dnakit 0.1.0.dev0__py3-none-any.whl

dnakit-0.1.0.dev0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: dnakit
+Version: 0.1.0.dev0
+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://github.com/mapengsen/DNAKit/tree/main/docs
+Project-URL: Repository, https://github.com/mapengsen/DNAKit
+Project-URL: Issues, https://github.com/mapengsen/DNAKit/issues
+Project-URL: Changelog, https://github.com/mapengsen/DNAKit/blob/main/CHANGELOG.md
+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
+License-File: THIRD_PARTY_NOTICES.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: 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: 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<0.6,>=0.5.3; extra == "neural-evo2"
+Dynamic: license-file
+
+<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://pypi.org/project/dnakit/">
+    <img src="https://img.shields.io/pypi/v/dnakit?include_prereleases&amp;label=PyPI" alt="PyPI version">
+  </a>
+  <a href="https://github.com/mapengsen/DNAKit/actions/workflows/ci.yml">
+    <img src="https://github.com/mapengsen/DNAKit/actions/workflows/ci.yml/badge.svg" alt="CI status">
+  </a>
+  <a href="https://pypi.org/project/dnakit/">
+    <img src="https://img.shields.io/pypi/pyversions/dnakit" alt="Supported Python versions">
+  </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>
+
+# 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 基础模型提取 rep 后进行 k-means 聚类；不集成启动子活性、表达量、TF 结合强度或 CRISPR 编辑效率等任务型深度学习预测模型。
+
+# 安装与快速入门
+
+安装当前开发预览版：
+
+```bash
+pip install dnakit==0.1.0.dev0
+```
+
+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
+```
+
+随后可以阅读 [Python 快速入门指南](https://github.com/mapengsen/DNAKit/blob/main/docs/quickstart.md)。
+
+更详细的依赖、可选后端和安装说明见 [安装文档](https://github.com/mapengsen/DNAKit/blob/main/docs/installation.md)。
+
+# 文档
+
+完整文档位于 [DNAKit 文档首页](https://github.com/mapengsen/DNAKit/blob/main/docs/index.md) 和仓库的 [`docs`](https://github.com/mapengsen/DNAKit/tree/main/docs) 目录。
+
+所有功能模块可在 [功能树总览](https://github.com/mapengsen/DNAKit/blob/main/docs/api/features/function_tree.md) 中查看，常见问题见 [FAQ](https://github.com/mapengsen/DNAKit/blob/main/docs/faq.md)。
+
+# 支持与社区
+
+如果有问题、意见或建议，可以先查看：
+
+- [常见问题](https://github.com/mapengsen/DNAKit/blob/main/docs/faq.md)
+- [贡献指南](https://github.com/mapengsen/DNAKit/blob/main/CONTRIBUTING.md)
+- [GitHub Issues](https://github.com/mapengsen/DNAKit/issues)
+
+如果发现缺陷或希望增加功能，请按照 [贡献指南](https://github.com/mapengsen/DNAKit/blob/main/CONTRIBUTING.md) 中的要求记录问题和复现信息。
+
+DNAKit 当前处于开发预览阶段，公开接口在正式版本发布前可能调整。

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dnakit-0.1.0.dev0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (84.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

dnakit-0.1.0.dev0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+dnakit = dnakit.cli.app:run

dnakit-0.1.0.dev0.dist-info/licenses/DISCLAIMER.md

@@ -0,0 +1,26 @@
+# DNAKit 免责声明 / Disclaimer
+
+## 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 `THIRD_PARTY_NOTICES.md`。
+
+## 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 `THIRD_PARTY_NOTICES.md`.

dnakit-0.1.0.dev0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Pengsen Ma
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

dnakit-0.1.0.dev0.dist-info/licenses/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,73 @@
+# DNAKit Third-Party Notices
+
+Last reviewed: 2026-08-23.
+
+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.
+
+## Distribution boundary
+
+The DNAKit wheel and sdist do **not** bundle DiProDB numerical tables, Primer3, NUPACK, DSSR/3DNA, Dashing, BLAST, MMseqs2, sourmash, REBASE, JASPAR, DNA foundation-model checkpoints, NCBI, Ensembl, ENA, ENCODE, UCSC, or their databases. External programs are never downloaded automatically. Public-data adapters access providers only when explicitly called. Where an executable adapter exists, the user must install the tool separately and provide an explicit executable or installation path. A model checkpoint is downloaded to the local `ckpt/` directory only when the user explicitly invokes the representation API; it is not redistributed in DNAKit artifacts.
+
+Python dependencies declared in `pyproject.toml` are resolved as separate distributions by the installer; their source code is not vendored into the DNAKit wheel. This inventory covers direct dependencies. Users and redistributors must also inspect resolved transitive dependencies for their actual environment and versions.
+
+## Direct Python dependencies
+
+| Scope | Component | License identifier or upstream label | DNAKit use |
+| --- | --- | --- | --- |
+| Runtime | PyYAML | MIT | YAML configuration |
+| Runtime | Rich | MIT | terminal rendering and progress |
+| Runtime | Typer | MIT | command-line interface |
+| Runtime, Python <3.11 | tomli | MIT | TOML parsing |
+| `viz` extra | CairoSVG | LGPL-3.0-or-later | optional SVG conversion |
+| `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 |
+| `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 |
+| `neural-evo2` extra | evo2 and transitive dependencies | verify the installed version and official repository | optional Evo 2 runtime |
+| `docs` extra | MkDocs | BSD-2-Clause | documentation build |
+| `docs` extra | Material for MkDocs | MIT | documentation theme |
+| `docs` extra | mkdocstrings | ISC | API documentation |
+| `docs` extra | nbmake | Apache-2.0 | notebook test gate |
+| `dev` extra | build | MIT | local package build |
+| `dev` extra | Hypothesis | MPL-2.0 | tests |
+| `dev` extra | mypy | MIT | type checking |
+| `dev` extra | pytest | MIT | tests |
+| `dev` extra | pytest-cov | MIT | coverage |
+| `dev` extra | Ruff | MIT | lint and formatting |
+| `dev` extra | twine | Apache-2.0 | local distribution checks |
+| `dev` extra | types-PyYAML | Apache-2.0 | type stubs |
+
+Exact versions and license texts must be checked in the distributions actually installed. Useful upstream locations include [PyPI](https://pypi.org/), [Biopython licensing](https://biopython.org/DIST/docs/LICENSE), and each project repository.
+
+## User-installed tools and supplied data
+
+| Resource | DNAKit integration and distribution | Terms/cost warning |
+| --- | --- | --- |
+| 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). |
+| Dashing | User supplies an explicit executable; no binary/source is included in distributions | GPL-3.0; verify the installed version in the [official repository](https://github.com/dnbaker/dashing). |
+| DiProDB-derived or other dinucleotide tables | DNAKit supplies only a JSON schema and loader. It contains no DiProDB numerical values. | No redistribution permission for the public table has been assumed. The user must obtain or create a table they are entitled to use and cite its actual source. See [DiProDB](https://diprodb.fli-leibniz.de/). |
+| BLAST, MMseqs2, sourmash and external databases | Not installed or bundled; registered capabilities are conditional and version-specific | Verify each program and database license separately. Database access does not imply redistribution rights. |
+| NCBI, Ensembl, ENA, ENCODE and UCSC public services/data | Queried or downloaded only on explicit user calls; source URLs and checksums are recorded; no remote dataset is embedded in distributions | Check provider usage, attribution, privacy, controlled-access and redistribution terms. dbGaP and other controlled data still require formal authorization. |
+| Hugging Face DNA-model checkpoints | Downloaded into `ckpt/` after explicit model selection with a source manifest; weights are not bundled in wheel/sdist | DNABERT-2, NTv2, HyenaDNA, Caduceus, GROVER, LucaOne, GENERator, Enformer, and Evo 2 may have different terms. Review the official links on the [clustering feature page](docs/api/features/10_clustering.md#data-027-neural-clustering). |
+| AlphaGenome | Loaded only after the user accepts access terms, obtains the checkpoint, and installs the official research code | The checkpoint is gated and carries non-commercial model terms. Review the [official repository](https://github.com/google-deepmind/alphagenome_research) and current model page. |
+| JanusDNA | Official Harvard Dataverse file is downloaded with MD5 verification; the user must also supply the official source environment | Review the [official repository](https://github.com/Qihao-Duan/JanusDNA), [Dataverse DOI](https://doi.org/10.7910/DVN/HDT0RN), and applicable code/data terms. |
+
+The DNABERT-2, NTv2, HyenaDNA, Caduceus, LucaOne, and GENERator Transformers
+checkpoints include Python code required by their loaders. DNAKit rejects that execution by
+default. It is enabled only after the user reviews the source and explicitly sets
+`allow_remote_code=True`. This opt-in does not replace a code audit, dependency lock, or
+license review.
+
+Keeping a tool in a separate process or asking the user to install it reduces bundling and automatic-distribution risk, but it is not a legal conclusion that every intended use is permitted. Commercial deployment, hosted services, redistribution, or journal supplementary archives require a new review of the exact artifacts being distributed.
+
+## Scientific attribution
+
+Methods, papers, databases, and websites used as scientific foundations are listed in `docs/acknowledgements.md`. Those citations document provenance; they do not replace software/data licenses. Runtime provenance should record the actual tool/table name, version, source, parameters, and checksum.
+
+## No assurance of zero cost or zero risk
+
+DNAKit does not promise that any optional tool, database, or future version is free of charge. Terms, availability, and fees can change. Before each release, archive, hosted deployment, or commercial use, repeat the dependency and artifact audit and retain copies of the applicable license texts.

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