semvec/pypi-packages huggingface dataset:
farm-memory 0.1.2
Filesystem As Remote Memory - Agent memory storage system
Requires Python: >=3.10

# FARM - Filesystem As Remote Memory

为 AI Agent 设计的持久化记忆系统。让 Agent 能够跨会话记住重要信息，并通过语义搜索快速检索。

## 核心功能

- **记忆存储**: 保存对话摘要、用户偏好、学习到的知识
- **多模式搜索**: 支持语义搜索、全文搜索、混合搜索
- **多接口**: MCP Server (Claude)、REST API、CLI

## 技术栈

- **向量搜索**: DuckDB + VSS 扩展 (HNSW 索引)
- **Embedding**: `BAAI/bge-small-zh-v1.5` (中文优化)
- **全文搜索**: 关键词匹配

## 快速开始

```bash
# 安装
pip install farm-memory
# 或
uv add farm-memory

# 初始化存储
farm init

# 添加记忆
farm add "用户偏好 Vue 框架" --tag preference

# 搜索记忆
farm search "前端框架" --mode semantic
farm search "Vue" --mode text
farm search "前端" --mode hybrid

# 启动 API 服务
farm serve
```

## Claude 集成

添加到 Claude 配置 (`~/.claude.json`):

```json
{
  "mcpServers": {
    "farm": {
      "command": "uvx",
      "args": ["farm-memory", "mcp"]
    }
  }
}
```

## 文档

- [快速入门](docs/getting-started.md)
- [CLI 命令](docs/cli.md)
- [REST API](docs/api.md)
- [MCP Server](docs/mcp.md)

## License

MIT
tact 0.8.0
Taxonomic addition for complete trees: Adds tips to a backbone phylogeny using taxonomy simulated with birth-death models
Requires Python: <4,>=3.11

# TACT: Taxonomic Addition for Complete Trees

[![PyPI](https://img.shields.io/pypi/v/tact.svg)](https://pypi.org/project/tact/)
[![Build status](https://github.com/jonchang/tact/workflows/Python%20package/badge.svg)](https://github.com/jonchang/tact/actions)
[![Docker Hub](https://img.shields.io/docker/pulls/jonchang/tact.svg)](https://hub.docker.com/r/jonchang/tact)

TACT is a tool for stochastic polytomy resolution, and generates complete phylogenies from incomplete ones. It uses birth-death-sampling estimators across an ultrametric phylogeny to generate branching times for unsampled taxa, using taxonomic information to compatibly place these unsampled taxa onto a backbone phylogeny.

## Getting started with TACT

* [Install TACT](https://tact.jonathanchang.org/install/)
* [Read the background](https://tact.jonathanchang.org/background/)
* [Try the tutorial](https://tact.jonathanchang.org/tutorial/)
* [Check the commands](https://tact.jonathanchang.org/commands/)
* [Solutions to common problems](https://tact.jonathanchang.org/troubleshooting/)

## Citation

If you use TACT in your research, please cite:

* Chang, J., Rabosky, D. L., & Alfaro, M. E. (2019). Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions. Systematic Biology. doi:[10.1093/sysbio/syz081](https://doi.org/10.1093/sysbio/syz081)

TACT builds on foundational work in stochastic polytomy resolution, particularly:

* Thomas, G. H., Hartmann, K., Jetz, W., Joy, J. B., Mimoto, A., & Mooers, A. O. (2013). PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences. Methods in Ecology and Evolution, 4(11), 1011–1017. doi:[10.1111/2041-210x.12117](https://doi.org/10.1111/2041-210X.12117)

* Cusimano, N., Stadler, T., & Renner, S. S. (2012). A New Method for Handling Missing Species in Diversification Analysis Applicable to Randomly or Nonrandomly Sampled Phylogenies. Systematic Biology, 61(5), 785–792. doi:[10.1093/sysbio/sys031](https://doi.org/10.1093/sysbio/sys031)

## Sponsorship

Please consider sponsoring the ongoing maintenance of TACT via [GitHub Sponsors](https://github.com/sponsors/jonchang).

Initial development was supported by a National Science Foundation Doctoral Dissertation Improvement Grant (DEB-1601830).