Bump prettier

GMOD · Jul 17, 2023 · a8409c4 · a8409c4
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commit a8409c4
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Showing 31 changed files with 744 additions and 516 deletions.
diff --git a/.eslintrc.json b/.eslintrc.json
@@ -45,7 +45,9 @@
     "testing-library/prefer-screen-queries": 0,
 
     "unicorn/no-new-array": 0,
+    "unicorn/no-empty-file": 0,
     "unicorn/prefer-type-error": 0,
+    "unicorn/prefer-modern-math-apis": 0,
     "unicorn/prefer-node-protocol": 0,
     "unicorn/no-unreadable-array-destructuring": 0,
     "unicorn/no-abusive-eslint-disable": 0,

diff --git a/component_tests/cgv/public/index.html b/component_tests/cgv/public/index.html
@@ -1,4 +1,4 @@
-<!DOCTYPE html>
+<!doctype html>
 <html lang="en">
   <head>
     <meta charset="utf-8" />

diff --git a/component_tests/lgv/public/index.html b/component_tests/lgv/public/index.html
@@ -1,4 +1,4 @@
-<!DOCTYPE html>
+<!doctype html>
 <html lang="en">
   <head>
     <meta charset="utf-8" />

diff --git a/component_tests/react-app/public/index.html b/component_tests/react-app/public/index.html
@@ -1,4 +1,4 @@
-<!DOCTYPE html>
+<!doctype html>
 <html lang="en">
   <head>
     <meta charset="utf-8" />

diff --git a/package.json b/package.json
@@ -93,7 +93,7 @@
     "@types/shortid": "^0.0.29",
     "@types/string-template": "^1.0.2",
     "@types/tmp": "^0.2.1",
-    "@typescript-eslint/parser": "^5.45.1",
+    "@typescript-eslint/parser": "^6.0.0",
     "babel-loader": "^9.1.0",
     "body-parser": "^1.20.2",
     "canvas": "^2.9.1",
@@ -103,18 +103,18 @@
     "cross-spawn": "^7.0.1",
     "crypto-js": "^3.0.0",
     "dependency-graph": "^0.11.0",
-    "electron": "25.2.0",
+    "electron": "25.3.0",
     "electron-builder": "^24.4.0",
     "electron-mock-ipc": "^0.3.8",
     "eslint": "^8.0.0",
     "eslint-config-prettier": "^8.5.0",
     "eslint-config-react-app": "^7.0.0",
     "eslint-plugin-cypress": "^2.12.1",
     "eslint-plugin-monorepo": "^0.3.2",
-    "eslint-plugin-prettier": "^4.0.0",
+    "eslint-plugin-prettier": "^5.0.0",
     "eslint-plugin-react-hooks": "^4.3.0",
     "eslint-plugin-tsdoc": "^0.2.4",
-    "eslint-plugin-unicorn": "^47.0.0",
+    "eslint-plugin-unicorn": "^48.0.0",
     "express": "^4.18.2",
     "express-basic-auth": "^1.2.1",
     "file-loader": "^6.2.0",
@@ -133,7 +133,7 @@
     "nock": "^13.2.1",
     "node-polyfill-webpack-plugin": "^2.0.1",
     "npm-run-all": "^4.1.5",
-    "prettier": "^2.5.1",
+    "prettier": "^3.0.0",
     "prop-types": "^15.0.0",
     "react": "^17.0.0",
     "react-dom": "^17.0.0",

diff --git a/packages/core/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.tsx b/packages/core/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.tsx
@@ -20,153 +20,152 @@ interface SeqPanelProps {
   mode: string
   intronBp?: number
 }
-const SeqPanel = React.forwardRef<HTMLDivElement, SeqPanelProps>(function (
-  props,
-  ref,
-) {
-  const { feature, mode, intronBp = 10 } = props
-  let {
-    sequence: { seq, upstream = '', downstream = '' },
-  } = props
-  const { subfeatures = [] } = feature
+const SeqPanel = React.forwardRef<HTMLDivElement, SeqPanelProps>(
+  function (props, ref) {
+    const { feature, mode, intronBp = 10 } = props
+    let {
+      sequence: { seq, upstream = '', downstream = '' },
+    } = props
+    const { subfeatures = [] } = feature
 
-  const children = subfeatures
-    .sort((a, b) => a.start - b.start)
-    .map(sub => ({
-      ...sub,
-      start: sub.start - feature.start,
-      end: sub.end - feature.start,
-    }))
+    const children = subfeatures
+      .sort((a, b) => a.start - b.start)
+      .map(sub => ({
+        ...sub,
+        start: sub.start - feature.start,
+        end: sub.end - feature.start,
+      }))
 
-  // we filter duplicate entries in cds and exon lists duplicate entries may be
-  // rare but was seen in Gencode v36 track NCList, likely a bug on GFF3 or
-  // probably worth ignoring here (produces broken protein translations if
-  // included)
-  //
-  // position 1:224,800,006..225,203,064 gene ENSG00000185842.15 first
-  // transcript ENST00000445597.6
-  //
-  // http://localhost:3000/?config=test_data%2Fconfig.json&session=share-FUl7G1isvF&password=HXh5Y
+    // we filter duplicate entries in cds and exon lists duplicate entries may be
+    // rare but was seen in Gencode v36 track NCList, likely a bug on GFF3 or
+    // probably worth ignoring here (produces broken protein translations if
+    // included)
+    //
+    // position 1:224,800,006..225,203,064 gene ENSG00000185842.15 first
+    // transcript ENST00000445597.6
+    //
+    // http://localhost:3000/?config=test_data%2Fconfig.json&session=share-FUl7G1isvF&password=HXh5Y
 
-  let cds = dedupe(children.filter(sub => sub.type === 'CDS'))
-  let utr = dedupe(children.filter(sub => sub.type.match(/utr/i)))
-  let exons = dedupe(children.filter(sub => sub.type === 'exon'))
+    let cds = dedupe(children.filter(sub => sub.type === 'CDS'))
+    let utr = dedupe(children.filter(sub => sub.type.match(/utr/i)))
+    let exons = dedupe(children.filter(sub => sub.type === 'exon'))
 
-  if (!utr.length && cds.length && exons.length) {
-    utr = calculateUTRs(cds, exons)
-  }
-  if (!utr.length && cds.length && !exons.length) {
-    utr = calculateUTRs2(cds, {
-      start: 0,
-      end: feature.end - feature.start,
-      type: 'gene',
-    })
-  }
+    if (!utr.length && cds.length && exons.length) {
+      utr = calculateUTRs(cds, exons)
+    }
+    if (!utr.length && cds.length && !exons.length) {
+      utr = calculateUTRs2(cds, {
+        start: 0,
+        end: feature.end - feature.start,
+        type: 'gene',
+      })
+    }
 
-  if (feature.strand === -1) {
-    // doing this in a single assignment is needed because downstream and
-    // upstream are swapped so this avoids a temp variable
-    ;[seq, upstream, downstream] = [
-      revcom(seq),
-      revcom(downstream),
-      revcom(upstream),
-    ]
-    cds = revlist(cds, seq.length)
-    exons = revlist(exons, seq.length)
-    utr = revlist(utr, seq.length)
-  }
-  const codonTable = generateCodonTable(defaultCodonTable)
+    if (feature.strand === -1) {
+      // doing this in a single assignment is needed because downstream and
+      // upstream are swapped so this avoids a temp variable
+      ;[seq, upstream, downstream] = [
+        revcom(seq),
+        revcom(downstream),
+        revcom(upstream),
+      ]
+      cds = revlist(cds, seq.length)
+      exons = revlist(exons, seq.length)
+      utr = revlist(utr, seq.length)
+    }
+    const codonTable = generateCodonTable(defaultCodonTable)
 
-  return (
-    <div ref={ref} data-testid="sequence_panel">
-      <div
-        style={{
-          /* raw styles instead of className so that html copy works */
-          fontFamily: 'monospace',
-          wordWrap: 'break-word',
-          overflow: 'auto',
-          color: 'black',
-          fontSize: 12,
-          maxWidth: 600,
-          maxHeight: 300,
-        }}
-      >
-        <span style={{ background: 'white' }}>
-          {`>${
-            feature.name ||
-            feature.id ||
-            `${feature.refName}:${feature.start + 1}-${feature.end}`
-          }-${mode}\n`}
-        </span>
-        <br />
-        {mode === 'genomic' ? (
-          <GenomicSequence sequence={seq} />
-        ) : mode === 'genomic_sequence_updownstream' ? (
-          <GenomicSequence
-            sequence={seq}
-            upstream={upstream}
-            downstream={downstream}
-          />
-        ) : mode === 'cds' ? (
-          <CDSSequence cds={cds} sequence={seq} />
-        ) : mode === 'cdna' ? (
-          <CDNASequence
-            exons={exons}
-            cds={cds}
-            utr={utr}
-            sequence={seq}
-            intronBp={intronBp}
-          />
-        ) : mode === 'protein' ? (
-          <ProteinSequence cds={cds} codonTable={codonTable} sequence={seq} />
-        ) : mode === 'gene' ? (
-          <CDNASequence
-            exons={exons}
-            cds={cds}
-            utr={utr}
-            sequence={seq}
-            includeIntrons
-            intronBp={intronBp}
-          />
-        ) : mode === 'gene_collapsed_intron' ? (
-          <CDNASequence
-            exons={exons}
-            cds={cds}
-            sequence={seq}
-            utr={utr}
-            includeIntrons
-            collapseIntron
-            intronBp={intronBp}
-          />
-        ) : mode === 'gene_updownstream' ? (
-          <CDNASequence
-            exons={exons}
-            cds={cds}
-            sequence={seq}
-            utr={utr}
-            upstream={upstream}
-            downstream={downstream}
-            includeIntrons
-            intronBp={intronBp}
-          />
-        ) : mode === 'gene_updownstream_collapsed_intron' ? (
-          <CDNASequence
-            exons={exons}
-            cds={cds}
-            sequence={seq}
-            utr={utr}
-            upstream={upstream}
-            downstream={downstream}
-            includeIntrons
-            collapseIntron
-            intronBp={intronBp}
-          />
-        ) : (
-          <div>Unknown type</div>
-        )}
+    return (
+      <div ref={ref} data-testid="sequence_panel">
+        <div
+          style={{
+            /* raw styles instead of className so that html copy works */
+            fontFamily: 'monospace',
+            wordWrap: 'break-word',
+            overflow: 'auto',
+            color: 'black',
+            fontSize: 12,
+            maxWidth: 600,
+            maxHeight: 300,
+          }}
+        >
+          <span style={{ background: 'white' }}>
+            {`>${
+              feature.name ||
+              feature.id ||
+              `${feature.refName}:${feature.start + 1}-${feature.end}`
+            }-${mode}\n`}
+          </span>
+          <br />
+          {mode === 'genomic' ? (
+            <GenomicSequence sequence={seq} />
+          ) : mode === 'genomic_sequence_updownstream' ? (
+            <GenomicSequence
+              sequence={seq}
+              upstream={upstream}
+              downstream={downstream}
+            />
+          ) : mode === 'cds' ? (
+            <CDSSequence cds={cds} sequence={seq} />
+          ) : mode === 'cdna' ? (
+            <CDNASequence
+              exons={exons}
+              cds={cds}
+              utr={utr}
+              sequence={seq}
+              intronBp={intronBp}
+            />
+          ) : mode === 'protein' ? (
+            <ProteinSequence cds={cds} codonTable={codonTable} sequence={seq} />
+          ) : mode === 'gene' ? (
+            <CDNASequence
+              exons={exons}
+              cds={cds}
+              utr={utr}
+              sequence={seq}
+              includeIntrons
+              intronBp={intronBp}
+            />
+          ) : mode === 'gene_collapsed_intron' ? (
+            <CDNASequence
+              exons={exons}
+              cds={cds}
+              sequence={seq}
+              utr={utr}
+              includeIntrons
+              collapseIntron
+              intronBp={intronBp}
+            />
+          ) : mode === 'gene_updownstream' ? (
+            <CDNASequence
+              exons={exons}
+              cds={cds}
+              sequence={seq}
+              utr={utr}
+              upstream={upstream}
+              downstream={downstream}
+              includeIntrons
+              intronBp={intronBp}
+            />
+          ) : mode === 'gene_updownstream_collapsed_intron' ? (
+            <CDNASequence
+              exons={exons}
+              cds={cds}
+              sequence={seq}
+              utr={utr}
+              upstream={upstream}
+              downstream={downstream}
+              includeIntrons
+              collapseIntron
+              intronBp={intronBp}
+            />
+          ) : (
+            <div>Unknown type</div>
+          )}
+        </div>
       </div>
-    </div>
-  )
-})
+    )
+  },
+)
 
 export default SeqPanel
diff --git a/packages/core/PluginManager.ts b/packages/core/PluginManager.ts
@@ -86,8 +86,8 @@ class TypeRecord<ElementClass extends PluggableElementBase> {
 
   constructor(
     public typeName: string,
-    public baseClass: // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    | { new (...args: any[]): ElementClass }
+    public baseClass:
+      | { new (...args: unknown[]): ElementClass }
       // covers abstract class case
       | (Function & {
           prototype: ElementClass