fix: accept numpy integers as chunk sizes

changes/4257.bugfix.md

@@ -0,0 +1 @@
+Numpy integers are accepted as chunk sizes again. Since 3.3.0 a per-dimension chunk size that was a numpy integer (e.g. `chunks=(np.int64(2), np.int64(2))`, as produced by any computed chunk shape) raised `TypeError: 'numpy.int64' object is not iterable`, because the scalar chunk path narrowed on `int` while its caller dispatched on `numbers.Integral`. Numpy arrays are now also accepted as chunk specifications, and a chunk specification that is neither an integer nor iterable now reports the offending value instead of failing with an opaque iteration error.

src/zarr/core/chunk_grids.py

@@ -729,17 +729,26 @@ def normalize_chunks_1d(
     overhang the span. The actual data extent of each chunk is determined
     by the chunk grid at runtime, not by this function.
     """
-    if chunks == -1:
-        return np.array([span], dtype=np.int64)
-    if isinstance(chunks, int):
-        if chunks <= 0:
-            raise ValueError(f"Chunk size must be positive, got {chunks}")
+    # `numbers.Integral` rather than `int` so that numpy integer scalars (which are not
+    # `int` subclasses) take the uniform-chunk path instead of being treated as a sequence.
+    if isinstance(chunks, numbers.Integral):
+        chunk_size = int(chunks)
+        if chunk_size == -1:
+            return np.array([span], dtype=np.int64)
+        if chunk_size <= 0:
+            raise ValueError(f"Chunk size must be positive, got {chunk_size}")
         if span == 0:
-            return np.array([chunks], dtype=np.int64)
-        n = ceildiv(span, chunks)
-        return np.full(n, chunks, dtype=np.int64)
+            return np.array([chunk_size], dtype=np.int64)
+        n = ceildiv(span, chunk_size)
+        return np.full(n, chunk_size, dtype=np.int64)
     else:
-        chunk_list = list(chunks)
+        try:
+            chunk_list = list(chunks)  # type: ignore[arg-type]
+        except TypeError:
+            raise TypeError(
+                f"Chunk specification must be an integer or an iterable of integers; got "
+                f"{chunks!r} of type {type(chunks).__name__}."
+            ) from None
         if not chunk_list:
             raise ValueError("Chunk specification must not be empty")
         non_int = [

tests/test_api.py

@@ -79,7 +79,7 @@ def test_create(memory_store: Store) -> None:
         z = create(shape=(400.5, 100), store=store, overwrite=True)  # type: ignore[arg-type]
 
     # create array with float chunk shape
-    with pytest.raises(TypeError, match="'float' object is not iterable"):
+    with pytest.raises(TypeError, match="Chunk specification must be an integer or an iterable"):
         z = create(shape=(400, 100), chunks=(16, 16.5), store=store, overwrite=True)  # type: ignore[arg-type]
 
 

tests/test_chunk_grids.py

@@ -68,6 +68,15 @@ def test_guess_chunks(shape: tuple[int, ...], itemsize: int) -> None:
         (10, (0,), ((10,),)),
         ((5, 10), (0, 100), ((5,), (10,) * 10)),
         ((5, 10), (20, 0), ((5, 5, 5, 5), (10,))),
+        # numpy integers are accepted anywhere a python int is, whether as the scalar
+        # convenience form, as per-dimension entries, or as the `-1` sentinel.
+        (np.int64(10), (100,), ((10,) * 10,)),
+        ((np.int64(2), np.int64(2)), (4, 4), ((2, 2), (2, 2))),
+        ((1, 3, np.int64(16), np.int64(16)), (1, 3, 32, 32), ((1,), (3,), (16, 16), (16, 16))),
+        ((np.int32(30), np.int64(-1)), (100, 20), ((30, 30, 30, 30), (20,))),
+        (np.array([10, 10]), (100, 100), ((10,) * 10, (10,) * 10)),
+        # rectilinear chunks given as numpy arrays
+        ((np.array([60, 40]), np.array([50, 50])), (100, 100), ((60, 40), (50, 50))),
     ],
 )
 def test_normalize_chunks(
@@ -142,7 +151,22 @@ def test_chunk_layout_nested() -> None:
             id="negative-uniform",
             msg="Chunk size must be positive",
         ),
+        ExpectFail(
+            input=(np.int64(0), 100),
+            exception=ValueError,
+            id="zero-uniform-numpy",
+            msg="Chunk size must be positive",
+        ),
         ExpectFail(input=([], 100), exception=ValueError, id="empty-list", msg="must not be empty"),
+        # Scalars that are neither integers nor iterable name themselves in the error,
+        # rather than surfacing an opaque "object is not iterable" from `list(chunks)`.
+        ExpectFail(
+            input=(2.5, 100),
+            exception=TypeError,
+            id="non-iterable-scalar",
+            msg="must be an integer or an iterable of integers; got 2.5 of type float",
+            escape=True,
+        ),
         ExpectFail(
             input=([10, -1, 10], 100),
             exception=ValueError,