# Ryu (SCI) Project .gitignore

# =============================================================================
# Python
# =============================================================================
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg

# Virtual environments
.venv/
venv/
ENV/
env/

# =============================================================================
# IDE and Editors
# =============================================================================
.idea/
.vscode/
*.swp
*.swo
*~
.project
.pydevproject
.settings/
*.sublime-project
*.sublime-workspace

# =============================================================================
# OS Generated
# =============================================================================
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db
desktop.ini

# =============================================================================
# Secrets and Credentials
# =============================================================================
.env
.env.*
!.env.example
*.pem
*.key
*.crt
api.keys
credentials.json
secrets.yaml
*.secret

# =============================================================================
# Data and Logs
# =============================================================================
*.log
*.log.*
logs/
*.csv
*.parquet
*.pkl
*.pickle
data/raw/
data/processed/

# =============================================================================
# Database
# =============================================================================
*.db
*.sqlite
*.sqlite3

# =============================================================================
# Docker Volumes (local data)
# =============================================================================
*_data/
*_postgres_data/
*_neo4j_data/
*_redis_data/

# =============================================================================
# Experiment Raw Data (keep reports, exclude raw data)
# =============================================================================
organisms/capital/experiments/*/results/
organisms/capital/experiments/*/data/
organisms/capital/experiments/*/logs/
!organisms/capital/experiments/*.md
!organisms/capital/experiments/*.yaml
!organisms/capital/experiments/*/comprehensive_report.md

# =============================================================================
# Build and Distribution
# =============================================================================
*.manifest
*.spec

# =============================================================================
# Jupyter Notebooks
# =============================================================================
.ipynb_checkpoints/
*.ipynb_checkpoints

# =============================================================================
# Coverage and Testing
# =============================================================================
htmlcov/
.tox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/
.pytest_cache/

# =============================================================================
# Type Checking
# =============================================================================
.mypy_cache/
.dmypy.json
dmypy.json

# =============================================================================
# Large Files (organism-specific)
# =============================================================================
organisms/capital/organism.log*
organisms/capital/organism.pid
organisms/capital/*.cypher
organisms/capital/poetry.lock

# =============================================================================
# Temporary Files
# =============================================================================
tmp/
temp/
*.tmp
*.temp
*.bak
*.backup

# =============================================================================
# Mount Points
# =============================================================================
mnt/

# =============================================================================
# Scripts that may contain sensitive info
# =============================================================================
organisms/capital/run_*.py
organisms/capital/check_*.py
organisms/capital/test_*.py
organisms/capital/debug_*.py
organisms/capital/verify_*.py
organisms/capital/warmup.py
organisms/capital/wipe_*.py
organisms/capital/reset_*.py
organisms/capital/flatten_*.py
organisms/capital/analyze_*.py
organisms/capital/update_*.py
organisms/capital/repro*.py
