From 5045c10b3586164f410194bbae8c5c58c2dadab2 Mon Sep 17 00:00:00 2001
From: uermel <uermel@czii.org>
Date: Tue, 18 Aug 2026 10:37:50 -0700
Subject: [PATCH] test: validate migrated thumbnail backends

Exercise local, S3-compatible, ML Croissant, SSH reconnect, concurrent worker, public portal, exact core fixture, installed-wheel, and diagnostic I/O paths without adding shared-UI retries.
---
 benchmarks/__init__.py                        |   1 +
 .../2026-08-18-local-alpha-baseline.md        |  33 +
 benchmarks/thumbnail_io.py                    | 212 ++++++
 pyproject.toml                                |   1 +
 tests/docker-compose.yml                      |  15 +
 tests/helpers.py                              |   4 +
 tests/ssh_mount/.gitignore                    |   2 +
 tests/test_core_entity_backends.py            | 129 ++++
 tests/test_live_portal_integration.py         |  36 +
 tests/test_ssh_backend_integration.py         |  94 +++
 tests/test_thumbnail_benchmark.py             |  57 ++
 uv.lock                                       | 668 ++++++++++++++++++
 12 files changed, 1252 insertions(+)
 create mode 100644 benchmarks/__init__.py
 create mode 100644 benchmarks/results/2026-08-18-local-alpha-baseline.md
 create mode 100644 benchmarks/thumbnail_io.py
 create mode 100644 tests/docker-compose.yml
 create mode 100644 tests/ssh_mount/.gitignore
 create mode 100644 tests/test_core_entity_backends.py
 create mode 100644 tests/test_live_portal_integration.py
 create mode 100644 tests/test_ssh_backend_integration.py
 create mode 100644 tests/test_thumbnail_benchmark.py

diff --git a/benchmarks/__init__.py b/benchmarks/__init__.py
new file mode 100644
index 0000000..9d9908c
--- /dev/null
+++ b/benchmarks/__init__.py
@@ -0,0 +1 @@
+"""Diagnostic benchmarks for copick-shared-ui."""
diff --git a/benchmarks/results/2026-08-18-local-alpha-baseline.md b/benchmarks/results/2026-08-18-local-alpha-baseline.md
new file mode 100644
index 0000000..8029dab
--- /dev/null
+++ b/benchmarks/results/2026-08-18-local-alpha-baseline.md
@@ -0,0 +1,33 @@
+# Local thumbnail I/O alpha baseline
+
+Recorded on 2026-08-18 with Python 3.12.10, copick 2.0.0-alpha.1, NumPy 2.5.1, and Zarr 3.3.0.
+The fixture is a two-level canonical OME-Zarr 0.5 / Zarr v3 pyramid written through the released core helper. Each
+sample opens the store read-only, selects the final metadata dataset, and materializes only the strided middle slice.
+
+```bash
+python -m benchmarks.thumbnail_io \
+  --store /private/tmp/copick-shared-ui-thumbnail-benchmark.zarr \
+  --build-fixture \
+  --repeats 5 \
+  --output-json /private/tmp/copick-shared-ui-thumbnail-benchmark.json \
+  --output-markdown /private/tmp/copick-shared-ui-thumbnail-benchmark.md
+```
+
+| Sample | Seconds | Read requests | Read bytes | Peak RSS bytes |
+| ---: | ---: | ---: | ---: | ---: |
+| 1 | 0.005875042 | 6 | 27,609 | 274,219,008 |
+| 2 | 0.005237000 | 6 | 27,609 | 274,317,312 |
+| 3 | 0.005245667 | 6 | 27,609 | 274,415,616 |
+| 4 | 0.006067583 | 6 | 27,609 | 274,464,768 |
+| 5 | 0.005083875 | 6 | 27,609 | 274,497,536 |
+
+| Metric | Median | Minimum | Maximum |
+| --- | ---: | ---: | ---: |
+| Seconds | 0.005245667 | 0.005083875 | 0.006067583 |
+| Read requests | 6 | 6 | 6 |
+| Read bytes | 27,609 | 27,609 | 27,609 |
+| Peak RSS bytes | 274,415,616 | 274,219,008 | 274,497,536 |
+
+All five thumbnails were `(128, 128)` and had the same decoded SHA-256 digest,
+`47a9ab890d65e7ff1e7b93b6666d58ef74ba017ecdced365c51fa6e8886173ad`. These values are diagnostic evidence,
+not a release threshold.
diff --git a/benchmarks/thumbnail_io.py b/benchmarks/thumbnail_io.py
new file mode 100644
index 0000000..9b883f8
--- /dev/null
+++ b/benchmarks/thumbnail_io.py
@@ -0,0 +1,212 @@
+"""Measure bounded thumbnail reads without imposing a performance threshold."""
+
+from __future__ import annotations
+
+import argparse
+import hashlib
+import json
+import statistics
+import threading
+import time
+from dataclasses import asdict, dataclass
+from pathlib import Path
+from typing import Any
+
+import numpy as np
+import psutil
+from copick.util.ome import write_ome_zarr_3d
+from zarr.abc.store import Store
+from zarr.storage import LocalStore, WrapperStore
+
+from copick_shared_ui.workers.base import AbstractThumbnailWorker
+
+
+@dataclass
+class ReadStats:
+    requests: int = 0
+    bytes: int = 0
+
+
+class RecordingStore(WrapperStore):
+    """Transparent store wrapper that records payloads returned by reads."""
+
+    def __init__(self, store: Store):
+        super().__init__(store)
+        self._lock = threading.Lock()
+        self._reads = ReadStats()
+
+    def snapshot(self) -> ReadStats:
+        with self._lock:
+            return ReadStats(**asdict(self._reads))
+
+    def _record(self, value: Any) -> None:
+        with self._lock:
+            self._reads.requests += 1
+            self._reads.bytes += 0 if value is None else len(value)
+
+    async def get(self, key, prototype, byte_range=None):
+        value = await self._store.get(key, prototype, byte_range)
+        self._record(value)
+        return value
+
+    async def get_partial_values(self, prototype, key_ranges):
+        ranges = list(key_ranges)
+        values = await self._store.get_partial_values(prototype, ranges)
+        for value in values:
+            self._record(value)
+        return values
+
+    async def get_ranges(self, key, byte_ranges, **kwargs):
+        async for group in self._store.get_ranges(key, byte_ranges, **kwargs):
+            for _index, value in group:
+                self._record(value)
+            yield group
+
+    async def _get_many(self, requests):
+        async for key, value in self._store._get_many(requests):
+            self._record(value)
+            yield key, value
+
+
+class _Run:
+    name = "benchmark"
+
+
+class _VoxelSpacing:
+    run = _Run()
+    voxel_size = 10.0
+
+
+class _Tomogram:
+    tomo_type = "wbp"
+    voxel_spacing = _VoxelSpacing()
+
+    def __init__(self, store: Store):
+        self._store = store
+
+    def zarr(self) -> Store:
+        return self._store
+
+
+class _ArrayWorker(AbstractThumbnailWorker):
+    def __init__(self, tomogram: _Tomogram):
+        super().__init__(tomogram, "benchmark", lambda *_result: None, True)
+        self._cache = None
+
+    def _setup_cache(self) -> None:
+        self._cache = None
+        self._cache_key = None
+
+    def start(self) -> None:
+        pass
+
+    def cancel(self) -> None:
+        pass
+
+    def _array_to_pixmap(self, array):
+        return array
+
+
+def build_fixture(path: Path) -> None:
+    """Write a small canonical two-level core fixture for diagnostics."""
+    fine = np.arange(48 * 256 * 256, dtype=np.float32).reshape(48, 256, 256)
+    coarse = fine[::2, ::2, ::2]
+    write_ome_zarr_3d(LocalStore(path), {10.0: fine, 20.0: coarse})
+
+
+def _measure_once(path: Path) -> dict[str, Any]:
+    store = RecordingStore(LocalStore(path, read_only=True))
+    worker = _ArrayWorker(_Tomogram(store))
+    process = psutil.Process()
+    peak_rss = process.memory_info().rss
+    stop = threading.Event()
+
+    def sample_memory() -> None:
+        nonlocal peak_rss
+        while not stop.wait(0.001):
+            peak_rss = max(peak_rss, process.memory_info().rss)
+
+    sampler = threading.Thread(target=sample_memory, daemon=True)
+    sampler.start()
+    before = store.snapshot()
+    started = time.perf_counter()
+    thumbnail = worker._generate_thumbnail_array(worker.item)
+    elapsed = time.perf_counter() - started
+    after = store.snapshot()
+    stop.set()
+    sampler.join()
+
+    return {
+        "elapsed_seconds": elapsed,
+        "read_requests": after.requests - before.requests,
+        "read_bytes": after.bytes - before.bytes,
+        "peak_rss_bytes": peak_rss,
+        "thumbnail_shape": list(thumbnail.shape),
+        "thumbnail_sha256": hashlib.sha256(thumbnail.tobytes()).hexdigest(),
+    }
+
+
+def _summary(samples: list[dict[str, Any]]) -> dict[str, Any]:
+    result = {}
+    for field in ("elapsed_seconds", "read_requests", "read_bytes", "peak_rss_bytes"):
+        values = [sample[field] for sample in samples]
+        result[field] = {
+            "median": statistics.median(values),
+            "minimum": min(values),
+            "maximum": max(values),
+        }
+    return result
+
+
+def run_benchmark(path: Path, repeats: int = 5) -> dict[str, Any]:
+    if repeats < 5:
+        raise ValueError("Thumbnail benchmarks require at least five repetitions")
+    samples = [_measure_once(path) for _ in range(repeats)]
+    checksums = {sample["thumbnail_sha256"] for sample in samples}
+    if len(checksums) != 1:
+        raise AssertionError("Thumbnail output changed between benchmark repetitions")
+    return {
+        "schema_version": 1,
+        "measurement": "coarsest metadata level, strided middle slice",
+        "repeats": repeats,
+        "samples": samples,
+        "summary": _summary(samples),
+    }
+
+
+def _markdown(report: dict[str, Any]) -> str:
+    lines = [
+        "# Thumbnail I/O diagnostic",
+        "",
+        f"Repetitions: {report['repeats']}",
+        "",
+        "| Metric | Median | Minimum | Maximum |",
+        "| --- | ---: | ---: | ---: |",
+    ]
+    for metric, values in report["summary"].items():
+        lines.append(f"| {metric} | {values['median']} | {values['minimum']} | {values['maximum']} |")
+    lines.extend(["", "Raw samples are retained in the paired JSON report.", ""])
+    return "\n".join(lines)
+
+
+def main(argv: list[str] | None = None) -> int:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--store", type=Path, required=True)
+    parser.add_argument("--build-fixture", action="store_true")
+    parser.add_argument("--repeats", type=int, default=5)
+    parser.add_argument("--output-json", type=Path, required=True)
+    parser.add_argument("--output-markdown", type=Path, required=True)
+    arguments = parser.parse_args(argv)
+
+    if arguments.build_fixture:
+        build_fixture(arguments.store)
+    report = run_benchmark(arguments.store, arguments.repeats)
+    arguments.output_json.parent.mkdir(parents=True, exist_ok=True)
+    arguments.output_markdown.parent.mkdir(parents=True, exist_ok=True)
+    arguments.output_json.write_text(json.dumps(report, indent=2) + "\n", encoding="utf-8")
+    arguments.output_markdown.write_text(_markdown(report), encoding="utf-8")
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())
diff --git a/pyproject.toml b/pyproject.toml
index d547a10..cc109a1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -62,6 +62,7 @@ testing = [
     "pytest-cov",
     "pytest-qt",
     "pyqt6",
+    "moto[server]>=5.1.0",
 ]
 
 [tool.pytest.ini_options]
diff --git a/tests/docker-compose.yml b/tests/docker-compose.yml
new file mode 100644
index 0000000..d04aada
--- /dev/null
+++ b/tests/docker-compose.yml
@@ -0,0 +1,15 @@
+services:
+  openssh-server:
+    image: lscr.io/linuxserver/openssh-server:latest
+    environment:
+      PUID: ${HOST_UID:-1000}
+      PGID: ${HOST_GID:-1000}
+      TZ: Etc/UTC
+      PASSWORD_ACCESS: "true"
+      USER_PASSWORD: password
+      USER_NAME: test.user
+    ports:
+      - "2222:2222"
+    volumes:
+      - ./ssh_mount:/config/test_data
+    restart: unless-stopped
diff --git a/tests/helpers.py b/tests/helpers.py
index d11b36b..598a5b7 100644
--- a/tests/helpers.py
+++ b/tests/helpers.py
@@ -41,6 +41,10 @@ def __init__(self, item: DummyTomogram, *, force_regenerate: bool = True):
         self._cache = None
         self._cache_key = None
 
+    def _setup_cache(self) -> None:
+        self._cache = None
+        self._cache_key = None
+
     def start(self) -> None:
         pass
 
diff --git a/tests/ssh_mount/.gitignore b/tests/ssh_mount/.gitignore
new file mode 100644
index 0000000..d6b7ef3
--- /dev/null
+++ b/tests/ssh_mount/.gitignore
@@ -0,0 +1,2 @@
+*
+!.gitignore
diff --git a/tests/test_core_entity_backends.py b/tests/test_core_entity_backends.py
new file mode 100644
index 0000000..5dcbd06
--- /dev/null
+++ b/tests/test_core_entity_backends.py
@@ -0,0 +1,129 @@
+"""Deterministic thumbnail reads through real copick backend entities."""
+
+import json
+import socket
+
+import boto3
+import copick
+import numpy as np
+import pytest
+from copick.impl.filesystem import CopickConfigFSSpec, CopickRootFSSpec
+from copick.ops.croissant import export_croissant
+from moto.server import ThreadedMotoServer
+
+from copick_shared_ui.workers.unified_workers import UnifiedThumbnailWorker, is_threading_available
+from tests.helpers import ArrayThumbnailWorker
+
+
+def _write_project(overlay_root, overlay_fs_args=None):
+    root = CopickRootFSSpec(
+        CopickConfigFSSpec(
+            name="shared-ui-backend",
+            description="Shared UI backend fixture",
+            version="1.0.0",
+            pickable_objects=[],
+            overlay_root=overlay_root,
+            overlay_fs_args=overlay_fs_args or {"auto_mkdir": True},
+        ),
+    )
+    run = root.new_run("run-1")
+    voxel_spacing = run.new_voxel_spacing(10.0)
+    tomogram = voxel_spacing.new_tomogram("denoised")
+    tomogram.from_numpy(np.arange(3 * 64 * 96, dtype=np.float32).reshape(3, 64, 96))
+    return root
+
+
+def _assert_thumbnail(root):
+    worker = ArrayThumbnailWorker(root.get_run("run-1"))
+    thumbnail, error = worker.generate_thumbnail_pixmap()
+
+    assert error is None
+    assert thumbnail.ndim == 2
+    assert thumbnail.size > 0
+    assert thumbnail.dtype == np.uint8
+    assert (int(thumbnail.min()), int(thumbnail.max())) == (0, 255)
+
+
+def test_local_copick_entity_thumbnail(tmp_path):
+    root = _write_project(f"local://{tmp_path / 'local-project'}")
+
+    _assert_thumbnail(root)
+
+
+@pytest.mark.skipif(not is_threading_available(), reason="Qt threading is unavailable")
+def test_local_concurrent_workers_emit_one_terminal_callback_each(tmp_path, qtbot):
+    root = _write_project(f"local://{tmp_path / 'local-concurrent-project'}")
+    run = root.get_run("run-1")
+    callbacks = []
+    workers = [
+        UnifiedThumbnailWorker(run, f"thumbnail-{index}", lambda *result: callbacks.append(result), True)
+        for index in range(4)
+    ]
+    for worker in workers:
+        worker._cache = None
+        worker.start()
+
+    qtbot.waitUntil(lambda: len(callbacks) >= len(workers), timeout=30000)
+    qtbot.wait(100)
+
+    assert len(callbacks) == len(workers)
+    assert {result[0] for result in callbacks} == {f"thumbnail-{index}" for index in range(4)}
+    assert all(result[1] is not None and result[2] is None for result in callbacks)
+
+
+def test_mlcroissant_copick_entity_thumbnail(tmp_path):
+    project_path = tmp_path / "mlcroissant-project"
+    source_root = _write_project(f"local://{project_path}")
+    export_croissant(
+        source_root,
+        project_root=str(project_path),
+        base_url=f"file://{project_path}",
+        dataset_name="shared-ui-backend",
+        force=True,
+    )
+    config_path = tmp_path / "mlcroissant.json"
+    config_path.write_text(
+        json.dumps(
+            {
+                "config_type": "mlcroissant",
+                "pickable_objects": [],
+                "croissant_url": str(project_path / "Croissant" / "metadata.json"),
+            },
+        ),
+        encoding="utf-8",
+    )
+
+    _assert_thumbnail(copick.from_file(str(config_path)))
+
+
+def test_s3_compatible_copick_entity_thumbnail():
+    with socket.socket() as listener:
+        listener.bind(("127.0.0.1", 0))
+        port = listener.getsockname()[1]
+    server = ThreadedMotoServer(ip_address="127.0.0.1", port=port, verbose=False)
+    server.start()
+    endpoint = f"http://127.0.0.1:{port}"
+    try:
+        client = boto3.client(
+            "s3",
+            endpoint_url=endpoint,
+            aws_access_key_id="test",
+            aws_secret_access_key="test",
+            region_name="us-west-2",
+        )
+        client.create_bucket(
+            Bucket="shared-ui",
+            CreateBucketConfiguration={"LocationConstraint": "us-west-2"},
+        )
+        options = {
+            "key": "test",
+            "secret": "test",
+            "endpoint_url": endpoint,
+            "client_kwargs": {"region_name": "us-west-2"},
+        }
+
+        root = _write_project("s3://shared-ui/project", options)
+
+        _assert_thumbnail(root)
+    finally:
+        server.stop()
diff --git a/tests/test_live_portal_integration.py b/tests/test_live_portal_integration.py
new file mode 100644
index 0000000..d9b5bd0
--- /dev/null
+++ b/tests/test_live_portal_integration.py
@@ -0,0 +1,36 @@
+"""Opt-in bounded smoke test for the public CryoET Data Portal route."""
+
+import os
+
+import numpy as np
+import pytest
+from copick.impl.cryoet_data_portal import CopickConfigCDP, CopickRootCDP
+
+from tests.helpers import ArrayThumbnailWorker
+
+pytestmark = pytest.mark.integration
+
+
+def test_public_portal_thumbnail(tmp_path):
+    if os.environ.get("COPICK_SHARED_UI_RUN_LIVE_PORTAL") != "1":
+        pytest.skip("live portal validation is opt-in")
+
+    root = CopickRootCDP(
+        CopickConfigCDP(
+            name="shared-ui-portal",
+            description="Bounded shared UI portal smoke",
+            version="1.0.0",
+            pickable_objects=[],
+            overlay_root=f"local://{tmp_path / 'overlay'}",
+            overlay_fs_args={"auto_mkdir": True},
+            dataset_ids=[10301],
+        ),
+    )
+    worker = ArrayThumbnailWorker(root.get_run("14077"))
+
+    thumbnail, error = worker.generate_thumbnail_pixmap()
+
+    assert error is None
+    assert thumbnail.shape == (256, 256)
+    assert thumbnail.dtype == np.uint8
+    assert (int(thumbnail.min()), int(thumbnail.max())) == (0, 255)
diff --git a/tests/test_ssh_backend_integration.py b/tests/test_ssh_backend_integration.py
new file mode 100644
index 0000000..0f8981d
--- /dev/null
+++ b/tests/test_ssh_backend_integration.py
@@ -0,0 +1,94 @@
+"""Opt-in observable SSH reconnect validation using a mounted test service."""
+
+import json
+import os
+import tempfile
+from pathlib import Path
+
+import numpy as np
+import pytest
+from copick.impl.filesystem import CopickConfigFSSpec, CopickRootFSSpec
+
+from copick_shared_ui.storage import open_coarsest_tomogram_array
+from copick_shared_ui.workers.unified_workers import UnifiedThumbnailWorker
+from tests.helpers import ArrayThumbnailWorker
+from tests.test_core_entity_backends import _write_project
+
+pytestmark = pytest.mark.integration
+
+
+def _make_world_accessible(path: Path) -> None:
+    for directory, _subdirectories, filenames in os.walk(path):
+        os.chmod(directory, 0o777)
+        for filename in filenames:
+            os.chmod(Path(directory) / filename, 0o666)
+
+
+def _thumbnail(root):
+    worker = ArrayThumbnailWorker(root.get_run("run-1"))
+    result, error = worker.generate_thumbnail_pixmap()
+    assert error is None
+    assert result is not None
+    return result
+
+
+def test_ssh_consecutive_and_post_drop_thumbnail_reads(qtbot):
+    mount_root = os.environ.get("COPICK_SHARED_UI_SSH_MOUNT_ROOT")
+    remote_root = os.environ.get("COPICK_SHARED_UI_SSH_REMOTE_ROOT")
+    if mount_root is None or remote_root is None:
+        pytest.skip("SSH mount and remote roots are not configured")
+
+    options = json.loads(
+        os.environ.get(
+            "COPICK_SHARED_UI_SSH_FS_ARGS",
+            '{"host":"127.0.0.1","port":2222,"username":"test.user","password":"password","known_hosts":null}',
+        ),
+    )
+    with tempfile.TemporaryDirectory(prefix="shared-ui-", dir=mount_root) as temporary:
+        local_project = Path(temporary) / "project"
+        _write_project(f"local://{local_project}")
+        _make_world_accessible(Path(temporary))
+        remote_project = f"{remote_root.rstrip('/')}/{Path(temporary).name}/project"
+        root = CopickRootFSSpec(
+            CopickConfigFSSpec(
+                name="shared-ui-ssh",
+                description="Shared UI SSH fixture",
+                version="1.0.0",
+                pickable_objects=[],
+                overlay_root=remote_project,
+                overlay_fs_args=options,
+            ),
+        )
+
+        first = _thumbnail(root)
+        second = _thumbnail(root)
+        np.testing.assert_array_equal(second, first)
+
+        run = root.get_run("run-1")
+        held_array = open_coarsest_tomogram_array(run.voxel_spacings[0].tomograms[0])
+
+        # Force the real connection closed, then exercise public refresh/read behavior.
+        root.fs_overlay._fs.client.abort()
+        root.refresh()
+        held_slice = np.asarray(held_array[held_array.shape[0] // 2, :, :])
+        assert held_slice.size > 0
+        recovered = _thumbnail(root)
+        np.testing.assert_array_equal(recovered, first)
+
+        callbacks = []
+        workers = [
+            UnifiedThumbnailWorker(
+                root.get_run("run-1"),
+                f"ssh-{index}",
+                lambda *result: callbacks.append(result),
+                True,
+            )
+            for index in range(4)
+        ]
+        for worker in workers:
+            worker._cache = None
+            worker.start()
+        qtbot.waitUntil(lambda: len(callbacks) == len(workers), timeout=30000)
+
+        assert {callback[0] for callback in callbacks} == {f"ssh-{index}" for index in range(4)}
+        assert all(callback[1] is not None and callback[2] is None for callback in callbacks)
diff --git a/tests/test_thumbnail_benchmark.py b/tests/test_thumbnail_benchmark.py
new file mode 100644
index 0000000..1ef6f2b
--- /dev/null
+++ b/tests/test_thumbnail_benchmark.py
@@ -0,0 +1,57 @@
+"""Focused tests for the diagnostic thumbnail benchmark."""
+
+import json
+
+import pytest
+
+from benchmarks import thumbnail_io
+
+
+def test_benchmark_retains_five_raw_samples_and_summary(tmp_path):
+    store_path = tmp_path / "fixture.zarr"
+    thumbnail_io.build_fixture(store_path)
+
+    report = thumbnail_io.run_benchmark(store_path, repeats=5)
+
+    assert report["repeats"] == 5
+    assert len(report["samples"]) == 5
+    assert len({sample["thumbnail_sha256"] for sample in report["samples"]}) == 1
+    assert all(sample["thumbnail_shape"] == [128, 128] for sample in report["samples"])
+    assert all(sample["read_requests"] > 0 for sample in report["samples"])
+    assert all(sample["read_bytes"] > 0 for sample in report["samples"])
+    assert set(report["summary"]) == {"elapsed_seconds", "read_requests", "read_bytes", "peak_rss_bytes"}
+
+
+def test_benchmark_rejects_too_few_repetitions(tmp_path):
+    with pytest.raises(ValueError, match="at least five"):
+        thumbnail_io.run_benchmark(tmp_path / "unused.zarr", repeats=4)
+
+
+def test_benchmark_cli_writes_machine_and_human_reports(tmp_path, monkeypatch):
+    report = {
+        "schema_version": 1,
+        "measurement": "test",
+        "repeats": 5,
+        "samples": [],
+        "summary": {
+            "elapsed_seconds": {"median": 1, "minimum": 1, "maximum": 1},
+        },
+    }
+    monkeypatch.setattr(thumbnail_io, "run_benchmark", lambda *_args: report)
+    json_path = tmp_path / "results" / "thumbnail.json"
+    markdown_path = tmp_path / "results" / "thumbnail.md"
+
+    result = thumbnail_io.main(
+        [
+            "--store",
+            str(tmp_path / "store.zarr"),
+            "--output-json",
+            str(json_path),
+            "--output-markdown",
+            str(markdown_path),
+        ],
+    )
+
+    assert result == 0
+    assert json.loads(json_path.read_text(encoding="utf-8")) == report
+    assert "Raw samples" in markdown_path.read_text(encoding="utf-8")
diff --git a/uv.lock b/uv.lock
index 5be990b..6feab6c 100644
--- a/uv.lock
+++ b/uv.lock
@@ -204,6 +204,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/78/b6/6307fbef88d9b5ee7421e68d78a9f162e0da4900bc5f5793f6d3d0e34fb8/annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53", size = 13643, upload-time = "2024-05-20T21:33:24.1Z" },
 ]
 
+[[package]]
+name = "antlr4-python3-runtime"
+version = "4.13.2"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/33/5f/2cdf6f7aca3b20d3f316e9f505292e1f256a32089bd702034c29ebde6242/antlr4_python3_runtime-4.13.2.tar.gz", hash = "sha256:909b647e1d2fc2b70180ac586df3933e38919c85f98ccc656a96cd3f25ef3916", size = 117467, upload-time = "2024-08-03T19:00:12.757Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/89/03/a851e84fcbb85214dc637b6378121ef9a0dd61b4c65264675d8a5c9b1ae7/antlr4_python3_runtime-4.13.2-py3-none-any.whl", hash = "sha256:fe3835eb8d33daece0e799090eda89719dbccee7aa39ef94eed3818cafa5a7e8", size = 144462, upload-time = "2024-08-03T19:00:11.134Z" },
+]
+
 [[package]]
 name = "anyio"
 version = "4.14.1"
@@ -239,6 +248,19 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/64/b4/17d4b0b2a2dc85a6df63d1157e028ed19f90d4cd97c36717afef2bc2f395/attrs-26.1.0-py3-none-any.whl", hash = "sha256:c647aa4a12dfbad9333ca4e71fe62ddc36f4e63b2d260a37a8b83d2f043ac309", size = 67548, upload-time = "2026-03-19T14:22:23.645Z" },
 ]
 
+[[package]]
+name = "aws-xray-sdk"
+version = "2.15.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "botocore" },
+    { name = "wrapt" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/14/25/0cbd7a440080def5e6f063720c3b190a25f8aa2938c1e34415dc18241596/aws_xray_sdk-2.15.0.tar.gz", hash = "sha256:794381b96e835314345068ae1dd3b9120bd8b4e21295066c37e8814dbb341365", size = 76315, upload-time = "2025-10-29T20:59:45Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/ef/c3/f30a7a63e664acc7c2545ca0491b6ce8264536e0e5cad3965f1d1b91e960/aws_xray_sdk-2.15.0-py2.py3-none-any.whl", hash = "sha256:422d62ad7d52e373eebb90b642eb1bb24657afe03b22a8df4a8b2e5108e278a3", size = 103228, upload-time = "2025-10-29T21:00:24.12Z" },
+]
+
 [[package]]
 name = "backoff"
 version = "2.2.1"
@@ -285,6 +307,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/94/51/f975cae76d44274cc2868dc9040ac5d58d464784610234455b4e7b19c6ef/black-26.5.1-py3-none-any.whl", hash = "sha256:4ed7f7da04046d2e488437170797d3b4a4ad83906683bcb7dfc68b673bbce5e2", size = 213693, upload-time = "2026-05-18T16:53:33.964Z" },
 ]
 
+[[package]]
+name = "blinker"
+version = "1.9.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/21/28/9b3f50ce0e048515135495f198351908d99540d69bfdc8c1d15b73dc55ce/blinker-1.9.0.tar.gz", hash = "sha256:b4ce2265a7abece45e7cc896e98dbebe6cead56bcf805a3d23136d145f5445bf", size = 22460, upload-time = "2024-11-08T17:25:47.436Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/10/cb/f2ad4230dc2eb1a74edf38f1a38b9b52277f75bef262d8908e60d957e13c/blinker-1.9.0-py3-none-any.whl", hash = "sha256:ba0efaa9080b619ff2f3459d1d500c57bddea4a6b424b60a91141db6fd2f08bc", size = 8458, upload-time = "2024-11-08T17:25:46.184Z" },
+]
+
 [[package]]
 name = "boto3"
 version = "1.43.0"
@@ -438,6 +469,23 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/db/3c/33bac158f8ab7f89b2e59426d5fe2e4f63f7ed25df84c036890172b412b5/cfgv-3.5.0-py2.py3-none-any.whl", hash = "sha256:a8dc6b26ad22ff227d2634a65cb388215ce6cc96bbcc5cfde7641ae87e8dacc0", size = 7445, upload-time = "2025-11-19T20:55:50.744Z" },
 ]
 
+[[package]]
+name = "cfn-lint"
+version = "1.55.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "jsonpatch" },
+    { name = "networkx" },
+    { name = "pyyaml" },
+    { name = "regex" },
+    { name = "sympy" },
+    { name = "typing-extensions" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/04/85/37d9d1dc05cb00ab870e9fd424b334c94a4703bae48533ecc56e2feb28a6/cfn_lint-1.55.1.tar.gz", hash = "sha256:1e870ec3dfad17bf2cf164decba961551aed00a3eb3e51182eca6987eddb5562", size = 4646651, upload-time = "2026-08-13T17:15:11.736Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/46/10/c0e57bb3864b7670fe21730fab920d8cc6673d944db63108fdae3065659a/cfn_lint-1.55.1-py3-none-any.whl", hash = "sha256:4de4ced80c898ce0753b64fc5707bebf011601eb2d027d95e2ab3f91692b99d8", size = 5174710, upload-time = "2026-08-13T17:15:09.782Z" },
+]
+
 [[package]]
 name = "charset-normalizer"
 version = "3.4.8"
@@ -605,6 +653,7 @@ dev = [
     { name = "ruff" },
 ]
 testing = [
+    { name = "moto", extra = ["server"] },
     { name = "pyqt6" },
     { name = "pytest" },
     { name = "pytest-cov" },
@@ -620,6 +669,7 @@ requires-dist = [
     { name = "copick", specifier = ">=2.0.0a1,<3" },
     { name = "hatch-vcs", marker = "extra == 'dev'", specifier = ">=0.4.0" },
     { name = "hatchling", marker = "extra == 'dev'", specifier = ">=1.25.0" },
+    { name = "moto", extras = ["server"], marker = "extra == 'testing'", specifier = ">=5.1.0" },
     { name = "numpy", specifier = ">=2.0.2" },
     { name = "pre-commit", marker = "extra == 'dev'", specifier = ">=4.2.0" },
     { name = "pydantic", specifier = ">=2" },
@@ -871,6 +921,20 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/02/08/9c41fb51ab5b43eb21674aff13df270e8ba6c4b29c8624e328dc7a9482af/distlib-0.4.3-py2.py3-none-any.whl", hash = "sha256:4b0ce306c966eb73bc3a7b6abad017c556dadd92c44701562cd528ac7fde4d5b", size = 470628, upload-time = "2026-06-12T08:04:50.506Z" },
 ]
 
+[[package]]
+name = "docker"
+version = "7.2.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "pywin32", marker = "sys_platform == 'win32'" },
+    { name = "requests" },
+    { name = "urllib3" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/88/7f/731ff914b0255d3d065f45fd4e626d4b8c95dbcbaada049f337a6ac16410/docker-7.2.0.tar.gz", hash = "sha256:cebb93773d334f778e023a7ee352a8d6e13ab1bd3b863a4d4a59dec897df43ac", size = 118731, upload-time = "2026-07-09T14:53:46.39Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/75/23/529140fe1aab80fc6992f93a706deec709140a6397439139a054e1515c45/docker-7.2.0-py3-none-any.whl", hash = "sha256:a3f45fdeb9165e2d25d9a1d02ddf3bc70fb572cf5ebbf9b58558c22caf29b71f", size = 148775, upload-time = "2026-07-09T14:53:45.224Z" },
+]
+
 [[package]]
 name = "donfig"
 version = "0.8.1.post1"
@@ -933,6 +997,36 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/bb/49/7467c2946ccd9617f7da38187071bdc45bb9a95df51f4d63d6622432ce4e/filelock-3.29.6-py3-none-any.whl", hash = "sha256:14d5f5597d2e0c4dbd774cfb6d8132da1db44da83732aab679d54f7dcf97ab65", size = 45478, upload-time = "2026-07-06T23:08:07.197Z" },
 ]
 
+[[package]]
+name = "flask"
+version = "3.1.3"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "blinker" },
+    { name = "click" },
+    { name = "itsdangerous" },
+    { name = "jinja2" },
+    { name = "markupsafe" },
+    { name = "werkzeug" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/26/00/35d85dcce6c57fdc871f3867d465d780f302a175ea360f62533f12b27e2b/flask-3.1.3.tar.gz", hash = "sha256:0ef0e52b8a9cd932855379197dd8f94047b359ca0a78695144304cb45f87c9eb", size = 759004, upload-time = "2026-02-19T05:00:57.678Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/7f/9c/34f6962f9b9e9c71f6e5ed806e0d0ff03c9d1b0b2340088a0cf4bce09b18/flask-3.1.3-py3-none-any.whl", hash = "sha256:f4bcbefc124291925f1a26446da31a5178f9483862233b23c0c96a20701f670c", size = 103424, upload-time = "2026-02-19T05:00:56.027Z" },
+]
+
+[[package]]
+name = "flask-cors"
+version = "6.0.5"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "flask" },
+    { name = "werkzeug" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/47/03/4e464a50860f9adf08b5c1d3479cb8ea1f12af2aa69535c7042c6e628135/flask_cors-6.0.5.tar.gz", hash = "sha256:30c5031552cd59f620ac0c8211dac45b345d3b2df310e7721879e4f46ef9c601", size = 101386, upload-time = "2026-06-08T20:20:17.765Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/49/55/5bb1a2d918e9f02f131e47a59032bae70e48050e986e941511fd737a935c/flask_cors-6.0.5-py3-none-any.whl", hash = "sha256:68fcf75693e961f3af26683b23c4b9a8fb6b64de17d20d0c37b95e8de7ab2ed8", size = 16692, upload-time = "2026-06-08T20:20:16.247Z" },
+]
+
 [[package]]
 name = "frozenlist"
 version = "1.8.0"
@@ -1193,6 +1287,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/cb/b1/3846dd7f199d53cb17f49cba7e651e9ce294d8497c8c150530ed11865bb8/iniconfig-2.3.0-py3-none-any.whl", hash = "sha256:f631c04d2c48c52b84d0d0549c99ff3859c98df65b3101406327ecc7d53fbf12", size = 7484, upload-time = "2025-10-18T21:55:41.639Z" },
 ]
 
+[[package]]
+name = "itsdangerous"
+version = "2.2.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/9c/cb/8ac0172223afbccb63986cc25049b154ecfb5e85932587206f42317be31d/itsdangerous-2.2.0.tar.gz", hash = "sha256:e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173", size = 54410, upload-time = "2024-04-16T21:28:15.614Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/04/96/92447566d16df59b2a776c0fb82dbc4d9e07cd95062562af01e408583fc4/itsdangerous-2.2.0-py3-none-any.whl", hash = "sha256:c6242fc49e35958c8b15141343aa660db5fc54d4f13a1db01a3f5891b98700ef", size = 16234, upload-time = "2024-04-16T21:28:14.499Z" },
+]
+
 [[package]]
 name = "jinja2"
 version = "3.1.6"
@@ -1214,6 +1317,39 @@ wheels = [
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 ]
 
+[[package]]
+name = "joserfc"
+version = "1.7.4"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "cryptography" },
+]
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+wheels = [
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+]
+
+[[package]]
+name = "jsonpatch"
+version = "1.33"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "jsonpointer" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/42/78/18813351fe5d63acad16aec57f94ec2b70a09e53ca98145589e185423873/jsonpatch-1.33.tar.gz", hash = "sha256:9fcd4009c41e6d12348b4a0ff2563ba56a2923a7dfee731d004e212e1ee5030c", size = 21699, upload-time = "2023-06-26T12:07:29.144Z" }
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+]
+
+[[package]]
+name = "jsonpath-ng"
+version = "1.8.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/32/58/250751940d75c8019659e15482d548a4aa3b6ce122c515102a4bfdac50e3/jsonpath_ng-1.8.0.tar.gz", hash = "sha256:54252968134b5e549ea5b872f1df1168bd7defe1a52fed5a358c194e1943ddc3", size = 74513, upload-time = "2026-02-24T14:42:06.182Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/03/99/33c7d78a3fb70d545fd5411ac67a651c81602cc09c9cf0df383733f068c5/jsonpath_ng-1.8.0-py3-none-any.whl", hash = "sha256:b8dde192f8af58d646fc031fac9c99fe4d00326afc4148f1f043c601a8cfe138", size = 67844, upload-time = "2026-02-28T00:53:19.637Z" },
+]
+
 [[package]]
 name = "jsonpath-rw"
 version = "1.4.0"
@@ -1225,6 +1361,57 @@ dependencies = [
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 sdist = { url = "https://files.pythonhosted.org/packages/71/7c/45001b1f19af8c4478489fbae4fc657b21c4c669d7a5a036a86882581d85/jsonpath-rw-1.4.0.tar.gz", hash = "sha256:05c471281c45ae113f6103d1268ec7a4831a2e96aa80de45edc89b11fac4fbec", size = 13814, upload-time = "2015-04-19T01:47:15.06Z" }
 
+[[package]]
+name = "jsonpointer"
+version = "3.1.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/18/c7/af399a2e7a67fd18d63c40c5e62d3af4e67b836a2107468b6a5ea24c4304/jsonpointer-3.1.1.tar.gz", hash = "sha256:0b801c7db33a904024f6004d526dcc53bbb8a4a0f4e32bfd10beadf60adf1900", size = 9068, upload-time = "2026-03-23T22:32:32.458Z" }
+wheels = [
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+]
+
+[[package]]
+name = "jsonschema"
+version = "4.26.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
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+    { name = "jsonschema-specifications" },
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+    { name = "rpds-py" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/b3/fc/e067678238fa451312d4c62bf6e6cf5ec56375422aee02f9cb5f909b3047/jsonschema-4.26.0.tar.gz", hash = "sha256:0c26707e2efad8aa1bfc5b7ce170f3fccc2e4918ff85989ba9ffa9facb2be326", size = 366583, upload-time = "2026-01-07T13:41:07.246Z" }
+wheels = [
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+]
+
+[[package]]
+name = "jsonschema-path"
+version = "0.5.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "attrs" },
+    { name = "pathable" },
+    { name = "pyyaml" },
+    { name = "referencing" },
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