upgrade to capacitor 6

[yxu-lanl]

Migrate capacitor 5 to 6 Capacitor 6 sets a deployment target of iOS 13 and Android 14 (SDK 34)

1. update capacitor to 6 https://capacitorjs.com/docs/updating/6-0 Using the CLI to Migrate npm i -D @capacitor/cli@latest npx cap migrate

2. Update plugins to 6 https://capacitorjs.com/docs/updating/plugins/6-0 Using @capacitor/plugin-migration-v5-to-v6 npx @capacitor/plugin-migration-v5-to-v6@latest

3. Sync (copy + update) an Ionic project ionic cap sync

[yxu-lanl]

@pkalita-lbl I couldn't figure out why the unit test failed. There is no any change inside the src directory.

[pkalita-lbl]

It looks like the failure is happening when running npm run build, before it even gets to the unit tests. Do you see the error locally when running npm run build?

[yxu-lanl]

No.

> nmdc-field-notes@0.0.1 build
> tsc && vite build

vite v5.2.11 building for production...
✓ 823 modules transformed.
dist/assets/web-legacy-C7W-XhZu.js                 0.46 kB │ gzip:   0.30 kB
dist/assets/status-tap-legacy-7fB9rwAc.js          0.60 kB │ gzip:   0.40 kB
dist/assets/web-legacy-D1jaVo-u.js                 0.76 kB │ gzip:   0.39 kB
dist/assets/swipe-back-legacy-puD0-1n1.js          0.78 kB │ gzip:   0.52 kB
dist/assets/web-legacy-ZgV_DYjn.js                 0.99 kB │ gzip:   0.51 kB
dist/assets/focus-visible-legacy-CdO5cX4I.js       1.09 kB │ gzip:   0.55 kB
dist/assets/md.transition-legacy-iFp7HxjL.js       1.13 kB │ gzip:   0.61 kB
dist/assets/index9-legacy-CyCUJo2M.js              1.74 kB │ gzip:   0.87 kB
dist/assets/input-shims-legacy-Dy5TMB-4.js         4.73 kB │ gzip:   2.08 kB
dist/assets/ios.transition-legacy-CkAsW4xI.js     10.64 kB │ gzip:   3.03 kB
dist/assets/polyfills-legacy-Dw99Pvtb.js          68.93 kB │ gzip:  27.38 kB
dist/assets/index-legacy-BVVo-Rpu.js           1,261.13 kB │ gzip: 304.75 kB

(!) Some chunks are larger than 500 kB after minification. Consider:
- Using dynamic import() to code-split the application
- Use build.rollupOptions.output.manualChunks to improve chunking: https://rollupjs.org/configuration-options/#output-manualchunks
- Adjust chunk size limit for this warning via build.chunkSizeWarningLimit.
dist/index.html                                  4.13 kB │ gzip:   1.71 kB
dist/assets/logo-text-DQe-ClQo.svg               6.52 kB │ gzip:   1.86 kB
dist/assets/NMDC_microbe_light-CnrD6x0E.png    538.52 kB
dist/assets/NMDC_microbe_dark-BdaioxqE.png     539.26 kB
dist/assets/index-CyW8DWhf.css                  33.37 kB │ gzip:   6.37 kB
dist/assets/web-CNtCtqRu.js                      0.38 kB │ gzip:   0.25 kB
dist/assets/status-tap-B3Kgygg_.js               0.48 kB │ gzip:   0.34 kB
dist/assets/web-BrTeqAOd.js                      0.67 kB │ gzip:   0.33 kB
dist/assets/swipe-back-Dgz2aUDn.js               0.68 kB │ gzip:   0.47 kB
dist/assets/web-Ufj_jgVm.js                      0.91 kB │ gzip:   0.46 kB
dist/assets/focus-visible-supuXXMI.js            0.99 kB │ gzip:   0.51 kB
dist/assets/md.transition-kWh3BLAl.js            1.07 kB │ gzip:   0.57 kB
dist/assets/index9-B7lzdqak.js                   1.63 kB │ gzip:   0.83 kB
dist/assets/input-shims-Dy297fLT.js              4.82 kB │ gzip:   2.08 kB
dist/assets/ios.transition-DPdIA-8W.js          11.21 kB │ gzip:   3.10 kB
dist/assets/index-2qqnZN4y.js                1,204.44 kB │ gzip: 302.25 kB

(!) Some chunks are larger than 500 kB after minification. Consider:
- Using dynamic import() to code-split the application
- Use build.rollupOptions.output.manualChunks to improve chunking: https://rollupjs.org/configuration-options/#output-manualchunks
- Adjust chunk size limit for this warning via build.chunkSizeWarningLimit.
✓ built in 14.74s

[yxu-lanl]

But 'npm run test.unit' failed.

FAIL  src/queries.test.tsx > useSubmission should replace paused mutations when offline
AssertionError: expected 'TEST 1' to be 'UPDATE 2' // Object.is equality

- Expected
+ Received

- UPDATE 2
+ TEST 1

 ❯ src/queries.test.tsx:191:5
    189|   expect(
    190|     result.current.query.data?.metadata_submission.studyForm.studyName,
    191|   ).toBe("UPDATE 2");
       |     ^
    192| });
    193| 

⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯[1/1]⎯

 Test Files  1 failed | 9 passed (10)
      Tests  1 failed | 62 passed (63)

[eecavanna]

Thanks for working on this, @yxu-lanl. I'll take a look at these errors now, too.

---

Notes

$ node --version
v20.8.1

$ npm install
$ npm run test.unit

I reproduced the error locally:

 FAIL  src/queries.test.tsx > useSubmission should replace paused mutations when offline
AssertionError: expected 'TEST 1' to be 'UPDATE 2' // Object.is equality

- Expected
+ Received

- UPDATE 2
+ TEST 1

 ❯ src/queries.test.tsx:191:5
    189|   expect(
    190|     result.current.query.data?.metadata_submission.studyForm.studyName,
    191|   ).toBe("UPDATE 2");
       |     ^
    192| });
    193| 

The failing test is defined here: https://github.com/microbiomedata/nmdc-field-notes/blob/d1a22d2dc76e2e62f0da79e864a9e764fe7c5122/src/queries.test.tsx#L143C7-L192

I wonder whether it uses something that is dependent upon the version of Capacitor or one of its plugins.

The expect(patchCount).toBe(1); statement (which comes before the failing one) is not failing; so I know that patchCount is 1 at that point. However, the value in the studyName field (in the failing expect() statement) is what I would expect if 0 patches had been applied, since the value matches the original value (as opposed to matching either of the patch values).

I'll defer to @pkalita-lbl on this as he wrote the original test (which is passing on the tip of the main branch). If it remains unresolved in a few days, I'll look at it more at that time.

[eecavanna]

I, too, am able to $ npm run build this branch locally with no issues. I am using $ node --version v20.8.1 on an M1 Mac. I think the GitHub Actions runner is an x86/x64 Linux machine.

[eecavanna]

I just looked at the GitHub Actions log and saw that the error was:

When I first checked out this branch, I also got an error (I think it was the same error) when I ran $ npm install locally. I ended up deleting package-lock.json and the entire node_modules folder and re-running $ npm install, at which point it ran OK.

I'll look into how a similar "workaround" can be applied to the GitHub Actions runner.

[eecavanna]

Possibly related to the build error: https://github.com/vitejs/vite/discussions/15532#discussioncomment-8141236 — the workaround ("patch") described there is to add the following object to package.json and then run $ npm install:

  "optionalDependencies": {
    "@rollup/rollup-linux-x64-gnu": "4.9.5"
  }

Edit: I confirmed that this works around the build error.

[pkalita-lbl]

Sorry I've been occupied with other tasks. It looks like the build error has been resolved, but there's still a test failure. I can try to take a look and see if I can tell what's going on.

[pkalita-lbl]

Looking at the diff between what npm list shows in main versus this branch I see, in part:

< ├── @tanstack/eslint-plugin-query@5.18.0
< ├── @tanstack/query-async-storage-persister@5.18.0
< ├── @tanstack/react-query-devtools@5.18.0
< ├── @tanstack/react-query-persist-client@5.18.0
< ├── @tanstack/react-query@5.18.0
---
> ├── @tanstack/eslint-plugin-query@5.32.1
> ├── @tanstack/query-async-storage-persister@5.35.1
> ├── @tanstack/react-query-devtools@5.35.1
> ├── @tanstack/react-query-persist-client@5.35.1
> ├── @tanstack/react-query@5.35.1

So it looks like the changes to package-lock.json in this branch increment the locked versions of more than just the Capacitor dependencies. I don't know if that was intentional or not. But I'm almost certain that some change introduced between versions 5.18 and 5.35 of the TanStack query dependencies is what's causing the test failure. It's something that we should definitely investigate some time (maybe we could bisect it down to a specific version and go from there). But if we don't need to change the locked version of those dependencies now, let's not.

[yxu-lanl]

Changed all 'node_modules/@tanstack' versions to '5.18.0' inside the package-lock.json. The unit test issue got fixed.