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from_array silently discards the source array's fill_value and attributes #4287
Description
Zarr version
3.3.1.dev34+gd44f9f92
Numcodecs version
0.16.5
Python Version
3.12
Operating System
Linux
Installation
uv run with zarr installed from git main
Description
zarr.from_array documents both fill_value and attributes as defaulting to the
source array's values, but it discards both, using the dtype's default scalar and {}
instead.
Expected vs. actual
Copying an array created with fill_value=42 and attributes={"units": "K"}:
| source | from_array copy |
expected | |
|---|---|---|---|
fill_value |
42 |
0 |
42 |
attributes |
{"units": "K"} |
{} |
{"units": "K"} |
Every other keep-parameter already defaults to the source
array. These two are the exception.
Affected versions
The fill_value defect is a regression from #3198 (released in 3.1.0), which
introduced the DEFAULT_FILL_VALUE sentinel. The line is unchanged since, so
3.1.0 through main are affected.
The attributes defect is not a regression — it has been present since from_array
was added.
Steps to reproduce
# /// script
# requires-python = ">=3.12"
# dependencies = [
# "zarr@git+https://github.com/zarr-developers/zarr-python.git@main",
# ]
# ///
#
# This script automatically imports the development branch of zarr to check for issues
import zarr
src = zarr.create_array({}, shape=(4,), dtype="int32", fill_value=42, attributes={"units": "K"})
copy = zarr.from_array({}, data=src)
print(f"fill_value: {copy.fill_value} expected 42")
print(f"attrs: {dict(copy.attrs)} expected {{'units': 'K'}}")
# The fill value is not just metadata: it decides what unwritten regions read.
meta_only = zarr.from_array({}, data=src, write_data=False)
print(f"write_data=False reads: {meta_only[:]} expected [42 42 42 42]")
# An explicit None *does* keep the source's fill value -- the exact inverse.
explicit_none = zarr.from_array({}, data=src, fill_value=None)
print(f"fill_value=None: {explicit_none.fill_value} keeps 42, inverted")
assert copy.fill_value == 42, "BUG: fill_value not kept"Additional output
fill_value: 0 expected 42
attrs: {} expected {'units': 'K'}
write_data=False reads: [0 0 0 0] expected [42 42 42 42]
fill_value=None: 42 keeps 42, inverted
AssertionError: BUG: fill_value not kept
Activity
fix: keep fill value and attributes in from_array
fix: keep fill value and attributes in from_array
fix: keep fill value and attributes in from_array (zarr-developers#4288)