Adjust Nextclade to Auspice 2.61+

[ivan-aksamentov]

Fixes build https://github.com/nextstrain/nextclade/actions/runs/11903714964/job/33171209422?pr=1553#step:18:146

This attempts to adjust Nextclade to changes introduced in Auspice 2.61.0 and above.

This involves a few moved files and making sure ts files are included into monkey patching.

Sadly, entropy panel permanently shows "data loading" after any interaction with the tree (e.g. clicking on a branch or using filters)

I made an isolated /tree-debug page to reproduce and investigate the issue further:

nextclade/packages/nextclade-web/src/pages/tree-debug.tsx

Lines 21 to 34 in 1b7917a

	const auspiceJson: AuspiceJsonV2 = useAxiosQuery(
	'https://raw.githubusercontent.com/nextstrain/nextclade_data/refs/heads/master/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/tree.json',
	)
	const dispatch = useDispatch()
	const auspiceState = createAuspiceState(auspiceJson, dispatch)
	dispatch(auspiceStartClean(auspiceState))
	dispatch(changeColorBy())
	// dispatch(treeFilterByNodeType(['New']))
	return (
	<Layout>
	<TreePageContent />
	</Layout>

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Name	Status	Preview	Updated (UTC)
nextclade	✅ Ready (Inspect)	Visit Preview	Nov 20, 2024 2:36am

[jameshadfield]

Sadly, entropy panel permanently shoes "data loading" after any interaction with the tree (e.g. clicking on a branch or using filters)

This is presumably due to this conditional where we skip the updating of the data behind the entropy panel if the panel's not rendered or off-screen. I'd guess the intersection observer we use to know if it's off-screen isn't working as expected within Nextclade. But it may also be the former if Nextclade doesn't use <reduxState>.controls.panelsToDisplay like vanilla Auspice does.

[ivan-aksamentov]

@jameshadfield Wow, thanks! Yes, I've been trying to identify which additional parts of redux state and logic I need to hook up. Will look into it.

[ivan-aksamentov]

@jameshadfield Alternatively, do you see an easy way to opt out of this optimization and render the entropy always, as before?

[jameshadfield]

Alternatively, do you see an easy way to opt out of this optimization and render the entropy always, as before?

You could change the source code to modify the conditional to if (false) {, i.e. within monkeyPatch.ts. It's been a long time since I properly looked at how Nextclade uses Auspice, but skimming through things now makes me think you're using a very cut-down version of the (redux) controls state and adding panelsToDisplay: ['tree'] may be enough.