More informative error when subsetting results in no observations retained in Visium HD #1096

Activity

1. LucaMarconato commented on Sep 13, 2026

   

   LucaMarconato

   on Sep 13, 2026

   Member

   More actions

   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.

   I re-attempted to reproduce this issue on the current main branch (commit ccf1ea048d054b6624214bf618008a9f9ae223e0) as part of a triage pass over open issues, and confirmed it reproduces.

   Reproduction script (PEP 723 inline metadata; run with uv run repro.py, no other setup needed):

   # /// script
   # requires-python = ">=3.12"
   # dependencies = [
   #     "spatialdata @ git+https://github.com/scverse/spatialdata.git@ccf1ea048d054b6624214bf618008a9f9ae223e0",
   # ]
   # ///
   """#1096: a table filtered to zero observations fails validation with a misleading 'Regions ... do not match' error."""
   import warnings
   import numpy as np
   import pandas as pd
   from anndata import AnnData
   from spatialdata import SpatialData
   from spatialdata.models import Labels2DModel, TableModel
   
   warnings.simplefilter("ignore")
   labels = Labels2DModel.parse(np.array([[0, 1], [2, 3]], dtype=np.uint16))
   obs = pd.DataFrame({"region": pd.Categorical(["labels"] * 3), "instance_id": [1, 2, 3], "n_counts": [10, 20, 30]})
   table = TableModel.parse(AnnData(X=np.ones((3, 2)), obs=obs), region="labels", region_key="region", instance_key="instance_id")
   sdata = SpatialData(labels={"labels": labels}, tables={"table": table})
   mask = table.obs["n_counts"] >= 500  # too strict: keeps nothing
   empty = table[mask].copy()
   print("filtered table shape:", empty.shape)
   try:
       sdata.tables["filtered"] = empty
       print("assigning the empty table: OK")
       bug = False
   except Exception as e:  # noqa: BLE001
       print("assigning the empty table:", type(e).__name__, str(e)[:120])
       bug = "do not match" in str(e)
   print("VERDICT:", "REPRODUCED (misleading error for an empty table)" if bug else "NOT REPRODUCED")

   Environment: uv run --no-project --python 3.13, which resolves spatialdata from git+https://github.com/scverse/spatialdata.git@ccf1ea048d054b6624214bf618008a9f9ae223e0 (extra dependencies, if any, are pinned in the script's inline metadata above).

   Output (verbatim, only uv package-resolution/install log lines removed):

   filtered table shape: (0, 2)
   assigning the empty table: ValueError Regions in the AnnData object and `region` do not match.
   VERDICT: REPRODUCED (misleading error for an empty table)
   exit=0
   

   Agent's severity assessment: low (see the priority: * label added to this issue).

   ---

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

   added

   priority: lowLow priorityLow priority

   needs: triage

   on Sep 13, 2026