Add types to tree component #1864

victorlin · 2024-10-08T18:54:29Z

Description of proposed changes

Adding types to link things together.

For later: b37a77c, 260ba00

Checklist

Checks pass
~~If making user-facing changes, add a message in CHANGELOG.md summarizing the changes in this PR~~
(to be done by a Nextstrain team member) Create preview PRs on downstream repositories.

jameshadfield · 2024-10-09T00:47:02Z

@genehack could you take a look at the types added / used here if you have a chance? 🙏

ES2015 allows iteration of sets which is used in this codebase.

jameshadfield · 2024-10-25T23:38:01Z

src/util/globals.js

-export const strainSymbol = Symbol('strain');
-export const genotypeSymbol = Symbol('genotype');
-export const measurementIdSymbol = Symbol('measurementId');
+export const strainSymbol = 'strain';


I presume this change is to make types easier?

I'd prefer to keep symbols - they are perfect for this use case. One downside to them is that they are skipped with things like Object.keys(), but I'd hope TS would be kind enough to flag this up for us?

Yeah mainly for ease of typing. I can look into working with them as-is.

Addressed with with 3c3ef2d

victorlin · 2024-10-25T23:52:54Z

Progress update: I think I've renamed all the files that need to be renamed for sufficient types. I've temporarily turned off strictNullChecks to focus on the other typing issues and have addressed those. There are still several FIXMEs and any types that I'll come back to next week.

Use named imports from the package instead of direct imports from source. This allows proper typing by the external types/d3 package.

For improved readability.

Converted most but not all tree-related files. There are some type errors exposed by conversion - those will be addressed by subsequent commits.

The conversion done in the previous commit came with 443 violations of this rule. While some could be addressed by better types, I think the types as-is are acceptable and we can live without these checks.

Passing a number to parseInt is a type error. The extra function call is not necessary since the number is already base 10.

calcTipRadii takes a key name of tipSelectedIdx. Previously, the value of idx was unused.

svgPropsToUpdate is Set<string>, not Set<string[]>.

This should be a boolean, not whatever value newDistance is when defined.

This should be a boolean, not whatever value ReduxNode.parentInfo.original is when defined.

The extra value `true` had no effect.

Not [string], [], [[string], [string]], or [string, [string]].

Previously, there was no guarantee that an unknown error would produce a helpful message.

Not sure how this worked previously. I briefly searched for a test dataset that goes through any of these conditions but couldn't find one.

Only KeyboardEvent has the shiftKey property.

This is easier for the compiler to understand.

These were initialized with default values but unused in the code.

There is a default value set in modifyControlsStateViaTree, but this is the only property that doesn't have an explicit default set by getDefaultControlsState. Add it for consistency.

There is a type error that prevents this from working properly: includes() takes a single string, but an array of PhyloNodes is given. It's not used on any existing calls to updateTipRadii, so just remove it entirely.

This prevents type errors when calling setState.

jameshadfield · 2024-10-30T01:03:26Z

tsconfig.json

@@ -31,6 +32,7 @@ Visit https://aka.ms/tsconfig.json for a detailed list of options.

    /* Type Checking */
    "strict": true,                                      /* Enable all strict type-checking options. */
+    "strictNullChecks": false,                           /* Allow unhandled false/null/undefined values to make incremental TypeScript adoption easier. */


Eslint has the option of disabling a rule for a particular file - does tsc / typescript-eslint have the same? If so, that may be better as we can add a "todo" comment in those files and then incrementally move to adhering to this rule

I haven't read the whole Typescript issue thread, but the answer to this seems to be somewhere between "no" and "kinda via a PITA workaround". See this SO question which leads to a Typescript issue.

(The PITA workaround is "make the general config non-strict and then 'mask' that with strict configs that are limited to a subset of files" which is kinda 🤮, I think?)

Thanks for digging @genehack. The closest thing I could find in TypeScript docs is ts-nocheck which means "disable all rules for this file" (not great).

Another bad alternative is the per-line ts-ignore/ts-expect-error:

This disables all rules for the line, which is similarly not great

Doing this for 443 violations of strictNullChecks seems overkill

I can update the commit message of 8a0f4fa to note that we've considered these alternatives.

Thanks for the responses - pity about the answers tho!

I can update the commit message of 8a0f4fa to note that we've considered these alternatives.

Sounds good. Ideally we would turn this rule on in the future as I think it'll catch a whole lot of bugs. 443 is daunting tho!

victorlin self-assigned this Oct 8, 2024

nextstrain-bot temporarily deployed to auspice-victorlin-tree--ntadob October 8, 2024 18:54 Inactive

victorlin force-pushed the victorlin/tree-typing branch from 34d10ba to 38b94d4 Compare October 8, 2024 20:49

victorlin temporarily deployed to auspice-victorlin-tree--ntadob October 8, 2024 20:49 Inactive

victorlin force-pushed the victorlin/tree-typing branch from 38b94d4 to 4b25ff9 Compare October 8, 2024 22:47

victorlin temporarily deployed to auspice-victorlin-tree--ntadob October 8, 2024 22:47 Inactive

victorlin temporarily deployed to auspice-victorlin-tree--ntadob October 9, 2024 17:56 Inactive

victorlin mentioned this pull request Oct 10, 2024

tree: Add toggle to focus on selected #1373

Merged

16 tasks

victorlin mentioned this pull request Oct 21, 2024

Code refactoring #1874

Open

4 tasks

victorlin force-pushed the victorlin/tree-typing branch 2 times, most recently from e27d5d2 to 864ed12 Compare October 25, 2024 02:10

Compile for ES2015

7ebe2bc

ES2015 allows iteration of sets which is used in this codebase.

jameshadfield reviewed Oct 25, 2024

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victorlin mentioned this pull request Oct 25, 2024

Migrate to modern Redux #1711

Open

8 tasks

victorlin force-pushed the victorlin/tree-typing branch from 864ed12 to 0962aa8 Compare October 25, 2024 23:46

Fix imports from d3-scale

773ef45

Use named imports from the package instead of direct imports from source. This allows proper typing by the external types/d3 package.

victorlin force-pushed the victorlin/tree-typing branch from 0d16114 to 0523c8f Compare October 29, 2024 00:20

victorlin added 11 commits October 29, 2024 17:29

Remove non-existent parameter from docstring

7759619

render(): Convert from positional to named parameters

87740d5

For improved readability.

Add tree-related types

947aa9f

Converted most but not all tree-related files. There are some type errors exposed by conversion - those will be addressed by subsequent commits.

tsconfig: Disable strictNullChecks

8a0f4fa

The conversion done in the previous commit came with 443 violations of this rule. While some could be addressed by better types, I think the types as-is are acceptable and we can live without these checks.

Use number directly

69659f1

Passing a number to parseInt is a type error. The extra function call is not necessary since the number is already base 10.

Use proper key name

2b9987a

calcTipRadii takes a key name of tipSelectedIdx. Previously, the value of idx was unused.

Properly check for stroke-width

0f95a95

svgPropsToUpdate is Set<string>, not Set<string[]>.

Properly set timeSliceHasPotentiallyChanged

f82ea72

This should be a boolean, not whatever value newDistance is when defined.

Properly set isSubtreeRoot

0acc466

This should be a boolean, not whatever value ReduxNode.parentInfo.original is when defined.

Remove unused parameter to numDate

97dccaf

The extra value `true` had no effect.

Ensure PhyloNode.branch is [string, string]

64aaca3

Not [string], [], [[string], [string]], or [string, [string]].

victorlin added 9 commits October 29, 2024 17:49

Handle unknown errors when creating color scales

2cab811

Previously, there was no guarantee that an unknown error would produce a helpful message.

Convert RGBColor to hex string

f6fbaf4

Not sure how this worked previously. I briefly searched for a test dataset that goes through any of these conditions but couldn't find one.

Ensure window.event is a KeyboardEvent

52296da

Only KeyboardEvent has the shiftKey property.

Prefix unused variables with _

86ecc82

Use separate variable for array and set of legend values

9b0afd7

This is easier for the compiler to understand.

Remove unused mapLegendOpen, treeLegendOpen from controls state

b92feb6

These were initialized with default values but unused in the code.

Add a default value for coloringsPresentOnTree

4e96a16

There is a default value set in modifyControlsStateViaTree, but this is the only property that doesn't have an explicit default set by getDefaultControlsState. Add it for consistency.

Remove broken/unused searchNodes parameter

5595762

There is a type error that prevents this from working properly: includes() takes a single string, but an array of PhyloNodes is given. It's not used on any existing calls to updateTipRadii, so just remove it entirely.

Allow all parts of state to be undefined

701d856

This prevents type errors when calling setState.

victorlin force-pushed the victorlin/tree-typing branch from 0523c8f to 701d856 Compare October 30, 2024 00:51

victorlin marked this pull request as ready for review October 30, 2024 00:52

victorlin requested a review from jameshadfield October 30, 2024 00:52

jameshadfield reviewed Oct 30, 2024

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Add types to tree component #1864

Add types to tree component #1864

victorlin commented Oct 8, 2024 •

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jameshadfield commented Oct 9, 2024

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victorlin commented Oct 25, 2024

jameshadfield Oct 30, 2024

genehack Oct 30, 2024 •

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victorlin commented Oct 8, 2024 • edited Loading

Description of proposed changes

Checklist

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victorlin commented Oct 25, 2024

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victorlin commented Oct 8, 2024 •

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genehack Oct 30, 2024 •

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