dnakit 0.1.0.dev0__tar.gz → 0.1.3__tar.gz

dnakit-0.1.3/CHANGELOG.md

@@ -0,0 +1,28 @@
+# Changelog。
+
+## [Unreleased]
+
+## [0.1.3] - 2026-09-01
+
+- 新增 AlphaGenome、Enformer、Evo 2、GENERator、LucaOneTasks 和 SegmentNT 的预训练性质预测接口，并对模型下载、远程代码和输出大小设置显式边界。
+- 新增 Ensembl VEP、ClinVar、dbSNP、gnomAD、dN/dS 和 Golden Gate 等按功能命名的可选生物信息 API。
+- 新增 `dnakit[agent]` 可选依赖、`dnakit-mcp` 服务和紧凑工具目录，使支持 MCP 的 Agent 可以搜索、查看并有界调用 DNAKit 公开功能。
+- 新增中英文微信社区页面和文档导航入口。
+
+## [0.1.2] - 2026-08-30
+
+- 新增 Bioconda、GNU Guix 与 Galaxy Tool Shed 的发布适配文件。
+- 可视化统一导出接口新增 JPG，支持通过 `image_type` 选择 PNG、SVG 或 JPG，无扩展名时默认导出 PNG；`SequencePlotConfig` 新增 `column_spacing`、`line_spacing` 和 `symbol_map`，可控制文字列间距、序列行间距及 DNA/IUPAC 显示字符；所有绘图改为无装饰性图内标题的正方形画布。
+- GitHub 仓库首页和 PyPI 项目说明默认改为英文，并保留简体中文切换入口。
+- 文档站提供完整中英文页面、导航和独立搜索结果，站内跳转保持当前语言。
+- 精简不再对外展示的旧规划、演示和交付报告文档。
+
+## [0.1.1] - 2026-08-29
+
+- 发布首个不含开发版本后缀的 DNAKit 版本。
+- 精简仓库根目录文件，将第三方声明合并到 `DISCLAIMER.md`，将引用信息移至 `README.md`。
+- 更新 README、安装文档、打包配置和 GitHub 发布工作流。
+
+## [0.1.0.dev0] - 2026-08-28
+
+初始版本

dnakit-0.1.0.dev0/THIRD_PARTY_NOTICES.md → dnakit-0.1.3/DISCLAIMER.md

@@ -1,6 +1,33 @@
-# DNAKit Third-Party Notices
+# DNAKit 免责声明 / Disclaimer
 
-Last reviewed: 2026-08-23.
+## 中文
+
+DNAKit 是研究与教学用途的软件，不是医疗器械，也不用于临床诊断、治疗、患者管理、实验安全决策或其他高风险用途。软件输出可能不完整、不准确或不适用于特定实验；使用者必须独立验证计算、参数、输入数据和实验结论。
+
+DNAKit 按仓库 `LICENSE` 中的 MIT 许可证提供。该许可证已经包含“按原样提供”、无明示或默示担保以及责任限制条款。本文件用于进一步说明使用边界，不替代、缩减或修改 MIT 许可证，也不构成法律、医疗或合规意见。
+
+DNAKit 自身采用 MIT 许可证，允许研究和商业使用。因此，“本项目仅供学术研究”只是当前开发目的说明，不能被解释为对下游使用者施加非商业限制，也不能自动免除作者或使用者的法律责任。
+
+使用者负责：
+
+- 确认其提供的数据、参数表、数据库和外部程序具有适用的访问、使用与再分发权限；
+- 遵守第三方许可证、订阅条款、署名/引用要求、出口管制、隐私、伦理、生物安全及所在司法辖区的法律法规；
+- 在论文、软件或服务中准确披露实际使用的方法、版本、参数、限制和第三方来源；
+- 在依赖结果开展实验、发表、部署或商业活动前完成独立验证和必要的专业审查。
+
+DNAKit 不保证任何第三方资源免费、持续可用、适合商业用途或允许再分发。第三方条款和费用可能变化；请在使用时核对其官方许可证和价格页面。详见下文“第三方声明”章节。
+
+## English
+
+DNAKit is research and educational software. It is not a medical device and is not intended for clinical diagnosis, treatment, patient management, laboratory-safety decisions, or other high-risk uses. Results may be incomplete, inaccurate, or unsuitable for a particular experiment and must be independently validated.
+
+DNAKit is provided under the MIT License in `LICENSE`, including its “AS IS” warranty disclaimer and limitation of liability. This document clarifies scope; it does not replace, narrow, or modify the MIT License and is not legal, medical, or regulatory advice.
+
+Users are responsible for verifying their rights to all supplied data, parameter tables, databases, and external software; complying with applicable third-party terms, citation requirements, privacy, ethics, biosafety, export-control, and other laws; and independently validating results before publication, deployment, experimentation, or commercial use. DNAKit does not warrant that third-party resources are free, continuously available, commercially usable, or redistributable. See the Third-Party Notices section below.
+
+# DNAKit 第三方声明 / Third-Party Notices
+
+Last reviewed: 2026-09-01.
 
 This file is an engineering compliance inventory, not legal advice. DNAKit itself is licensed under MIT. A dependency, external executable, database, paper, or user-supplied parameter table keeps its own terms; citing a paper does not by itself grant permission to redistribute its software or data.
 
@@ -22,6 +49,8 @@ Python dependencies declared in `pyproject.toml` are resolved as separate distri
 | `viz` extra | Pillow | MIT-CMU | optional raster export |
 | `io` extra | PyArrow | Apache-2.0 | optional Parquet I/O |
 | `validation` extra | Biopython | Biopython License Agreement | validation only |
+| `external-tools` extra | ToolUniverse | Apache-2.0; verify the installed release and transitive dependencies | optional allowlisted scientific-function backend |
+| `agent` extra | FastMCP | Apache-2.0; verify the installed release and transitive dependencies | optional local MCP server |
 | `neural` extra | Hugging Face Hub, NumPy, scikit-learn, PyTorch, Transformers | Apache-2.0, BSD-family, and Apache-2.0 labels; verify resolved versions | checkpoint retrieval, inference, and k-means |
 | `neural-caduceus` extra | mamba-ssm | Apache-2.0 label; verify resolved version | optional Caduceus runtime |
 | `neural-enformer` extra | enformer-pytorch | MIT label; verify resolved version | optional Enformer runtime |
@@ -45,6 +74,7 @@ Exact versions and license texts must be checked in the distributions actually i
 
 | Resource | DNAKit integration and distribution | Terms/cost warning |
 | --- | --- | --- |
+| ToolUniverse | Optional Python dependency; DNAKit loads only an allowlisted function after an explicit call and does not vendor its source | Apache-2.0 code; remote Ensembl, NCBI, gnomAD, and EMBL-EBI services retain their own terms and availability limits. See the [official repository](https://github.com/mims-harvard/ToolUniverse). |
 | Primer3 CLI (`primer3_core`, `oligotm`, `ntthal`) | Pure external CLI adapter; explicit paths; no Python binding and no bundled binary | Primer3 source files state GPL-2.0-or-later; verify the installed release and comply with its license. See the [official repository](https://github.com/primer3-org/primer3) and [manual](https://github.com/primer3-org/primer3/blob/main/src/primer3_manual.htm). |
 | NUPACK | User installs separately; DNAKit does not download, bundle, or expose it as a hosted service | Separate NUPACK terms/subscription apply and access may require payment. Academic and commercial terms differ. Check the [official download and licensing page](https://www.nupack.org/download/overview) before use. |
 | DSSR/3DNA | User installs separately; DNAKit only parses explicitly supplied output | Academic and commercial permissions differ; free academic availability is still subject to the issued license. Check the [official DSSR licensing notice](https://home.x3dna.org/highlights/x3dna-dssr-is-funded-and-dssr-basic-academic-is-free). |

{dnakit-0.1.0.dev0 → dnakit-0.1.3}/MANIFEST.in

@@ -1,10 +1,8 @@
 include README.md
+include README_CN.md
 include CHANGELOG.md
-include CITATION.cff
-include CONTRIBUTING.md
 include LICENSE
 include DISCLAIMER.md
-include THIRD_PARTY_NOTICES.md
 include pyproject.toml
 include environment-dev.yml
 recursive-include src *.py py.typed
@@ -13,6 +11,7 @@ recursive-include benchmarks *.py *.md *.json
 recursive-include validation *.py *.md *.json
 recursive-include examples *.json *.fasta *.yml *.md
 recursive-include docs *.md *.json *.csv
+recursive-include overrides *.html
 include mkdocs.yml
 recursive-include notebooks *.ipynb
 

dnakit-0.1.3/PKG-INFO

@@ -0,0 +1,199 @@
+Metadata-Version: 2.4
+Name: dnakit
+Version: 0.1.3
+Summary: Deterministic tools for DNA sequence analysis
+Author: DNAKit contributors
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/mapengsen/DNAKit
+Project-URL: Documentation, https://mapengsen.github.io/DNAKit/en/
+Project-URL: Repository, https://github.com/mapengsen/DNAKit
+Project-URL: Issues, https://github.com/mapengsen/DNAKit/issues
+Project-URL: Changelog, https://mapengsen.github.io/DNAKit/en/changelog/
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+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
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: DISCLAIMER.md
+Requires-Dist: PyYAML>=6.0
+Requires-Dist: rich>=13.7
+Requires-Dist: tomli>=2.0; python_version < "3.11"
+Requires-Dist: typer>=0.12
+Provides-Extra: dev
+Requires-Dist: build>=1.2; extra == "dev"
+Requires-Dist: hypothesis>=6.100; extra == "dev"
+Requires-Dist: mypy>=1.11; extra == "dev"
+Requires-Dist: numpy<3,>=1.26; extra == "dev"
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: pytest-cov>=5.0; extra == "dev"
+Requires-Dist: ruff>=0.8; extra == "dev"
+Requires-Dist: twine>=5.0; extra == "dev"
+Requires-Dist: types-PyYAML>=6.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs<2,>=1.6; extra == "docs"
+Requires-Dist: mkdocs-material<10,>=9.5; extra == "docs"
+Requires-Dist: mkdocs-static-i18n<2,>=1.3.1; extra == "docs"
+Requires-Dist: mkdocstrings[python]<1,>=0.27; extra == "docs"
+Requires-Dist: nbmake<2,>=1.5; extra == "docs"
+Provides-Extra: viz
+Requires-Dist: CairoSVG<3,>=2.7; extra == "viz"
+Requires-Dist: Pillow<13,>=10; extra == "viz"
+Provides-Extra: io
+Requires-Dist: pyarrow<26,>=19; extra == "io"
+Provides-Extra: validation
+Requires-Dist: biopython<2,>=1.85; extra == "validation"
+Provides-Extra: external-tools
+Requires-Dist: tooluniverse<2,>=1.4; extra == "external-tools"
+Provides-Extra: agent
+Requires-Dist: fastmcp<4,>=3.4.5; extra == "agent"
+Provides-Extra: neural
+Requires-Dist: huggingface-hub<2,>=0.28; extra == "neural"
+Requires-Dist: numpy<3,>=1.26; extra == "neural"
+Requires-Dist: scikit-learn<2,>=1.5; extra == "neural"
+Requires-Dist: torch<3,>=2.5; extra == "neural"
+Requires-Dist: transformers<5,>=4.49; extra == "neural"
+Provides-Extra: neural-caduceus
+Requires-Dist: mamba-ssm<3,>=2.2; extra == "neural-caduceus"
+Provides-Extra: neural-enformer
+Requires-Dist: enformer-pytorch<1,>=0.8.11; extra == "neural-enformer"
+Provides-Extra: neural-evo2
+Requires-Dist: evo2<0.7,>=0.5.3; (python_version >= "3.11" and python_version < "3.13") and extra == "neural-evo2"
+Dynamic: license-file
+
+<p align="right">
+  <a href="https://github.com/mapengsen/DNAKit/blob/main/README_CN.md">简体中文</a> | <strong>English</strong>
+</p>
+
+<p align="center">
+  <img alt="DNAKit logo" src="https://raw.githubusercontent.com/mapengsen/DNAKit/main/docs/assets/images/DNAKit-icon.png" width="40%">
+</p>
+
+<p align="center">
+  <a href="https://github.com/mapengsen/DNAKit/actions/workflows/ci.yml">
+    <img src="https://github.com/mapengsen/DNAKit/actions/workflows/ci.yml/badge.svg?branch=main&amp;event=push" alt="CI status">
+  </a>
+  <a href="https://mapengsen.github.io/DNAKit/en/">
+    <img src="https://img.shields.io/badge/docs-GitHub%20Pages-4051b5" alt="Documentation">
+  </a>
+  <a href="https://www.python.org/downloads/">
+    <img src="https://img.shields.io/badge/Python-3.10%2B-3776AB" alt="Python 3.10+">
+  </a>
+  <a href="https://github.com/mapengsen/DNAKit/blob/main/LICENSE">
+    <img src="https://img.shields.io/github/license/mapengsen/DNAKit" alt="MIT license">
+  </a>
+</p>
+
+<p align="center">
+  <a href="https://pypi.org/project/dnakit/">
+    <img src="https://img.shields.io/pypi/v/dnakit?include_prereleases=true&amp;label=PyPI&amp;logo=pypi&amp;cacheSeconds=300" alt="PyPI version">
+  </a>
+  <a href="https://github.com/mapengsen/DNAKit/tree/main/packaging/bioconda">
+    <img src="https://img.shields.io/badge/Bioconda-recipe-43B02A?logo=anaconda&amp;logoColor=white" alt="Bioconda recipe">
+  </a>
+  <a href="https://github.com/mapengsen/DNAKit/tree/main/galaxy/dnakit">
+    <img src="https://img.shields.io/badge/Galaxy-wrapper-2C3143?logo=galaxy&amp;logoColor=white" alt="Galaxy wrapper">
+  </a>
+  <a href="https://github.com/mapengsen/DNAKit/tree/main/packaging/guix">
+    <img src="https://img.shields.io/badge/GNU%20Guix-package-A42E2B?logo=gnu&amp;logoColor=white" alt="GNU Guix package">
+  </a>
+</p>
+
+<p align="center">
+  <a href="https://mapengsen.github.io/DNAKit/">
+    <img src="https://img.shields.io/badge/MCP_Server-Available-blue" alt="DNAKit MCP server">
+  </a>
+  <a href="https://mapengsen.github.io/DNAKit/">
+    <img src="https://img.shields.io/badge/Website-DNAKit-blue" alt="DNAKit website">
+  </a>
+  <a href="https://mapengsen.github.io/DNAKit/en/wechat/">
+    <img src="https://img.shields.io/badge/WeChat-Community-07C160" alt="WeChat community">
+  </a>
+  <a href="https://x.com/PengsenMa">
+    <img src="https://img.shields.io/badge/X-Follow-000000" alt="Follow Pengsen Ma on X">
+  </a>
+</p>
+
+<p align="center">
+  <strong>DNAKit: A Comprehensive Toolkit for Efficient DNA Research</strong>
+</p>
+
+# What is DNAKit?
+
+DNAKit is a reproducible Python toolkit for DNA sequence analysis, positioned as an "RDKit for
+DNA." It covers standardization, sequence and annotation formats, basic operations, descriptors,
+pattern scanning, thermodynamics, fingerprints, similarity analysis, clustering and dataset
+splitting, comprehensive evaluation, molecular-biology simulation, and visualization. DNA
+foundation models can optionally be used for direct property prediction or to extract
+representations for k-means clustering.
+
+# Installation and quick start
+
+Install the current release:
+
+```bash
+pip install dnakit==0.1.3
+```
+
+Install the optional VEP, ClinVar, dbSNP, gnomAD, dN/dS, and Golden Gate
+backend with `pip install "dnakit[external-tools]"`.
+
+To expose DNAKit to an MCP-capable Agent, install `dnakit[agent]` and configure the
+`dnakit-mcp` command in the Agent client.
+
+To contribute to development, clone the repository and create the complete Conda environment:
+
+```bash
+conda env create -f environment-dev.yml
+conda activate dnakit-dev
+```
+
+Then explore the [feature tree](https://mapengsen.github.io/DNAKit/en/api/features/function_tree/).
+
+# Additional distribution platforms
+
+The repository provides [Bioconda and GNU Guix recipes](https://github.com/mapengsen/DNAKit/tree/main/packaging)
+and a [Galaxy Tool Shed wrapper](https://github.com/mapengsen/DNAKit/tree/main/galaxy/dnakit).
+These files target `0.1.1`. Until they are reviewed and published by their respective platforms,
+use the PyPI installation method above.
+
+# Documentation
+
+The complete English documentation is available from the
+[DNAKit documentation homepage](https://mapengsen.github.io/DNAKit/en/), including the
+[feature tree](https://mapengsen.github.io/DNAKit/en/api/features/function_tree/) and
+[FAQ](https://mapengsen.github.io/DNAKit/en/faq/).
+
+# Support and community
+
+**GitHub repository:**
+
+[github.com/mapengsen/DNAKit](https://github.com/mapengsen/DNAKit)
+
+For questions, feedback, or suggestions, see:
+
+- [FAQ](https://mapengsen.github.io/DNAKit/en/faq/)
+- [GitHub Issues](https://github.com/mapengsen/DNAKit/issues)
+
+# Changelog
+
+See [CHANGELOG.md](https://github.com/mapengsen/DNAKit/blob/main/CHANGELOG.md) for release notes.
+
+# Citation
+
+The DNAKit project paper has not yet been published. Cite the current version as:
+
+```text
+DNAKit contributors. DNAKit 0.1.3, 2026. https://github.com/mapengsen/DNAKit
+```
+
+This section will be updated after the paper is published. When using specific algorithms,
+databases, or optional backends, cite their corresponding sources as well.

dnakit-0.1.3/README.md

@@ -0,0 +1,128 @@
+<p align="right">
+  <a href="https://github.com/mapengsen/DNAKit/blob/main/README_CN.md">简体中文</a> | <strong>English</strong>
+</p>
+
+<p align="center">
+  <img alt="DNAKit logo" src="https://raw.githubusercontent.com/mapengsen/DNAKit/main/docs/assets/images/DNAKit-icon.png" width="40%">
+</p>
+
+<p align="center">
+  <a href="https://github.com/mapengsen/DNAKit/actions/workflows/ci.yml">
+    <img src="https://github.com/mapengsen/DNAKit/actions/workflows/ci.yml/badge.svg?branch=main&amp;event=push" alt="CI status">
+  </a>
+  <a href="https://mapengsen.github.io/DNAKit/en/">
+    <img src="https://img.shields.io/badge/docs-GitHub%20Pages-4051b5" alt="Documentation">
+  </a>
+  <a href="https://www.python.org/downloads/">
+    <img src="https://img.shields.io/badge/Python-3.10%2B-3776AB" alt="Python 3.10+">
+  </a>
+  <a href="https://github.com/mapengsen/DNAKit/blob/main/LICENSE">
+    <img src="https://img.shields.io/github/license/mapengsen/DNAKit" alt="MIT license">
+  </a>
+</p>
+
+<p align="center">
+  <a href="https://pypi.org/project/dnakit/">
+    <img src="https://img.shields.io/pypi/v/dnakit?include_prereleases=true&amp;label=PyPI&amp;logo=pypi&amp;cacheSeconds=300" alt="PyPI version">
+  </a>
+  <a href="https://github.com/mapengsen/DNAKit/tree/main/packaging/bioconda">
+    <img src="https://img.shields.io/badge/Bioconda-recipe-43B02A?logo=anaconda&amp;logoColor=white" alt="Bioconda recipe">
+  </a>
+  <a href="https://github.com/mapengsen/DNAKit/tree/main/galaxy/dnakit">
+    <img src="https://img.shields.io/badge/Galaxy-wrapper-2C3143?logo=galaxy&amp;logoColor=white" alt="Galaxy wrapper">
+  </a>
+  <a href="https://github.com/mapengsen/DNAKit/tree/main/packaging/guix">
+    <img src="https://img.shields.io/badge/GNU%20Guix-package-A42E2B?logo=gnu&amp;logoColor=white" alt="GNU Guix package">
+  </a>
+</p>
+
+<p align="center">
+  <a href="https://mapengsen.github.io/DNAKit/">
+    <img src="https://img.shields.io/badge/MCP_Server-Available-blue" alt="DNAKit MCP server">
+  </a>
+  <a href="https://mapengsen.github.io/DNAKit/">
+    <img src="https://img.shields.io/badge/Website-DNAKit-blue" alt="DNAKit website">
+  </a>
+  <a href="https://mapengsen.github.io/DNAKit/en/wechat/">
+    <img src="https://img.shields.io/badge/WeChat-Community-07C160" alt="WeChat community">
+  </a>
+  <a href="https://x.com/PengsenMa">
+    <img src="https://img.shields.io/badge/X-Follow-000000" alt="Follow Pengsen Ma on X">
+  </a>
+</p>
+
+<p align="center">
+  <strong>DNAKit: A Comprehensive Toolkit for Efficient DNA Research</strong>
+</p>
+
+# What is DNAKit?
+
+DNAKit is a reproducible Python toolkit for DNA sequence analysis, positioned as an "RDKit for
+DNA." It covers standardization, sequence and annotation formats, basic operations, descriptors,
+pattern scanning, thermodynamics, fingerprints, similarity analysis, clustering and dataset
+splitting, comprehensive evaluation, molecular-biology simulation, and visualization. DNA
+foundation models can optionally be used for direct property prediction or to extract
+representations for k-means clustering.
+
+# Installation and quick start
+
+Install the current release:
+
+```bash
+pip install dnakit==0.1.3
+```
+
+Install the optional VEP, ClinVar, dbSNP, gnomAD, dN/dS, and Golden Gate
+backend with `pip install "dnakit[external-tools]"`.
+
+To expose DNAKit to an MCP-capable Agent, install `dnakit[agent]` and configure the
+`dnakit-mcp` command in the Agent client.
+
+To contribute to development, clone the repository and create the complete Conda environment:
+
+```bash
+conda env create -f environment-dev.yml
+conda activate dnakit-dev
+```
+
+Then explore the [feature tree](https://mapengsen.github.io/DNAKit/en/api/features/function_tree/).
+
+# Additional distribution platforms
+
+The repository provides [Bioconda and GNU Guix recipes](https://github.com/mapengsen/DNAKit/tree/main/packaging)
+and a [Galaxy Tool Shed wrapper](https://github.com/mapengsen/DNAKit/tree/main/galaxy/dnakit).
+These files target `0.1.1`. Until they are reviewed and published by their respective platforms,
+use the PyPI installation method above.
+
+# Documentation
+
+The complete English documentation is available from the
+[DNAKit documentation homepage](https://mapengsen.github.io/DNAKit/en/), including the
+[feature tree](https://mapengsen.github.io/DNAKit/en/api/features/function_tree/) and
+[FAQ](https://mapengsen.github.io/DNAKit/en/faq/).
+
+# Support and community
+
+**GitHub repository:**
+
+[github.com/mapengsen/DNAKit](https://github.com/mapengsen/DNAKit)
+
+For questions, feedback, or suggestions, see:
+
+- [FAQ](https://mapengsen.github.io/DNAKit/en/faq/)
+- [GitHub Issues](https://github.com/mapengsen/DNAKit/issues)
+
+# Changelog
+
+See [CHANGELOG.md](https://github.com/mapengsen/DNAKit/blob/main/CHANGELOG.md) for release notes.
+
+# Citation
+
+The DNAKit project paper has not yet been published. Cite the current version as:
+
+```text
+DNAKit contributors. DNAKit 0.1.3, 2026. https://github.com/mapengsen/DNAKit
+```
+
+This section will be updated after the paper is published. When using specific algorithms,
+databases, or optional backends, cite their corresponding sources as well.

dnakit-0.1.3/README_CN.md

@@ -0,0 +1,101 @@
+<p align="right">
+  <strong>简体中文</strong> | <a href="https://github.com/mapengsen/DNAKit/blob/main/README.md">English</a>
+</p>
+
+<p align="center">
+  <img alt="DNAKit logo" src="https://raw.githubusercontent.com/mapengsen/DNAKit/main/docs/assets/images/DNAKit-icon.png" width="40%">
+</p>
+
+<p align="center">
+  <a href="https://github.com/mapengsen/DNAKit/actions/workflows/ci.yml">
+    <img src="https://github.com/mapengsen/DNAKit/actions/workflows/ci.yml/badge.svg?branch=main&event=push" alt="CI status">
+  </a>
+  <a href="https://mapengsen.github.io/DNAKit/">
+    <img src="https://img.shields.io/badge/docs-GitHub%20Pages-4051b5" alt="Documentation">
+  </a>
+  <a href="https://www.python.org/downloads/">
+    <img src="https://img.shields.io/badge/Python-3.10%2B-3776AB" alt="Python 3.10+">
+  </a>
+  <a href="https://github.com/mapengsen/DNAKit/blob/main/LICENSE">
+    <img src="https://img.shields.io/github/license/mapengsen/DNAKit" alt="MIT license">
+  </a>
+</p>
+
+<p align="center">
+  <a href="https://pypi.org/project/dnakit/">
+    <img src="https://img.shields.io/pypi/v/dnakit?include_prereleases=true&label=PyPI&logo=pypi&cacheSeconds=300" alt="PyPI version">
+  </a>
+  <a href="https://github.com/mapengsen/DNAKit/tree/main/packaging/bioconda">
+    <img src="https://img.shields.io/badge/Bioconda-recipe-43B02A?logo=anaconda&logoColor=white" alt="Bioconda recipe">
+  </a>
+  <a href="https://github.com/mapengsen/DNAKit/tree/main/galaxy/dnakit">
+    <img src="https://img.shields.io/badge/Galaxy-wrapper-2C3143?logo=galaxy&logoColor=white" alt="Galaxy wrapper">
+  </a>
+  <a href="https://github.com/mapengsen/DNAKit/tree/main/packaging/guix">
+    <img src="https://img.shields.io/badge/GNU%20Guix-package-A42E2B?logo=gnu&logoColor=white" alt="GNU Guix package">
+  </a>
+</p>
+
+<p align="center">
+  <strong>DNAkit: A Comprehensive Toolkit for Efficient DNA Research</strong>
+</p>
+
+# DNAKit 是什么？
+
+DNAKit 是面向 DNA 序列的可复现 Python 工具包，定位类似“DNA 领域的 RDKit”。它覆盖标准化、文件与注释格式、基础操作、描述符、模式扫描、热力学、指纹、相似度、聚类与数据划分、综合评价、分子生物学模拟和可视化，并可选用 DNA 基础模型直接预测性质或提取 rep 后进行 k-means 聚类等各种各样的操作。
+
+# 安装与快速入门
+
+Pypi安装当前版本：
+
+```bash
+pip install dnakit==0.1.3
+```
+
+如需 VEP、ClinVar、dbSNP、gnomAD、dN/dS 和 Golden Gate
+功能，可执行 `pip install "dnakit[external-tools]"` 安装可选后端。
+
+如需让支持 MCP 的 Agent 调用 DNAKit，可执行 `pip install "dnakit[agent]"`，然后在 Agent
+中配置 `dnakit-mcp` 命令。
+
+如果需要参与开发，克隆仓库后通过 Conda 创建完整环境：
+
+```bash
+conda env create -f environment-dev.yml
+conda activate dnakit-dev
+```
+
+# 文档
+
+完整文档位于 [DNAKit 文档首页](https://mapengsen.github.io/DNAKit/)，所有功能模块可在 [功能树总览](https://mapengsen.github.io/DNAKit/api/features/function_tree/) 中查看，常见问题见 [FAQ](https://mapengsen.github.io/DNAKit/faq/)。
+
+# 支持与社区
+
+**Github仓库：**
+
+[github.com/mapengsen/DNAKit](https://github.com/mapengsen/DNAKit)
+
+如果有问题、意见或建议，可以先查看：
+
+- [常见问题](https://mapengsen.github.io/DNAKit/faq/)
+- [GitHub Issues](https://github.com/mapengsen/DNAKit/issues)
+
+# 更多发布平台
+
+仓库已提供 [Bioconda 与 GNU Guix 配方](https://github.com/mapengsen/DNAKit/tree/main/packaging)
+以及 [Galaxy Tool Shed 包装器](https://github.com/mapengsen/DNAKit/tree/main/galaxy/dnakit)。这些文件已固定对应
+`0.1.1`；在各平台审核通过前，仍请使用上面的 PyPI 安装方式。
+
+# 更新日志
+
+详细版本更新记录请查看 [CHANGELOG.md](https://github.com/mapengsen/DNAKit/blob/main/CHANGELOG.md)。
+
+# 引用
+
+DNAKit 的项目论文尚未发表。当前版本可引用为：
+
+```text
+DNAKit contributors. DNAKit 0.1.3, 2026. https://github.com/mapengsen/DNAKit
+```
+
+正式论文发表后，此处将更新为论文引用信息。使用具体算法、数据库或可选后端时，还应引用其对应来源。