Metadata-Version: 2.4
Name: reader-workbench
Version: 1.0.0
Summary: Validated, traceable analysis workflows for experimental instrument data
Author: Eric J. South
License-Expression: MIT
Project-URL: Documentation, https://github.com/e-south/reader/tree/main/docs
Project-URL: Issues, https://github.com/e-south/reader/issues
Project-URL: Repository, https://github.com/e-south/reader
Keywords: data-analysis,data-pipelines,scientific-computing,workbench
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering
Requires-Python: <3.13,>=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.26
Requires-Dist: matplotlib>=3.8
Requires-Dist: pandas>=2.1
Requires-Dist: pydantic>=2.6
Requires-Dist: pyyaml>=6.0.2
Requires-Dist: typer>=0.16.0
Requires-Dist: click>=8.3.3
Requires-Dist: rich>=13.7
Requires-Dist: pyarrow>=23.0.1
Requires-Dist: openpyxl>=3.1
Requires-Dist: seaborn>=0.13
Requires-Dist: pillow>=12.3.0
Requires-Dist: polars>=1.36.1
Requires-Dist: flowio>=1.4.0
Requires-Dist: filelock<4,>=3.20.3
Dynamic: license-file

# ![Reader data workbench](https://raw.githubusercontent.com/e-south/reader/v1.0.0/assets/reader-banner.png)

[![Checks](https://github.com/e-south/reader/actions/workflows/checks.yaml/badge.svg?branch=main)](https://github.com/e-south/reader/actions/workflows/checks.yaml)
[![Python 3.12](https://img.shields.io/badge/python-3.12-3776AB.svg)](https://www.python.org/downloads/release/python-3120/)
[![MIT license](https://img.shields.io/badge/license-MIT-3D8068.svg)](https://github.com/e-south/reader/blob/main/LICENSE)

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

Install Reader as a command-line tool:

```bash
uv tool install reader-workbench
```

For development, install from a checkout:

```bash
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`:

```bash
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](https://github.com/e-south/reader/blob/main/docs/guides/getting_started.md) — install Reader, run the
  demo, and scaffold a first experiment.
- [Common tasks](https://github.com/e-south/reader/blob/main/docs/guides/common_routes.md) — shortest commands for
  discovery, validation, execution, and automation.
- [Python API](https://github.com/e-south/reader/blob/main/docs/core/python_api.md) — typed, task-oriented experiment and
  plugin interfaces for integrations.
- [Documentation index](https://github.com/e-south/reader/blob/main/docs/README.md) — complete user, reference, and
  maintainer documentation.

Reader is available under the [MIT license](https://github.com/e-south/reader/blob/main/LICENSE).
