# NuCSI Project Gitignore
# =======================

# Manuscript_files

METHODS_DRAFT.md

# 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

# Conda
.conda/
conda-meta/

# Jupyter Notebook
.ipynb_checkpoints

# Environment variables
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

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

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

# Logs
*.log
*.tmp
*.temp

# Data files (protect sensitive data)
*.bam
*.bai
*.sam
*.fastq
*.fastq.gz
*.fq
*.fq.gz
*.fa
*.fasta
*.fa.gz
*.fasta.gz

# Results and analysis files (protect analysis results)
*.png
*.jpg
*.jpeg
*.pdf
*.svg
*.csv
*.tsv

# Allow specific files
!requirements.txt
!README.md
!nucsi.py
!scripts/*.py
