unpad_raster() (public API) raises 'Please report this bug' on any all-zero raster #1239

Summary

unpad_raster(Image2DModel.parse(np.zeros((1, 5, 5)))) → ValueError: Expected maximum coordinate for axis y to be4,but got 4.5. Please report this bug. (note also the message formatting).

Severity (agent's assessment): low/medium — an all-zero raster (empty mask, blank tile) is a legitimate input

Where: src/spatialdata/_utils.py::unpad_raster._compute_paddings (coordinate checks against 0 and shape-1 while compute_coordinates uses pixel centres 0.5, 1.5, ...; also if not min_coordinate != 0 is inverted)

Expected behaviour

The raster is returned unchanged (nothing to unpad).

Reproduction

Save as repro.py and run uv run repro.py (the PEP 723 header pins spatialdata to the commit the bug was found on; replace the URL fragment with @main to test the current main branch).

# /// script
# requires-python = ">=3.12"
# dependencies = [
#     "spatialdata @ git+https://github.com/scverse/spatialdata.git@ccf1ea048d054b6624214bf618008a9f9ae223e0",
# ]
# ///
"""unpad_raster() raises 'Please report this bug' on any all-zero raster."""
import warnings
import numpy as np
from spatialdata import unpad_raster
from spatialdata.models import Image2DModel, Labels2DModel

warnings.simplefilter("ignore")
bug = False
for name, el in [("all-zero image", Image2DModel.parse(np.zeros((1, 5, 5)))), ("all-zero labels", Labels2DModel.parse(np.zeros((5, 5), dtype=np.uint8))), ("non-zero image (control)", Image2DModel.parse(np.ones((1, 5, 5))))]:
    try:
        out = unpad_raster(el)
        print(f"{name:25s}: OK, shape {out.shape}")
    except Exception as e:  # noqa: BLE001
        print(f"{name:25s}: {type(e).__name__}: {e}")
        bug = True
print("VERDICT:", "BUG REPRODUCED" if bug else "NOT REPRODUCED")

Observed output

all-zero image           : ValueError: Expected maximum coordinate for axis y to be4,but got 4.5. Please report this bug.
all-zero labels          : ValueError: Expected maximum coordinate for axis y to be4,but got 4.5. Please report this bug.
non-zero image (control) : OK, shape (1, 5, 5)
VERDICT: BUG REPRODUCED

Possible fix direction (unverified)

Remove the two coordinate assertions (or compare against 0.5 / shape − 0.5) and fix the message.

Environment

uv run repro.py with the PEP 723 metadata in the script (fresh, isolated environment; spatialdata built from main @ ccf1ea0 (2026-08-28); Python 3.13, latest releases of the dependencies at run time: pandas 3.0, anndata 0.13, zarr 3.3, dask 2026.8, numpy 2.5, geopandas 1.1, shapely 2.1). macOS (arm64). Also reproduced in a second environment with pandas 2.3.3 / anndata 0.12.11 / numpy 2.4.4 / zarr 3.2.1.

Automatically generated; discovered by an AI agent (Claude) and not yet reviewed by a human.