# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# Testing and coverage
.pytest_cache/
.coverage*
htmlcov/
.tox/
coverage.xml
*.cover

# Profiling and analysis outputs
analysis/profiling_results/
optimization_results/
profile_results.txt
*.prof

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

# IDEs
.vscode/
.idea/
*.swp
*.swo

# OS generated
.DS_Store
Thumbs.db

# Documentation builds
docs/build/
docs/_build/

# Temporary files
temp_*.py

# Jupyter Notebook
.ipynb_checkpoints
*.ipynb_checkpoints/

# Data files
*.csv
*.json
*.pkl
*.npy
*.npz
*.png  # Plot files
_temporary/research/analysis_scripts/**/results/
_temporary/research/r_comparisons/results/
benchmarks/**/*.csv
benchmarks/**/*.json

# Analysis outputs
analysis/plots/**/*.png
analysis/**/*.json

# R files
.Rhistory
.RData
*.Rout
*.Rproj.user/
*.Rproj

# Specific project directories
archive/legacy_config/
.cadence/
.junie/
.qodo/
.windsurf/
.gemini/
.agent_guidelines/
.claude/

# Additional cache directories
.mypy_cache/
.ruff_cache/
.hypothesis/

# Windsurf-specific files
.windsurfrules

# Jupyter notebooks (except example notebooks)
**/*.ipynb
!examples/**/*.ipynb
!docs/user_guide/examples/**/*.ipynb

# Log files
*.log
*.out
results_*.txt

# Compiled extensions
*.so
*.pyd
*.dll
