Misc

GMOD · Sep 18, 2023 · c0c5eef · c0c5eef
1 parent 857e62f
commit c0c5eef
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Showing 14 changed files with 1,519 additions and 1,391 deletions.
diff --git a/.eslintrc.json b/.eslintrc.json
@@ -31,6 +31,7 @@
     "@typescript-eslint/camelcase": "off",
     "@typescript-eslint/explicit-function-return-type": "off",
     "@typescript-eslint/explicit-module-boundary-types": "off",
+    "@typescript-eslint/no-base-to-string": "off",
     "@typescript-eslint/no-empty-function": "off",
     "@typescript-eslint/no-unused-vars": ["warn"],
     "@typescript-eslint/no-floating-promises": "error",

diff --git a/README.md b/README.md
@@ -2,7 +2,6 @@
 
 A multiple sequence alignment viewer
 
-
 ## Docs
 
 See [user guide](docs/user_guide.md)
@@ -20,7 +19,6 @@ This page is a deployment of the `app` directory in this repo, which uses the
 
 ![](docs/media/image15.png)
 
-
 ## Developers
 
 The lib folder contains the NPM package, and the `app` folder contains an

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

diff --git a/app/package.json b/app/package.json
@@ -6,23 +6,25 @@
   "scripts": {
     "dev": "vite",
     "build": "tsc && vite build",
-    "preview": "vite preview"
+    "preview": "vite preview",
+    "predeploy": "npm run build",
+    "deploy": "gh-pages -d dist"
   },
   "dependencies": {
     "@emotion/react": "^11.10.8",
     "@emotion/styled": "^11.10.8",
     "@jbrowse/core": "^2.4.2",
     "@mui/material": "^5.12.3",
-    "@mui/x-data-grid": "^5.0.0",
-    "@testing-library/jest-dom": "^5.11.4",
-    "@testing-library/react": "^11.1.0",
-    "@testing-library/user-event": "^12.1.10",
+    "@mui/x-data-grid": "^6.14.0",
+    "@testing-library/jest-dom": "^6.1.3",
+    "@testing-library/react": "^14.0.0",
+    "@testing-library/user-event": "^14.5.1",
     "@types/jest": "^29.5.1",
-    "@types/node": "^18.16.3",
+    "@types/node": "^20.6.2",
     "buffer": "^6.0.3",
-    "gh-pages": "^5.0.0",
+    "gh-pages": "^6.0.0",
     "mobx": "^6.9.0",
-    "mobx-react": "^7.6.0",
+    "mobx-react": "^9.0.1",
     "mobx-state-tree": "5.1.8",
     "ngl": "^2.0.0",
     "react": "^18.2.0",

diff --git a/lib/package.json b/lib/package.json
@@ -14,7 +14,6 @@
     "node": ">=10"
   },
   "scripts": {
-    "lint": "eslint src",
     "clean": "rimraf dist",
     "prebuild": "npm run clean",
     "prepublishOnly": "node -p \"'export const version = ' + JSON.stringify(require('./package.json').version) + ';'\" > src/version.ts",
@@ -33,7 +32,7 @@
     "react-dom": ">=16.8.0"
   },
   "devDependencies": {
-    "@rollup/plugin-commonjs": "^24.1.0",
+    "@rollup/plugin-commonjs": "^25.0.4",
     "@rollup/plugin-json": "^6.0.0",
     "@rollup/plugin-node-resolve": "^15.0.2",
     "@rollup/plugin-replace": "^5.0.2",
@@ -49,11 +48,16 @@
     "typescript": "^5.0.4"
   },
   "dependencies": {
+    "@typescript-eslint/eslint-plugin": "^6.7.2",
+    "@typescript-eslint/parser": "^6.7.2",
     "clustal-js": "^1.0.3",
-    "color": "^3.1.3",
+    "color": "^4.2.3",
     "copy-to-clipboard": "^3.3.1",
     "d3-array": "^3.2.3",
     "d3-hierarchy": "^3.1.2",
+    "eslint": "^8.39.0",
+    "eslint-plugin-import": "^2.27.5",
+    "eslint-plugin-react": "^7.32.2",
     "normalize-wheel": "^1.0.1",
     "rbush": "^3.0.1",
     "stockholm-js": "^1.0.10",

diff --git a/lib/src/components/MSAView.tsx b/lib/src/components/MSAView.tsx
@@ -48,7 +48,15 @@ const MouseoverCanvas = observer(function ({ model }: { model: MsaViewModel }) {
       ctx.fillStyle = 'rgba(100,100,100,0.5)'
       ctx.fillRect(x, 0, colWidth, height)
     }
-  }, [mouseCol, colWidth, scrollX, height, resizeHandleWidth, treeAreaWidth, width])
+  }, [
+    mouseCol,
+    colWidth,
+    scrollX,
+    height,
+    resizeHandleWidth,
+    treeAreaWidth,
+    width,
+  ])
 
   return (
     <canvas

diff --git a/lib/src/components/TreeCanvas.tsx b/lib/src/components/TreeCanvas.tsx
@@ -104,25 +104,23 @@ const TreeMenu = observer(function ({
           )
         })}
 
-        {
-          // @ts-expect-error
-          nodeDetails?.data.accession?.map((accession: string) => (
-            <MenuItem
-              dense
-              key={accession}
-              onClick={() => {
-                model.addUniprotTrack({
-                  // @ts-expect-error
-                  name: nodeDetails?.data.name,
-                  accession,
-                })
-                onClose()
-              }}
-            >
-              Open UniProt track ({accession})
-            </MenuItem>
-          ))
-        }
+        {// @ts-expect-error
+        nodeDetails?.data.accession?.map((accession: string) => (
+          <MenuItem
+            dense
+            key={accession}
+            onClick={() => {
+              model.addUniprotTrack({
+                // @ts-expect-error
+                name: nodeDetails?.data.name,
+                accession,
+              })
+              onClose()
+            }}
+          >
+            Open UniProt track ({accession})
+          </MenuItem>
+        ))}
       </Menu>
     </>
   )

diff --git a/lib/src/components/util.ts b/lib/src/components/util.ts
@@ -55,7 +55,6 @@ export function makeTicks(
   }
 
   if (bpPerPx < 0) {
-    // eslint-disable-next-line @typescript-eslint/no-extra-semi
     ;[minBase, maxBase] = [maxBase, minBase]
   }
 

diff --git a/lib/src/parseNewick.ts b/lib/src/parseNewick.ts
@@ -72,7 +72,7 @@ export default function parse(s: string) {
         tree = subtree
         break
       case ',': // another branch
-        ancestors[ancestors.length - 1].branchset.push(subtree)
+        ancestors.at(-1)?.branchset.push(subtree)
         tree = subtree
         break
       case ')': // optional name next

diff --git a/lib/src/parsers/FastaMSA.ts b/lib/src/parsers/FastaMSA.ts
@@ -9,7 +9,7 @@ function parseSmallFasta(text: string) {
       const [id, ...description] = defLine.split(' ')
       const descriptionStr = description.join(' ')
       const seqLinesStr = seqLines.join('')
-      const sequence = seqLinesStr.replace(/\s/g, '')
+      const sequence = seqLinesStr.replaceAll(/\s/g, '')
       return { id, description: descriptionStr, sequence }
     })
 }

diff --git a/lib/src/parsers/StockholmMSA.ts b/lib/src/parsers/StockholmMSA.ts
@@ -81,7 +81,7 @@ export default class StockholmMSA {
         return { id, pdb, chain, startPos, endPos }
       })
 
-    const ret = {} as Record<string, Omit<typeof args[0], 'id'>[]>
+    const ret = {} as Record<string, Omit<(typeof args)[0], 'id'>[]>
     for (const entry of args) {
       const { id, ...rest } = entry
       if (!ret[id]) {

diff --git a/lib/src/version.ts b/lib/src/version.ts
@@ -1 +1 @@
-export const version = "2.0.0";
+export const version = '2.0.0'
diff --git a/package.json b/package.json
@@ -6,20 +6,17 @@
     "app"
   ],
   "scripts": {
-    "predeploy": "cd lib; npm run build",
-    "deploy": "cd app; npm run deploy",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts,.jsx,.tsx .",
-    "predopublish": "cd lib; yarn build",
-    "dopublish": "cd lib; yarn publish"
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts,.jsx,.tsx ."
   },
   "devDependencies": {
     "@types/rbush": "^3.0.0",
-    "@typescript-eslint/eslint-plugin": "^5.59.2",
-    "@typescript-eslint/parser": "^5.59.2",
+    "@typescript-eslint/eslint-plugin": "^6.7.2",
+    "@typescript-eslint/parser": "^6.7.2",
     "eslint": "^8.39.0",
     "eslint-plugin-import": "^2.27.5",
     "eslint-plugin-react": "^7.32.2",
     "eslint-plugin-react-hooks": "^4.6.0",
-    "eslint-plugin-unicorn": "^46.0.0"
+    "eslint-plugin-unicorn": "^48.0.1",
+    "prettier": "^3.0.3"
   }
 }