# 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:

```powershell
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:

```text
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:

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

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