Invalid "selection" values in "read_zarr()" should raise an error #1172

Activity

1. Tomaz-Vieira commented on Aug 5, 2026

   

   Tomaz-Vieira

   on Aug 5, 2026

   Collaborator

   More actions

   I actually think the right fix would be to tighten the type of selection to:

   Tuple[Literal["images", "labels", "shapes", "points", "tables"], ...] | None

   so we can catch these errors statically. If we want to be extremely nice towards people not using a type checker, we could also assert that, since passing anything other than Literal["images", "labels", ...] is a violation of the preconditions of the function, and therefore a bug, not a recoverable exception.

   👍React with 👍2Reacted by Alberto Fabbri and LucaMarconato
2. 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",
   # ]
   # ///
   """Issue #1172: invalid `selection` values passed to `read_zarr()` are silently ignored."""
   import tempfile
   from pathlib import Path
   
   import numpy as np
   
   from spatialdata import SpatialData, read_zarr
   from spatialdata.models import Image2DModel
   
   path = Path(tempfile.mkdtemp()) / "s.zarr"
   SpatialData(images={"img": Image2DModel.parse(np.zeros((1, 8, 8), dtype=np.uint8))}).write(path)
   for sel in (("table",), ("imagez",), "images"):
       try:
           sd = read_zarr(path, selection=sel)
           print(f"selection={sel!r:12} -> loaded elements: {[n for _, n, _ in sd.gen_elements()]}")
       except Exception as e:  # noqa: BLE001
           print(f"selection={sel!r:12} -> {type(e).__name__}: {str(e)[:100]}")
   sd = read_zarr(path, selection=("table",))
   if not list(sd.gen_elements()):
       print("VERDICT: REPRODUCED (invalid selection values are silently ignored and an empty object is returned)")
   else:
       print("VERDICT: 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):

   selection=('table',)   -> loaded elements: []
   selection=('imagez',)  -> loaded elements: []
   selection='images'     -> loaded elements: []
   VERDICT: REPRODUCED (invalid selection values are silently ignored and an empty object is returned)
   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.
3. LucaMarconato

   added

   priority: lowLow priorityLow priority

   needs: triage

   on Sep 13, 2026