Reader ingests instrument files and experiment metadata, applies declared transformations, and writes validated records, plots, exports, and notebooks. Every unit of work—including a cross-experiment aggregate—has an owned directory beneath experiments/, with source material in inputs/, a reader/v8 contract in config.yaml, and generated artifacts in outputs/. The distribution and import package are named reader-workbench and reader_workbench; the installed command remains reader.

Install

Reader has not yet been published to PyPI. Install the current source release as a command-line tool:

uv tool install git+https://github.com/e-south/reader.git

For development, install from a checkout:

git clone https://github.com/e-south/reader.git
cd reader
uv sync --locked --group dev
uv run reader demo

The installed command is reader:

reader demo
reader protocols
reader init ./experiments/my_experiment --protocol plate_reader/single_reporter_screen

The demo prints a guided command tour. It does not execute a pipeline or write files. Every generated starter can be inspected and validated before data is added.

Learn more

• Getting started — install Reader, run the demo, and scaffold a first experiment.
• Common tasks — shortest commands for discovery, validation, execution, and automation.
• Python API — typed, task-oriented experiment and plugin interfaces for integrations.
• Documentation index — complete user, reference, and maintainer documentation.

Reader is available under the MIT license.