API Examples

• Examples showing how to interact with the Pipe|bio REST api through python.
• See https://docs.pipebio.com for full API documentation.
• See PyPi for our SDK which wraps some methods in the API
• Examples currently wrap our API endpoints in python only, you can of course use the endpoints in any language (java, javascript, c#, etc)
• All endpoints are under heavy development and subject to change. Use at your own risk.

Installation

• Python3 or just brew install python@3.7
• Install uv: pip install uv or follow uv installation guide
• Create a virtual environment and install dependencies in one step: uv venv && source venv/bin/activate && uv pip install -r requirements.txt
• Alternatively, step by step:
  • Create a virtual environment: uv venv
  • Activate the venv: source venv/bin/activate
  • Install dependencies: uv pip install -r requirements.txt

Getting started

• Check out the files with names in the examples directory; to run them use python examples/upload_fasta.py for example.
• Before running the examples, make sure to set the required environment variables:

  export TARGET_FOLDER_ID="your_folder_id"
  export TARGET_SHAREABLE_ID="your_shareable_id"
  export TARGET_DOCUMENT_ID="your_document_id"

• Please contact support@pipebio.com for help.

Running Tests

To ensure these examples work correctly, we have integration tests that run each example:

# Install pytest
uv pip install pytest

# Run the integration tests
python -m pytest -c pytest.ini -v

The tests will check that each example script can run to completion without errors.

Contributing

• Issues and pull requests are welcome.