riverine 0.7.0

Many-component mix library for molecular programming

For DNA 28, our poster as a Jupyter notebook is available here. Our documentation is in the process of being written (latest git documentation is here); we also have a tutorial notebook (WIP).

Riverine is a Python library to systematically, efficiently, and safely design recipes for mixes of many components, intended primarily for DNA computation experiments. The library recursively tracks individual components through layers of intermediate mixes, performs checks to ensure those layers of mixes are possible, and allows verification that final samples will contain the correct components at the correct concentrations. Incorporating reference information from files such as DNA synthesis order details, the library generates recipes for straightforward pipetting, even in mixes with many components at different concentrations spread across several plates.

Changelog

v0.7.0

• Renames the package from alhambra-mixes to riverine.
• Replaces Mix.buffer_name and Mix.fixed_total_volume with a more flexible FillToVolume action, like the existing EchoFillToVolume. The existing keywords should remain functional for backwards compatibility: they now add and modify a FillToVolume action as needed (or modify an EchoFillToVolume action if it already exists).
• Deprecates Python 3.9 support.
• Several bug fixes.

v0.6.1

• Adds html_with_borders_tablefmt again (and import printing).

v0.6.0

• ECHO liquid handler support now included by default. Uses kithairon, which does require Python ≥ 3.10.

v0.5.0

An interim version release while larger changes are being made, so that users can make use of several important new features, and the pypi-available version fits well with the latest documentation.

• Adds an Experiment class that can hold mixes and components, and keep track of volumes, etc.
• Adds volume/consumption tracking.
• Adds master/split mix functions.
• Fixes numerous minor bugs.