chore: update to slim 0.45.1

.eslintrc.strict.cjs

@@ -0,0 +1,41 @@
+/**
+ * ESLint config that approximates DeepSource + SonarQube rules.
+ * Run with: bun run lint:strict  (or: bunx eslint --config .eslintrc.strict.cjs src/)
+ *
+ * DeepSource's JavaScript analyzer uses ESLint under the hood and supports
+ * style_guide (e.g. "standard"). SonarQube rules are available via eslint-plugin-sonarjs.
+ * This config enables rules that catch the kinds of issues both report.
+ */
+module.exports = {
+  root: true,
+  extends: [
+    'react-app',
+    'react-app/jest',
+    'plugin:sonarjs/recommended',
+  ],
+  plugins: ['sonarjs'],
+  overrides: [
+    {
+      files: ['src/**/*.{ts,tsx,js,jsx}'],
+      rules: {
+        // DeepSource JS-0050: use === and !==
+        eqeqeq: ['error', 'always'],
+        // Avoid console in browser code (DeepSource JS-0002)
+        'no-console': ['warn', { allow: ['warn', 'error'] }],
+        // Object shorthand (DeepSource JS-0240)
+        'object-shorthand': ['warn', 'always'],
+        // Empty callbacks (DeepSource JS-0321)
+        'no-empty-function': ['warn', { allow: ['arrowFunctions'] }],
+        // Prefer named exports when re-exporting (DeepSource JS-P1003)
+        'sonarjs/prefer-single-boolean-return': 'warn',
+      },
+    },
+  ],
+  ignorePatterns: [
+    'build/',
+    'node_modules/',
+    'coverage/',
+    '*.config.js',
+    '*.config.cjs',
+  ],
+};

.github/workflows/deploy-to-firebase.yml

@@ -15,19 +15,16 @@ jobs:
       - name: Checkout to repository
         uses: actions/checkout@v4.2.2
 
-      - name: Setup Node
-        uses: actions/setup-node@v4.4.0
+      - name: Setup Bun
+        uses: oven-sh/setup-bun@v2
         with:
-          node-version: 20.8.1
-
-      - name: Install Yarn
-        run: sudo npm i -g yarn
+          bun-version: latest
 
       - name: Install dependencies
-        run: yarn
+        run: bun install --frozen-lockfile
 
       - name: Build
-        run: REACT_APP_CONFIG=preview PUBLIC_URL=/ yarn build
+        run: REACT_APP_CONFIG=preview PUBLIC_URL=/ bun run build
 
       - name: Deploy
         uses: FirebaseExtended/action-hosting-deploy@v0

.github/workflows/deploy-to-github-pages.yml

@@ -14,20 +14,17 @@ jobs:
       - name: Checkout to repository
         uses: actions/checkout@v4.2.2
 
-      - name: Setup Node
-        uses: actions/setup-node@v4.4.0
+      - name: Setup Bun
+        uses: oven-sh/setup-bun@v2
         with:
-          node-version: 20.8.1
-
-      - name: Install Yarn
-        run: sudo npm i -g yarn
+          bun-version: latest
 
       - name: Install dependencies
-        run: yarn
+        run: bun install --frozen-lockfile
 
       - name: Build and deploy to GitHub Pages
         run: |
           git remote set-url origin https://git:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git
-          yarn deploy -- -u "github-actions-bot <support+actions@github.com>"
+          bun run deploy -- -u "github-actions-bot <support+actions@github.com>"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/release.yml

@@ -16,16 +16,16 @@ jobs:
           ref: master
           persist-credentials: false
 
-      - name: Setup Node
-        uses: actions/setup-node@v4.4.0
+      - name: Setup Bun
+        uses: oven-sh/setup-bun@v2
         with:
-          node-version: 20.8.1
+          bun-version: latest
 
       - name: Install dependencies
-        run: yarn
+        run: bun install --frozen-lockfile
 
       - name: Build
-        run: yarn build
+        run: bun run build
 
       - name: Zip build
         run: zip -r build.zip build
@@ -37,4 +37,4 @@ jobs:
           GIT_AUTHOR_EMAIL: ${{ vars.RELEASE_GIT_AUTHOR_EMAIL }}
           GIT_COMMITTER_NAME: ${{ vars.RELEASE_GIT_COMMITTER_NAME }}
           GIT_COMMITTER_EMAIL: ${{ vars.RELEASE_GIT_COMMITTER_EMAIL }}
-        run: npx semantic-release --branches master
+        run: bunx semantic-release --branches master

.github/workflows/unit-tests.yml

@@ -14,19 +14,19 @@ jobs:
       - name: Checkout to repository
         uses: actions/checkout@v4.2.2
 
-      - name: Setup Node
-        uses: actions/setup-node@v4.4.0
+      - name: Setup Bun
+        uses: oven-sh/setup-bun@v2
         with:
-          node-version: 20.8.1
+          bun-version: latest
 
       - name: Install dependencies
-        run: yarn
+        run: bun install --frozen-lockfile
 
       - name: Build
-        run: yarn build
+        run: bun run build
 
       - name: Lint
-        run: yarn lint
+        run: bun run lint
 
       - name: Test
-        run: yarn test
+        run: bun run test

.gitignore

@@ -12,6 +12,8 @@
 /coverage
 .env
 
+.cursorrules
+
 # production
 /build
 
@@ -28,7 +30,7 @@ public/config/*
 .env.production.local
 
 npm-debug.log*
-yarn-debug.log*
-yarn-error.log*
+bun-debug.log*
+bun-error.log*
 
 /.github

.husky/pre-commit

@@ -0,0 +1,3 @@
+#!/usr/bin/env sh
+# Block commit if typecheck or lint fails
+bun run typecheck && bun run lint

CONTRIBUTING.md

@@ -31,15 +31,17 @@ The app is built using [craco](https://github.com/gsoft-inc/craco) (with the [cr
 
 Tests are written and run using the [jest](https://jestjs.io/) framework.
 
-The [yarn](https://yarnpkg.com/) package manager is used to manage dependencies and run scripts specified in `package.json` (`build`, `lint`, `test`, etc.).
+The [Bun](https://bun.sh/) runtime and package manager is used to manage dependencies and run scripts specified in `package.json` (`build`, `lint`, `test`, etc.).
 
 ## Coding style
 
-Source code is linted using [ts-standard](https://github.com/standard/ts-standard) (based on [eslint](https://eslint.org/)) and TypeScript is used with [strict type checking compiler options](https://www.typescriptlang.org/tsconfig#Strict_Type_Checking_Options_6173) enabled.
+Source code is linted and formatted using [Biome](https://biomejs.dev/). TypeScript is used with [strict type checking compiler options](https://www.typescriptlang.org/tsconfig#Strict_Type_Checking_Options_6173) enabled. Semicolons are not used at the end of statements (Biome uses `asNeeded`).
 
-Use the following command to identify potential coding style and type annotation violations:
+Use the following commands to check and fix style:
 
-    $ yarn lint
+    $ bun run lint        # check for issues
+    $ bun run lint:fix    # auto-fix issues
+    $ bun run fmt         # format code
 
 
 ### Documentation

Dockerfile

@@ -10,28 +10,27 @@ RUN apt-get update && \
     curl \
     dumb-init \
     gnupg \
-    nginx && \
+    nginx \
+    unzip && \
     apt-get clean
 
 RUN curl -fsSL https://deb.nodesource.com/setup_21.x | bash - && \
-    curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | apt-key add - && \
-    echo "deb https://dl.yarnpkg.com/debian/ stable main" | tee /etc/apt/sources.list.d/yarn.list && \
-    curl -sS https://deb.nodesource.com/setup_21.x | bash - && \
     apt-get update && \
     apt-get install -y --no-install-suggests --no-install-recommends \
-    nodejs \
-    yarn && \
+    nodejs && \
     apt-get clean
 
+# Install Bun (matches packageManager in package.json)
+ENV BUN_INSTALL=/usr/local
+RUN curl -fsSL https://bun.sh/install | bash -
+
 WORKDIR /usr/local/share/mghcomputationalpathology/slim
 
 # Install dependencies first and then include code for efficient caching
 COPY package.json .
-COPY yarn.lock .
+COPY bun.lock .
 
-# There are sometimes weird network errors. Increasing the network timeout
-#  seems to help (see https://github.com/yarnpkg/yarn/issues/5259)
-RUN yarn install --frozen-lockfile --network-timeout 100000
+RUN bun install --frozen-lockfile
 
 COPY craco.config.js .
 COPY tsconfig.json .
@@ -57,7 +56,7 @@ RUN addgroup --system --gid 101 nginx && \
             --shell /bin/false \
             nginx
 
-RUN NODE_OPTIONS=--max_old_space_size=8192 yarn run build && \
+RUN NODE_OPTIONS=--max_old_space_size=8192 bun run build && \
         mkdir -p /var/www/html && \
         cp -R build/* /var/www/html/
 
@@ -82,4 +81,4 @@ RUN useradd -m -s /bin/bash tester && \
 
 USER tester
 
-ENTRYPOINT ["/usr/bin/dumb-init", "--", "yarn", "test"]
+ENTRYPOINT ["/usr/bin/dumb-init", "--", "bun", "run", "test"]