Create comprehensive BioNanomics project template with multi-language support and development workflows

.editorconfig

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+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+indent_style = space
+indent_size = 4
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.{yml,yaml}]
+indent_size = 2
+
+[*.{json,js,ts}]
+indent_size = 2
+
+[*.md]
+trim_trailing_whitespace = false
+
+[Makefile]
+indent_style = tab

.env.example

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+# Environment Configuration Template
+# Copy this file to .env and update with your specific values
+
+# Application Settings
+APP_NAME=YourProjectName
+DEBUG=false
+LOG_LEVEL=INFO
+SECRET_KEY=your-secret-key-here
+
+# Database Configuration
+DATABASE_URL=sqlite:///app.db
+# For PostgreSQL: postgresql://user:password@localhost:5432/dbname
+# For MySQL: mysql://user:password@localhost:3306/dbname
+
+# External Services
+API_KEY=your-api-key-here
+EXTERNAL_SERVICE_URL=https://api.example.com
+
+# Email Configuration (if applicable)
+EMAIL_HOST=smtp.gmail.com
+EMAIL_PORT=587
+EMAIL_USER=your-email@example.com
+EMAIL_PASSWORD=your-email-password
+
+# Redis Configuration (if applicable)
+REDIS_URL=redis://localhost:6379/0
+
+# File Storage (if applicable)
+MEDIA_ROOT=/path/to/media/files
+STATIC_ROOT=/path/to/static/files
+
+# Security Settings
+ALLOWED_HOSTS=localhost,127.0.0.1,your-domain.com
+CORS_ALLOWED_ORIGINS=http://localhost:3000,https://your-frontend.com
+
+# Feature Flags
+ENABLE_FEATURE_X=false
+ENABLE_DEBUG_TOOLBAR=false

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: '[BUG] '
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Environment (please complete the following information):**
+ - OS: [e.g. Ubuntu 20.04, Windows 10, macOS 12.0]
+ - Version: [e.g. 1.2.3]
+ - Python/Node.js version: [e.g. Python 3.9, Node.js 18.0]
+
+**Additional context**
+Add any other context about the problem here.
+
+**Possible Solution**
+If you have ideas on how to fix the issue, please describe them here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: '[FEATURE] '
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Use Cases**
+Describe specific use cases where this feature would be beneficial.
+
+**Implementation Ideas**
+If you have ideas on how this could be implemented, please describe them here.
+
+**Additional context**
+Add any other context, mockups, or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

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+## Description
+
+Please include a summary of the changes and the related issue. Please also include relevant motivation and context.
+
+Fixes # (issue)
+
+## Type of change
+
+Please delete options that are not relevant.
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] This change requires a documentation update
+
+## How Has This Been Tested?
+
+Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce.
+
+- [ ] Test A
+- [ ] Test B
+
+**Test Configuration**:
+* Operating System:
+* Python/Node.js version:
+* Dependencies version:
+
+## Checklist:
+
+- [ ] My code follows the style guidelines of this project
+- [ ] I have performed a self-review of my own code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have made corresponding changes to the documentation
+- [ ] My changes generate no new warnings
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing unit tests pass locally with my changes
+- [ ] Any dependent changes have been merged and published in downstream modules
+
+## Additional Notes
+
+Add any additional notes, concerns, or considerations here.

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # Customize based on your project's needs
+        python-version: [3.8, 3.9, "3.10", "3.11"]
+        # node-version: [16, 18, 20]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    # Python setup example - uncomment and customize as needed
+    # - name: Set up Python ${{ matrix.python-version }}
+    #   uses: actions/setup-python@v4
+    #   with:
+    #     python-version: ${{ matrix.python-version }}
+
+    # - name: Install dependencies
+    #   run: |
+    #     python -m pip install --upgrade pip
+    #     pip install -r requirements.txt
+    #     pip install -r requirements-dev.txt
+
+    # - name: Lint with flake8
+    #   run: |
+    #     # stop the build if there are Python syntax errors or undefined names
+    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+    # - name: Test with pytest
+    #   run: |
+    #     pytest
+
+    # Node.js setup example - uncomment and customize as needed
+    # - name: Use Node.js ${{ matrix.node-version }}
+    #   uses: actions/setup-node@v4
+    #   with:
+    #     node-version: ${{ matrix.node-version }}
+
+    # - name: Install dependencies
+    #   run: npm ci
+
+    # - name: Run linter
+    #   run: npm run lint
+
+    # - name: Run tests
+    #   run: npm test
+
+    # Placeholder step - replace with actual CI steps
+    - name: Placeholder CI step
+      run: |
+        echo "Replace this with your actual CI steps"
+        echo "Examples: linting, testing, building"
+        echo "Current directory contents:"
+        ls -la

.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    tags:
+      - 'v*'  # Trigger on version tags like v1.0.0
+
+jobs:
+  create-release:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # Fetch full history for changelog
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+
+    # Python build example
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build twine
+
+    - name: Build package
+      run: python -m build
+
+    - name: Check package
+      run: twine check dist/*
+
+    # Node.js build example (uncomment if using Node.js)
+    # - name: Set up Node.js
+    #   uses: actions/setup-node@v4
+    #   with:
+    #     node-version: '18'
+    #     registry-url: 'https://registry.npmjs.org'
+
+    # - name: Install dependencies
+    #   run: npm ci
+
+    # - name: Build package
+    #   run: npm run build
+
+    # - name: Run tests
+    #   run: npm test
+
+    - name: Extract release notes
+      id: extract-release-notes
+      run: |
+        # Extract release notes from CHANGELOG.md
+        version=${GITHUB_REF#refs/tags/}
+        awk -v version="$version" '
+        /^## \[/ { 
+          if ($0 ~ version) { 
+            found=1; next 
+          } else if (found) { 
+            exit 
+          } 
+        } 
+        found && /^## \[/ { exit } 
+        found { print }
+        ' CHANGELOG.md > release_notes.txt
+
+    - name: Create Release
+      uses: actions/create-release@v1
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        tag_name: ${{ github.ref }}
+        release_name: Release ${{ github.ref }}
+        body_path: release_notes.txt
+        draft: false
+        prerelease: false
+
+    # Python package publishing (uncomment if publishing to PyPI)
+    # - name: Publish to PyPI
+    #   env:
+    #     TWINE_USERNAME: __token__
+    #     TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+    #   run: twine upload dist/*
+
+    # Node.js package publishing (uncomment if publishing to npm)
+    # - name: Publish to npm
+    #   run: npm publish
+    #   env:
+    #     NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
+
+    # Docker image publishing (uncomment if publishing Docker images)
+    # - name: Set up Docker Buildx
+    #   uses: docker/setup-buildx-action@v2
+
+    # - name: Login to Docker Hub
+    #   uses: docker/login-action@v2
+    #   with:
+    #     username: ${{ secrets.DOCKERHUB_USERNAME }}
+    #     password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+    # - name: Build and push Docker image
+    #   uses: docker/build-push-action@v4
+    #   with:
+    #     context: .
+    #     push: true
+    #     tags: |
+    #       your-username/your-project:latest
+    #       your-username/your-project:${{ github.ref_name }}
+
+  # Notify about release
+  notify:
+    needs: create-release
+    runs-on: ubuntu-latest
+    if: always()
+
+    steps:
+    - name: Notify success
+      if: needs.create-release.result == 'success'
+      run: |
+        echo "✅ Release ${{ github.ref }} created successfully!"
+        # Add notification logic here (Slack, Discord, email, etc.)
+
+    - name: Notify failure
+      if: needs.create-release.result == 'failure'
+      run: |
+        echo "❌ Release ${{ github.ref }} failed!"
+        # Add failure notification logic here