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": "4.6.0",
   "$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",
@@ -42,33 +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",
-    "ts-jest": "^29.1.1",
-    "ts-loader": "9.4.4",
-    "tslib": "2.6.0",
-    "typescript": "5.1.6",
-    "webpack": "5.88.1"
+    "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": "29.1.2",
+    "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-heatmap/test/__snapshots__/nightingale-heatmap.test.ts.snap

@@ -36,10 +36,10 @@ exports[`nightingale-navigation tests it should display the heatmap correctly 1`
   display-start="1"
   height="200"
   highlight-color="#fc1e1e"
+  length="153"
   min-height="10"
   min-width="10"
   style="width: 100%; display: block; line-height: 0;"
-  width="100"
 >
   <!---->
 

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"
   }
 }