concatenate(): orphan tables crash the dict form; a generator input gives a misleading error

[LucaMarconato]

Note

This whole message is AI-generated. The issue was automatically discovered and reported by an AI agent (Claude) during an autonomous bug hunt on the spatialdata code base. It has not been verified or triaged by a human yet; the needs: triage label is set so that a maintainer can confirm it. The reproduction script below was executed by the agent in an isolated environment (see Environment) and its output is pasted verbatim.

Summary

1. A table without spatialdata_attrs (orphan table, supported elsewhere via include_orphan_tables) makes concatenate({...}) raise ValueError: No spatialdata_attrs key found in table.uns. 2. The signature accepts Iterable[SpatialData] but a generator is exhausted after the first pass, so the length check fails with KeyError: 'Images must have unique names across the SpatialData objects to concatenate...'.

Severity (agent's assessment): low

Where: src/spatialdata/_core/concatenate.py (_fix_ensure_unique_element_names calls get_table_keys(table) unconditionally; concatenate iterates sdatas several times)

Expected behaviour

Orphan tables are carried over (renamed with the suffix); generators are materialised with list(sdatas) or the type hint is Sequence.

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",
# ]
# ///
"""concatenate(): orphan tables crash the dict form; a generator input gives a misleading error."""
import warnings
import numpy as np
from anndata import AnnData
from spatialdata import SpatialData, concatenate
from spatialdata.models import Image2DModel

warnings.simplefilter("ignore")


def mk():
    return SpatialData(images={"img": Image2DModel.parse(np.zeros((1, 4, 4), dtype=np.uint8))})


bug = False
s1, s2 = mk(), mk()
s1.tables["orphan"] = AnnData(X=np.zeros((2, 1)))  # table without spatialdata_attrs (allowed elsewhere)
try:
    m = concatenate({"a": s1, "b": s2})
    print("dict form with an orphan table: OK ->", list(m.tables))
except Exception as e:  # noqa: BLE001
    print("dict form with an orphan table:", type(e).__name__, str(e)[:100])
    bug = True
try:
    concatenate(s for s in [mk(), mk()])
    print("generator input: OK")
except Exception as e:  # noqa: BLE001
    print("generator input:", type(e).__name__, str(e)[:100])
    bug = True
print("VERDICT:", "BUG REPRODUCED" if bug else "NOT REPRODUCED")

Observed output

dict form with an orphan table: ValueError No spatialdata_attrs key found in table.uns, therefore, no table keys found. Please parse the table.
generator input: KeyError 'Images must have unique names across the SpatialData objects to concatenate. Please pass a `dict[st
VERDICT: BUG REPRODUCED

Possible fix direction (unverified)

See above.

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.

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