# 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
MANIFEST

# Rust
/target/
**/*.rs.bk
Cargo.lock

# HDF5 files
*.h5
*.hdf5

# Jupyter Notebook
.ipynb_checkpoints

# Virtual environments
venv/
env/
ENV/
env.bak/
venv.bak/
.env
.venv

# IDE files
.idea/
.vscode/
*.swp
*.swo
.DS_Store

# Coverage reports
htmlcov/
.tox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/
.pytest_cache/

# Logs
*.log
logs/

# Temporary files
*.tmp
*.temp
tmp/
temp/

# Data files
*.fasta
*.fa
*.fna
*.ffn
*.faa
*.frn
*.gbk
*.gb
*.gbff
*.gff
*.gff3
*.gtf
*.bed
*.vcf
*.vcf.gz
*.tbi
*.bam
*.bai
*.sam
*.fastq
*.fastq.gz
*.fq
*.fq.gz

# Exceptions for test data
!tests/data/*.fasta
!tests/data/*.h5
!tests/data/*.gff3
!tests/data/*.gb
