# 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

# Testing
.pytest_cache/
.coverage
htmlcov/
.tox/

# Local config files (for testing)
config/full_training_config.yaml

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

# OS
.DS_Store
Thumbs.db

# Claude Code
.claude/
**/CLAUDE.md

# Temporary files
*.tmp
*.bak

# Validation and test outputs
validation_outputs/
*.iic
*.iic.png
intronIC_patched.py
run.log
comparison_outputs/
homo_sapiens_*.log
homo_sapiens_*.*
# Test run logs
tiny_*.log
small_*.log
micro_*.log
refactored_*.log
original_*.log
*_output.log
*_test.log
*_fix.log 
comparison_test/
test_verification/
*.log

# Documentation (keep only specific .md files tracked)
/docs/
/*.md
!/README.md
!/QUICKSTART.md
!/SRC_LAYOUT_MIGRATION.md
!/TODO.md
!/FEATURE_SELECTION_IMPLEMENTATION_PLAN.md
!/CONTRIBUTING.md

# Test output directories
run_tests/
test_*_output/
*_test/
*_validation*/
celegans_*/
test_chr19_output/

# Model files from development
*.model.pkl
!src/intronIC/data/default_pretrained.model.pkl
*.model.metadata.json
homo_sapiens.d*.model.*
homo_sapiens.default*.model.*

# Archive (not tracked)
archive/

# Old refactored directory (purged from history)
intronIC_refactored/
