chore: Biome linting with auto-fixes [DT-7060] (#53)

.github/workflows/ci.yml

@@ -57,8 +57,6 @@ jobs:
     lint:
         name: Lint
         runs-on: ubuntu-latest
-        # Skip job until we get a linter added
-        if: false
 
         steps:
             - uses: actions/checkout@v4
@@ -77,7 +75,7 @@ jobs:
               run: pnpm install --frozen-lockfile
 
             - name: Lint
-              run: echo "Add pnpm lint command here"
+              run: pnpm lint:check
 
     test:
         name: Test

biome.json

@@ -7,7 +7,7 @@
     },
     "files": {
         "ignoreUnknown": false,
-        "ignore": []
+        "ignore": ["**/dist/*"]
     },
     "formatter": {
         "enabled": true,

examples/src/app.tsx

@@ -1,8 +1,8 @@
 import React from 'react';
 import { BrowserRouter, Route, Routes } from 'react-router';
+import { DziDemo } from './dzi/dzi-demo';
 import { Home } from './home';
 import { OmezarrDemo } from './omezarr/omezarr-demo';
-import { DziDemo } from './dzi/dzi-demo';
 
 export function App() {
     return (

examples/src/common/image-renderer.ts

@@ -1,5 +1,6 @@
 import type { vec2, vec4 } from '@alleninstitute/vis-geometry';
-import REGL, { type Framebuffer2D } from 'regl';
+import type REGL from 'regl';
+import type { Framebuffer2D } from 'regl';
 
 type Props = {
     target: Framebuffer2D | null;

examples/src/common/loaders/ome-zarr/fetchSlice.worker.ts

@@ -1,6 +1,6 @@
+import { type ZarrDataset, type ZarrRequest, getSlice } from '@alleninstitute/vis-omezarr';
 // a web-worker which fetches slices of data, decodes them, and returns the result as a flat float32 array, using transferables
 import type { Chunk } from 'zarrita';
-import { type ZarrDataset, type ZarrRequest, getSlice } from '@alleninstitute/vis-omezarr';
 
 const ctx = self;
 type ZarrSliceRequest = {
@@ -11,7 +11,7 @@ type ZarrSliceRequest = {
     layerIndex: number;
 };
 function isSliceRequest(payload: any): payload is ZarrSliceRequest {
-    return typeof payload === 'object' && payload['type'] === 'ZarrSliceRequest';
+    return typeof payload === 'object' && payload.type === 'ZarrSliceRequest';
 }
 ctx.onmessage = (msg: MessageEvent<unknown>) => {
     const { data } = msg;

examples/src/common/loaders/ome-zarr/sliceWorkerPool.ts

@@ -1,5 +1,5 @@
-import { uniqueId } from 'lodash';
 import type { ZarrDataset, ZarrRequest } from '@alleninstitute/vis-omezarr';
+import { uniqueId } from 'lodash';
 
 type PromisifiedMessage = {
     requestCacheKey: string;

examples/src/common/loaders/scatterplot/data.ts

@@ -1,16 +1,16 @@
 // todo rename this file
 
-import { Box2D, visitBFS, type box2D, type vec2 } from '@alleninstitute/vis-geometry';
+import { Box2D, type box2D, type vec2, visitBFS } from '@alleninstitute/vis-geometry';
+import type REGL from 'regl';
 import {
-    fetchColumn,
     type ColumnData,
     type ColumnRequest,
     type ColumnarNode,
     type ColumnarTree,
     type SlideViewDataset,
+    fetchColumn,
     type loadDataset,
 } from './scatterbrain-loader';
-import REGL from 'regl';
 export type Dataset = ReturnType<typeof loadDataset>;
 export type RenderSettings = {
     dataset: Dataset;
@@ -27,7 +27,7 @@ function isVisible(view: box2D, sizeLimit: number, tree: ColumnarTree<vec2>) {
 }
 export function getVisibleItems(dataset: Dataset, view: box2D, sizeLimit: number) {
     const hits: ColumnarTree<vec2>[] = [];
-    let tree = 'slides' in dataset ? Object.values(dataset.slides)[0].tree : dataset.tree;
+    const tree = 'slides' in dataset ? Object.values(dataset.slides)[0].tree : dataset.tree;
     visitBFS(
         tree,
         (t: ColumnarTree<vec2>) => t.children,

examples/src/common/loaders/scatterplot/scatterbrain-loader.ts

@@ -1,6 +1,6 @@
 import { Box2D, Box3D, Vec3, type box, type box3D, type vec2, type vec3 } from '@alleninstitute/vis-geometry';
-import { MakeTaggedBufferView, type TaggedTypedArray, type WebGLSafeBasicType } from '../../typed-array';
 import type REGL from 'regl';
+import { MakeTaggedBufferView, type TaggedTypedArray, type WebGLSafeBasicType } from '../../typed-array';
 
 type volumeBound = {
     lx: number;

examples/src/data-renderers/annotation-renderer.ts

@@ -1,14 +1,14 @@
-import type REGL from 'regl';
-import type { RenderCallback } from './types';
 import { Box2D, Vec2, type box2D, type vec2, type vec4 } from '@alleninstitute/vis-geometry';
+import { type AsyncDataCache, type FrameLifecycle, beginLongRunningFrame } from '@alleninstitute/vis-scatterbrain';
+import type REGL from 'regl';
+import type { Camera } from '~/common/camera';
+import type { AnnotationGrid } from '~/data-sources/annotation/annotation-grid';
+import { MeshFromAnnotation } from '~/data-sources/annotation/annotation-to-mesh';
+import { fetchAnnotation } from '~/data-sources/annotation/fetch-annotation';
 import type { AnnotationMesh, GPUAnnotationMesh } from '~/data-sources/annotation/types';
-import type { buildLoopRenderer, buildMeshRenderer } from './mesh-renderer';
 import type { OptionalTransform } from '~/data-sources/types';
-import { AsyncDataCache, beginLongRunningFrame, type FrameLifecycle } from '@alleninstitute/vis-scatterbrain';
-import { fetchAnnotation } from '~/data-sources/annotation/fetch-annotation';
-import { MeshFromAnnotation } from '~/data-sources/annotation/annotation-to-mesh';
-import type { AnnotationGrid } from '~/data-sources/annotation/annotation-grid';
-import type { Camera } from '~/common/camera';
+import type { buildLoopRenderer, buildMeshRenderer } from './mesh-renderer';
+import type { RenderCallback } from './types';
 
 type SlideId = string;
 

examples/src/data-renderers/dynamicGridSlideRenderer.ts

@@ -1,13 +1,13 @@
-import { beginLongRunningFrame, type AsyncDataCache } from '@alleninstitute/vis-scatterbrain';
-import type REGL from 'regl';
-import { buildRenderer as buildScatterplotRenderer } from './scatterplot';
 import { Box2D, Vec2, type vec2 } from '@alleninstitute/vis-geometry';
-import { applyOptionalTrn } from './utils';
+import { type AsyncDataCache, beginLongRunningFrame } from '@alleninstitute/vis-scatterbrain';
+import type REGL from 'regl';
+import type { Camera } from '~/common/camera';
+import { fetchItem, getVisibleItemsInSlide } from '~/common/loaders/scatterplot/data';
+import type { ColumnRequest, ColumnarTree } from '~/common/loaders/scatterplot/scatterbrain-loader';
 import type { DynamicGrid, DynamicGridSlide } from '../data-sources/scatterplot/dynamic-grid';
+import type { buildRenderer as buildScatterplotRenderer } from './scatterplot';
 import type { RenderCallback } from './types';
-import { fetchItem, getVisibleItemsInSlide } from '~/common/loaders/scatterplot/data';
-import type { ColumnarTree, ColumnRequest } from '~/common/loaders/scatterplot/scatterbrain-loader';
-import type { Camera } from '~/common/camera';
+import { applyOptionalTrn } from './utils';
 type CacheContentType = {
     type: 'vbo';
     data: REGL.Buffer;

examples/src/data-renderers/lineRenderer.ts

@@ -1,5 +1,6 @@
 import type { box2D, vec2, vec4 } from '@alleninstitute/vis-geometry';
-import REGL, { type AttributeConfig } from 'regl';
+import type REGL from 'regl';
+import type { AttributeConfig } from 'regl';
 import type { ColumnData } from '~/common/loaders/scatterplot/scatterbrain-loader';
 
 type Attrs = { pos: REGL.AttributeConfig };
@@ -75,7 +76,7 @@ export function buildPathRenderer(regl: REGL.Regl) {
         settings: { view: box2D; target: REGL.Framebuffer2D | null },
         tasks: Record<string, ColumnData | object | undefined>,
     ) => {
-        const pos = tasks['position'];
+        const pos = tasks.position;
         const { view, target } = settings;
         if (pos && 'type' in pos && pos.type === 'float') {
             cmd(pos.data, item.color, view, target);

examples/src/data-renderers/mesh-renderer.ts

@@ -1,5 +1,5 @@
-import type { vec4, vec2 } from '@alleninstitute/vis-geometry';
-import REGL from 'regl';
+import type { vec2, vec4 } from '@alleninstitute/vis-geometry';
+import type REGL from 'regl';
 
 const frag = `
 precision highp float;

examples/src/data-renderers/scatterplot.ts

@@ -1,7 +1,8 @@
-import REGL, { type Framebuffer2D } from 'regl';
 import { Box2D, type box2D, type vec2, type vec4 } from '@alleninstitute/vis-geometry';
-import type { ColumnarTree, ColumnBuffer } from '~/common/loaders/scatterplot/scatterbrain-loader';
+import type REGL from 'regl';
+import type { Framebuffer2D } from 'regl';
 import type { RenderSettings } from '~/common/loaders/scatterplot/data';
+import type { ColumnBuffer, ColumnarTree } from '~/common/loaders/scatterplot/scatterbrain-loader';
 
 type Props = {
     view: vec4;

examples/src/data-renderers/simpleAnnotationRenderer.ts

@@ -1,12 +1,12 @@
-import type REGL from 'regl';
-import { beginLongRunningFrame, type AsyncDataCache } from '@alleninstitute/vis-scatterbrain';
-import type { RenderCallback } from './types';
 import { Box2D, type box2D } from '@alleninstitute/vis-geometry';
-import type { Path, buildPathRenderer } from './lineRenderer';
+import { type AsyncDataCache, beginLongRunningFrame } from '@alleninstitute/vis-scatterbrain';
 import { flatten } from 'lodash';
-import type { OptionalTransform } from '../data-sources/types';
+import type REGL from 'regl';
 import type { Camera } from '~/common/camera';
 import type { ColumnData } from '~/common/loaders/scatterplot/scatterbrain-loader';
+import type { OptionalTransform } from '../data-sources/types';
+import type { Path, buildPathRenderer } from './lineRenderer';
+import type { RenderCallback } from './types';
 
 type Renderer = ReturnType<typeof buildPathRenderer>;
 

examples/src/data-renderers/utils.ts

@@ -1,6 +1,6 @@
 import { Box2D, Vec2, type box2D, type vec2 } from '@alleninstitute/vis-geometry';
 
-export function applyOptionalTrn(box: box2D, trn: undefined | { offset: vec2 }, inv: boolean = false) {
+export function applyOptionalTrn(box: box2D, trn: undefined | { offset: vec2 }, inv = false) {
     // todo scale...
     return trn ? Box2D.translate(box, Vec2.scale(trn.offset, inv ? -1 : 1)) : box;
 }

examples/src/data-renderers/versa-renderer.ts

@@ -1,15 +1,16 @@
-import REGL, { type Framebuffer2D } from 'regl';
 import { Box2D, type Interval, Vec2, type box2D, type vec2, type vec4 } from '@alleninstitute/vis-geometry';
-import { omit } from 'lodash';
 import {
+    type ZarrDataset,
+    type ZarrRequest,
     pickBestScale,
     planeSizeInVoxels,
     sizeInUnits,
-    type ZarrDataset,
-    type ZarrRequest,
 } from '@alleninstitute/vis-omezarr';
-import { getSlicePool } from '~/common/loaders/ome-zarr/sliceWorkerPool';
+import { omit } from 'lodash';
+import type REGL from 'regl';
+import type { Framebuffer2D } from 'regl';
 import type { Camera } from '~/common/camera';
+import { getSlicePool } from '~/common/loaders/ome-zarr/sliceWorkerPool';
 
 const TILE_SIZE = 256;
 

examples/src/data-renderers/volumeSliceRenderer.ts

@@ -1,28 +1,28 @@
+import { type AsyncDataCache, beginLongRunningFrame } from '@alleninstitute/vis-scatterbrain';
 import type REGL from 'regl';
-import { beginLongRunningFrame, type AsyncDataCache } from '@alleninstitute/vis-scatterbrain';
 import type { RenderCallback } from './types';
 
-import { applyOptionalTrn } from './utils';
 import { Box2D, Vec2, type vec2 } from '@alleninstitute/vis-geometry';
-import type { AxisAlignedZarrSlice } from '../data-sources/ome-zarr/planar-slice';
-import type { AxisAlignedZarrSliceGrid } from '../data-sources/ome-zarr/slice-grid';
 import {
     pickBestScale,
     sizeInUnits,
     sizeInVoxels,
     sliceDimensionForPlane,
     uvForPlane,
 } from '@alleninstitute/vis-omezarr';
+import type { Camera } from '~/common/camera';
+import type { AxisAlignedZarrSlice } from '../data-sources/ome-zarr/planar-slice';
+import type { AxisAlignedZarrSliceGrid } from '../data-sources/ome-zarr/slice-grid';
+import { applyOptionalTrn } from './utils';
 import {
-    cacheKeyFactory,
-    getVisibleTiles,
-    requestsForTile,
     type AxisAlignedPlane,
-    type buildVersaRenderer,
     type VoxelSliceRenderSettings,
     type VoxelTile,
+    type buildVersaRenderer,
+    cacheKeyFactory,
+    getVisibleTiles,
+    requestsForTile,
 } from './versa-renderer';
-import type { Camera } from '~/common/camera';
 
 type Renderer = ReturnType<typeof buildVersaRenderer>;
 type CacheContentType = { type: 'texture2D'; data: REGL.Texture2D };
@@ -113,7 +113,7 @@ export function renderGrid<C extends CacheContentType | object>(
     for (let i = 0; i < slices; i++) {
         const gridIndex: vec2 = [i % rowSize, Math.floor(i / rowSize)];
 
-        let param = i / slices;
+        const param = i / slices;
         const slice: AxisAlignedZarrSlice = {
             ...grid,
             type: 'AxisAlignedZarrSlice',

examples/src/data-sources/annotation/annotation-codec.ts

@@ -1,5 +1,5 @@
+import { compileSchema, parseSchema } from 'kiwi-schema';
 import type { AnnotationCodec } from './annotation-schema-type';
-import { parseSchema, compileSchema } from 'kiwi-schema';
 
 export const AnnotationSchema = `
 enum PathCommandType {

examples/src/data-sources/annotation/annotation-to-mesh.ts

@@ -1,4 +1,4 @@
-import { type box2D, type vec2, Box2D, Vec2, Vec4 } from '@alleninstitute/vis-geometry';
+import { Box2D, Vec2, Vec4, type box2D, type vec2 } from '@alleninstitute/vis-geometry';
 import type { Annotation, Path, PathCommand } from './annotation-schema-type';
 import type { AnnotationMesh, AnnotationPolygon, ClosedLoop } from './types';
 // a helper function, which does a first path over commands, grouping them into closed loops

examples/src/data-sources/annotation/types.ts

@@ -1,4 +1,4 @@
-import type { vec4, box2D } from '@alleninstitute/vis-geometry';
+import type { box2D, vec4 } from '@alleninstitute/vis-geometry';
 import type REGL from 'regl';
 
 export type ClosedLoop = {

examples/src/data-sources/ome-zarr/planar-slice.ts

@@ -1,4 +1,4 @@
-import { loadMetadata, type ZarrDataset } from '@alleninstitute/vis-omezarr';
+import { type ZarrDataset, loadMetadata } from '@alleninstitute/vis-omezarr';
 import type { AxisAlignedPlane } from '~/data-renderers/versa-renderer';
 import type { ColorMapping } from '../../data-renderers/types';
 import type { OptionalTransform, Simple2DTransform } from '../types';

examples/src/data-sources/ome-zarr/slice-grid.ts

@@ -1,4 +1,4 @@
-import { loadMetadata, type ZarrDataset } from '@alleninstitute/vis-omezarr';
+import { type ZarrDataset, loadMetadata } from '@alleninstitute/vis-omezarr';
 import type { AxisAlignedPlane } from '~/data-renderers/versa-renderer';
 import type { ColorMapping } from '../../data-renderers/types';
 import type { OptionalTransform, Simple2DTransform } from '../types';

examples/src/data-sources/scatterplot/dynamic-grid.ts

@@ -1,9 +1,9 @@
 import {
     type ColumnRequest,
     type SlideViewDataset,
-    loadScatterbrainJson,
     isSlideViewData,
     loadDataset,
+    loadScatterbrainJson,
 } from '~/common/loaders/scatterplot/scatterbrain-loader';
 import type { OptionalTransform, Simple2DTransform } from '../types';
 

examples/src/dzi/dzi-demo.tsx

@@ -1,10 +1,10 @@
+import type { DziImage, DziRenderSettings } from '@alleninstitute/vis-dzi';
+import { Box2D, type box2D, type vec2 } from '@alleninstitute/vis-geometry';
 import { useEffect, useMemo, useRef, useState } from 'react';
-import { RenderServerProvider } from '../common/react/render-server-provider';
 import React from 'react';
-import type { DziImage, DziRenderSettings } from '@alleninstitute/vis-dzi';
-import { Box2D, Vec2, type box2D, type vec2 } from '@alleninstitute/vis-geometry';
-import { DziViewer } from './dzi-viewer';
 import { pan, zoom } from '~/common/camera';
+import { RenderServerProvider } from '../common/react/render-server-provider';
+import { DziViewer } from './dzi-viewer';
 
 // We know the sizes and formats ahead of time for these examples,
 // if you'd like to see how to get this data from an endpoint with a dzi file check out use-dzi-image.ts
@@ -90,7 +90,7 @@ export function DziDemo() {
             <p>Scroll below to view image</p>
             <div style={{ display: 'flex', flexDirection: 'row' }}>
                 {images.map((v) => (
-                    <div style={{ width: screenSize[0], height: screenSize[1] }}>
+                    <div key={v.imagesUrl} style={{ width: screenSize[0], height: screenSize[1] }}>
                         <DziViewer
                             id={v.imagesUrl}
                             dzi={v}

examples/src/dzi/dzi-viewer.tsx

@@ -1,16 +1,15 @@
-import { useContext, useEffect, useRef, useState } from 'react';
 import {
-    buildDziRenderer,
+    type GpuProps as CachedPixels,
     type DziImage,
     type DziRenderSettings,
     type DziTile,
-    type GpuProps as CachedPixels,
     buildAsyncDziRenderer,
+    buildDziRenderer,
 } from '@alleninstitute/vis-dzi';
-import { buildAsyncRenderer, type RenderFrameFn } from '@alleninstitute/vis-scatterbrain';
 import { Vec2, type vec2 } from '@alleninstitute/vis-geometry';
+import type { RenderFrameFn, buildAsyncRenderer } from '@alleninstitute/vis-scatterbrain';
+import { useContext, useEffect, useRef, useState } from 'react';
 import { renderServerContext } from '~/common/react/render-server-provider';
-import React from 'react';
 
 type Props = {
     id: string;
@@ -36,7 +35,7 @@ export function DziViewer(props: Props) {
         >();
 
     useEffect(() => {
-        if (server && server.regl) {
+        if (server?.regl) {
             renderer.current = buildAsyncDziRenderer(server.regl);
         }
         return () => {
@@ -74,13 +73,13 @@ export function DziViewer(props: Props) {
             server.beginRendering(
                 renderMyData,
                 (e) => {
-                    if (e.status == 'begin') {
+                    if (e.status === 'begin') {
                         server.regl?.clear({
                             framebuffer: e.target,
                             color: [0, 0, 0, 0],
                             depth: 1,
                         });
-                    } else if (e.status == 'progress' || e.status == 'finished') {
+                    } else if (e.status === 'progress' || e.status === 'finished') {
                         e.server.copyToClient(compose);
                     }
                 },