Metadata-Version: 2.4
Name: zeztz-flow
Version: 0.1.1
Summary: Self-contained flow cytometry analysis helpers with a slim vendored Cytoflow runtime.
License-Expression: GPL-2.0-or-later
License-File: LICENSE.txt
License-File: THIRD_PARTY_NOTICES.md
Author: Xiaoyu Wu
Requires-Python: >=3.9
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Provides-Extra: tables
Requires-Dist: bottleneck
Requires-Dist: marimo
Requires-Dist: matplotlib (>=3.8)
Requires-Dist: mpl-scatter-density
Requires-Dist: natsort
Requires-Dist: numba (>=0.59)
Requires-Dist: numexpr
Requires-Dist: numpy (>=1.26)
Requires-Dist: pandas (>=2.1)
Requires-Dist: scikit-learn (>=1.3)
Requires-Dist: scipy (>=1.11)
Requires-Dist: seaborn (>=0.13)
Requires-Dist: six
Requires-Dist: statsmodels (>=0.14)
Requires-Dist: tabulate ; extra == "tables"
Requires-Dist: traits
Description-Content-Type: text/markdown

# zeztz-flow

`zeztz-flow` is an marimo-compatible flow-cytometry FCS analysis package.
Derived from `cytoflow`, this package is designed to become a minimal platform, allowing users to perform vibe analysis with their own AI agents.

Features:
- FCS import with automatic well-plate metadata
- Cleanup gating: scatter, doublet removal, polygon, custom thresholds
- Density plots, faceted histograms, ridgeline plots
- Subset by row, column, or well
- Median-fluorescence export
- Self-contained — vendored Cytoflow runtime, no extra installs
- Pure Python — no compiled extensions
- Designed for AI-assisted analysis

## Installation

```bash
pip install zeztz-flow
```

For local development: `mamba env create -f environment.yml`

## Quick Start

Open a [marimo](https://marimo.io) notebook, import `zeztzflow`, and
describe your analysis to your AI agent. The agent reads `AGENTS.md`
and `PROJECT_GUIDE.md` to generate the right code — from loading FCS
files to gating, plotting, and exporting results.

## Documentation

- [PROJECT_GUIDE.md](PROJECT_GUIDE.md) — API reference, workflows, testing, publishing
- [AGENTS.md](AGENTS.md) — guide for AI coding agents
- [llms.txt](llms.txt) — machine-readable project map

## Testing

```bash
MPLCONFIGDIR=/tmp/mplconfig python test/package_smoke_test.py
```

## License

GPL-compatible. See [LICENSE.txt](LICENSE.txt) and
[THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md).

