Add all IDR images to fixtures by AlexSurtees · Pull Request #82 · BioNGFF/vizarr

AlexSurtees · 2026-05-18T10:16:41Z

Description

Adds the full suite of IDR images to the test suite, with a flag for whether they are 'testable'. Images that are not flagged as 'testable' are not currently supported by the viewer and therefore are not tested. These can be changed to 'testable' when support is added.

Thought needs to be given to how exactly to organise the test suites. As a baseline all images in the IDR dataset should go through a 'generic' test. In addition to these tests it is likely that we will want additional tests with more concrete/specific expectations, possibly but not necessarily with data from other sources, whether that is external or internally created test datasets.

The .yaml files should be organised in some way, e.g. all IDR images in a single directory, in order to facilitate giving a snapshot of the current capabilities of the viewer.

Type of change

🐛 Bug fix (non-breaking change that resolves an issue)
✨ New feature (non-breaking change that adds functionality)
⚡ Optimisation (non-breaking improvement to performance or efficiency)
🧩 Documentation (adds or improves documentation)
[x ] 🧱 Maintenance (refactor, dependency update, CI/CD, etc.)
🔥 Breaking change (fix or feature that causes existing functionality to change)

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codecov · 2026-05-18T10:20:35Z

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✅ All modified and coverable lines are covered by tests.

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AlexSurtees · 2026-05-19T13:28:24Z

Name of fixture file derived from URL (rather than ID) - hash/uuid

Copilot

Pull request overview

Adds a “generic” fixtures suite for IDR (and related) Zarr sources and updates the viewer test harness to only run against fixtures flagged as testable, so unsupported datasets can be included without failing CI.

Changes:

Add testable flag to YAML fixture metadata and gate the generic “can read without error” test on it.
Move the generic test fixture lookup to fixtures/generic and add many new generic fixture YAMLs.
Add a Codecov config to ignore viewer/tests/.

Reviewed changes

Copilot reviewed 95 out of 97 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
viewer/tests/metadata.js	Adds `testable` to generated metadata and introduces an untestable-yaml writer helper.
viewer/tests/images.test.js	Switches tests to `fixtures/generic` and skips fixtures where `testable` is false.
pnpm-workspace.yaml	Formatting-only change.
fixtures/kingsnake.yaml	Adds `testable: true` to existing root fixture.
fixtures/6001240_labels.yaml	Adds `testable: true` to existing root fixture.
.github/codecov.yml	Ignores `viewer/tests/` in Codecov.
fixtures/generic/ffa293ab-7bea-4464-9865-b5dfea286ab9.yaml	Adds generic fixture entry (untestable).
fixtures/generic/fcd03633-67ec-4089-9732-20e39d95a1f5.yaml	Adds generic fixture entry (testable).
fixtures/generic/fa237fbb-6a92-4998-85d3-1ec795baf516.yaml	Adds generic fixture entry (testable).
fixtures/generic/f960e2d2-3c9a-48c5-9721-1f57af27abec.yaml	Adds generic fixture entry (untestable).
fixtures/generic/f8545197-952d-4c23-94fa-af1e9fdb9f7d.yaml	Adds generic fixture entry (testable).
fixtures/generic/f2d97fd4-c825-47bf-9f33-19a8d2b9da88.yaml	Adds generic fixture entry (testable).
fixtures/generic/ef272493-28b8-4a46-a5b4-744ab8556e13.yaml	Adds generic fixture entry (testable).
fixtures/generic/dacb2378-aa3d-4835-8878-37e6737cee9e.yaml	Adds generic fixture entry (untestable).
fixtures/generic/d283bb51-3b33-413a-af55-0ce861858e59.yaml	Adds generic fixture entry (testable).
fixtures/generic/cb2244ef-3881-4736-858f-fad8f3aef12e.yaml	Adds generic fixture entry (testable).
fixtures/generic/ca28beae-f25a-45d9-baeb-d82dd6a33f61.yaml	Adds generic fixture entry (testable).
fixtures/generic/c4904df5-0005-4a80-953e-62b1ede447b4.yaml	Adds generic fixture entry (testable).
fixtures/generic/c4163d01-b3d0-4c7c-939f-f2390d68ceea.yaml	Adds generic fixture entry (testable).
fixtures/generic/bbfb44b9-5505-401b-8d82-318f646cd06f.yaml	Adds generic fixture entry (testable).
fixtures/generic/bacb4799-7d22-4e2b-89bc-0fb6af476b8a.yaml	Adds generic fixture entry (testable).
fixtures/generic/b9bd91c9-a7a6-481c-9dfd-d0950a71a477.yaml	Adds generic fixture entry (testable).
fixtures/generic/b702ca85-9fd8-4598-8d90-64b484a1b695.yaml	Adds generic fixture entry (testable).
fixtures/generic/b34c35db-3e0e-4951-b765-ed8b6617fb2f.yaml	Adds generic fixture entry (untestable).
fixtures/generic/b0d67e24-de5b-4866-8fbd-cf51a00cdbcf.yaml	Adds generic fixture entry (testable).
fixtures/generic/b019a099-9205-489c-ae84-1d95c43c3b0a.yaml	Adds generic fixture entry (testable).
fixtures/generic/ae184d89-7410-4ea0-a0ad-267590eaf7e4.yaml	Adds generic fixture entry (testable).
fixtures/generic/a9da3c6c-d2a1-42d4-9bc0-2b3dfefc2012.yaml	Adds generic fixture entry (testable).
fixtures/generic/a8dc80a9-a3a7-47d0-bfbe-62245e9e2019.yaml	Adds generic fixture entry (testable).
fixtures/generic/a6e4722e-85c7-40e2-8e8f-84ec55117186.yaml	Adds generic fixture entry (testable).
fixtures/generic/a410e397-651e-4eea-a6f2-f30aa8d8a9f0.yaml	Adds generic fixture entry (testable).
fixtures/generic/a105f5b7-7e76-42cc-9652-5c051e122f59.yaml	Adds generic fixture entry (untestable).
fixtures/generic/9f8b6511-3a57-4945-8ff4-11ad1fdde54b.yaml	Adds generic fixture entry (testable).
fixtures/generic/9f1a11eb-29ae-469b-93fd-a404b28755ee.yaml	Adds generic fixture entry (testable).
fixtures/generic/9eacd3fe-9f15-432c-8b2b-9b3e54b06828.yaml	Adds generic fixture entry (testable).
fixtures/generic/9bd6b892-fdf9-4caf-931b-186f535885f7.yaml	Adds generic fixture entry (testable).
fixtures/generic/9b5b4fc7-de59-42f9-b161-2fe47c89b3a0.yaml	Adds generic fixture entry (testable).
fixtures/generic/91ab4871-f9fc-4174-abec-866a14ea0ce3.yaml	Adds generic fixture entry (untestable).
fixtures/generic/90f2c920-90f7-4b28-bf21-b1367a009940.yaml	Adds generic fixture entry (untestable).
fixtures/generic/8eadf4da-2c9a-4743-bdb8-f2082ab9a062.yaml	Adds generic fixture entry (testable).
fixtures/generic/8a38b941-51b1-4d63-ba43-64b688e7d576.yaml	Adds generic fixture entry (testable).
fixtures/generic/883cb4c2-e5ce-46f2-aa8c-464af9704e8c.yaml	Adds generic fixture entry (untestable).
fixtures/generic/86c1338f-59aa-4627-a352-2bf3334b39ae.yaml	Adds generic fixture entry (untestable).
fixtures/generic/7953a88e-2110-44b4-a41f-4c4d13f17065.yaml	Adds generic fixture entry (testable).
fixtures/generic/77aa71ae-e067-41e4-a24a-8c694160f8f7.yaml	Adds generic fixture entry (testable).
fixtures/generic/74cbdfb2-dfd1-4e28-b09a-2c3eacc2d1ea.yaml	Adds generic fixture entry (testable).
fixtures/generic/747e9ae7-6eae-4bb7-897a-e2180e703616.yaml	Adds generic fixture entry (testable).
fixtures/generic/710d0093-e694-4cfe-aa49-9e03cd439c5d.yaml	Adds generic fixture entry (untestable).
fixtures/generic/6c3ca6ef-7570-4126-9e53-7e9436ed54d1.yaml	Adds generic fixture entry (testable).
fixtures/generic/698053e3-d485-4469-9245-caa6c3ec9fe1.yaml	Adds generic fixture entry (testable).
fixtures/generic/68d9072d-da3c-4670-ab93-40164d34f962.yaml	Adds generic fixture entry (testable).
fixtures/generic/65b1be90-370e-4661-b35a-6f20417a8b55.yaml	Adds generic fixture entry (testable).
fixtures/generic/64075c0b-45d6-48cb-87b2-6e8c30ef9d69.yaml	Adds generic fixture entry (testable).
fixtures/generic/623fb91b-1389-4eff-ac1a-b637f67bddc8.yaml	Adds generic fixture entry (testable).
fixtures/generic/60ad7d2e-64ca-4680-8be4-ce8cadaa57b4.yaml	Adds generic fixture entry (testable).
fixtures/generic/5e24ceaa-6c15-4c83-aeef-2eef5cda9767.yaml	Adds generic fixture entry (testable).
fixtures/generic/5e1df35f-6417-4ca5-8dd9-19a1efdf87eb.yaml	Adds generic fixture entry (testable).
fixtures/generic/5d3e3fb3-05eb-43d6-8061-9ad463612d4e.yaml	Adds generic fixture entry (untestable).
fixtures/generic/5c2bd073-a256-4047-be0a-1768938caf61.yaml	Adds generic fixture entry (testable).
fixtures/generic/5bcaa16a-1468-4ee9-822b-87866483bba6.yaml	Adds generic fixture entry (testable).
fixtures/generic/5a273ada-1109-4948-a3f5-8703a6d0e3fb.yaml	Adds generic fixture entry (testable).
fixtures/generic/55fa5fb3-8ea9-4725-afe9-2591e8d5489b.yaml	Adds generic fixture entry (testable).
fixtures/generic/55e542b3-8927-4719-8ec0-b1d33cd8bd41.yaml	Adds generic fixture entry (testable).
fixtures/generic/55abbf8f-2813-4d5e-86b8-8dca71b44103.yaml	Adds generic fixture entry (testable).
fixtures/generic/5359e36c-c6a3-4d0c-ae75-d8d189c95f18.yaml	Adds generic fixture entry (testable).
fixtures/generic/52f36829-a6c1-4f56-9982-c29610d15f85.yaml	Adds generic fixture entry (testable).
fixtures/generic/50622cae-103d-4d14-ad48-4a4379e4b885.yaml	Adds generic fixture entry (testable).
fixtures/generic/4bfbd46d-30d6-4b9e-a842-cc9d6ea2f713.yaml	Adds generic fixture entry (testable).
fixtures/generic/4611aa11-c9c4-4459-bf61-b97d68693627.yaml	Adds generic fixture entry (testable).
fixtures/generic/4101281b-abe0-4199-9fa7-2ea96a200c29.yaml	Adds generic fixture entry (testable).
fixtures/generic/3e33a0e8-d4ea-4027-ba2a-e64150d957d8.yaml	Adds generic fixture entry (untestable).
fixtures/generic/3dd517fc-9b4b-4aae-bb90-afb2f334b60f.yaml	Adds generic fixture entry (testable).
fixtures/generic/2d52ade7-81eb-426e-9181-3aca6e1e18d8.yaml	Adds generic fixture entry (untestable).
fixtures/generic/2ca15d77-3970-4fe5-ba52-ac5773c13466.yaml	Adds generic fixture entry (testable).
fixtures/generic/2c35dfdf-0206-4d1e-a9a5-7899407918ad.yaml	Adds generic fixture entry (testable).
fixtures/generic/2bc2e49d-8771-40c4-87e4-5b141da5c66f.yaml	Adds generic fixture entry (testable).
fixtures/generic/2abeddbb-e0fd-411d-81c9-40f49eb457a2.yaml	Adds generic fixture entry (untestable).
fixtures/generic/2a6ef65b-82c3-4840-b2aa-48b5421e010a.yaml	Adds generic fixture entry (testable).
fixtures/generic/2a5229a7-d6e3-4288-a6c0-1c0a8351cbb7.yaml	Adds generic fixture entry (testable).
fixtures/generic/273ac7ef-8a87-425e-9c70-1f3f5000023e.yaml	Adds generic fixture entry (testable).
fixtures/generic/2729b5d9-5d5a-4869-a49e-fbae7bfc981e.yaml	Adds generic fixture entry (testable).
fixtures/generic/26aa2b14-b04e-4abb-b080-6e8dcc3e8406.yaml	Adds generic fixture entry (testable).
fixtures/generic/25ac3825-bd3f-458d-8966-090c4894314e.yaml	Adds generic fixture entry (testable).
fixtures/generic/2486d06d-4081-430e-9d00-d2c0dd8b3757.yaml	Adds generic fixture entry (testable).
fixtures/generic/1ec4fbba-11db-42c2-948c-f373d7a0b6e8.yaml	Adds generic fixture entry (testable).
fixtures/generic/1c0fbd52-7971-4095-9f90-669cc6728973.yaml	Adds generic fixture entry (untestable).
fixtures/generic/1bc4a58c-392a-4168-8713-94a85df1832a.yaml	Adds generic fixture entry (testable).
fixtures/generic/1ae8a9db-3c11-4cd4-85e0-205240e0fc37.yaml	Adds generic fixture entry (testable).
fixtures/generic/19e98a94-27af-481a-8aea-0ce09df4b145.yaml	Adds generic fixture entry (untestable).
fixtures/generic/13834ee8-6e10-4898-8cd5-76545ba98793.yaml	Adds generic fixture entry (testable).
fixtures/generic/123062e1-46ad-474a-b308-d488073ccb7d.yaml	Adds generic fixture entry (testable).
fixtures/generic/0d8964be-d8ed-4642-b490-8733bc4cb588.yaml	Adds generic fixture entry (testable).
fixtures/generic/0d594022-23f2-4c61-9141-0a5a433e6606.yaml	Adds generic fixture entry (untestable).
fixtures/generic/0a11ad7d-ed50-4cbe-affa-0355148c9595.yaml	Adds generic fixture entry (testable).
fixtures/generic/0838583a-af6a-488a-b93d-3e86a912219a.yaml	Adds generic fixture entry (testable).
fixtures/generic/0259e1da-a6f6-4966-977f-8a6eda01a9c6.yaml	Adds generic fixture entry (untestable).

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

+export function writeUntestableYaml(url, imageName, savePath, testable) {
+  fs.writeFileSync(
+    path.join(savePath, `${imageName}.yaml`),
+    stringify({
+      source: url,
+      name: imageName,
+      testable: false,
+    }),


davehorsfall · 2026-05-21T16:37:31Z

 import { createSourceData } from "../src/io";
-import { getYamlFileNames, writeImageYaml } from "./metadata";
+import { getYamlFileNames, writeImageYaml, writeUntestableYaml } from "./metadata";



+    test(`Can read ${description.name} without error`, async () => {
+      await createSourceData({
+        source: description.source,
+      });
+      await writeImageYaml(description.source, description.name, imagesPath);
+    }, 20000);


davehorsfall · 2026-05-21T16:34:24Z

+source: https://livingobjects.ebi.ac.uk/idr/zarr/v0.5/idr0157/Asterella gracilis
+  SWE/IMG_1033-1112 Asterella gracilis (Mannia gracilis) stature.ome.zarr
+name: 15154182
+testable: true


Happy for this to be a follow up, but spaces in URLs (who does this?) is a valid point to raise.

 files.map(async (file) => {
  const filePath = path.join(imagesPath, file);
  const description = yaml.parse(fs.readFileSync(filePath, "utf8"));
-  test(`Can read ${description.name} without error`, async () => {
-    await createSourceData({
-      source: description.source,
-    });
-    await writeImageYaml(description.source, description.name, imagesPath);
-  }, 20000);
+
+  if (description.testable) {
+    test(`Can read ${description.name} without error`, async () => {


 source: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2-ozx/kingsnake.ozx
 name: kingsnake
+testable: true
 type: dask_image_gaussian


davehorsfall · 2026-05-21T16:35:42Z

@@ -1,5 +1,6 @@
 source: https://livingobjects.ebi.ac.uk/idr/zarr/v0.5/idr0062A/6001240_labels.zarr
 name: 6001240_labels
+testable: true


This URL does appear to be included in fixtures, so perhaps this needs to be removed before merge?

+  if (description.testable) {
+    test(`Can read ${description.name} without error`, async () => {
+      await createSourceData({
+        source: description.source,
+      });
+      await writeImageYaml(description.source, description.name, imagesPath);
+    }, 20000);


davehorsfall

@AlexSurtees I've approved so you can merge and proceed with stuff next week. However, there are couple of remedial points that have been picked up by co-pilot that would be good to address. Please review them, make changes, and then merge when you're happy thanks.

davehorsfall · 2026-05-21T16:34:24Z

+source: https://livingobjects.ebi.ac.uk/idr/zarr/v0.5/idr0157/Asterella gracilis
+  SWE/IMG_1033-1112 Asterella gracilis (Mannia gracilis) stature.ome.zarr
+name: 15154182
+testable: true


Happy for this to be a follow up, but spaces in URLs (who does this?) is a valid point to raise.

davehorsfall · 2026-05-21T16:35:42Z

@@ -1,5 +1,6 @@
 source: https://livingobjects.ebi.ac.uk/idr/zarr/v0.5/idr0062A/6001240_labels.zarr
 name: 6001240_labels
+testable: true


This URL does appear to be included in fixtures, so perhaps this needs to be removed before merge?

davehorsfall · 2026-05-21T16:36:51Z

@@ -1,5 +1,6 @@
 source: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2-ozx/kingsnake.ozx


Again, this URL does appear to be replicated in fixtures, so assuming these are legacy copies and can probably be removed?

davehorsfall · 2026-05-21T16:37:31Z

 import { createSourceData } from "../src/io";
-import { getYamlFileNames, writeImageYaml } from "./metadata";
+import { getYamlFileNames, writeImageYaml, writeUntestableYaml } from "./metadata";



Add all IDR images to fixtures

223a8d1

Lin

c29be66

Ignore tests in code coverage

97338fc

Alex Surtees and others added 6 commits May 21, 2026 09:17

UUIDs for generic fixtures

695a8a8

Remove accidentally added files

b5d616c

Restore accidentally removed file

30e94bf

Add accidentally removed file

3b6b215

Update lockfile

857b9d4

Merge branch 'dev' into idr_image_tests

568ce95

AlexSurtees requested a review from davehorsfall May 21, 2026 09:42

AlexSurtees marked this pull request as ready for review May 21, 2026 09:44

davehorsfall requested a review from Copilot May 21, 2026 16:16

Copilot started reviewing on behalf of davehorsfall May 21, 2026 16:16 View session

Copilot AI reviewed May 21, 2026

View reviewed changes

davehorsfall approved these changes May 21, 2026

View reviewed changes

Alex Surtees added 2 commits May 27, 2026 08:10

Clean up of tests

1f1faca

Address comments

268dcf4

AlexSurtees merged commit bf3c117 into dev May 27, 2026
7 checks passed

AlexSurtees deleted the idr_image_tests branch May 27, 2026 07:16

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Add all IDR images to fixtures#82

Add all IDR images to fixtures#82
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		@@ -1,5 +1,6 @@
		source: https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.5/96x2-ozx/kingsnake.ozx

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