QQsci-skill/README.md

QQsci

QQsci is a Codex skill for materials-science manuscript writing, submission-package audit, literature-grounded revision, and Word DOI-only citation comments.

It is designed for workflows that combine:

• manuscript and Supporting Information .docx files
• main figures, SI figures, and TOC .pptx files
• Zotero literature items and AI-generated Zotero child notes
• QQnote-generated literature summaries or comparison tables
• target-journal positioning and reviewer-style pre-submission audit

Scope

QQsci owns the manuscript-facing reasoning:

• extract manuscript keywords from topic, draft, figures, SI, or cover material
• classify strongly and weakly related papers
• compare the manuscript with strongly related papers
• audit missing experiments, controls, mechanisms, benchmarks, and statistics
• check figures, captions, SI consistency, formatting, spelling, and terminology
• produce Markdown reviewer reports
• add Word native citation comments containing DOI strings only

QQsci does not directly insert Zotero Word fields. For Word manuscripts, citation suggestions are added as native comments with one DOI per line.

QQnote Relationship

QQnote is used only as the literature-note input tool.

QQnote may:

• generate or refresh Zotero child-note summaries
• summarize selected Zotero papers into Markdown comparison tables

QQsci then consumes those notes/tables and makes the manuscript decisions. QQnote should not decide whether a paper is strongly related, weakly related, necessary for citation, or sufficient as reviewer evidence.

When QQsci calls QQnote, use:

py "$env:USERPROFILE\.codex\skills\qqsci\scripts\run_qqnote_with_qqsci_config.py" --script summarize_zotero_table -- --vault "C:\Users\qyh15\Documents\Obsidian Vault" --item-keys "SXAIQUJT X7GJZ627"

Configuration

Use config/config.template.json as the public template and create a private local file:

config/config.local.json

Do not commit config/config.local.json.

QQsci is the top-level configuration owner for manuscript workflows. It maps its DeepSeek and Zotero settings into QQnote-compatible environment variables when calling QQnote:

• deepseek.api_key -> AWESOMEGPT_API_KEY
• deepseek.base_url -> AWESOMEGPT_BASE_URL
• deepseek.model -> AWESOMEGPT_MODEL
• zotero.web_api_key -> ZOTERO_API_KEY
• zotero.user_id -> ZOTERO_USER_ID

QQnote remains independently usable through its own environment variables, vault .env, or AwesomeGPT/Zotero preferences.

Submission Package Audit

For a full submission package, QQsci checks files in this order:

1. Manuscript.docx
2. Figures.pptx
3. Supplementary Information.docx
4. Supplementary Information.pptx
5. Highlights.docx
6. CoverLetter.docx
7. TOC.pptx

The manuscript and main figures define the story. SI, highlights, cover letter, and TOC must stay consistent with that story.

Installed Location

For Codex discovery, install under:

C:\Users\qyh15\.codex\skills\qqsci

The source repository is maintained separately and can be pushed to Gitea.