# =============================================================================
# Universal Biomedical Skills - Git Ignore
# =============================================================================

# 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/
ENV/
env/
.venv/
test_demonstration/venv/

# Environment Variables
.env
.env.local
*.env

# Jupyter Notebooks
.ipynb_checkpoints/
*.ipynb_checkpoints

# IDEs and Editors
.idea/
.vscode/
*.swp
*.swo
*~
.project
.pydevproject
.settings/

# OS Files
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db

# =============================================================================
# Data Files (Large/Generated)
# =============================================================================
*.h5ad
*.h5
*.mtx
*.mtx.gz
*.tsv.gz
*.csv.gz

# Test Data Directories
scRNAsedata/
analyzed_data/
qc_results/
qc_results_demo/

# =============================================================================
# Archive (External References & Old Versions)
# =============================================================================
archive/

# =============================================================================
# Sensitive Files
# =============================================================================
token.txt
*.token
credentials.json
secrets.yaml
*.pem
*.key

# =============================================================================
# Temporary Files
# =============================================================================
*.tmp
*.temp
*.log
*.bak
.~lock.*

# =============================================================================
# Build Outputs
# =============================================================================
platform/build/
platform/output/
platform/reports/

# =============================================================================
# Claude Code
# =============================================================================
.claude/