# =============================================================================
# Agent / Workflow artifacts
# =============================================================================
.agents/

# =============================================================================
# Python
# =============================================================================
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST
pip-log.txt
pip-delete-this-directory.txt

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

# =============================================================================
# IDEs / Editors
# =============================================================================
.idea/
*.swp
*.swo
*~
*.sublime-project
*.sublime-workspace
.project
.pydevproject
.settings/

# =============================================================================
# OS
# =============================================================================
.DS_Store
Thumbs.db
desktop.ini

# =============================================================================
# Testing / Coverage
# =============================================================================
.pytest_cache/
.coverage
.coverage.*
htmlcov/
.tox/
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/

# =============================================================================
# Type checking / Linting
# =============================================================================
.ruff_cache/
.mypy_cache/
.dmypy.json
dmypy.json

# =============================================================================
# Environment / Secrets
# =============================================================================
.env
.env.local
.env.*.local
!.env.example
secrets.yaml
secrets.yml
*.pem
*.key

# =============================================================================
# SQLite databases
# =============================================================================
*.db
*.db-journal
*.sqlite
*.sqlite3

# =============================================================================
# Bioinformatics / Data artifacts
# =============================================================================
*.fasta
*.fastq
*.faa
*.fna
*.sam
*.bam
*.cram
*.vcf
*.bcf
*.gff
*.gff3
*.bed
*.bw
*.bigWig
*.pdb
*.pdbqt
*.mol2
*.sdf
*.xtc
*.trr
*.edr
*.gro
*.tpr
*.log

# =============================================================================
# LakeFS / S3 staging
# =============================================================================
/tmp/biodock/
.staging/

# =============================================================================
# Snakemake
# =============================================================================
.snakemake/
*.snakemake.log

# =============================================================================
# Docker
# =============================================================================
.dockerignore

# =============================================================================
# Jupyter / Notebooks
# =============================================================================
.ipynb_checkpoints/
*.ipynb

# =============================================================================
# mkdocs / Documentation build
# =============================================================================
site/

# =============================================================================
# Misc
# =============================================================================
*.bak
*.tmp
*.temp
