunks, strict=True)):
+        event("smaller last chunk")
+
+    return chunks
+
 
 @st.composite  # type: ignore[misc]
 def shard_shapes(
@@ -211,7 +234,7 @@ def arrays(
     shapes: st.SearchStrategy[tuple[int, ...]] = array_shapes,
     compressors: st.SearchStrategy = compressors,
     stores: st.SearchStrategy[StoreLike] = stores,
-    paths: st.SearchStrategy[str | None] = paths,
+    paths: st.SearchStrategy[str | None] = paths(),  # noqa: B008
     array_names: st.SearchStrategy = array_names,
     arrays: st.SearchStrategy | None = None,
     attrs: st.SearchStrategy = attrs,
@@ -267,23 +290,56 @@ def arrays(
     return a
 
 
+@st.composite  # type: ignore[misc]
+def simple_arrays(
+    draw: st.DrawFn,
+    *,
+    shapes: st.SearchStrategy[tuple[int, ...]] = array_shapes,
+) -> Any:
+    return draw(
+        arrays(
+            shapes=shapes,
+            paths=paths(max_num_nodes=2),
+            array_names=short_node_names,
+            attrs=st.none(),
+            compressors=st.sampled_from([None, "default"]),
+        )
+    )
+
+
 def is_negative_slice(idx: Any) -> bool:
     return isinstance(idx, slice) and idx.step is not None and idx.step < 0
 
 
+@st.composite  # type: ignore[misc]
+def end_slices(draw: st.DrawFn, *, shape: tuple[int]) -> Any:
+    """
+    A strategy that slices ranges that include the last chunk.
+    This is intended to stress-test handling of a possibly smaller last chunk.
+    """
+    slicers = []
+    for size in shape:
+        start = draw(st.integers(min_value=size // 2, max_value=size - 1))
+        length = draw(st.integers(min_value=0, max_value=size - start))
+        slicers.append(slice(start, start + length))
+    event("drawing end slice")
+    return tuple(slicers)
+
+
 @st.composite  # type: ignore[misc]
 def basic_indices(draw: st.DrawFn, *, shape: tuple[int], **kwargs: Any) -> Any:
     """Basic indices without unsupported negative slices."""
-    return draw(
-        npst.basic_indices(shape=shape, **kwargs).filter(
-            lambda idxr: (
-                not (
-                    is_negative_slice(idxr)
-                    or (isinstance(idxr, tuple) and any(is_negative_slice(idx) for idx in idxr))
-                )
+    strategy = npst.basic_indices(shape=shape, **kwargs).filter(
+        lambda idxr: (
+            not (
+                is_negative_slice(idxr)
+                or (isinstance(idxr, tuple) and any(is_negative_slice(idx) for idx in idxr))
             )
         )
     )
+    if math.prod(shape) >= 3:
+        strategy = end_slices(shape=shape) | strategy
+    return draw(strategy)
 
 
 @st.composite  # type: ignore[misc]

tests/test_indexing.py

@@ -424,6 +424,18 @@ def test_orthogonal_indexing_fallback_on_getitem_2d(
     np.testing.assert_array_equal(z[index], expected_result)
 
 
+@pytest.mark.skip(reason="fails on ubuntu, windows; numpy=2.2; in CI")
+def test_setitem_repeated_index():
+    array = zarr.array(data=np.zeros((4,)), chunks=(1,))
+    indexer = np.array([-1, -1, 0, 0])
+    array.oindex[(indexer,)] = [0, 1, 2, 3]
+    np.testing.assert_array_equal(array[:], np.array([3, 0, 0, 1]))
+
+    indexer = np.array([-1, 0, 0, -1])
+    array.oindex[(indexer,)] = [0, 1, 2, 3]
+    np.testing.assert_array_equal(array[:], np.array([2, 0, 0, 3]))
+
+
 Index = list[int] | tuple[slice | int | list[int], ...]
 
 
@@ -815,6 +827,25 @@ def test_set_orthogonal_selection_1d(store: StorePath) -> None:
         _test_set_orthogonal_selection(v, a, z, selection)
 
 
+def test_set_item_1d_last_two_chunks():
+    # regression test for GH2849
+    g = zarr.open_group("foo.zarr", zarr_format=3, mode="w")
+    a = g.create_array("bar", shape=(10,), chunks=(3,), dtype=int)
+    data = np.array([7, 8, 9])
+    a[slice(7, 10)] = data
+    np.testing.assert_array_equal(a[slice(7, 10)], data)
+
+    z = zarr.open_group("foo.zarr", mode="w")
+    z.create_array("zoo", dtype=float, shape=())
+    z["zoo"][...] = np.array(1)  # why doesn't [:] work?
+    np.testing.assert_equal(z["zoo"][()], np.array(1))
+
+    z = zarr.open_group("foo.zarr", mode="w")
+    z.create_array("zoo", dtype=float, shape=())
+    z["zoo"][...] = 1  # why doesn't [:] work?
+    np.testing.assert_equal(z["zoo"][()], np.array(1))
+
+
 def _test_set_orthogonal_selection_2d(
     v: npt.NDArray[np.int_],
     a: npt.NDArray[np.int_],

tests/test_properties.py

@@ -1,3 +1,4 @@
+import numpy as np
 import pytest
 from numpy.testing import assert_array_equal
 
@@ -18,6 +19,7 @@
     basic_indices,
     numpy_arrays,
     orthogonal_indices,
+    simple_arrays,
     stores,
     zarr_formats,
 )
@@ -50,13 +52,13 @@ def test_array_creates_implicit_groups(array):
 
 @given(data=st.data())
 def test_basic_indexing(data: st.DataObject) -> None:
-    zarray = data.draw(arrays())
+    zarray = data.draw(simple_arrays())
     nparray = zarray[:]
     indexer = data.draw(basic_indices(shape=nparray.shape))
     actual = zarray[indexer]
     assert_array_equal(nparray[indexer], actual)
 
-    new_data = data.draw(npst.arrays(shape=st.just(actual.shape), dtype=nparray.dtype))
+    new_data = data.draw(numpy_arrays(shapes=st.just(actual.shape), dtype=nparray.dtype))
     zarray[indexer] = new_data
     nparray[indexer] = new_data
     assert_array_equal(nparray, zarray[:])
@@ -65,15 +67,19 @@ def test_basic_indexing(data: st.DataObject) -> None:
 @given(data=st.data())
 def test_oindex(data: st.DataObject) -> None:
     # integer_array_indices can't handle 0-size dimensions.
-    zarray = data.draw(arrays(shapes=npst.array_shapes(max_dims=4, min_side=1)))
+    zarray = data.draw(simple_arrays(shapes=npst.array_shapes(max_dims=4, min_side=1)))
     nparray = zarray[:]
 
     zindexer, npindexer = data.draw(orthogonal_indices(shape=nparray.shape))
     actual = zarray.oindex[zindexer]
     assert_array_equal(nparray[npindexer], actual)
 
     assume(zarray.shards is None)  # GH2834
-    new_data = data.draw(npst.arrays(shape=st.just(actual.shape), dtype=nparray.dtype))
+    for idxr in npindexer:
+        if isinstance(idxr, np.ndarray) and idxr.size != np.unique(idxr).size:
+            # behaviour of setitem with repeated indices is not guaranteed in practice
+            assume(False)
+    new_data = data.draw(numpy_arrays(shapes=st.just(actual.shape), dtype=nparray.dtype))
     nparray[npindexer] = new_data
     zarray.oindex[zindexer] = new_data
     assert_array_equal(nparray, zarray[:])
@@ -82,7 +88,7 @@ def test_oindex(data: st.DataObject) -> None:
 @given(data=st.data())
 def test_vindex(data: st.DataObject) -> None:
     # integer_array_indices can't handle 0-size dimensions.
-    zarray = data.draw(arrays(shapes=npst.array_shapes(max_dims=4, min_side=1)))
+    zarray = data.draw(simple_arrays(shapes=npst.array_shapes(max_dims=4, min_side=1)))
     nparray = zarray[:]
 
     indexer = data.draw(