Deps bump

.github/workflows/test-and-publish-app.yml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-node@v3
         with:
-          node-version: 16
+          node-version: 18
       - name: 🔧 Install
         run: |
           yarn

.gitignore

@@ -10,4 +10,5 @@ package-lock.json
 *.tgz
 .DS_Store
 .vscode
-rollup.config-*.cjs
+rollup.config-*.cjs
+.nx/

.nvmrc

@@ -1 +1 @@
-lts/gallium
+lts/hydrogen

lerna.json

@@ -1,7 +1,5 @@
 {
-  "packages": [
-    "packages/*"
-  ],
+  "packages": ["packages/*"],
   "npmClient": "yarn",
   "version": "4.5.2",
   "$schema": "node_modules/lerna/schemas/lerna-schema.json"

nx.json

@@ -3,32 +3,20 @@
     "default": {
       "runner": "nx/tasks-runners/default",
       "options": {
-        "cacheableOperations": [
-          "build",
-          "test"
-        ]
+        "cacheableOperations": ["build", "test"]
       }
     }
   },
   "targetDefaults": {
     "build": {
-      "dependsOn": [
-        "^build"
-      ],
-      "outputs": [
-        "{projectRoot}/dist"
-      ]
+      "dependsOn": ["^build"],
+      "outputs": ["{projectRoot}/dist"]
     }
   },
   "$schema": "./node_modules/nx/schemas/nx-schema.json",
   "namedInputs": {
-    "default": [
-      "{projectRoot}/**/*",
-      "sharedGlobals"
-    ],
+    "default": ["{projectRoot}/**/*", "sharedGlobals"],
     "sharedGlobals": [],
-    "production": [
-      "default"
-    ]
+    "production": ["default"]
   }
-}
+}

package.json

@@ -23,17 +23,16 @@
   },
   "license": "MIT",
   "resolutions": {
-    "@storybook/{app}/webpack": "5.88.1"
+    "@storybook/{app}/webpack": "5.91.0"
   },
   "devDependencies": {
-    "@babel/core": "^7.22.9",
-    "@codesandbox/sandpack-react": "2.6.9",
-    "@custom-elements-manifest/analyzer": "0.8.3",
-    "@rollup/plugin-commonjs": "25.0.2",
-    "@rollup/plugin-json": "6.0.0",
-    "@rollup/plugin-node-resolve": "15.1.0",
-    "@rollup/plugin-replace": "5.0.2",
-    "@rollup/plugin-typescript": "11.1.2",
+    "@babel/core": "7.24.5",
+    "@codesandbox/sandpack-react": "2.13.10",
+    "@custom-elements-manifest/analyzer": "0.10.2",
+    "@rollup/plugin-commonjs": "25.0.7",
+    "@rollup/plugin-json": "6.1.0",
+    "@rollup/plugin-node-resolve": "15.2.3",
+    "@rollup/plugin-typescript": "11.1.6",
     "@storybook/addon-a11y": "6.5.16",
     "@storybook/addon-actions": "^6.5.16",
     "@storybook/addon-essentials": "6.5.16",
@@ -42,34 +41,33 @@
     "@storybook/builder-webpack5": "^6.5.16",
     "@storybook/manager-webpack5": "^6.5.16",
     "@storybook/web-components": "6.5.16",
-    "@types/d3": "7.4.0",
-    "@types/jest": "29.5.3",
-    "@types/lodash-es": "4.17.7",
-    "@typescript-eslint/eslint-plugin": "6.0.0",
-    "@typescript-eslint/parser": "6.0.0",
-    "@web/dev-server": "0.3.0",
-    "@web/dev-server-legacy": "2.0.0",
-    "@web/dev-server-rollup": "0.5.2",
+    "@types/d3": "7.4.3",
+    "@types/jest": "29.5.12",
+    "@types/lodash-es": "4.17.12",
+    "@typescript-eslint/eslint-plugin": "7.8.0",
+    "@typescript-eslint/parser": "7.8.0",
+    "@web/dev-server": "0.4.4",
+    "@web/dev-server-rollup": "0.6.2",
     "@webcomponents/webcomponentsjs": "2.8.0",
     "babel-loader": "9.1.3",
-    "eslint": "8.44.0",
-    "eslint-plugin-jest": "27.2.2",
-    "jest": "^29.6.1",
-    "jest-canvas-mock": "^2.5.2",
-    "jest-environment-jsdom": "29.6.1",
-    "lerna": "7.1.3",
-    "lit-analyzer": "1.2.1",
-    "prettier": "3.0.0",
-    "rimraf": "5.0.1",
-    "rollup": "3.26.2",
-    "rollup-plugin-css-only": "^4.3.0",
-    "rollup-plugin-terser": "^7.0.2",
+    "eslint": "8.57.0",
+    "eslint-plugin-jest": "28.5.0",
+    "jest": "29.7.0",
+    "jest-canvas-mock": "2.5.2",
+    "jest-environment-jsdom": "29.7.0",
+    "lerna": "8.1.2",
+    "lit-analyzer": "2.0.3",
+    "prettier": "3.2.5",
+    "rimraf": "5.0.5",
+    "rollup": "4.17.2",
+    "rollup-plugin-css-only": "4.5.2",
+    "rollup-plugin-terser": "7.0.2",
     "rollup-plugin-web-worker-loader": "1.6.1",
-    "ts-jest": "^29.1.1",
-    "ts-loader": "9.4.4",
-    "tslib": "2.6.0",
-    "typescript": "5.1.6",
-    "webpack": "5.88.1"
+    "ts-jest": "29.1.2",
+    "ts-loader": "9.5.1",
+    "tslib": "2.6.2",
+    "typescript": "5.4.5",
+    "webpack": "5.91.0"
   },
   "workspaces": [
     "packages/*"

packages/nightingale-colored-sequence/package.json

@@ -19,7 +19,7 @@
   "dependencies": {
     "@nightingale-elements/nightingale-new-core": "^4.5.0",
     "@nightingale-elements/nightingale-sequence": "^4.5.0",
-    "d3": "7.8.5"
+    "d3": "7.9.0"
   },
   "repository": {
     "type": "git",

packages/nightingale-heatmap/package.json

@@ -33,6 +33,6 @@
   "homepage": "https://ebi-webcomponents.github.io/nightingale/",
   "dependencies": {
     "@nightingale-elements/nightingale-new-core": "^4.5.0",
-    "d3": "7.8.5"
+    "d3": "7.9.0"
   }
 }

packages/nightingale-interpro-track/package.json

@@ -35,7 +35,7 @@
   "dependencies": {
     "@nightingale-elements/nightingale-new-core": "^4.5.0",
     "@nightingale-elements/nightingale-track": "^4.5.0",
-    "d3": "7.8.5",
+    "d3": "7.9.0",
     "lodash-es": "^4.17.15"
   }
 }

packages/nightingale-interpro-track/src/coverage/index.ts

@@ -129,13 +129,12 @@ export const getCoverage = (
   if (createEmptyFragments) {
     coverage = addContributor({ start: 1, end: length, value: 0 }, coverage);
   }
-  contributors.forEach(
-    (f) =>
-      f.locations?.forEach((loc) =>
-        loc.fragments.forEach((fr) => {
-          coverage = addContributor(fr, coverage);
-        }),
-      ),
+  contributors.forEach((f) =>
+    f.locations?.forEach((loc) =>
+      loc.fragments.forEach((fr) => {
+        coverage = addContributor(fr, coverage);
+      }),
+    ),
   );
   return coverage;
 };

packages/nightingale-linegraph-track/package.json

@@ -33,6 +33,6 @@
   },
   "dependencies": {
     "@nightingale-elements/nightingale-new-core": "^4.5.0",
-    "d3": "7.8.5"
+    "d3": "7.9.0"
   }
 }

packages/nightingale-links/package.json

@@ -32,7 +32,7 @@
   "dependencies": {
     "@nightingale-elements/nightingale-new-core": "^4.5.0",
     "@nightingale-elements/nightingale-track": "^4.5.0",
-    "d3": "7.8.5",
+    "d3": "7.9.0",
     "lodash-es": "^4.17.15"
   }
 }

packages/nightingale-links/src/nightingale-links.ts

@@ -60,8 +60,8 @@ class NightingaleLinks extends NightingaleTrack {
           filterContacts(
             this._rawData,
             this.minDistance || 0,
-            this.minProbability || DEFAULT_PROBABILITY
-          )
+            this.minProbability || DEFAULT_PROBABILITY,
+          ),
         );
         this.createTrack();
       }
@@ -80,8 +80,8 @@ class NightingaleLinks extends NightingaleTrack {
       filterContacts(
         this._rawData,
         this.minDistance || 0,
-        this.minProbability || DEFAULT_PROBABILITY
-      )
+        this.minProbability || DEFAULT_PROBABILITY,
+      ),
     );
     this.createTrack();
   }
@@ -255,4 +255,4 @@ class NightingaleLinks extends NightingaleTrack {
   }
 }
 
-export default NightingaleLinks;
+export default NightingaleLinks;

packages/nightingale-links/tsconfig.json

@@ -3,7 +3,5 @@
   "compilerOptions": {
     "outDir": "./dist"
   },
-  "include": [
-    "./src"
-  ]
-}
+  "include": ["./src"]
+}

packages/nightingale-manager/src/nightingale-manager.ts

@@ -154,4 +154,4 @@ class NightingaleManager extends NightingaleElement {
   }
 }
 
-export default NightingaleManager;
+export default NightingaleManager;

packages/nightingale-msa/package.json

@@ -30,6 +30,6 @@
   "homepage": "https://ebi-webcomponents.github.io/nightingale/",
   "dependencies": {
     "@nightingale-elements/nightingale-new-core": "^4.5.0",
-    "d3": "7.8.5"
+    "d3": "7.9.0"
   }
 }

packages/nightingale-msa/src/components/Canvas/SequenceViewer.ts

@@ -97,12 +97,12 @@ class SequenceViewerComponent extends DraggingComponent {
       currentViewSequence: clamp(
         floor(position.yPos / this.tileHeight),
         0,
-        (this.sequences?.length || 1) - 1
+        (this.sequences?.length || 1) - 1,
       ),
       currentViewSequencePosition: clamp(
         floor(position.xPos / this.tileWidth),
         0,
-        this.sequences?.maxLength || 0
+        this.sequences?.maxLength || 0,
       ),
       ...position,
     };
@@ -217,7 +217,7 @@ class SequenceViewerComponent extends DraggingComponent {
     if (!positions) {
       if (debug)
         console.error(
-          "Failed to draw scene because couldn't get the tile positions"
+          "Failed to draw scene because couldn't get the tile positions",
         );
       return;
     }
@@ -233,14 +233,14 @@ class SequenceViewerComponent extends DraggingComponent {
       this.ctx.canvas.dispatchEvent(
         new CustomEvent("drawCompleted", {
           bubbles: true,
-        })
+        }),
       );
     }
     if (debug) {
       const elapsed = Date.now() - this.redrawStarted;
       if (elapsed > 5) {
         console.log(
-          `Took ${elapsed} msecs to redraw for ${positions.startXTile} ${positions.startYTile} (redrawnTiles: ${this.redrawnTiles})`
+          `Took ${elapsed} msecs to redraw for ${positions.startXTile} ${positions.startYTile} (redrawnTiles: ${this.redrawnTiles})`,
         );
       }
     }
@@ -251,19 +251,19 @@ class SequenceViewerComponent extends DraggingComponent {
     if (!this.position || !this.sequences || !this.stats) return null;
     const startXTile = Math.max(
       0,
-      this.position.currentViewSequencePosition - this.props.cacheElements
+      this.position.currentViewSequencePosition - this.props.cacheElements,
     );
     const startYTile = Math.max(
       0,
-      this.position.currentViewSequence - this.props.cacheElements
+      this.position.currentViewSequence - this.props.cacheElements,
     );
     const endYTile = Math.min(
       this.sequences.length,
-      startYTile + this.stats.nrYTiles + 2 * this.props.cacheElements
+      startYTile + this.stats.nrYTiles + 2 * this.props.cacheElements,
     );
     const endXTile = Math.min(
       this.sequences.maxLength,
-      startXTile + this.stats.nrXTiles + 2 * this.props.cacheElements
+      startXTile + this.stats.nrXTiles + 2 * this.props.cacheElements,
     );
     return { startXTile, startYTile, endXTile, endYTile };
   }
@@ -330,7 +330,7 @@ class SequenceViewerComponent extends DraggingComponent {
           xPos,
           yPos,
           width,
-          height
+          height,
         );
       }
     }
@@ -397,7 +397,7 @@ class SequenceViewerComponent extends DraggingComponent {
       xPosFrom,
       yPosFrom,
       regionWidth,
-      regionHeight
+      regionHeight,
     );
   }
   movePosition = (m: Movement) => {
@@ -424,14 +424,14 @@ class SequenceViewerComponent extends DraggingComponent {
     const seqNr = clamp(
       floor((this.position.yPos + pos.yPos) / this.tileHeight),
       0,
-      sequences.length - 1
+      sequences.length - 1,
     );
     const sequence = sequences[seqNr];
 
     const position = clamp(
       floor((this.position.xPos + pos.xPos) / this.tileWidth),
       0,
-      sequence.sequence.length - 1
+      sequence.sequence.length - 1,
     );
     return {
       i: seqNr,
@@ -452,7 +452,7 @@ class SequenceViewerComponent extends DraggingComponent {
           sequencePosition.position >= feature.residues.from - 1 &&
           sequencePosition.position <= feature.residues.to - 1 &&
           sequencePosition.i >= feature.sequences.from &&
-          sequencePosition.i <= feature.sequences.to
+          sequencePosition.i <= feature.sequences.to,
       )
       .map((feature) => feature.id || "");
   }
@@ -477,7 +477,7 @@ class SequenceViewerComponent extends DraggingComponent {
         new CustomEvent(name, {
           bubbles: true,
           detail: data,
-        })
+        }),
       );
     }
 
@@ -566,7 +566,7 @@ class SequenceViewerComponent extends DraggingComponent {
       sequences: this.sequences,
     } as TileOptions);
     this.residueTileCache.updateTileSpecs(
-      residueTileSpecs as ResidueTileOptions
+      residueTileSpecs as ResidueTileOptions,
     );
   }