# NP Replica

This project provides a local Chinese web replica of the core NUPACK `analysis/input` workflow.

## Run

```bash
docker compose up --build -d
```

Open `http://127.0.0.1:18765`.

## Reverse Proxy

The service listens on port `18765`. You can later reverse proxy `np.lihato.icu` to this port from your public server.

## Endpoints

- `GET /`
- `GET /health`
- `GET /api/example`
- `POST /api/analyze`
- `POST /api/jobs`
- `GET /api/jobs/<job_id>`

## Notes

- `tube` mode supports strand concentrations and `SetSpec(max_size=...)`.
- `complex` mode supports explicit complex definitions such as `A+B`.
- Pair matrices are returned as a preview block to keep responses manageable.
- The Docker image compiles ViennaRNA `RNAplot` from `rna/ViennaRNA-2.7.2.tar.gz` and embeds SVG structure plots into MFE results.
- Multistrand MFE plots now use a split-strand layout by default when a structure contains `+`, with `RNAplot` retained as the fallback path.
- The web UI now supports Chinese and English switching, browser-side history, result export, and async polling for submitted jobs.
- Docker now starts three services: `np-replica`, `np-worker`, and `redis`.
- Async jobs use Redis-backed storage and queueing when `NP_REDIS_URL` is configured; otherwise the app falls back to the older in-memory mode.
- The browser-facing API and page behavior stay the same after enabling Redis-backed jobs.
- Worker concurrency is controlled by `NP_WORKER_CONCURRENCY` and defaults to `2`.
- Per-job native thread usage is capped by `NP_PER_JOB_THREAD_LIMIT` and defaults to `1` to prevent a single analysis from monopolizing the machine.
- `NP_STRUCTURE_PLOT_MODE` supports `auto` (default), `split`, and `rnaplot`.
- Static pages are served with ETag-based browser caching; JSON API responses remain uncached.
- The force-directed structure viewer lazy-loads D3 only when that view is opened, so the initial page load is not blocked by the external CDN.
- `/health` uses Redis queue length plus a running-job set instead of scanning every historical job on each poll.



  现在 `docker-compose.yml` 面向 64 核 / 64G WSL 服务器的并发策略是：

  - 最多同时跑 16 个任务
  - 每个任务最多用 4 个计算线程
  - 后续任务进入队列等待
  - 理论上最多占用约 64 个 native 计算线程，避免 16 × 8 这类过度超卖

  如果后面你发现机器还会被压满，最直接的调法就是在 docker-compose.yml 里继续压：

  - 把 NP_WORKER_CONCURRENCY 改小
  - 或保持并发不变，把 NP_PER_JOB_THREAD_LIMIT 改成 2 或 1