Metadata-Version: 2.4
Name: phenoradar
Version: 0.3.0
Summary: Macroevolutionary phenotype predictor
Author-email: Tomoya Nishiguchi <t.nishiguchi5@gmail.com>
License-File: LICENSE
Requires-Python: >=3.12
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Description-Content-Type: text/markdown

# phenoradar

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> [!WARNING]
> This repository is under active development and may change without notice.

## Overview

PhenoRadar is a CLI tool for binary phenotype prediction from orthogroup-level TPM.

## Install

```bash
pip install phenoradar
```

## Fastest Run

Fetch compact test data, materialize default config, then run:

```bash
phenoradar dataset
phenoradar config
phenoradar run -c config.yml
```

## Documentation (Recommended Order)

1. [docs/quickstart.md](docs/quickstart.md): first successful run, full run, and prediction.
2. [docs/data-format.md](docs/data-format.md): required metadata/expression TSV schema.
3. [docs/configuration.md](docs/configuration.md): config behavior, defaults, and key-by-key definitions.
4. [docs/cli-reference.md](docs/cli-reference.md): all commands and options.
5. [docs/output-artifacts.md](docs/output-artifacts.md): output files, column-level details, and interpretation guidance.
6. [docs/pipeline-details.md](docs/pipeline-details.md): internal execution behavior.
