biotailor 0.1.5

Python SDK for the Biotailor bioinformatics pipeline platform

biotailor

Python SDK for the Biotailor bioinformatics pipeline platform.

Installation

pip install biotailor

Quickstart

from biotailor import BiotailorClient, Pipeline

# 1. Create a client (get your API key from the Biotailor website)
client = BiotailorClient(api_key="btk_xxx.sk_yyy")

# 2. Discover available tools
tools = client.list_tools()
for t in tools:
    print(f"{t.toolid}: {t.display_name}")

# 3. Build a pipeline
tool = client.get_tool("fastp-single")

pipeline = (
    Pipeline(name="QC my reads", tool=tool)
    .set_input("input", "reads.fastq")
    .set_param("qualified_quality_phred", 20)
)

# 4. Run and wait
job = client.run_and_wait(pipeline, output_dir="./results")
print(f"Job {job.jobid} finished with status: {job.job_status.value}")

Development

# Install in dev mode
pip install -e ".[dev]"

# Run tests
pytest tests/ -v

# Lint
ruff check src/ tests/

Publishing to PyPI

# 1. Install build tools
pip install build twine

# 2. Clean old builds and build the package
rm -rf dist/
python -m build

# 3. (Optional) Test on TestPyPI first
twine upload --repository testpypi dist/*

# 4. Upload to PyPI
twine upload dist/*

Note: Bump version in pyproject.toml before each release — PyPI rejects duplicate versions. Use a PyPI API token for authentication (username: __token__).