More lint fixes

.eslintrc.json

@@ -32,6 +32,7 @@
     "@typescript-eslint/ban-types": "off",
     "@typescript-eslint/camelcase": "off",
     "@typescript-eslint/explicit-function-return-type": "off",
+    "@typescript-eslint/prefer-nullish-coalescing": "off",
     "@typescript-eslint/no-base-to-string": "off",
     "@typescript-eslint/explicit-module-boundary-types": "off",
     "@typescript-eslint/no-empty-function": "off",

docs/util.ts

@@ -73,10 +73,10 @@ export function extractWithComment(
       'action',
       'method',
     ]
-    for (let i = 0; i < list.length; i++) {
-      const type = '#' + list[i]
+    for (const entry of list) {
+      const type = '#' + entry
       if (fulltext.includes(type) && r.comment.includes(type)) {
-        cb({ type: list[i], ...r })
+        cb({ type: entry, ...r })
       }
     }
   }

package.json

@@ -52,6 +52,7 @@
     "@storybook/react": "^7.0.0",
     "@storybook/react-webpack5": "^7.0.0",
     "@svgr/webpack": "^8.1.0",
+    "@testing-library/dom": "^8.0.0",
     "@testing-library/jest-dom": "^5.16.5",
     "@testing-library/react": "^12.0.0",
     "@testing-library/user-event": "^14.4.3",
@@ -174,6 +175,7 @@
     "typescript": "^5.1.3",
     "web-encoding": "^1.1.5",
     "webpack": "^5.64.4",
+    "webpack-cli": "^5.1.4",
     "webpack-dev-server": "^4.6.0",
     "webpack-manifest-plugin": "^4.0.2"
   },

packages/core/data_adapters/dataAdapterCache.ts

@@ -34,10 +34,13 @@ export async function getAdapter(
   // cache the adapter object
   const cacheKey = adapterConfigCacheKey(adapterConfigSnapshot)
   if (!adapterCache[cacheKey]) {
-    const adapterType = (adapterConfigSnapshot || {}).type
+    const adapterType = adapterConfigSnapshot?.type
+
     if (!adapterType) {
       throw new Error(
-        'could not determine adapter type from adapter config snapshot',
+        `could not determine adapter type from adapter config snapshot ${JSON.stringify(
+          adapterConfigSnapshot,
+        )}`,
       )
     }
     const dataAdapterType = pluginManager.getAdapterType(adapterType)

packages/core/pluggableElementTypes/renderers/util/serializableFilterChain.ts

@@ -25,10 +25,10 @@ export default class SerializableFilterChain {
 
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
   passes(...args: any[]) {
-    for (let i = 0; i < this.filterChain.length; i += 1) {
+    for (const entry of this.filterChain) {
       if (
         // @ts-expect-error
-        !this.filterChain[i].expr.evalSync({ feature: args[0] })
+        !entry.expr.evalSync({ feature: args[0] })
       ) {
         return false
       }

packages/core/ui/FileSelector/LocalFileChooser.tsx

@@ -46,7 +46,7 @@ function LocalFileChooser(props: {
               type="file"
               hidden
               onChange={({ target }) => {
-                const file = target && target.files && target.files[0]
+                const file = target?.files?.[0]
                 if (file) {
                   if (isElectron) {
                     setLocation({

packages/core/util/dedupe.ts

@@ -5,8 +5,7 @@ export function dedupe<T>(list: T[], hasher: Hasher<T> = JSON.stringify) {
   const clone: T[] = []
   const lookup = new Set<string>()
 
-  for (let i = 0; i < list.length; i++) {
-    const entry = list[i]
+  for (const entry of list) {
     const hashed = hasher(entry)
 
     if (!lookup.has(hashed)) {

packages/core/util/index.ts

@@ -1260,24 +1260,24 @@ export function localStorageSetItem(str: string, item: string) {
 
 export function max(arr: number[], init = -Infinity) {
   let max = init
-  for (let i = 0; i < arr.length; i++) {
-    max = arr[i] > max ? arr[i] : max
+  for (const entry of arr) {
+    max = entry > max ? entry : max
   }
   return max
 }
 
 export function min(arr: number[], init = Infinity) {
   let min = init
-  for (let i = 0; i < arr.length; i++) {
-    min = arr[i] < min ? arr[i] : min
+  for (const entry of arr) {
+    min = entry < min ? entry : min
   }
   return min
 }
 
 export function sum(arr: number[]) {
   let sum = 0
-  for (let i = 0; i < arr.length; i++) {
-    sum += arr[i]
+  for (const entry of arr) {
+    sum += entry
   }
   return sum
 }

packages/core/util/layouts/GranularRectLayout.test.js

@@ -39,8 +39,8 @@ describe('GranularRectLayout', () => {
       ['1,32', 239691, 245015, 16],
     ]
 
-    for (let i = 0; i < testRects.length; i += 1) {
-      const top = l.addRect(...testRects[i])
+    for (const rect of testRects) {
+      const top = l.addRect(...rect)
       expect(top).toEqual(0)
     }
   })

packages/core/util/layouts/GranularRectLayout.ts

@@ -457,8 +457,7 @@ export default class GranularRectLayout<T> implements BaseLayout<T> {
     const pLeft = Math.floor(left / this.pitchX)
     const pRight = Math.floor(right / this.pitchX)
     const { bitmap } = this
-    for (let y = 0; y < bitmap.length; y += 1) {
-      const row = bitmap[y]
+    for (const row of bitmap) {
       if (row) {
         row.discardRange(pLeft, pRight)
       }

packages/text-indexing/src/types/vcfAdapter.ts

@@ -68,8 +68,7 @@ export async function* indexVcf(
       .filter((f): f is string => !!f)
 
     const ids = id.split(',')
-    for (let i = 0; i < ids.length; i++) {
-      const id = ids[i]
+    for (const id of ids) {
       const attrs = [id]
       const record = JSON.stringify([
         encodeURIComponent(locStr),

packages/text-indexing/src/util.ts

@@ -85,7 +85,9 @@ export interface VcfAdapter {
   type: 'VcfAdapter'
   vcfLocation: UriLocation | LocalPathLocation
 }
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
 export type Track = Record<string, any>
+
 export interface TextSearching {
   indexingFeatureTypesToExclude?: string[]
   indexingAttributes?: string[]

plugins/alignments/src/CramAdapter/util.ts

@@ -28,9 +28,7 @@ export function readFeaturesToMismatches(
   let sublen = 0
   let lastPos = start
 
-  for (let i = 0; i < readFeatures.length; i++) {
-    const f = readFeatures[i]
-    const { code, pos, data, sub, ref } = f
+  for (const { refPos: p, code, pos, data, sub, ref } of readFeatures) {
     sublen = refPos - lastPos
     lastPos = refPos
 
@@ -43,7 +41,7 @@ export function readFeaturesToMismatches(
       }
       insLen = 0
     }
-    refPos = f.refPos - 1 - start
+    refPos = p - 1 - start
 
     if (code === 'X') {
       // substitution
@@ -150,8 +148,7 @@ export function readFeaturesToCIGAR(
   let sublen = 0
   let insLen = 0
   if (readFeatures !== undefined) {
-    for (let i = 0; i < readFeatures.length; i++) {
-      const { code, refPos, sub, data } = readFeatures[i]
+    for (const { code, refPos, sub, data } of readFeatures) {
       sublen = refPos - lastPos
       seq += ref.slice(lastPos - refStart, refPos - refStart)
       lastPos = refPos

plugins/alignments/src/LinearReadCloudDisplay/drawPairChains.ts

@@ -94,8 +94,7 @@ export function drawPairChains({
   const maxD = Math.log(max(coords.map(c => c.distance)))
   const minD = Math.max(Math.log(min(coords.map(c => c.distance))) - 1, 0)
   const scaler = (self.height - 20) / (maxD - minD)
-  for (let i = 0; i < coords.length; i++) {
-    const { r1e, r1s, r2e, r2s, distance, v0, v1 } = coords[i]
+  for (const { r1e, r1s, r2e, r2s, distance, v0, v1 } of coords) {
     const w1 = Math.max(r1e - r1s, 2)
     const w2 = Math.max(r2e - r2s, 2)
     const [fill, stroke] = getPairedColor({ type, v0, v1, stats }) || []

plugins/alignments/src/MismatchParser/index.ts

@@ -179,15 +179,15 @@ export function mdToMismatches(
 
   // now actually parse the MD string
   const md = mdstring.match(mdRegex) || []
-  for (let i = 0; i < md.length; i++) {
-    const token = md[i]
+  for (const token of md) {
     const num = +token
     if (!Number.isNaN(num)) {
       curr.start += num
     } else if (token.startsWith('^')) {
       curr.start += token.length - 1
     } else {
       // mismatch
+      // eslint-disable-next-line @typescript-eslint/prefer-for-of
       for (let j = 0; j < token.length; j += 1) {
         curr.length = 1
 
@@ -315,8 +315,7 @@ export function getModificationPositions(
   const seq = fstrand === -1 ? revcom(fseq) : fseq
   const mods = mm.split(';').filter(mod => !!mod)
   const result = []
-  for (let i = 0; i < mods.length; i++) {
-    const mod = mods[i]
+  for (const mod of mods) {
     const [basemod, ...skips] = mod.split(',')
 
     // regexes based on parse_mm.pl from hts-specs
@@ -340,12 +339,11 @@ export function getModificationPositions(
     // sequence of the read, if we have a modification type e.g. C+m;2 and a
     // sequence ACGTACGTAC we skip the two instances of C and go to the last
     // C
-    for (let j = 0; j < types.length; j++) {
-      const type = types[j]
+    for (const type of types) {
       let i = 0
       const positions = []
-      for (let k = 0; k < skips.length; k++) {
-        let delta = +skips[k]
+      for (const d of skips) {
+        let delta = +d
         do {
           if (base === 'N' || base === seq[i]) {
             delta--

plugins/alignments/src/PileupRenderer/layoutFeature.ts

@@ -36,8 +36,7 @@ export function layoutFeature({
     const mismatches = feature.get('mismatches') as Mismatch[]
     const seq = feature.get('seq') as string
     if (seq) {
-      for (let i = 0; i < mismatches.length; i += 1) {
-        const { type, start, cliplen = 0 } = mismatches[i]
+      for (const { type, start, cliplen = 0 } of mismatches) {
         if (type === 'softclip') {
           start === 0 ? (expansionBefore = cliplen) : (expansionAfter = cliplen)
         }

plugins/alignments/src/PileupRenderer/renderMismatches.ts

@@ -51,8 +51,7 @@ export function renderMismatches({
 
   // two pass rendering: first pass, draw all the mismatches except wide
   // insertion markers
-  for (let i = 0; i < mismatches.length; i += 1) {
-    const mismatch = mismatches[i]
+  for (const mismatch of mismatches) {
     const mstart = start + mismatch.start
     const mlen = mismatch.length
     const mbase = mismatch.base
@@ -164,8 +163,7 @@ export function renderMismatches({
 
   // second pass, draw wide insertion markers on top
   if (drawIndels) {
-    for (let i = 0; i < mismatches.length; i += 1) {
-      const mismatch = mismatches[i]
+    for (const mismatch of mismatches) {
       const mstart = start + mismatch.start
       const mlen = mismatch.length
       const [leftPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx)

plugins/alignments/src/SNPCoverageRenderer/SNPCoverageRenderer.ts

@@ -113,8 +113,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     // Use two pass rendering, which helps in visualizing the SNPs at higher
     // bpPerPx First pass: draw the gray background
     ctx.fillStyle = colorForBase.total
-    for (let i = 0; i < coverage.length; i++) {
-      const feature = coverage[i]
+    for (const feature of coverage) {
       const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)
       const w = rightPx - leftPx + fudgeFactor
       const score = feature.get('score') as number
@@ -136,8 +135,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     // which can be wider than the actual bpPerPx This reduces overdrawing of
     // the grey background over the SNPs
 
-    for (let i = 0; i < coverage.length; i++) {
-      const feature = coverage[i]
+    for (const feature of coverage) {
       const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)
 
       const score = feature.get('score') as number
@@ -147,8 +145,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
       const keys = Object.keys(snpinfo.cov).sort()
 
       let curr = 0
-      for (let i = 0; i < keys.length; i++) {
-        const base = keys[i]
+      for (const base of keys) {
         const { total } = snpinfo.cov[base]
         ctx.fillStyle =
           colorForBase[base] ||
@@ -170,8 +167,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
       const indicatorHeight = 4.5
       if (drawInterbaseCounts) {
         let curr = 0
-        for (let i = 0; i < interbaseEvents.length; i++) {
-          const base = interbaseEvents[i]
+        for (const base of interbaseEvents) {
           const { total } = snpinfo.noncov[base]
           const r = 0.6
           ctx.fillStyle = colorForBase[base]
@@ -189,8 +185,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
         let accum = 0
         let max = 0
         let maxBase = ''
-        for (let i = 0; i < interbaseEvents.length; i++) {
-          const base = interbaseEvents[i]
+        for (const base of interbaseEvents) {
           const { total } = snpinfo.noncov[base]
           accum += total
           if (total > max) {
@@ -219,8 +214,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     }
 
     if (drawArcs) {
-      for (let i = 0; i < skips.length; i++) {
-        const f = skips[i]
+      for (const f of skips) {
         const [left, right] = bpSpanPx(
           f.get('start'),
           f.get('end'),

plugins/breakpoint-split-view/src/BreakpointSplitView/components/Translocations.tsx

@@ -68,8 +68,7 @@ const Translocations = observer(function ({
         // we follow a path in the list of chunks, not from top to bottom,
         // just in series following x1,y1 -> x2,y2
         const ret = []
-        for (let i = 0; i < chunk.length; i += 1) {
-          const { layout: c1, feature: f1, level: level1 } = chunk[i]
+        for (const { layout: c1, feature: f1, level: level1 } of chunk) {
           const level2 = level1 === 0 ? 1 : 0
           const id = f1.id()
           if (!c1) {

plugins/breakpoint-split-view/src/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.tsx

@@ -48,8 +48,7 @@ function getTrackOffsets(
 ) {
   const offsets = {} as Record<string, number>
   let curr = textOffset
-  for (let i = 0; i < view.tracks.length; i++) {
-    const track = view.tracks[i]
+  for (const track of view.tracks) {
     offsets[track.configuration.trackId] = curr + extra
     curr += track.displays[0].height + textOffset
   }

plugins/breakpoint-split-view/src/BreakpointSplitView/util.ts

@@ -35,7 +35,7 @@ function heightFromSpecificLevel(
 }
 
 export function getPxFromCoordinate(view: LGV, refName: string, coord: number) {
-  return ((view.bpToPx({ refName, coord }) || {}).offsetPx || 0) - view.offsetPx
+  return (view.bpToPx({ refName, coord })?.offsetPx || 0) - view.offsetPx
 }
 
 // get's the yposition of a layout record in a track

plugins/circular-view/src/CircularView/models/viewportVisibleRegion.ts

@@ -114,8 +114,7 @@ export function viewportVisibleSection(
       [viewR, viewB],
     ]
     let maxRho = -Infinity
-    for (let i = 0; i < vertices.length; i += 1) {
-      const [x, y] = vertices[i]
+    for (const [x, y] of vertices) {
       const rho = Math.sqrt(x * x + y * y)
       if (rho > maxRho) {
         maxRho = rho
@@ -231,9 +230,8 @@ export function viewportVisibleSection(
   let rhoMax = -Infinity
   let thetaMin = Infinity
   let thetaMax = -Infinity
-  for (let i = 0; i < vertices.length; i += 1) {
+  for (const [vx, vy] of vertices) {
     // ignore vertex if outside the viewport
-    const [vx, vy] = vertices[i]
     if (vx >= viewL && vx <= viewR && vy >= viewT && vy <= viewB) {
       const [rho, theta] = cartesianToPolar(vx * reflect, vy * reflect)
       // ignore vertex if outside the circle

plugins/comparative-adapters/src/DeltaAdapter/util.ts

@@ -93,8 +93,8 @@ export function paf_delta2paf(buffer: Buffer) {
             throw new Error(`inconsistent alignment on line ${i}`)
           }
           cigar.push((re - rs - x) << 4)
-          for (let i = 0; i < cigar.length; ++i) {
-            const rlen = cigar[i] >> 4
+          for (const entry of cigar) {
+            const rlen = entry >> 4
             blen += rlen
             cigar_str.push(rlen + 'MID'.charAt(cigar[i] & 0xf))
           }