# BBAV20311 Open Source .gitignore
# Strategy: Only Agent system is open-sourced

# ============================================================================
# CLOSED-SOURCE COMPONENTS - DO NOT COMMIT
# ============================================================================

# Analysis scripts (based on course materials)
apps/cli/
scripts/
gfa_core/tools/

# Local data directories
input/
workspace/
output/
logs/
*.log

# Bioinformatics data files
*.fa
*.fasta
*.fna
*.faa
*.gff
*.gff3
*.gtf
*.bed
*.vcf
*.bam
*.sam
*.cram

# HMM and BLAST databases
*.hmm
*.h3f
*.h3i
*.h3m
*.h3p
*.phr
*.pin
*.pog
*.psd
*.psi
*.psq
*.ptf
*.pto

# ============================================================================
# PYTHON
# ============================================================================

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

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

# PyInstaller
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/
.pytest_cache/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

# ============================================================================
# IDE
# ============================================================================

# PyCharm
.idea/
*.iml
*.iws
*.ipr

# VSCode
.vscode/
*.code-workspace

# Sublime Text
*.sublime-project
*.sublime-workspace

# Vim
*.swp
*.swo
*~

# Emacs
*~
\#*\#
.\#*

# ============================================================================
# OS
# ============================================================================

# macOS
.DS_Store
.AppleDouble
.LSOverride

# Windows
Thumbs.db
ehthumbs.db
Desktop.ini
$RECYCLE.BIN/

# Linux
*~
.nfs*

# ============================================================================
# PROJECT SPECIFIC
# ============================================================================

# Configuration with sensitive data
config/api_keys.yaml
config/secrets.yaml

# Database
*.db
*.sqlite
*.sqlite3

# Temporary files
tmp/
temp/
*.tmp

# Large files
*.tar.gz
*.zip
*.rar
*.7z

# Model files
*.pkl
*.pth
*.h5
*.onnx
*.pb

# Documentation builds
docs/_build/
docs/_static/
docs/_templates/