Add bamjs BAM file viewer

.github/workflows/manual-publish.yml

@@ -0,0 +1,93 @@
+name: Manual Package Publish
+
+on:
+  workflow_dispatch:
+    inputs:
+      package:
+        description: 'Package to publish (e.g., heatmap, plotly)'
+        required: true
+        type: string
+      dry-run:
+        description: 'Dry run (do not actually publish)'
+        required: false
+        type: boolean
+        default: false
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Validate package exists
+        run: |
+          if [ ! -d "packages/${{ github.event.inputs.package }}" ]; then
+            echo "Error: Package 'packages/${{ github.event.inputs.package }}' does not exist"
+            exit 1
+          fi
+
+          if [ ! -f "packages/${{ github.event.inputs.package }}/package.json" ]; then
+            echo "Error: Package 'packages/${{ github.event.inputs.package }}' has no package.json"
+            exit 1
+          fi
+
+      - name: Setup pnpm
+        uses: pnpm/action-setup@v5
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v5
+        with:
+          node-version: 22
+          registry-url: 'https://registry.npmjs.org'
+
+      - name: Install dependencies
+        run: pnpm install --frozen-lockfile
+
+      - name: Build package
+        working-directory: packages/${{ github.event.inputs.package }}
+        run: |
+          if grep -q '"build"' package.json; then
+            pnpm build
+          else
+            echo "No build script found, skipping"
+          fi
+
+      - name: Check package info
+        working-directory: packages/${{ github.event.inputs.package }}
+        run: |
+          package_name=$(jq -r '.name' package.json)
+          package_version=$(jq -r '.version' package.json)
+
+          echo "Package: $package_name"
+          echo "Version: $package_version"
+
+          if npm view "$package_name@$package_version" version 2>/dev/null; then
+            echo "Warning: $package_name@$package_version is already published"
+            echo "published=true" >> $GITHUB_ENV
+          else
+            echo "$package_name@$package_version is not yet published"
+            echo "published=false" >> $GITHUB_ENV
+          fi
+
+      - name: Dry run
+        if: github.event.inputs.dry-run == 'true'
+        working-directory: packages/${{ github.event.inputs.package }}
+        run: |
+          echo "DRY RUN - Would publish:"
+          npm pack --dry-run
+
+      - name: Publish to npm
+        if: github.event.inputs.dry-run == 'false' && env.published == 'false'
+        working-directory: packages/${{ github.event.inputs.package }}
+        env:
+          NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
+        run: |
+          package_name=$(jq -r '.name' package.json)
+          package_version=$(jq -r '.version' package.json)
+
+          echo "Publishing $package_name@$package_version"
+          npm publish --access public
+
+      - name: Skip publishing
+        if: github.event.inputs.dry-run == 'false' && env.published == 'true'
+        run: echo "Skipping publish - package already exists at this version"

.github/workflows/publish-packages.yml

@@ -0,0 +1,98 @@
+name: Publish Updated Packages
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  detect-changes:
+    runs-on: ubuntu-latest
+    outputs:
+      changed-packages: ${{ steps.detect.outputs.packages }}
+      has-changes: ${{ steps.detect.outputs.has-changes }}
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          fetch-depth: 2
+
+      - name: Detect package version changes
+        id: detect
+        run: |
+          changed_files=$(git diff --name-only HEAD~1 HEAD | grep "packages/.*/package.json" || true)
+
+          if [ -z "$changed_files" ]; then
+            echo "has-changes=false" >> $GITHUB_OUTPUT
+            echo "No package.json files changed"
+            exit 0
+          fi
+
+          packages_json="[]"
+
+          for file in $changed_files; do
+            package_dir=$(dirname "$file")
+            package_name=$(basename "$package_dir")
+
+            old_version=$(git show HEAD~1:"$file" 2>/dev/null | jq -r '.version' 2>/dev/null || echo "")
+            new_version=$(jq -r '.version' "$file" 2>/dev/null || echo "")
+
+            if [ "$old_version" != "$new_version" ] && [ -n "$new_version" ] && [ "$new_version" != "null" ]; then
+              echo "Package $package_name version changed: $old_version -> $new_version"
+              packages_json=$(echo "$packages_json" | jq -c --arg pkg "$package_name" '. + [$pkg]')
+            fi
+          done
+
+          if [ "$packages_json" != "[]" ]; then
+            echo "has-changes=true" >> $GITHUB_OUTPUT
+            echo "packages=$packages_json" >> $GITHUB_OUTPUT
+            echo "Changed packages: $packages_json"
+          else
+            echo "has-changes=false" >> $GITHUB_OUTPUT
+            echo "No version changes detected"
+          fi
+
+  publish:
+    needs: detect-changes
+    if: needs.detect-changes.outputs.has-changes == 'true'
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        package: ${{ fromJson(needs.detect-changes.outputs.changed-packages) }}
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Setup pnpm
+        uses: pnpm/action-setup@v5
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v5
+        with:
+          node-version: 22
+          registry-url: 'https://registry.npmjs.org'
+
+      - name: Install dependencies
+        run: pnpm install --frozen-lockfile
+
+      - name: Build package
+        working-directory: packages/${{ matrix.package }}
+        run: |
+          if grep -q '"build"' package.json; then
+            pnpm build
+          else
+            echo "No build script found, skipping"
+          fi
+
+      - name: Publish to npm
+        working-directory: packages/${{ matrix.package }}
+        env:
+          NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
+        run: |
+          package_name=$(jq -r '.name' package.json)
+          package_version=$(jq -r '.version' package.json)
+
+          if npm view "$package_name@$package_version" version 2>/dev/null; then
+            echo "Package $package_name@$package_version already published, skipping"
+            exit 0
+          fi
+
+          echo "Publishing $package_name@$package_version"
+          npm publish --access public

.github/workflows/test_visualizations.yml

@@ -15,7 +15,7 @@ jobs:
       playwright_packages: ${{ steps.set-packages.outputs.playwright_packages }}
     steps:
       - uses: actions/checkout@v5
-      
+
       - name: Discover packages with tests
         id: set-packages
         run: |
@@ -43,10 +43,10 @@ jobs:
           done
           packages=$(printf '%s\n' "${regular_packages[@]}" | jq -R -s -c 'split("\n") | map(select(length > 0))')
           echo "packages=$packages" >> $GITHUB_OUTPUT
-          
+
           playwright_packages_json=$(printf '%s\n' "${playwright_packages[@]}" | jq -R -s -c 'split("\n") | map(select(length > 0))')
           echo "playwright_packages=$playwright_packages_json" >> $GITHUB_OUTPUT
-          
+
           echo ""
           echo "✅ Regular packages with test script (${#regular_packages[@]}):"
           printf '  - %s\n' "${regular_packages[@]}"
@@ -65,22 +65,28 @@ jobs:
       fail-fast: false
       matrix:
         package: ${{ fromJson(needs.discover.outputs.packages) }}
-    
+
     steps:
       - uses: actions/checkout@v5
 
+      - name: Setup pnpm
+        uses: pnpm/action-setup@v5
+
       - name: Setup Node.js
         uses: actions/setup-node@v5
         with:
-          node-version: 20
+          node-version: 22
 
-      - name: Cache dependencies
+      - name: Cache pnpm store
         uses: actions/cache@v4
         with:
-          path: packages/${{ matrix.package }}/node_modules
-          key: ${{ runner.os }}-node-${{ matrix.package }}-${{ hashFiles(format('packages/{0}/package-lock.json', matrix.package)) }}
+          path: ~/.local/share/pnpm/store/v10
+          key: ${{ runner.os }}-pnpm-${{ hashFiles('pnpm-lock.yaml') }}
           restore-keys: |
-            ${{ runner.os }}-node-${{ matrix.package }}-
+            ${{ runner.os }}-pnpm-
+
+      - name: Install dependencies
+        run: pnpm install --frozen-lockfile
 
       - name: Check for requirements.txt
         id: check-python
@@ -105,13 +111,9 @@ jobs:
         working-directory: packages/${{ matrix.package }}
         run: pip install -r requirements.txt
 
-      - name: Install Node dependencies
-        working-directory: packages/${{ matrix.package }}
-        run: npm install
-
       - name: Run tests
         working-directory: packages/${{ matrix.package }}
-        run: npm test
+        run: pnpm test
 
   test-playwright:
     needs: discover
@@ -121,31 +123,37 @@ jobs:
       fail-fast: false
       matrix:
         package: ${{ fromJson(needs.discover.outputs.playwright_packages) }}
-    
+
     steps:
       - uses: actions/checkout@v5
 
+      - name: Setup pnpm
+        uses: pnpm/action-setup@v5
+
       - name: Setup Node.js
         uses: actions/setup-node@v5
         with:
-          node-version: 20
+          node-version: 22
 
-      - name: Cache Node dependencies
+      - name: Cache pnpm store
         uses: actions/cache@v4
         with:
-          path: packages/${{ matrix.package }}/node_modules
-          key: ${{ runner.os }}-node-${{ matrix.package }}-${{ hashFiles(format('packages/{0}/package-lock.json', matrix.package)) }}
+          path: ~/.local/share/pnpm/store/v10
+          key: ${{ runner.os }}-pnpm-${{ hashFiles('pnpm-lock.yaml') }}
           restore-keys: |
-            ${{ runner.os }}-node-${{ matrix.package }}-
+            ${{ runner.os }}-pnpm-
 
       - name: Cache Playwright browsers
         uses: actions/cache@v4
         with:
           path: ~/.cache/ms-playwright
-          key: ${{ runner.os }}-playwright-${{ hashFiles(format('packages/{0}/package-lock.json', matrix.package)) }}
+          key: ${{ runner.os }}-playwright-${{ hashFiles('pnpm-lock.yaml') }}
           restore-keys: |
             ${{ runner.os }}-playwright-
 
+      - name: Install dependencies
+        run: pnpm install --frozen-lockfile
+
       - name: Check for requirements.txt
         id: check-python
         working-directory: packages/${{ matrix.package }}
@@ -169,22 +177,18 @@ jobs:
         working-directory: packages/${{ matrix.package }}
         run: pip install -r requirements.txt
 
-      - name: Install Node dependencies
-        working-directory: packages/${{ matrix.package }}
-        run: npm install
-
       - name: Install Playwright browsers
         working-directory: packages/${{ matrix.package }}
-        run: npx playwright install --with-deps chromium
+        run: pnpm exec playwright install --with-deps chromium
 
       - name: Build
         working-directory: packages/${{ matrix.package }}
-        run: npm run build
+        run: pnpm build
 
       - name: Start Server in background
         working-directory: packages/${{ matrix.package }}
         run: |
-          nohup npm run dev > server.log 2>&1 &
+          nohup pnpm dev > server.log 2>&1 &
           echo $! > server.pid
 
       - name: Wait for Server to be ready
@@ -207,7 +211,7 @@ jobs:
 
       - name: Run Playwright Tests
         working-directory: packages/${{ matrix.package }}
-        run: npm test
+        run: pnpm test
 
       - name: Stop Server
         if: always()

.gitignore

@@ -5,4 +5,7 @@ node_modules
 .cache
 .DS_Store
 lerna-debug.log
+pnpm-debug.log
 packages/**/static
+**/test-results/
+**/playwright-report/

.prettierignore

@@ -0,0 +1,4 @@
+pnpm-lock.yaml
+**/dist/
+**/static/
+**/node_modules/