From 6965fe26aa012a761cbb2ca928d7acb0ee98d155 Mon Sep 17 00:00:00 2001
From: uermel <uermel@czii.org>
Date: Tue, 18 Aug 2026 10:25:36 -0700
Subject: [PATCH] feat!: adopt metadata-driven Zarr 3 thumbnails

Use the published copick 2.0 alpha runtime, resolve coarsest tomogram levels from OME metadata, and preserve precise errors through existing public callback shapes.

BREAKING CHANGE: copick-shared-ui now requires Python 3.11, copick 2.0 alpha, NumPy 2, and Zarr 3.
---
 .github/workflows/tests.yml              |   11 +
 pyproject.toml                           |   13 +-
 src/copick_shared_ui/storage.py          |   52 +
 src/copick_shared_ui/workers/base.py     |   79 +-
 src/copick_shared_ui/workers/chimerax.py |    4 +-
 tests/helpers.py                         |   47 +-
 tests/inspect_wheel_metadata.py          |   30 +
 tests/test_core_direct_reader_fixture.py |   42 +
 tests/test_package_metadata.py           |   20 +
 tests/test_storage.py                    |  164 +++
 tests/test_thumbnail_baseline.py         |    3 -
 tests/test_thumbnail_errors.py           |   63 ++
 tests/test_worker_callbacks.py           |   34 +
 uv.lock                                  | 1249 ++++------------------
 14 files changed, 725 insertions(+), 1086 deletions(-)
 create mode 100644 src/copick_shared_ui/storage.py
 create mode 100644 tests/inspect_wheel_metadata.py
 create mode 100644 tests/test_core_direct_reader_fixture.py
 create mode 100644 tests/test_package_metadata.py
 create mode 100644 tests/test_storage.py
 create mode 100644 tests/test_thumbnail_errors.py
 create mode 100644 tests/test_worker_callbacks.py

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 46293e8..139229a 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -48,6 +48,14 @@ jobs:
           assert sys.version_info[:2] == expected, sys.version;
           assert sys.version_info.releaselevel == 'final', sys.version"
 
+      - name: Verify Zarr selection
+        run: >
+          uv run --no-sync python -c
+          "import sys, zarr;
+          expected = '3.1.6' if sys.version_info[:2] == (3, 11) else None;
+          assert expected is None or zarr.__version__ == expected, zarr.__version__;
+          print(zarr.__version__)"
+
       - name: Run tests
         run: uv run --no-sync pytest -q --cov=copick_shared_ui --cov-branch --cov-report=term-missing
 
@@ -56,3 +64,6 @@ jobs:
 
       - name: Build artifacts
         run: uv build
+
+      - name: Inspect wheel metadata
+        run: uv run --no-sync python tests/inspect_wheel_metadata.py dist/*.whl
diff --git a/pyproject.toml b/pyproject.toml
index db8edf6..d547a10 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "copick-shared-ui"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = [
     "Development Status :: 2 - Pre-Alpha",
     "Intended Audience :: Developers",
@@ -13,21 +13,20 @@ classifiers = [
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Programming Language :: Python :: Implementation :: CPython",
-    "Programming Language :: Python :: Implementation :: PyPy",
     "Topic :: Scientific/Engineering :: Image Processing",
 ]
 dynamic = ["version"]
 dependencies = [
     "qtpy",
     "pydantic>=2",
-    "copick[all]>=1.25.3",
-    "zarr<3",
-    "numpy>=1.21.0",
+    "copick>=2.0.0a1,<3",
+    "zarr>=3.1.6,<4",
+    "numpy>=2.0.2",
     "superqt"
 ]
 authors = [
@@ -69,7 +68,7 @@ testing = [
 addopts = "--strict-config --strict-markers"
 testpaths = ["tests"]
 markers = [
-    "migration_expected_failure: behavior intentionally fixed by the next migration stack layer",
+    "integration: validation requiring a separately published artifact or live service",
 ]
 
 [tool.hatch.version]
diff --git a/src/copick_shared_ui/storage.py b/src/copick_shared_ui/storage.py
new file mode 100644
index 0000000..3f8f38e
--- /dev/null
+++ b/src/copick_shared_ui/storage.py
@@ -0,0 +1,52 @@
+"""Read-only storage helpers used by shared UI components."""
+
+from typing import TYPE_CHECKING, Any
+
+import zarr
+from copick.util.ome import get_level_path, get_multiscales
+
+if TYPE_CHECKING:
+    from copick.models import CopickTomogram
+
+
+def open_coarsest_tomogram_array(tomogram: "CopickTomogram") -> Any:
+    """Open the final metadata-defined tomogram pyramid level without loading it.
+
+    The ordered OME multiscale metadata is the sole authority for pyramid
+    selection. Array labels and root iteration order are deliberately ignored.
+    """
+    group = zarr.open_group(store=tomogram.zarr(), mode="r")
+    try:
+        multiscales = get_multiscales(group)
+    except KeyError as error:
+        raise ValueError("OME-Zarr multiscales metadata not found") from error
+    if not isinstance(multiscales, list) or not multiscales:
+        raise ValueError("OME-Zarr multiscales metadata is empty")
+
+    first_multiscale = multiscales[0]
+    if not isinstance(first_multiscale, dict):
+        raise ValueError("OME-Zarr first multiscale entry is malformed")
+
+    datasets = first_multiscale.get("datasets")
+    if not isinstance(datasets, list) or not datasets:
+        raise ValueError("OME-Zarr first multiscale has no datasets")
+
+    level = len(datasets) - 1
+    try:
+        dataset_path = get_level_path(group, level)
+    except (KeyError, IndexError, TypeError) as error:
+        raise ValueError("OME-Zarr coarsest dataset path is missing") from error
+    if not isinstance(dataset_path, str) or not dataset_path:
+        raise ValueError("OME-Zarr coarsest dataset path is missing")
+
+    try:
+        array = group[dataset_path]
+    except KeyError as error:
+        raise ValueError(f"OME-Zarr dataset path {dataset_path!r} does not exist") from error
+
+    if not isinstance(array, zarr.Array):
+        raise TypeError(f"OME-Zarr dataset path {dataset_path!r} is not an array")
+    if array.ndim != 3:
+        raise ValueError(f"Tomogram dataset {dataset_path!r} must be three-dimensional, got {array.ndim} dimensions")
+
+    return array
diff --git a/src/copick_shared_ui/workers/base.py b/src/copick_shared_ui/workers/base.py
index 17ed22b..2d0b2a0 100644
--- a/src/copick_shared_ui/workers/base.py
+++ b/src/copick_shared_ui/workers/base.py
@@ -213,9 +213,10 @@ def generate_thumbnail_pixmap(self) -> tuple[Optional[Any], Optional[str]]:
                 return cached_pixmap, None
 
         # Generate thumbnail array
-        thumbnail_array = self._generate_thumbnail_array(tomogram)
-        if thumbnail_array is None:
-            return None, "Failed to generate thumbnail array"
+        try:
+            thumbnail_array = self._generate_thumbnail_array(tomogram)
+        except Exception as error:
+            return None, str(error)
 
         # Convert to pixmap
         pixmap = self._array_to_pixmap(thumbnail_array)
@@ -241,62 +242,36 @@ def _array_to_pixmap(self, array: Any) -> Optional[Any]:
         """Convert numpy array to platform-specific pixmap."""
         pass
 
-    def _generate_thumbnail_array(self, tomogram: "CopickTomogram") -> Optional[Any]:
+    def _generate_thumbnail_array(self, tomogram: "CopickTomogram") -> Any:
         """Generate thumbnail array from tomogram data."""
-        try:
-            import numpy as np
-            import zarr
-
-            # Load tomogram data - handle multi-scale zarr properly
-            zarr_group = zarr.open(tomogram.zarr(), mode="r")
-
-            # Get the data array - handle multi-scale structure
-            if hasattr(zarr_group, "keys") and callable(zarr_group.keys):
-                # Multi-scale zarr group - get the HIGHEST binning level for faster thumbnails
-                scale_levels = sorted([k for k in zarr_group.keys() if k.isdigit()], key=int)  # noqa: SIM118
-                if scale_levels:
-                    # Use the highest scale level (most binned/smallest) for thumbnails
-                    highest_scale = scale_levels[-1]  # Last element is highest number = most binned
-                    tomo_data = zarr_group[highest_scale]
-                else:
-                    # Fallback to first key
-                    first_key = list(zarr_group.keys())[0]
-                    tomo_data = zarr_group[first_key]
-            else:
-                # Direct zarr array
-                tomo_data = zarr_group
-
-            # Calculate downsampling factor based on data size
-            target_size = 200
-            z_size, y_size, x_size = tomo_data.shape
+        import numpy as np
 
-            # Use middle slice for 2D thumbnail
-            mid_z = z_size // 2
+        from copick_shared_ui.storage import open_coarsest_tomogram_array
 
-            # Calculate downsampling for x and y dimensions
-            downsample_x = max(1, x_size // target_size)
-            downsample_y = max(1, y_size // target_size)
+        tomo_data = open_coarsest_tomogram_array(tomogram)
 
-            # Extract and downsample middle slice
-            slice_data = tomo_data[mid_z, ::downsample_y, ::downsample_x]
+        # Calculate downsampling factor based on data size
+        target_size = 200
+        z_size, y_size, x_size = tomo_data.shape
 
-            # Convert to numpy array
-            slice_array = np.array(slice_data)
+        # Use middle slice for 2D thumbnail
+        mid_z = z_size // 2
 
-            # Normalize to 0-255 range
-            slice_array = slice_array.astype(np.float32)
-            data_min, data_max = slice_array.min(), slice_array.max()
+        # Calculate downsampling for x and y dimensions
+        downsample_x = max(1, x_size // target_size)
+        downsample_y = max(1, y_size // target_size)
 
-            if data_max > data_min:
-                slice_array = ((slice_array - data_min) / (data_max - data_min) * 255).astype(np.uint8)
-            else:
-                slice_array = np.zeros_like(slice_array, dtype=np.uint8)
+        # Extract and downsample middle slice before materializing it.
+        slice_data = tomo_data[mid_z, ::downsample_y, ::downsample_x]
+        slice_array = np.array(slice_data)
 
-            return slice_array
+        # Normalize to 0-255 range
+        slice_array = slice_array.astype(np.float32)
+        data_min, data_max = slice_array.min(), slice_array.max()
 
-        except Exception as e:
-            print(f"Error generating thumbnail array: {e}")
-            import traceback
+        if data_max > data_min:
+            slice_array = ((slice_array - data_min) / (data_max - data_min) * 255).astype(np.uint8)
+        else:
+            slice_array = np.zeros_like(slice_array, dtype=np.uint8)
 
-            traceback.print_exc()
-            return None
+        return slice_array
diff --git a/src/copick_shared_ui/workers/chimerax.py b/src/copick_shared_ui/workers/chimerax.py
index d2b8576..f46f5d7 100644
--- a/src/copick_shared_ui/workers/chimerax.py
+++ b/src/copick_shared_ui/workers/chimerax.py
@@ -5,6 +5,7 @@
 from copick_shared_ui.workers.unified_workers import (
     QT_AVAILABLE,
     UnifiedDataWorker,
+    UnifiedThumbnailWorker,
     UnifiedWorkerManager,
     create_worker_manager,
     get_platform_info,
@@ -16,9 +17,8 @@
     from copick.models import CopickRun, CopickTomogram
 
 if is_threading_available():
-    from copick_shared_ui.workers.base import AbstractThumbnailWorker
 
-    class ChimeraXThumbnailWorker(AbstractThumbnailWorker):
+    class ChimeraXThumbnailWorker(UnifiedThumbnailWorker):
         """ChimeraX-specific thumbnail worker with enhanced UI responsiveness optimizations."""
 
         def __init__(
diff --git a/tests/helpers.py b/tests/helpers.py
index 2138852..d11b36b 100644
--- a/tests/helpers.py
+++ b/tests/helpers.py
@@ -56,14 +56,30 @@ def gradient_volume(offset: int = 0) -> np.ndarray:
     return np.arange(offset, offset + 3 * 6 * 8, dtype=np.float32).reshape(3, 6, 8)
 
 
-def write_ome_zarr_04(path: Path, datasets: dict[str, np.ndarray], declared_paths: list[str]) -> DummyTomogram:
-    """Build an OME-Zarr 0.4 / Zarr v2 fixture without using production helpers."""
-    group = zarr.open_group(str(path), mode="w")
+def write_ome_zarr(
+    path: Path,
+    datasets: dict[str, np.ndarray],
+    declared_paths: list[str],
+    *,
+    ome_version: str,
+    zarr_format: int,
+    chunks: tuple[int, ...] | None = None,
+    shards: tuple[int, ...] | None = None,
+    chunk_key_encoding: dict[str, Any] | None = None,
+) -> DummyTomogram:
+    """Build a format-specific OME-Zarr fixture without production helpers."""
+    group = zarr.open_group(store=str(path), mode="w", zarr_format=zarr_format)
     for name, values in datasets.items():
-        group.create_dataset(name, data=values, chunks=(1, 3, 4))
-    group.attrs["multiscales"] = [
+        options = {"chunks": chunks or tuple(max(1, size // 2) for size in values.shape)}
+        if shards is not None:
+            options["shards"] = shards
+        if chunk_key_encoding is not None:
+            options["chunk_key_encoding"] = chunk_key_encoding
+        group.create_array(name, data=values, **options)
+
+    multiscales = [
         {
-            "version": "0.4",
+            "version": ome_version,
             "axes": [
                 {"name": "z", "type": "space"},
                 {"name": "y", "type": "space"},
@@ -72,4 +88,23 @@ def write_ome_zarr_04(path: Path, datasets: dict[str, np.ndarray], declared_path
             "datasets": [{"path": dataset_path} for dataset_path in declared_paths],
         },
     ]
+    if ome_version == "0.4":
+        group.attrs["multiscales"] = multiscales
+    elif ome_version == "0.5":
+        group.attrs["ome"] = {"version": "0.5", "multiscales": multiscales}
+    else:
+        raise ValueError(f"Unsupported fixture OME-Zarr version: {ome_version}")
+
     return DummyTomogram(str(path))
+
+
+def write_ome_zarr_04(path: Path, datasets: dict[str, np.ndarray], declared_paths: list[str]) -> DummyTomogram:
+    """Build an OME-Zarr 0.4 / Zarr v2 fixture."""
+    return write_ome_zarr(
+        path,
+        datasets,
+        declared_paths,
+        ome_version="0.4",
+        zarr_format=2,
+        chunks=(1, 3, 4),
+    )
diff --git a/tests/inspect_wheel_metadata.py b/tests/inspect_wheel_metadata.py
new file mode 100644
index 0000000..96ebad3
--- /dev/null
+++ b/tests/inspect_wheel_metadata.py
@@ -0,0 +1,30 @@
+"""Inspect built wheel metadata for the shared-UI alpha runtime contract."""
+
+import argparse
+import email
+import zipfile
+from pathlib import Path
+
+
+def inspect_wheel(path: Path) -> None:
+    with zipfile.ZipFile(path) as archive:
+        metadata_name = next(name for name in archive.namelist() if name.endswith(".dist-info/METADATA"))
+        metadata = email.message_from_bytes(archive.read(metadata_name))
+
+    requirements = metadata.get_all("Requires-Dist", [])
+    assert metadata["Requires-Python"] == ">=3.11"
+    assert any(requirement.startswith("copick<3,>=2.0.0a1") for requirement in requirements), requirements
+    assert any(requirement.startswith("numpy>=2.0.2") for requirement in requirements), requirements
+    assert any(requirement.startswith("zarr<4,>=3.1.6") for requirement in requirements), requirements
+    assert all("copick[all]" not in requirement for requirement in requirements), requirements
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("wheel", type=Path)
+    arguments = parser.parse_args()
+    inspect_wheel(arguments.wheel)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/tests/test_core_direct_reader_fixture.py b/tests/test_core_direct_reader_fixture.py
new file mode 100644
index 0000000..afd9f25
--- /dev/null
+++ b/tests/test_core_direct_reader_fixture.py
@@ -0,0 +1,42 @@
+"""Validation against the exact artifact published by the copick core alpha."""
+
+import hashlib
+import json
+import os
+import zipfile
+from pathlib import Path
+
+import pytest
+
+from copick_shared_ui.storage import open_coarsest_tomogram_array
+from tests.helpers import ArrayThumbnailWorker, DummyTomogram
+
+CORE_ALPHA_REVISION = "5b3aff2ae4bf9bcf85b4a1d4132205640171f85b"
+CORE_FIXTURE_SHA256 = "c6f8e58c9d89c4d4d76208c08563ad34ed9838952666c49f43b5c0c68652f51b"
+
+
+@pytest.mark.integration
+def test_published_core_alpha_direct_reader_fixture(tmp_path):
+    configured_path = os.environ.get("COPICK_DIRECT_READER_FIXTURE")
+    if configured_path is None:
+        pytest.skip("COPICK_DIRECT_READER_FIXTURE does not name the published core artifact")
+
+    archive_path = Path(configured_path)
+    assert hashlib.sha256(archive_path.read_bytes()).hexdigest() == CORE_FIXTURE_SHA256
+    with zipfile.ZipFile(archive_path) as archive:
+        archive.extractall(tmp_path)
+
+    fixture_root = tmp_path / "copick-v3-direct-reader-fixture"
+    manifest = json.loads((fixture_root / "manifest.json").read_text(encoding="utf-8"))
+    assert manifest["producer"]["source_revision"] == CORE_ALPHA_REVISION
+
+    for case in ("boolean", "floating", "integer"):
+        store_path = fixture_root / manifest["stores"][case]["path"]
+        tomogram = DummyTomogram(str(store_path))
+
+        array = open_coarsest_tomogram_array(tomogram)
+        thumbnail = ArrayThumbnailWorker(tomogram)._generate_thumbnail_array(tomogram)
+
+        assert array.path == manifest["stores"][case]["multiscale"]["datasets"][-1]["path"]
+        assert thumbnail.ndim == 2
+        assert thumbnail.size > 0
diff --git a/tests/test_package_metadata.py b/tests/test_package_metadata.py
new file mode 100644
index 0000000..f1e73db
--- /dev/null
+++ b/tests/test_package_metadata.py
@@ -0,0 +1,20 @@
+"""Runtime metadata gates for the shared-UI 2.0 alpha line."""
+
+import tomllib
+from pathlib import Path
+
+PROJECT_ROOT = Path(__file__).parents[1]
+
+
+def test_alpha_runtime_contract_is_explicit():
+    project = tomllib.loads((PROJECT_ROOT / "pyproject.toml").read_text(encoding="utf-8"))["project"]
+
+    assert project["requires-python"] == ">=3.11"
+    assert set(project["dependencies"]) >= {
+        "copick>=2.0.0a1,<3",
+        "numpy>=2.0.2",
+        "zarr>=3.1.6,<4",
+    }
+    assert all("copick[all]" not in requirement for requirement in project["dependencies"])
+    assert "Programming Language :: Python :: 3.10" not in project["classifiers"]
+    assert "Programming Language :: Python :: 3.14" in project["classifiers"]
diff --git a/tests/test_storage.py b/tests/test_storage.py
new file mode 100644
index 0000000..6b6fd47
--- /dev/null
+++ b/tests/test_storage.py
@@ -0,0 +1,164 @@
+"""Tests for metadata-defined, layout-agnostic tomogram reads."""
+
+import hashlib
+from pathlib import Path
+
+import numpy as np
+import pytest
+import zarr
+
+from copick_shared_ui.storage import open_coarsest_tomogram_array
+from tests.helpers import DummyTomogram, gradient_volume, write_ome_zarr
+
+
+def _snapshot(path: Path) -> dict[str, str]:
+    return {
+        str(item.relative_to(path)): hashlib.sha256(item.read_bytes()).hexdigest()
+        for item in sorted(path.rglob("*"))
+        if item.is_file()
+    }
+
+
+@pytest.mark.parametrize(
+    ("ome_version", "zarr_format", "paths"),
+    [
+        ("0.4", 2, ["0", "1"]),
+        ("0.4", 2, ["s0", "s1"]),
+        ("0.5", 3, ["0", "1"]),
+        ("0.5", 3, ["fine", "coarse"]),
+    ],
+)
+def test_coarsest_array_follows_ordered_metadata(tmp_path, ome_version, zarr_format, paths):
+    fine = gradient_volume(1000)
+    coarse = gradient_volume()
+    store_path = tmp_path / f"ome-{ome_version}-zarr-{zarr_format}.zarr"
+    tomogram = write_ome_zarr(
+        store_path,
+        {paths[0]: fine, paths[1]: coarse},
+        paths,
+        ome_version=ome_version,
+        zarr_format=zarr_format,
+        chunks=(1, 3, 4),
+    )
+    before = _snapshot(store_path)
+
+    array = open_coarsest_tomogram_array(tomogram)
+
+    assert array.path == paths[-1]
+    np.testing.assert_array_equal(array[:], coarse)
+    assert _snapshot(store_path) == before
+
+
+@pytest.mark.parametrize(
+    ("chunks", "shards", "chunk_key_encoding"),
+    [
+        ((1, 3, 4), None, None),
+        ((1, 3, 4), (3, 6, 8), {"name": "v2", "configuration": {"separator": "."}}),
+        ((1, 3, 4), (2, 3, 4), None),
+        ((1, 2, 2), None, {"name": "v2", "configuration": {"separator": "."}}),
+    ],
+)
+def test_reader_ignores_valid_zarr_v3_layout_choices(tmp_path, chunks, shards, chunk_key_encoding):
+    values = gradient_volume()
+    tomogram = write_ome_zarr(
+        tmp_path / "layout.zarr",
+        {"arbitrary-level": values},
+        ["arbitrary-level"],
+        ome_version="0.5",
+        zarr_format=3,
+        chunks=chunks,
+        shards=shards,
+        chunk_key_encoding=chunk_key_encoding,
+    )
+
+    array = open_coarsest_tomogram_array(tomogram)
+
+    np.testing.assert_array_equal(array[1, ::2, ::3], values[1, ::2, ::3])
+
+
+@pytest.mark.parametrize(
+    ("metadata", "message"),
+    [
+        ({"ome": {"version": "0.5", "multiscales": []}}, "multiscales metadata is empty"),
+        (
+            {"ome": {"version": "0.5", "multiscales": [{}]}},
+            "first multiscale has no datasets",
+        ),
+        (
+            {"ome": {"version": "0.5", "multiscales": [{"datasets": []}]}},
+            "first multiscale has no datasets",
+        ),
+        (
+            {"ome": {"version": "0.5", "multiscales": [{"datasets": [{}]}]}},
+            "coarsest dataset path is missing",
+        ),
+    ],
+)
+def test_empty_or_malformed_metadata_fails_clearly(tmp_path, metadata, message):
+    store_path = tmp_path / "invalid.zarr"
+    group = zarr.open_group(store=str(store_path), mode="w", zarr_format=3)
+    group.attrs.update(metadata)
+    before = _snapshot(store_path)
+
+    with pytest.raises(ValueError, match=message):
+        open_coarsest_tomogram_array(DummyTomogram(str(store_path)))
+
+    assert _snapshot(store_path) == before
+
+
+def test_missing_metadata_fails_without_mutating_store(tmp_path):
+    store_path = tmp_path / "missing-metadata.zarr"
+    zarr.open_group(store=str(store_path), mode="w", zarr_format=3)
+    before = _snapshot(store_path)
+
+    with pytest.raises(ValueError, match="multiscales metadata not found"):
+        open_coarsest_tomogram_array(DummyTomogram(str(store_path)))
+
+    assert _snapshot(store_path) == before
+
+
+def test_missing_declared_path_fails_clearly(tmp_path):
+    tomogram = write_ome_zarr(
+        tmp_path / "missing-path.zarr",
+        {"fine": gradient_volume()},
+        ["fine", "absent"],
+        ome_version="0.5",
+        zarr_format=3,
+    )
+
+    with pytest.raises(ValueError, match="dataset path 'absent' does not exist"):
+        open_coarsest_tomogram_array(tomogram)
+
+
+def test_non_three_dimensional_dataset_is_rejected(tmp_path):
+    tomogram = write_ome_zarr(
+        tmp_path / "two-dimensional.zarr",
+        {"preview": np.ones((6, 8), dtype=np.float32)},
+        ["preview"],
+        ome_version="0.5",
+        zarr_format=3,
+    )
+
+    with pytest.raises(ValueError, match="must be three-dimensional"):
+        open_coarsest_tomogram_array(tomogram)
+
+
+def test_empty_store_open_is_read_only(tmp_path):
+    store_path = tmp_path / "empty.zarr"
+    store_path.mkdir()
+
+    with pytest.raises(zarr.errors.GroupNotFoundError, match="No group found"):
+        open_coarsest_tomogram_array(DummyTomogram(str(store_path)))
+
+    assert list(store_path.iterdir()) == []
+
+
+def test_root_array_is_not_accepted_as_a_tomogram_group(tmp_path):
+    store_path = tmp_path / "root-array.zarr"
+    zarr.open_array(store=str(store_path), mode="w", shape=(3, 6, 8), dtype="f4", zarr_format=3)
+    before = _snapshot(store_path)
+
+    with pytest.raises(zarr.errors.ContainsArrayError, match="array already exists"):
+        open_coarsest_tomogram_array(DummyTomogram(str(store_path)))
+
+    assert _snapshot(store_path) == before
diff --git a/tests/test_thumbnail_baseline.py b/tests/test_thumbnail_baseline.py
index d64a942..cdd3862 100644
--- a/tests/test_thumbnail_baseline.py
+++ b/tests/test_thumbnail_baseline.py
@@ -1,7 +1,6 @@
 """Executable baseline for the storage-sensitive thumbnail behavior."""
 
 import numpy as np
-import pytest
 
 from tests.helpers import ArrayThumbnailWorker, gradient_volume, write_ome_zarr_04
 
@@ -30,8 +29,6 @@ def test_constant_middle_slice_normalizes_to_zero(tmp_path):
     np.testing.assert_array_equal(result, np.zeros((6, 8), dtype=np.uint8))
 
 
-@pytest.mark.migration_expected_failure
-@pytest.mark.xfail(strict=True, reason="phase 1 replaces numeric-key discovery with OME metadata")
 def test_metadata_path_wins_over_numeric_distractor(tmp_path):
     distractor = np.zeros((3, 6, 8), dtype=np.float32)
     declared = gradient_volume()
diff --git a/tests/test_thumbnail_errors.py b/tests/test_thumbnail_errors.py
new file mode 100644
index 0000000..d33b24b
--- /dev/null
+++ b/tests/test_thumbnail_errors.py
@@ -0,0 +1,63 @@
+"""Tests for thumbnail materialization and public error contracts."""
+
+import numpy as np
+import zarr
+
+from copick_shared_ui.workers.base import AbstractThumbnailWorker
+from tests.helpers import ArrayThumbnailWorker, DummyTomogram
+
+
+def test_public_synchronous_contract_returns_precise_storage_error(tmp_path):
+    store_path = tmp_path / "missing-metadata.zarr"
+    zarr.open_group(store=str(store_path), mode="w", zarr_format=3)
+    worker = ArrayThumbnailWorker(DummyTomogram(str(store_path)))
+
+    pixmap, error = worker.generate_thumbnail_pixmap()
+
+    assert pixmap is None
+    assert error == "OME-Zarr multiscales metadata not found"
+
+
+def test_thumbnail_materializes_only_the_strided_middle_slice(monkeypatch):
+    requests = []
+
+    class LazyArray:
+        shape = (5, 600, 400)
+
+        def __getitem__(self, selection):
+            requests.append(selection)
+            return np.arange(200 * 200, dtype=np.float32).reshape(200, 200)
+
+    monkeypatch.setattr("copick_shared_ui.storage.open_coarsest_tomogram_array", lambda _tomogram: LazyArray())
+    worker = ArrayThumbnailWorker(DummyTomogram("unused"))
+
+    result = worker._generate_thumbnail_array(worker.item)
+
+    assert requests == [(2, slice(None, None, 3), slice(None, None, 2))]
+    assert result.shape == (200, 200)
+    assert result.dtype == np.uint8
+
+
+def test_private_thumbnail_layer_does_not_swallow_storage_errors(monkeypatch):
+    def fail(_tomogram):
+        raise PermissionError("backend denied thumbnail read")
+
+    monkeypatch.setattr("copick_shared_ui.storage.open_coarsest_tomogram_array", fail)
+    worker = ArrayThumbnailWorker(DummyTomogram("unused"))
+
+    try:
+        worker._generate_thumbnail_array(worker.item)
+    except PermissionError as error:
+        assert str(error) == "backend denied thumbnail read"
+    else:
+        raise AssertionError("private thumbnail layer swallowed a storage error")
+
+
+def test_public_thumbnail_layer_preserves_return_shape(monkeypatch):
+    def fail(self, _tomogram):
+        raise PermissionError("backend denied thumbnail read")
+
+    monkeypatch.setattr(AbstractThumbnailWorker, "_generate_thumbnail_array", fail)
+    worker = ArrayThumbnailWorker(DummyTomogram("unused"))
+
+    assert worker.generate_thumbnail_pixmap() == (None, "backend denied thumbnail read")
diff --git a/tests/test_worker_callbacks.py b/tests/test_worker_callbacks.py
new file mode 100644
index 0000000..f434369
--- /dev/null
+++ b/tests/test_worker_callbacks.py
@@ -0,0 +1,34 @@
+"""Callback-shape tests for both supported thumbnail workers."""
+
+import pytest
+
+from copick_shared_ui.workers.chimerax import ChimeraXThumbnailWorker
+from copick_shared_ui.workers.unified_workers import UnifiedThumbnailWorker, is_threading_available
+from tests.helpers import DummyTomogram
+
+pytestmark = pytest.mark.skipif(not is_threading_available(), reason="Qt threading is unavailable")
+
+
+@pytest.mark.parametrize("worker_class", [UnifiedThumbnailWorker, ChimeraXThumbnailWorker])
+def test_worker_callback_retains_thumbnail_id_and_precise_error(qtbot, worker_class, monkeypatch):
+    callbacks = []
+    worker = worker_class(DummyTomogram("unused"), "thumb-17", lambda *result: callbacks.append(result), True)
+    worker._cache = None
+    monkeypatch.setattr(worker, "generate_thumbnail_pixmap", lambda: (None, "storage unavailable"))
+
+    worker.start()
+    qtbot.waitUntil(lambda: bool(callbacks), timeout=5000)
+
+    assert callbacks == [("thumb-17", None, "storage unavailable")]
+
+
+@pytest.mark.parametrize("worker_class", [UnifiedThumbnailWorker, ChimeraXThumbnailWorker])
+def test_cancelled_worker_does_not_emit_terminal_callback(worker_class):
+    callbacks = []
+    worker = worker_class(DummyTomogram("unused"), "thumb-17", lambda *result: callbacks.append(result), True)
+    worker._cache = None
+    worker._cancelled = True
+
+    worker._on_worker_finished((None, "Cancelled"))
+
+    assert callbacks == []
diff --git a/uv.lock b/uv.lock
index 6982834..5be990b 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,6 +1,6 @@
 version = 1
 revision = 3
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 resolution-markers = [
     "python_full_version >= '3.14' and sys_platform == 'win32'",
     "python_full_version >= '3.14' and sys_platform == 'emscripten'",
@@ -11,11 +11,12 @@ resolution-markers = [
     "python_full_version == '3.12.*' and sys_platform == 'win32'",
     "python_full_version == '3.12.*' and sys_platform == 'emscripten'",
     "python_full_version == '3.12.*' and sys_platform != 'emscripten' and sys_platform != 'win32'",
-    "python_full_version == '3.11.*' and sys_platform == 'win32'",
-    "python_full_version == '3.11.*' and sys_platform == 'emscripten'",
-    "python_full_version == '3.11.*' and sys_platform != 'emscripten' and sys_platform != 'win32'",
-    "python_full_version > '3.10' and python_full_version < '3.11'",
-    "python_full_version <= '3.10'",
+    "python_full_version > '3.11' and python_full_version < '3.12' and sys_platform == 'win32'",
+    "python_full_version > '3.11' and python_full_version < '3.12' and sys_platform == 'emscripten'",
+    "python_full_version > '3.11' and python_full_version < '3.12' and sys_platform != 'emscripten' and sys_platform != 'win32'",
+    "python_full_version <= '3.11' and sys_platform == 'win32'",
+    "python_full_version <= '3.11' and sys_platform == 'emscripten'",
+    "python_full_version <= '3.11' and sys_platform != 'emscripten' and sys_platform != 'win32'",
 ]
 
 [[package]]
@@ -38,7 +39,6 @@ dependencies = [
     { name = "jmespath" },
     { name = "multidict" },
     { name = "python-dateutil" },
-    { name = "typing-extensions", marker = "python_full_version < '3.11'" },
     { name = "wrapt" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/e7/75/42cce839c2ec263ff74b10b650fe36b066fbb124cbee6f247eac0983e1ab/aiobotocore-3.7.0.tar.gz", hash = "sha256:c64d871ed5491a6571948dd48eabd185b46c6c23b64e3afd0c059fc7593ada30", size = 127054, upload-time = "2026-05-09T10:02:52.332Z" }
@@ -62,7 +62,6 @@ source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohappyeyeballs" },
     { name = "aiosignal" },
-    { name = "async-timeout", marker = "python_full_version < '3.11'" },
     { name = "attrs" },
     { name = "frozenlist" },
     { name = "multidict" },
@@ -72,24 +71,6 @@ dependencies = [
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/82/78/8ea7308cac6934de8c74a14f3d5f65d1c89287426688be79538d0e5c013d/aiohttp-3.14.1.tar.gz", hash = "sha256:307f2cff90a764d329e77040603fa032db89c5c24fdad50c4c15334cba744035", size = 7955794, upload-time = "2026-06-07T21:09:35.529Z" }
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@@ -228,7 +209,6 @@ name = "anyio"
 version = "4.14.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
-    { name = "exceptiongroup", marker = "python_full_version < '3.11'" },
     { name = "idna" },
     { name = "typing-extensions", marker = "python_full_version < '3.13'" },
 ]
@@ -237,21 +217,6 @@ wheels = [
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 ]
 
-[[package]]
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-version = "0.3.3"
-source = { registry = "https://pypi.org/simple" }
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-
-[[package]]
-name = "async-timeout"
-version = "5.0.1"
-source = { registry = "https://pypi.org/simple" }
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-
 [[package]]
 name = "asyncssh"
 version = "2.24.0"
@@ -294,16 +259,9 @@ dependencies = [
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