# renunney

Clean working repository for:

- faithful replication of Leonard Nunney's 2003 cost-of-substitution results,
- orchestration of distributed sweep runs,
- later migration to a faster Rust-backed worker.

## Current Scope

This repository is the clean operational wrapper around the current work in:

- [`../collaborations/to_ptbc/evc/cost_of_substitution`](/mnt/CIFS/pengolodh/Docs/Projects/collaborations/to_ptbc/evc/cost_of_substitution)

The Track 1 simulation backend still lives there. The orchestration control
plane and the Track 1 runner/API boundary are now local to `renunney`.

`renunney` provides:

- a clean git repo,
- a stable working directory layout,
- a local orchestration CLI and library,
- local paper-scale Figure 1 submission configs,
- a local Track 1 runner and config/API layer,
- a local Track 1 analysis layer for tracking summaries and loci-regression,
- a local Track 1 threshold/search layer for Nunney-style threshold checks,
- a local Track 1 simulation kernel,
- a local Track 1 report generator,
- a local Track 1 extinction-model data layer,
- a local Track 1 dataset generator,
- a local Track 1 fit layer,
- a Makefile for common tasks,
- migration notes for pulling code into this repo in stages.

## Layout

- `docs/`
  - project and migration notes
- `config/`
  - configuration templates and examples
- `runs/state/`
  - SQLite registries and persistent orchestration state
- `runs/results/`
  - result artifacts collected by orchestration
- `runs/scratch/`
  - local worker scratch and cache files
- `src/renunney/`
  - future in-repo Python package and migration target
- `scripts/`
  - local CLI entrypoints
- `tests/`
  - local verification for migrated boundaries

## Start

Initialize the local run directories and SQLite registry:

```bash
make init
```

Submit a paper-scale Figure 1 treatment:

```bash
make submit-figure1-m10
```

Run one local Track 1 simulation through the migrated runner/API boundary:

```bash
make track1-sim-smoke
```

Run one worker loop locally:

```bash
make run-loop
```

Collate completed Figure 1 jobs:

```bash
make collate-figure1
```

## Status

The current state is split:

- orchestration control plane: local to `renunney`
- Track 1 runner and config/API layer: local to `renunney`
- Track 1 analysis layer: local to `renunney`
- Track 1 threshold/search layer: local to `renunney`
- Track 1 simulation kernel: local to `renunney`
- Track 1 report generator: local to `renunney`
- Track 1 extinction-model data layer: local to `renunney`
- Track 1 dataset generator: local to `renunney`
- Track 1 fit layer: local to `renunney`

This repo is now the clean operational entry point while the simulation code is
migrated in later stages.