@luffysolution/omnischolar-pi 0.1.12 → 0.1.13
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.en.md +129 -0
- package/README.md +77 -124
- package/README.zh-CN.md +1 -1
- package/docs/INSTALLATION.md +20 -0
- package/package.json +2 -1
- package/pi-extension/dist/index.js +1 -1
package/README.en.md
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# OmniScholar
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<!-- mcp-name: io.github.luffysolution-svg/omnischolar -->
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[中文](README.md) | English
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OmniScholar adds literature search, local Zotero reading, PDF parsing, citation tools, materials data, and scientific image generation to coding agents through a local Python MCP server.
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It can search public indexes, combine online records with your Zotero notes, send an approved PDF to MinerU, and publish Markdown into a regular folder or an Obsidian vault. Zotero access is read-only.
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## Features
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- Search Semantic Scholar, OpenAlex, PubMed/PMC, arXiv, Crossref, Unpaywall, easyScholar, Google Scholar, and Google Patents
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- Retrieve paper details, authors, citations, references, recommendations, snippets, datasets, and journal metrics
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- Read Zotero collections, items, notes, annotations, attachments, indexed text, and local PDF paths without changing the library
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- Parse selected PDFs with MinerU and keep text, formulas, tables, and figures together
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- Find citation candidates, check bibliographic identity, and format accepted references
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- Query Materials Project and export JSON, CSV, Markdown, or CIF
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- Generate or edit scientific illustrations with configured image services
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- Preserve local Markdown edits and place incoming conflict versions in `.conflicts/`
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OmniScholar exposes 38 tools. See the [tool list](docs/TOOLS.en.md).
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<details>
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<summary>Install and connect an agent</summary>
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Python 3.11 or newer is required:
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```sh
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uv tool install luffysolution-omnischolar
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# or
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pipx install luffysolution-omnischolar
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# or
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python -m pip install luffysolution-omnischolar
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```
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Check, update, or uninstall the Python command:
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```sh
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omnischolar --version
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omnischolar doctor --json
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uv tool upgrade luffysolution-omnischolar
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uv tool uninstall luffysolution-omnischolar
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```
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Codex plugin:
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```sh
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codex plugin marketplace add luffysolution-svg/omnischolar --ref main
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codex plugin add omnischolar@omnischolar
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codex plugin marketplace upgrade omnischolar
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codex plugin remove omnischolar@omnischolar
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```
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Claude Code plugin:
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```text
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/plugin marketplace add luffysolution-svg/omnischolar
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/plugin install omnischolar@omnischolar
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```
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Pi package:
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```sh
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pi install npm:@luffysolution/omnischolar-pi
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pi update npm:@luffysolution/omnischolar-pi
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pi remove npm:@luffysolution/omnischolar-pi
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```
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The standalone Skills CLI is optional because the plugins bundle their Skills:
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```sh
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npx skills add luffysolution-svg/omnischolar --skill '*' --agent codex --global --yes
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npx skills update --global --yes
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npx skills remove --skill '*' --agent codex --global --yes
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```
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The plugin and host configurations start the latest PyPI MCP with:
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```sh
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uvx --from luffysolution-omnischolar@latest omnischolar mcp
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```
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</details>
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## Agent configuration prompt
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Use this as a starting prompt for an agent:
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```text
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You are my research assistant using OmniScholar. Search and cite reliable scholarly sources, verify DOI and bibliographic identity, and clearly distinguish evidence from inference. You may read Zotero but must never modify it. Ask before uploading any PDF or reference image to an external service or making a paid request. For PDF reading, use MinerU only after I approve the upload. Save approved literature notes and generated artifacts to the configured output directory, preserve local edits, and report the exact output paths. Treat generated scientific figures as illustrations, never as experimental evidence.
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```
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## Configuration and examples
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On the first MCP start or installer run, OmniScholar creates a complete user-level `omnischolar.config.json` template. API keys can be entered directly as `apiKey`, or supplied through the named `apiKeyEnv` environment variable.
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The root [`mcp.json`](mcp.json) is a reusable MCP stdio example. It intentionally contains no API keys: the MCP process reads the global [`omnischolar.config.example.json`](omnischolar.config.example.json), which can be created with `omnischolar config init`. The plugin copy is [`.mcp.json`](.mcp.json).
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Configure the Obsidian output location, paper folders, Markdown files, and parsed image assets with `output.rootDirectory`, `output.literatureDirectory`, `output.folderNameTemplate`, `output.filenameTemplate`, `output.filenameSeparator`, and `output.assetFilenameTemplate`; see [literature and output configuration](docs/RESEARCH.en.md).
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## Try it
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```text
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Find five recent reviews about solid-state battery interfaces. Deduplicate by DOI and show open-access copies.
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Find this DOI in my Zotero library and summarize my notes and annotations without changing Zotero.
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After I approve the upload, parse this PDF with MinerU and save a reading note in my Obsidian vault.
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Query stable Li-Fe-P-O materials in Materials Project and export the selected records as CSV and CIF.
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Create a labelled illustration of this mechanism. Treat it as a draft, not experimental data.
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```
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## Documentation
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- [Installation and agent setup](docs/INSTALLATION.en.md)
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- [Configuration and service credentials](docs/CONFIGURATION.en.md)
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- [Literature, Zotero, MinerU, citations, and output](docs/RESEARCH.en.md)
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- [Materials and chemistry](docs/MATERIALS.en.md)
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- [Scientific image providers](docs/IMAGE_PROVIDERS.en.md)
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- [Tool list](docs/TOOLS.en.md)
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## Support and license
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OmniScholar is open source under the [MIT License](LICENSE). Open a [GitHub issue](https://github.com/luffysolution-svg/omnischolar/issues) or email `LuffySolution@gmail.com`. Remove keys, signed URLs, private paper content, and personal Zotero data before sending a report.
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Third-party services and datasets keep their own terms and licenses. See [`THIRD_PARTY_NOTICES.md`](THIRD_PARTY_NOTICES.md).
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<!-- mcp-name: io.github.luffysolution-svg/omnischolar -->
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[](https://pypi.org/project/luffysolution-omnischolar/)
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[](https://www.npmjs.com/package/@luffysolution/omnischolar-pi)
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[](https://www.npmjs.com/package/skills)
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[](https://github.com/luffysolution-svg/omnischolar/releases)
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简体中文 | [English](README.en.md)
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OmniScholar 通过本地 Python MCP 服务，为 Codex、Claude Code、Cursor、OpenCode、Hermes 和 Pi 提供文献检索、Zotero 读取、PDF 解析、引用处理、材料数据和科研绘图工具。
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它可以把在线文献记录与 Zotero 笔记放在一起处理，将经你确认的 PDF 交给 MinerU 解析，再把 Markdown 保存到普通文件夹或 Obsidian Vault。Zotero 全程只读。
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- Retrieve paper details, authors, citations, references, recommendations, snippets, datasets, and journal metrics
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- Read Zotero collections, items, notes, annotations, attachments, indexed text, and local PDF paths without changing the library
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- Parse selected PDFs with MinerU and keep text, formulas, tables, and figures together
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- Find citation candidates, check bibliographic identity, and format accepted references
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- Query Materials Project and export JSON, CSV, Markdown, or CIF
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- Generate or edit scientific illustrations with configured image services
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- Preserve local Markdown edits and place incoming conflict versions in `.conflicts/`
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## 功能
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- 检索 Semantic Scholar、OpenAlex、PubMed/PMC、arXiv、Crossref、Unpaywall、easyScholar、Google Scholar 和 Google Patents
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- 查询论文详情、作者、参考文献、施引文献、推荐、全文片段、数据集和期刊指标
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- 读取 Zotero 收藏夹、条目、笔记、批注、附件、索引文本和本地 PDF 路径，不修改文献库
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- 使用 MinerU 提取指定 PDF 的正文、公式、表格和图片
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- 查找引用候选，核对书目信息，再按要求生成参考文献
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- 查询 Materials Project，并导出 JSON、CSV、Markdown 或 CIF
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- 调用已配置的图片服务生成或编辑科研示意图
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- 保留手工修改过的 Markdown，把待合并版本放入 `.conflicts/`
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OmniScholar 共提供 38 个工具，完整列表见[工具目录](docs/TOOLS.md)。
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<details>
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<summary>安装与部署</summary>
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需要 Python 3.11 或更高版本。普通 Python 命令任选一种方式安装：
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```sh
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uv tool install luffysolution-omnischolar
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# 或
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pipx install luffysolution-omnischolar
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# 或
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python -m pip install luffysolution-omnischolar
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```
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The distribution name is `luffysolution-omnischolar`; the command and Python package are `omnischolar`.
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Check the installation:
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检查、更新和卸载：
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```sh
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omnischolar --version
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```
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uv tool uninstall luffysolution-omnischolar
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```
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如果希望用一条命令强制刷新并重装最新版：
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```sh
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uv tool install --reinstall luffysolution-omnischolar
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```
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### Codex 插件
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```sh
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codex plugin marketplace add luffysolution-svg/omnischolar --ref main
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codex plugin add omnischolar@omnischolar
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codex plugin marketplace upgrade omnischolar
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```
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The plugin bundles all eight Skills and starts its local MCP server from the latest PyPI release:
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ChatGPT 桌面应用中重启应用后打开 **Plugins**，选择 **OmniScholar** 并安装或启用；Codex CLI 可运行 `/plugins` 浏览插件。插件已经包含 Skills，并通过下面的命令启动 PyPI 最新 MCP：
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```sh
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uvx --from luffysolution-omnischolar@latest omnischolar mcp
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```
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### Claude Code 插件
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Install [`uv`](https://docs.astral.sh/uv/getting-started/installation/) first. In Claude Code, add the GitHub marketplace and install the plugin:
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在 Claude Code 会话中运行：
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```text
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```
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普通终端也可以运行：
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```sh
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```
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### Host configuration installer
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Preview the files that will change, then install the local MCP entry and Skills:
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```
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Replace `claude` with `codex`, `cursor`, `opencode`, `hermes`, `pi`, or `workbuddy`. Codex, Claude Code, Cursor, OpenCode, Pi, and WorkBuddy/CodeBuddy support both user and project scopes. Hermes supports user-level MCP configuration; project-level installation adds Skills and reports that MCP setup is manual.
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```
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For Pi, the full installer runs `pi install npm:@luffysolution/omnischolar-pi` and installs the bundled Skills separately. The npm Extension starts the matching PyPI MCP through `uvx`, discovers its tools, and registers them with Pi; a separate global Python CLI installation is not required. You can also install the Extension directly:
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### Pi Extension
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```sh
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```
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The direct latest MCP command is:
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### 通用安装器与独立 Skills
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```sh
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omnischolar install --dry-run claude
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omnischolar install claude
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omnischolar update claude
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omnischolar uninstall claude
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```
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Full host and update instructions are in [Installation](docs/INSTALLATION.en.md).
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### Standalone Skills CLI
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Plugins already bundle their declared Skills. Use the official Skills CLI separately when you want to install the repository's Skills directly into an agent:
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也可以使用官方 Skills CLI 单独安装 Skills；插件已经包含这些 Skills，通常不需要重复安装：
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```sh
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# User scope; replace codex with claude-code, pi, cursor, or another supported agent
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npx skills add luffysolution-svg/omnischolar --skill '*' --agent codex --global --yes
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npx skills update --global --yes
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npx skills remove --skill '*' --agent codex --global --yes
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```
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完整的各 Agent 路径、项目级安装和故障排查见[安装说明](docs/INSTALLATION.md)。
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Find five recent reviews about solid-state battery interfaces. Deduplicate by DOI and show open-access copies.
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+
</details>
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## Agent 配置提示词
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可以将下面的提示词作为 Agent 的项目级指令或系统提示词基础：
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Create a labelled illustration of this mechanism. Treat it as a draft, not experimental data.
|
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+
```text
|
|
122
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+
你是我的科研助理，使用 OmniScholar 完成文献检索、Zotero 阅读、PDF 解析、引用核对和科研资料整理。检索时优先使用可靠的学术来源，核对 DOI 与书目信息，并明确区分原文证据、推断和不确定内容。Zotero 只允许读取，禁止修改。上传 PDF、参考图或发起可能收费的请求前必须先征得我的确认；MinerU 只有在我确认后才能上传文件。将确认后的文献笔记和生成文件保存到配置的输出目录，保留已有手工修改，并报告最终文件路径。生成的科研图片只能作为示意图，不能当作实验数据或科研证据。
|
|
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|
```
|
|
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|
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-
##
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+
## 配置与 MCP 示例
|
|
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126
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|
|
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-
|
|
127
|
+
首次启动 MCP 或运行安装器时，如果没有可发现的配置，OmniScholar 会创建用户级 `omnischolar.config.json` 模板。API key 可以直接填写到 `apiKey`，也可以用 `apiKeyEnv` 指定环境变量。
|
|
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|
|
|
164
|
-
|
|
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|
-
|
|
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-
A small local configuration can start with Zotero and the output directory:
|
|
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根目录的 [`mcp.json`](mcp.json) 是可直接复制到支持 MCP 的 Agent 中的 stdio 示例，内容如下：
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```json
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{
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"
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|
|
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|
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|
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|
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|
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|
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"mcpServers": {
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|
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|
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"omnischolar": {
|
|
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|
+
"type": "stdio",
|
|
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+
"command": "uvx",
|
|
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|
+
"args": ["--from", "luffysolution-omnischolar@latest", "omnischolar", "mcp"]
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}
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+
}
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|
}
|
|
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141
|
```
|
|
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|
|
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|
-
|
|
143
|
+
`mcp.json` 只负责启动 MCP，不保存 API key；服务凭据和 Obsidian 输出位置填写在 [`omnischolar.config.example.json`](omnischolar.config.example.json) 对应字段中，可执行 `omnischolar config init` 创建实际配置。插件内部使用的配置文件是 [`.mcp.json`](.mcp.json)。文件夹、Markdown 文件和图片附件命名可通过 `output` 区块自定义，详见[文献与输出配置](docs/RESEARCH.md)。
|
|
144
|
+
|
|
145
|
+
## 使用示例
|
|
181
146
|
|
|
182
|
-
|
|
147
|
+
```text
|
|
148
|
+
查找 5 篇关于固态电池界面的近期综述，按 DOI 去重，并给出开放获取版本。
|
|
183
149
|
|
|
184
|
-
|
|
185
|
-
- MinerU receives a PDF only when `allowExternalUpload` is enabled in the config and confirmed again in that tool call.
|
|
186
|
-
- Image services receive prompts and any reference images selected for upload. Generation may use account credit.
|
|
187
|
-
- Ai4Scholar calls may use account credit. A stored key does not by itself approve a paid call.
|
|
188
|
-
- A failed paid request is not retried automatically when the provider may already have accepted it.
|
|
189
|
-
- Generated images are illustrations. They are not measurements, experimental evidence, or scientific results.
|
|
150
|
+
在我的 Zotero 中找到这个 DOI，汇总笔记和批注，不要修改 Zotero。
|
|
190
151
|
|
|
191
|
-
|
|
152
|
+
我确认上传后，用 MinerU 解析这份 PDF，并把阅读笔记保存到 Obsidian Vault。
|
|
192
153
|
|
|
193
|
-
|
|
154
|
+
查询 Materials Project 中稳定的 Li-Fe-P-O 材料，将选中的记录导出为 CSV 和 CIF。
|
|
194
155
|
|
|
195
|
-
|
|
196
|
-
|
|
197
|
-
| `omnischolar` | Choose and combine tools for a research request |
|
|
198
|
-
| `scholar-search` | Literature, patents, authors, citation graphs, journals, and datasets |
|
|
199
|
-
| `zotero-research` | Local Zotero matching, notes, annotations, and attachments |
|
|
200
|
-
| `paper-reading` | MinerU parsing and close reading of text, formulas, tables, and figures |
|
|
201
|
-
| `academic-citation` | Evidence checks, citation candidates, formatting, and bibliographies |
|
|
202
|
-
| `scientific-figure` | Image generation, editing, review, and scientific labelling |
|
|
203
|
-
| `materials-project` | Materials screening, properties, provenance, phase data, and export |
|
|
204
|
-
| `chemical-data` | CAS Common Chemistry records when an official interface description is configured |
|
|
156
|
+
为这个机理绘制带标签的示意图。图片只是草稿，不得写成实验数据。
|
|
157
|
+
```
|
|
205
158
|
|
|
206
|
-
##
|
|
159
|
+
## 文档
|
|
207
160
|
|
|
208
|
-
- [
|
|
209
|
-
- [
|
|
210
|
-
- [
|
|
211
|
-
- [
|
|
212
|
-
- [
|
|
213
|
-
- [
|
|
161
|
+
- [安装与 Agent 配置](docs/INSTALLATION.md)
|
|
162
|
+
- [配置与服务凭据](docs/CONFIGURATION.md)
|
|
163
|
+
- [文献、Zotero、MinerU、引用与输出](docs/RESEARCH.md)
|
|
164
|
+
- [材料与化学](docs/MATERIALS.md)
|
|
165
|
+
- [科研绘图服务](docs/IMAGE_PROVIDERS.md)
|
|
166
|
+
- [工具目录](docs/TOOLS.md)
|
|
214
167
|
|
|
215
|
-
##
|
|
168
|
+
## 支持与许可证
|
|
216
169
|
|
|
217
|
-
OmniScholar
|
|
170
|
+
OmniScholar 使用 [MIT License](LICENSE) 开源。可以在 [GitHub Issues](https://github.com/luffysolution-svg/omnischolar/issues) 提交问题，或发送邮件到 `LuffySolution@gmail.com`。报告问题前，请删除 API key、签名 URL、私人论文内容和个人 Zotero 数据。
|
|
218
171
|
|
|
219
|
-
|
|
172
|
+
第三方服务和数据遵循各自的条款与许可证，详见 [`THIRD_PARTY_NOTICES.md`](THIRD_PARTY_NOTICES.md)。
|
package/README.zh-CN.md
CHANGED
package/docs/INSTALLATION.md
CHANGED
|
@@ -12,6 +12,18 @@ pipx install luffysolution-omnischolar
|
|
|
12
12
|
python -m pip install luffysolution-omnischolar
|
|
13
13
|
```
|
|
14
14
|
|
|
15
|
+
如果该工具已经安装，`uv tool install` 会保持现有版本，不会自动升级。要获取 PyPI 最新版本，请使用：
|
|
16
|
+
|
|
17
|
+
```sh
|
|
18
|
+
uv tool upgrade luffysolution-omnischolar
|
|
19
|
+
```
|
|
20
|
+
|
|
21
|
+
需要强制刷新并重新安装时使用：
|
|
22
|
+
|
|
23
|
+
```sh
|
|
24
|
+
uv tool install --reinstall luffysolution-omnischolar
|
|
25
|
+
```
|
|
26
|
+
|
|
15
27
|
更新或卸载 Python 命令：
|
|
16
28
|
|
|
17
29
|
```sh
|
|
@@ -205,6 +217,14 @@ npx skills remove --skill '*' -a codex -y
|
|
|
205
217
|
|
|
206
218
|
这组命令只安装 Skills，不会安装 `omnischolar` Python 命令。通过 Codex/Claude plugin 或 Pi Extension 安装时，插件/安装器已经处理了对应 Skills，不需要重复执行。
|
|
207
219
|
|
|
220
|
+
## Agent 配置提示词
|
|
221
|
+
|
|
222
|
+
可以将下面的提示词作为 Agent 的项目级指令或系统提示词基础：
|
|
223
|
+
|
|
224
|
+
```text
|
|
225
|
+
你是我的科研助理，使用 OmniScholar 完成文献检索、Zotero 阅读、PDF 解析、引用核对和科研资料整理。检索时优先使用可靠的学术来源，核对 DOI 与书目信息，并明确区分原文证据、推断和不确定内容。Zotero 只允许读取，禁止修改。上传 PDF、参考图或发起可能收费的请求前必须先征得我的确认；MinerU 只有在我确认后才能上传文件。将确认后的文献笔记和生成文件保存到配置的输出目录，保留已有手工修改，并报告最终文件路径。生成的科研图片只能作为示意图，不能当作实验数据或科研证据。
|
|
226
|
+
```
|
|
227
|
+
|
|
208
228
|
## MCP 连接失败
|
|
209
229
|
|
|
210
230
|
1. 运行 `omnischolar --version`，确认 Agent 的 PATH 能找到该命令。
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@luffysolution/omnischolar-pi",
|
|
3
|
-
"version": "0.1.
|
|
3
|
+
"version": "0.1.13",
|
|
4
4
|
"description": "Pi MCP bridge for the OmniScholar research toolkit",
|
|
5
5
|
"type": "module",
|
|
6
6
|
"license": "MIT",
|
|
@@ -29,6 +29,7 @@
|
|
|
29
29
|
"files": [
|
|
30
30
|
"pi-extension/dist",
|
|
31
31
|
"README.md",
|
|
32
|
+
"README.en.md",
|
|
32
33
|
"README.zh-CN.md",
|
|
33
34
|
"LICENSE",
|
|
34
35
|
"PRIVACY.md",
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { Client } from "@modelcontextprotocol/sdk/client/index.js";
|
|
2
2
|
import { StdioClientTransport } from "@modelcontextprotocol/sdk/client/stdio.js";
|
|
3
3
|
import { Type } from "typebox";
|
|
4
|
-
const CLIENT_INFO = { name: "omnischolar-pi", version: "0.1.
|
|
4
|
+
const CLIENT_INFO = { name: "omnischolar-pi", version: "0.1.13" };
|
|
5
5
|
export function resultText(result) {
|
|
6
6
|
return result.content
|
|
7
7
|
.map((item) => {
|