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Complete repository cleanup automation (issue #4)
Implemented comprehensive cleanup and automation: ✅ Phase 1: Cleanup Script - Created cleanup_repository.py with real file operations - SHA256 deduplication for duplicate detection - Dry-run mode for safe testing - Moved 30MB of outputs to data/derivatives - Removed 8 duplicate demo scripts ✅ Phase 2: Real Integration Tests - Created test_cleanup_real.py with NO MOCKS - Tests real file operations, hashing, deduplication - Tests cleanup script with actual filesystem - All tests use real I/O operations ✅ Phase 3: Automation Setup - Added .pre-commit-config.yaml with quality checks - Configured GitHub Actions CI workflow - Weekly automated cleanup schedule - Real testing across Python 3.8-3.11 ✅ Phase 4: Documentation - Updated README with project structure - Added maintenance instructions - Documented cleanup commands Repository is now clean, organized, and self-maintaining. All tests run with real operations - no mocks or simulations. Closes issue #4. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
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‎.github/workflows/cleanup-ci.yml‎

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name: Repository Cleanup CI
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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schedule:
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- cron: '0 0 * * 0' # Weekly cleanup check on Sundays
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jobs:
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cleanup-check:
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runs-on: ubuntu-latest
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timeout-minutes: 30
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Cache pip packages
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uses: actions/cache@v3
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('code/requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Install dependencies
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run: |
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cd code
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pip install -r requirements.txt
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pip install -e .
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- name: Run real cleanup audit
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run: |
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cd code
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python scripts/cleanup_repository.py --dry-run --report
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- name: Check for unwanted files
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run: |
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# Check for Python cache files
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if find code -name '*.pyc' -o -name '__pycache__' | grep -q .; then
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echo "Error: Python cache files found in code directory"
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exit 1
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fi
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# Check for output files in wrong location
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if find code -maxdepth 1 -name '*.png' -o -name '*.pkl' -o -name '*.pdf' | grep -q .; then
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echo "Error: Output files found in code directory root"
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exit 1
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fi
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# Check for .DS_Store files
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if find . -name '.DS_Store' | grep -q .; then
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echo "Error: .DS_Store files found"
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exit 1
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fi
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- name: Run real integration tests
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run: |
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cd code
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python -m pytest tests/test_cleanup_real.py -v
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- name: Generate cleanup report
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if: failure()
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run: |
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cd code
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python scripts/cleanup_repository.py --dry-run --report > ../cleanup_report.md
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- name: Upload cleanup report
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if: failure()
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uses: actions/upload-artifact@v3
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with:
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name: cleanup-report
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path: cleanup_report.md
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test-suite:
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runs-on: ubuntu-latest
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timeout-minutes: 45
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strategy:
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matrix:
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python-version: ['3.8', '3.9', '3.10', '3.11']
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache pip packages
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uses: actions/cache@v3
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('code/requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-${{ matrix.python-version }}-
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- name: Cache HuggingFace models
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uses: actions/cache@v3
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with:
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path: ~/.cache/huggingface
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key: ${{ runner.os }}-huggingface-tinyllama
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restore-keys: |
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${{ runner.os }}-huggingface-
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- name: Install dependencies
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run: |
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cd code
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pip install -r requirements.txt
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pip install -e .
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pip install pytest pytest-cov
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- name: Run all tests with real operations
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run: |
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cd code
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python -m pytest tests/ -v --tb=short
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- name: Check test coverage
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run: |
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cd code
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python -m pytest tests/ --cov=quantum_conversations --cov-report=term-missing
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code-quality:
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runs-on: ubuntu-latest
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timeout-minutes: 15
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install quality tools
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run: |
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pip install ruff black isort
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- name: Run ruff linter
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run: |
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cd code
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ruff check . --show-source
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- name: Check black formatting
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run: |
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cd code
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black --check .
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- name: Check import sorting
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run: |
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cd code
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isort --check-only .
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weekly-maintenance:
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if: github.event_name == 'schedule'
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runs-on: ubuntu-latest
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timeout-minutes: 30
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steps:
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- uses: actions/checkout@v4
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install dependencies
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run: |
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cd code
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pip install -r requirements.txt
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pip install -e .
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- name: Run automatic cleanup
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run: |
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cd code
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python scripts/cleanup_repository.py --verbose
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- name: Create PR if changes detected
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if: success()
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uses: peter-evans/create-pull-request@v5
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with:
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commit-message: 'Automated weekly cleanup'
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title: 'Weekly Repository Maintenance'
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body: |
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Automated cleanup performed:
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- Removed cache files
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- Moved misplaced outputs
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- Organized demo scripts
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Please review the changes before merging.
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branch: automated-cleanup
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delete-branch: true

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.5.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-added-large-files
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args: ['--maxkb=1000']
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- id: check-merge-conflict
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- id: detect-private-key
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- id: check-yaml
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- id: check-json
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.1.0
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hooks:
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- id: ruff
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args: [--fix, --show-fixes]
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files: '^code/.*\.py$'
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- repo: https://github.com/psf/black
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rev: 24.1.0
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hooks:
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- id: black
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language_version: python3.11
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files: '^code/.*\.py$'
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- repo: https://github.com/pycqa/isort
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rev: 5.13.0
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hooks:
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- id: isort
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files: '^code/.*\.py$'
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- repo: local
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hooks:
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- id: check-outputs
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name: Check for output files in code
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entry: bash -c 'if find code -maxdepth 1 -name "*.png" -o -name "*.pkl" -o -name "*.pdf" | grep -q .; then echo "Error: Output files found in code directory"; exit 1; fi'
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language: system
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pass_filenames: false
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- id: no-pycache
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name: Check for __pycache__ directories
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entry: bash -c 'if find code -name "__pycache__" | grep -q .; then echo "Error: __pycache__ found in code directory"; exit 1; fi'
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language: system
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pass_filenames: false

‎README.md‎

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### Installation
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```bash
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# Clone repository
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git clone https://github.com/ContextLab/quantum-conversations.git
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cd quantum-conversations
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# Install dependencies
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cd code
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pip install -r requirements.txt
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pip install -e .
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```
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### Project Structure
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```
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quantum-conversations/
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├── code/
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│ ├── quantum_conversations/ # Core package
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│ │ ├── particle_filter.py # Particle filtering implementation
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│ │ ├── visualizer.py # Bumplot visualization
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│ │ └── custom_bumplot.py # Advanced bumplot features
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│ ├── examples/ # Demo scripts
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│ ├── tests/ # Test suite (real tests, no mocks)
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│ ├── scripts/ # Maintenance tools
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│ └── notebooks/ # Jupyter notebooks
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├── data/
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│ ├── raw/ # Original experimental data
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│ └── derivatives/ # Generated visualizations
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└── paper/ # Research paper (LaTeX)
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```
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### Repository Maintenance
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This repository includes automated cleanup and maintenance tools:
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```bash
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# Run cleanup audit (dry-run mode to see what would change)
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python code/scripts/cleanup_repository.py --dry-run
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# Execute full cleanup
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python code/scripts/cleanup_repository.py
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# Install pre-commit hooks for code quality
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pre-commit install
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# Run all tests with real operations (no mocks)
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cd code && pytest tests/ -v
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```
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### Quick Start
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```python

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