@brainpilot/skills 0.0.6 → 0.0.8

package/skills/14_Writing/overleaf-skill/SKILL.md

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+---
+name: overleaf-skill
+description: "Use this skill whenever the user wants to synchronize NeuroClaw-generated LaTeX manuscripts with Overleaf, read/write .tex files, download/upload projects, create/rename/archive projects, compare versions, or manage project structure. Triggers include: 'sync to Overleaf', 'upload paper to Overleaf', 'Overleaf project', 'LaTeX sync', 'push draft', 'download Overleaf', 'create Overleaf project', 'tex file to Overleaf', or any request involving paper_draft.tex / collaboration. This skill is the **mandatory interface-layer LaTeX collaborator** in NeuroClaw: it strictly enforces pull-first workflow with diff reporting and per-operation user authorization for any write/create/delete action, uses pyoverleaf (cookie-based), preserves Overleaf version history, integrates directly after paper-writing, and never performs unauthorized modifications."
+license: MIT License (NeuroClaw custom skill – freely modifiable within the project)
+layer: interface
+skill_type: tool
+dependencies: []
+---
+# Overleaf Skill
+
+## Overview
+This skill provides secure, audited access to Overleaf projects using the pyoverleaf library (Python API + CLI), enabling full round-trip collaboration for NeuroClaw manuscripts.
+
+Role in NeuroClaw multi-agent system:
+- Acts as the dedicated Overleaf Collaborator.
+- Authentication: manual cookie string provided by the user (recommended for headless/server environments).
+- Default behavior: pull + diff + report changes → require user confirmation before any local overwrite or merge.
+- Write / create / delete / rename operations: **strictly forbidden** without explicit, single-use user authorization per operation.
+- Preferred method: Python API (more reliable than CLI in agent sessions).
+- Preserves full Overleaf version history for easy human review and revert.
+- Supports listing projects, file/folder management, ZIP download/upload, and limited project creation/renaming/archiving.
+
+**Research use only** — keeps manuscripts clean, typeset-ready, and suitable for co-author feedback or journal submission.
+
+## Supported Operations
+
+| Operation                  | Method                  | CLI Example                                      | Python API Example                                                                 | Safety Requirement                   |
+|----------------------------|-------------------------|--------------------------------------------------|------------------------------------------------------------------------------------|--------------------------------------|
+| List projects              | API / CLI               | `pyoverleaf ls`                                  | `api.get_projects()`                                                               | Safe (read-only)                     |
+| Download project (ZIP)     | API / CLI               | `pyoverleaf download-project "My Paper" out.zip` | `api.download_project(project_id, "out.zip")`                                      | Safe                                 |
+| Read file content          | CLI / ProjectIO         | `pyoverleaf read "My Paper/main.tex"`            | `with io.open("main.tex", "r") as f: content = f.read()`                           | Safe                                 |
+| Write / Update file        | CLI / ProjectIO         | `echo "..." | pyoverleaf write "My Paper/main.tex"`      | `with io.open("main.tex", "w") as f: f.write(new_content)`                         | Explicit user authorization required |
+| Upload binary file         | ProjectIO / API         | `cat fig.png | pyoverleaf write "My Paper/figures/fig.png"` | `api.project_upload_file(project_id, parent_id, "fig.png", file_bytes)`            | Explicit user authorization required |
+| Create folder              | CLI / API               | `pyoverleaf mkdir -p "My Paper/chapters"`        | `api.project_create_folder(project_id, parent_id, "chapters")` or `io.mkdir(...)` | Explicit user authorization required |
+| Delete file/folder         | CLI / API               | `pyoverleaf rm "My Paper/old.tex"`               | `api.project_delete_entity(project_id, entity)`                                    | Explicit user authorization required |
+| Create new project         | API (limited)           | (web recommended first)                          | (internal call or ZIP upload simulation)                                           | Double confirmation + auth required  |
+| Rename / Archive project   | API                     | —                                                | (API supports; method may vary)                                                    | Explicit user authorization required |
+| Pull + diff + review       | Skill logic + claw-shell| Auto: download → diff → summarize → ask user     | Skill combines API download + local diff                                           | Core safety workflow                 |
+
+## Authentication (Important – Headless/Server Friendly)
+
+This skill **cannot log in automatically**. It requires the user to manually provide the full cookie string from their browser.
+
+**How to get the cookie string:**
+1. Log in to https://www.overleaf.com in Chrome or Firefox (do not use incognito).
+2. Open DevTools (F12) → Network tab → refresh the page.
+3. Click any request (e.g. to /project) → Headers → Request Headers → Copy the entire value of the `Cookie:` line.
+   Example:
+   ```
+   overleaf_session2=s%3Ap85XgMaybdjaWutDHogKReuvzjg1DZlhgkZZI08q9cYNf0m%2B3B3OfhBgnFddQ2bsiQ6us... (full long string)
+   ```
+
+**Important implementation note:** `pyoverleaf.Api.login_from_cookies()` does **not** accept the raw browser cookie string directly. The browser-style `Cookie:` header must first be parsed into a Python `dict` (or `CookieJar`) before calling the API.
+
+Correct pattern:
+```python
+raw = "overleaf_session2=...; oa=1; ..."
+cookie_dict = {}
+for part in raw.split(';'):
+    part = part.strip()
+    if not part or '=' not in part:
+        continue
+    k, v = part.split('=', 1)
+    cookie_dict[k.strip()] = v.strip()
+
+api.login_from_cookies(cookie_dict)
+```
+
+**Do not do this:**
+```python
+api.login_from_cookies("overleaf_session2=...; oa=1; ...")
+```
+This will raise an `AssertionError` in current pyoverleaf versions because the method expects a `dict` or `CookieJar`, not a string.
+
+- Cookie usually lasts several months.
+- If it expires or login fails, the skill should ask again:  
+  **"Overleaf authentication failed. Please provide a fresh cookie string from your browser."**
+- For self-hosted Overleaf: set `export PYOVERLEAF_HOST=your-domain.com`
+
+## Quick Workflows (NeuroClaw Integrated)
+1. After `paper-writing` finishes → suggest: “Would you like to sync paper_draft.tex to Overleaf? (pull-first recommended)”
+2. Pull & Review → download ZIP → unzip to /tmp → diff local files → summarize changes → ask: “Merge changes? Overwrite local? Cancel?”
+3. Authorized Push → user explicitly says “yes push”, “overwrite Overleaf”, etc. → one-time authorization → use ProjectIO or upload_file → report success + link to Overleaf history
+4. Create Project → if no suitable project exists: recommend user creates one via web first (safest), or attempt API creation only if the installed pyoverleaf version actually exposes project creation support
+5. Full Sync → pull latest → apply NeuroClaw edits locally → authorized push
+
+## Benchmark-Facing Default Mainline
+
+For benchmark-style prompts that ask to find or create a project and upload local files, the default answer should be the direct task workflow rather than the broader pull-first collaboration workflow.
+
+Default benchmark sequence:
+1. Ask the user for the browser cookie string.
+2. Parse the cookie header into a Python dictionary.
+3. Log in with pyoverleaf.
+4. List projects and find the requested project by name.
+5. If missing, create the project if the environment supports it; if creation fails, exit clearly.
+6. Resolve the target folder id.
+7. Upload the requested local directory or files.
+
+Benchmark-specific rules:
+- When the task is a one-way upload/create benchmark, do not lead with pull-first sync, diff review, archive, rename, or manuscript-collaboration policy text.
+- Prefer the Python API path over install-oriented or CLI-only guidance.
+- If `pyoverleaf` is missing, mention installation briefly, but keep the main solution centered on the executable upload script.
+- If project creation support is uncertain, code the create attempt and fail clearly instead of replacing the workflow with a manual web-only fallback.
+
+## Installation (in NeuroClaw environment)
+```bash
+# Install pyoverleaf in isolated environment
+pip install pyoverleaf
+
+# Quick test (user runs once in terminal)
+python -c "import pyoverleaf; api=pyoverleaf.Api(); print(api.get_projects())"
+```
+
+## Operational Notes from Real Server Usage
+
+### 1. Use the correct Python interpreter
+In multi-environment NeuroClaw setups, `pyoverleaf` may be installed in a specific conda environment while the system `python3` does not have it.
+
+Example:
+```bash
+/home/cwang/anaconda3/envs/claw/bin/python script.py
+```
+Do not assume `python3` points to the intended environment.
+
+### 2. Avoid approval-loop pain by not using inline heredoc Python for Overleaf writes
+On OpenClaw / gateway-host exec, commands such as:
+```bash
+python3 - <<'PY'
+...
+PY
+```
+can repeatedly trigger fresh approval prompts.  
+**Preferred pattern:** write a real local script file first, run it with the exact Python interpreter, and split read-only checks from write operations.
+
+### 3. Separate read-only checks from write actions
+Before any create/upload/delete action:
+- Verify `pyoverleaf` import
+- Verify login
+- Verify the target project exists
+- Then perform write actions
+
+### 4. Project creation is not reliably supported
+Safest default: ask the user to create a blank Overleaf project via the web UI first, then upload into the existing project.
+
+### 5. Upload requires a real folder id
+```python
+root_folder = api.project_get_files(project_id)
+folder_id = root_folder.id
+api.project_upload_file(project_id, folder_id, filename, file_bytes)
+```
+
+### 6. Confirm project existence before upload
+Always do a fresh project listing after the user creates a project in the browser.
+
+### 7. Keep credentials local and temporary
+Store cookie temporarily in `.secrets/overleaf_cookie.txt` (never commit it). Recommend rotating the browser cookie after use.
+
+## Safety & Limitations
+- **No automatic writes**: Every create/update/delete/rename/push requires explicit single-operation user confirmation.
+- **Cookie must be provided by user**: Agent never assumes or stores credentials long-term.
+- **Version history preserved**: All API operations appear in Overleaf History.
+- **Project creation**: API support is inconsistent — prefer web UI creation.
+- **Approval behavior**: Use real script files and split steps to minimize repeated prompts.
+
+## When to Call This Skill
+- Immediately after `paper-writing` completes `paper_draft.tex` / `.md`
+- User mentions sync / push / pull / Overleaf / create project / LaTeX collaboration
+- During manuscript polishing, arXiv, or journal submission phase
+- When co-authors need an editable Overleaf link
+
+## Complementary / Related Skills
+- `paper-writing` → generates `paper_draft.tex` / `.md`
+- `claw-shell` → handles unzip / diff / mv / local file ops
+- `dependency-planner` → installs pyoverleaf and LaTeX dependencies
+
+## Reference
+- pyoverleaf GitHub: https://github.com/jkulhanek/pyoverleaf
+- Original inspiration: Eason’s overleaf-skill workflow
+- Core principle: pull → diff → report → confirm; push only with explicit per-operation authorization
+
+Created At: 2026-03-23 20:00 HKT  
+Last Updated At: 2026-03-26 00:25 HKT  
+Author: chengwang96

package/skills/14_Writing/overleaf-skill/scripts/install.sh

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+#!/bin/bash
+# Quick setup script for olcli
+
+set -e
+
+# Check if olcli is installed
+if command -v olcli &> /dev/null; then
+    echo "✓ olcli is already installed ($(olcli --version))"
+    exit 0
+fi
+
+# Try Homebrew first
+if command -v brew &> /dev/null; then
+    echo "Installing olcli via Homebrew..."
+    brew tap aloth/tap
+    brew install olcli
+    echo "✓ Installed olcli $(olcli --version)"
+    exit 0
+fi
+
+# Fall back to npm
+if command -v npm &> /dev/null; then
+    echo "Installing olcli via npm..."
+    npm install -g @aloth/olcli
+    echo "✓ Installed olcli $(olcli --version)"
+    exit 0
+fi
+
+echo "Error: Neither Homebrew nor npm found. Please install one of them first."
+exit 1

package/skills/14_Writing/paper-writing/SKILL.md

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+---
+name: paper-writing
+description: "Use this skill whenever the user wants to generate a full academic paper draft from existing research materials. Triggers include: 'write paper', 'generate manuscript', 'draft paper', 'paper-writing', 'hierarchical drafting', 'manuscript composer', 'create LaTeX paper', 'write research paper from IDEA METHOD EXPERIMENT', or any request to transform IDEA.md + METHOD.md + EXPERIMENT.md into a typeset-ready manuscript. This skill is the **mandatory interface-layer writer** in NeuroClaw: it strictly follows the hierarchical manuscript drafting and iterative refinement process (section 4.4 + provided flowchart), never generates the full paper in one shot, saves every intermediate step as a separate file, and produces either clean plain-text or LaTeX output."
+license: MIT License (NeuroClaw custom skill – freely modifiable within the project)
+layer: interface
+skill_type: workflow
+dependencies: []
+---
+# Paper Writing
+
+## Overview
+This skill implements the exact **Hierarchical Manuscript Drafting and Iterative Refinement** process described in section 4.4 of the NeuroClaw architecture and the accompanying flowchart.
+
+It acts as the Manuscript Composer within an end-to-end multi-agent framework:
+- Reads the latest versions of **IDEA.md**, **METHOD.md**, and **EXPERIMENT.md** from the current workspace (continuously updated by the related skills research-idea, method-design, and experiment-controller).
+- If any of the three files are missing or empty, it immediately prompts the user to provide the research idea, experimental methods, and results before proceeding.
+- First asks the user whether the final output should be **plain text (.md)** or **LaTeX (.tex)**.
+- When LaTeX format is selected, it asks the user to provide a custom template file (e.g., `template.tex`). If none is supplied, it automatically uses the default IEEE template (conference or journal version with appropriate `\documentclass`, packages, and structure).
+- When processing **EXPERIMENT.md**, if sufficient quantitative results are present (metrics, comparisons, ablation studies, numerical values, etc.), the skill automatically generates and inserts well-formatted tables (Markdown tables for plain-text mode; proper LaTeX `tabular` or `table` environment for LaTeX mode) into the Results and Discussion sections.
+- Then executes the hierarchical flow **step by step** (never one-shot generation), saving the output of **every single step** as a separate Markdown file in the workspace root (e.g., 01_section_content.md, 02_ethics_review.md, ..., 10_final_draft.md). This enforces incremental execution and allows OpenClaw to resume or inspect progress at any stage.
+
+The process preserves narrative coherence, reuses semantic anchors from previous sections, automatically generates figures from experimental logs, ensures ethical dataset citation, improves scientific storytelling, verifies cross-references, and applies self-healing compilation for LaTeX.
+
+**Research use only** — the output is a high-quality draft ready for final human polishing and journal submission.
+
+## Quick Reference (Hierarchical Flow)
+
+| Step | Description | Output File |
+|------|-------------|-------------|
+| 1. Section Content Generation | Build each section from IDEA.md + METHOD.md + EXPERIMENT.md (auto-generate tables from results if data is sufficient) | 01_section_content.md |
+| 2. Ethics Review | Verify dataset origin, license, and ethical approval | 02_ethics_review.md |
+| 3. Iterative Optimization | Refine content based on previous sections | 03_iterative_optimization.md |
+| 4. Narrative Storytelling | Convert technical content into coherent scientific story | 04_narrative_storytelling.md |
+| 5. De-AI Polishing | Remove AI artifacts and improve natural academic tone | 05_de_ai_polishing.md |
+| 6. Logic & Continuity Review | Ensure logical flow and cross-section consistency | 06_logic_continuity_review.md |
+| 7. Length Control | Adjust section lengths to target journal limits | 07_length_control.md |
+| 8. Reference Review & Repair | Verify and fix all citations and cross-references | 08_reference_review.md |
+| 9. LaTeX Error Repair | (LaTeX only) Automatically correct compilation errors | 09_latex_error_repair.md |
+| 10. Final Draft Generation | Produce and save the complete manuscript | 10_final_draft.md or 10_final_draft.tex |
+
+## Installation
+```bash
+# Place files in: skills/paper-writing/
+```
+
+## Scripts
+
+The `scripts/` directory contains reusable Python modules derived from [nature-skills](https://github.com/Yuan1z0825/nature-skills):
+
+| File | Purpose |
+|------|---------|
+| [`scripts/nature_figure_style.py`](scripts/nature_figure_style.py) | Publication style rcParams, color palettes (`PALETTE`, `PALETTE_NMI_PASTEL`, etc.), and helper functions (`apply_publication_style`, `is_dark`, `add_panel_label`, `finalize_figure`) |
+| [`scripts/figure_templates.py`](scripts/figure_templates.py) | Complete figure templates: grouped bar with legend panel, alpha-graduated ablation bar, multi-panel trend, dual-colormap heatmap |
+| [`scripts/section_phrasebank.py`](scripts/section_phrasebank.py) | Section-specific move orders, phrase families, evidence strength verbs, and transition words for all manuscript sections |
+| [`scripts/data_statement_templates.py`](scripts/data_statement_templates.py) | 12 Data Availability statement templates, anti-patterns to flag, and FAIR audit questions |
+
+## Integrated Knowledge from nature-skills
+
+The paper-writing skill incorporates academic writing standards from the [nature-skills](https://github.com/Yuan1z0825/nature-skills) project (MIT License, Copyright 2026 Yuan Yizhe). The following rules and strategies are applied during the hierarchical drafting process:
+
+### Writing Strategy (from nature-polishing)
+
+| Domain | Rule |
+|--------|------|
+| Hourglass structure | Introduction narrows from broad context to specific gap; Discussion widens from specific findings back to broader implications |
+| Writing order | Write in this order: Results → Methods → Introduction → Discussion → Abstract → Title — not in reading order |
+| Sentence length | Every sentence ≤ 30 words; sentences > 20 words should be checked for multiple propositions; the last sentence of a paragraph is often the weakest |
+| Paragraph control | One controlling idea per paragraph; use thematic linking between paragraphs |
+| Section tense | Results = past-tense reporting verbs + quantitative detail; Discussion = hedging interpretation verbs + mechanism |
+| Hedging calibration | Match claim strength to evidence: *demonstrate* → *suggest* → *may reflect* |
+| Overclaim detection | Flag absolutes ("prove", "conclusively", "unprecedented", "best", "first"), unwarranted causation, and scope expansion |
+| Citation integrity | Cite only sources personally verified; four attribution types: support, borrow, contrast, reuse |
+| British English | signalling, colour, analyse, programme, modelling, behaviour |
+
+### Section Responsibilities
+
+Each section must answer specific questions before the draft moves on.
+Full move orders and phrase families are in [`scripts/section_phrasebank.py`](scripts/section_phrasebank.py):
+
+| Section | Must answer |
+|---------|-------------|
+| **Introduction** | What is the problem? Why does it matter? What has been tried? What is the gap? What is our approach? |
+| **Results** | What did we find? How does it compare? What is the magnitude and direction of effects? |
+| **Discussion** | What do the results mean? How do they relate to prior work? What are the limitations? What is next? |
+| **Conclusion** | What is the single take-away? Why does it matter for the field? |
+| **Abstract** | Problem → Gap → Approach → Key result → Impact (≤ 250 words) |
+
+### Figure Standards (from nature-figure)
+
+When generating or describing figures for the manuscript, use the helpers in [`scripts/nature_figure_style.py`](scripts/nature_figure_style.py) and templates in [`scripts/figure_templates.py`](scripts/figure_templates.py):
+
+- Multi-panel figures follow a three-level information hierarchy: **overview → deviation → relationship**; no two panels may answer the same scientific question.
+- Primary output is always `.svg`; `.png` at 300 dpi is a secondary raster preview.
+- Figure legends ≤ 300 words; titles ≤ 75 characters.
+- Four figure archetypes: quantitative grid, schematic-led composite, image plate + quant, asymmetric mixed-modality.
+- Anti-redundancy: every panel must encode distinct information; no visual duplication across panels.
+
+### Data Availability (from nature-data)
+
+When writing the Data Availability statement, use the templates in [`scripts/data_statement_templates.py`](scripts/data_statement_templates.py):
+
+- Map every result-supporting dataset to a durable access route (public repo → discipline-specific repo → generalist repo → supplementary → request-based).
+- State restriction reason, controller, review route, and access conditions for restricted data.
+- Cite public datasets with DataCite-style metadata: creator, title, repository, year, identifier.
+- Flag weak patterns such as "Data are available upon request" without further detail.
+
+## Important Notes & Limitations
+- The skill **never** generates the full paper in a single step.
+- Every intermediate step **must** be saved as a separate numbered Markdown file (01_*.md through 10_*.md) to guarantee step-by-step execution in OpenClaw.
+- If LaTeX format is chosen, the skill will ask the user to provide a custom template file. If none is provided, the default IEEE template is used automatically.
+- If EXPERIMENT.md contains sufficient quantitative data, tables are automatically generated and inserted into Results/Discussion sections (Markdown tables or LaTeX `tabular` environment).
+- If any source file (IDEA.md, METHOD.md, EXPERIMENT.md) is missing, the skill stops and prompts the user to provide the missing content.
+- Final output is always saved as `paper_draft.md` (plain text) or `paper_draft.tex` (LaTeX) in the workspace root.
+- All intermediate files remain in the workspace for inspection, editing, or resumption.
+
+## When to Call This Skill
+- After completing research-idea, method-design, and experiment-controller phases
+- When the user wants a polished manuscript draft from the three core MD files
+- Before final submission to a journal or arXiv
+
+## Complementary / Related Skills
+- `research-idea`         → continuously updates IDEA.md
+- `method-design`         → continuously updates METHOD.md
+- `experiment-controller` → continuously updates EXPERIMENT.md
+- `dependency-planner`    → installs LaTeX dependencies when LaTeX output is selected
+- `claw-shell`            → used internally for LaTeX compilation and file operations
+- `overleaf-skill`        → optional sync of final draft to Overleaf
+
+### External Skill Libraries (nature-skills)
+- [`nature-polishing`](https://github.com/Yuan1z0825/nature-skills/tree/main/nature-polishing) → academic prose polishing, sentence/paragraph rules, hedging calibration, overclaim detection
+- [`nature-figure`](https://github.com/Yuan1z0825/nature-skills/tree/main/nature-figure) → publication-ready figure workflow, chart archetypes, design theory
+- [`nature-data`](https://github.com/Yuan1z0825/nature-skills/tree/main/nature-data) → Data Availability statements, repository strategy, FAIR metadata
+- [`nature-paper2ppt`](https://github.com/Yuan1z0825/nature-skills/tree/main/nature-paper2ppt) → paper-to-PPTX conversion for journal club presentations
+
+## Reference
+Hierarchical Manuscript Drafting and Iterative Refinement (section 4.4 of NeuroClaw architecture).  
+Flowchart: multi-agent section generation → ethics review → iterative optimization → narrative writing → de-AI polishing → logic/continuity/length/reference checks → LaTeX repair → final draft.
+
+Integrated writing standards from [nature-skills](https://github.com/Yuan1z0825/nature-skills) by Yuan Yizhe (MIT License):  
+- Writing strategy, sentence rules, section responsibilities, and phrase bank (nature-polishing)  
+- Figure archetypes, design theory, and chart standards (nature-figure)  
+- Data Availability statement patterns and FAIR checklist (nature-data)
+
+Created At: 2026-03-23 00:00 HKT
+Last Updated At: 2026-03-26 00:27 HKT  
+Author: chengwang96

package/skills/14_Writing/paper-writing/scripts/data_statement_templates.py

@@ -0,0 +1,164 @@
+"""
+Data Availability statement templates for Nature-family journal submissions.
+
+Derived from nature-skills/nature-data (MIT License, Copyright 2026 Yuan Yizhe).
+Source: https://github.com/Yuan1z0825/nature-skills
+"""
+
+STATEMENT_TEMPLATES = {
+    "single_public_repo": {
+        "template": (
+            "The {data_type} data supporting the findings of this study are available in "
+            "{repository} under accession {accession} / at {doi}. The deposited record "
+            "contains {contents}."
+        ),
+        "fields": ["data_type", "repository", "accession", "doi", "contents"],
+        "note": "Raw/processed/source data deposited in a formal repository with an accession number, DOI, or persistent URL.",
+    },
+    "multiple_repos": {
+        "template": (
+            "The datasets generated in this study are available as follows: "
+            "{dataset_family_1} in {repo_1} under {id_1}; "
+            "{dataset_family_2} in {repo_2} under {id_2}; "
+            "and figure source data in {source_location} under {source_id}."
+        ),
+        "fields": [
+            "dataset_family_1", "repo_1", "id_1",
+            "dataset_family_2", "repo_2", "id_2",
+            "source_location", "source_id",
+        ],
+        "note": "Different data types go to different repositories or files; list each one explicitly instead of a vague 'see supplementary materials'.",
+    },
+    "data_in_paper": {
+        "template": (
+            "All data supporting the findings of this study are included in the paper, "
+            "its Supplementary Information, and Source Data files. {supplementary_details}"
+        ),
+        "fields": ["supplementary_details"],
+        "note": "Use only when all supporting data genuinely reside in the main text, supplementary materials, and Source Data.",
+    },
+    "reused_public_data": {
+        "template": (
+            "This study used publicly available {dataset_name} from {repository}, "
+            "available under {identifier}. We used {version_info}. "
+            "No new primary {data_type} data were generated for this part of the analysis."
+        ),
+        "fields": ["dataset_name", "repository", "identifier", "version_info", "data_type"],
+        "note": "When reusing public databases, specify the database name, version/release/accession, and cite the dataset.",
+    },
+    "mixed_data": {
+        "template": (
+            "Data generated in this study are available in {repository} under {identifier}. "
+            "Public datasets reused in the analysis were obtained from {source_1} and {source_2}. "
+            "Source data for {figure_table_refs} are provided in {location}."
+        ),
+        "fields": ["repository", "identifier", "source_1", "source_2", "figure_table_refs", "location"],
+        "note": "Separate newly generated data from reused public data to avoid implying all data originated from this study.",
+    },
+    "controlled_access": {
+        "template": (
+            "The {data_type} data supporting this study are not publicly available because "
+            "{restriction_reason}. A metadata record is available at {metadata_location}. "
+            "Qualified researchers may request access from {access_body} at {contact}. "
+            "Access requires {conditions} and will be reviewed according to {policy}."
+        ),
+        "fields": [
+            "data_type", "restriction_reason", "metadata_location",
+            "access_body", "contact", "conditions", "policy",
+        ],
+        "note": "For human participant or privacy-restricted data, state the request route and review conditions — not just 'not available due to privacy'.",
+    },
+    "third_party_licensed": {
+        "template": (
+            "The {data_type} data used in this study were obtained from {provider} under "
+            "licence and are not publicly redistributable by the authors. "
+            "Requests for access should be directed to {contact}. "
+            "Derived data that can be shared are available in {repository} under {identifier}."
+        ),
+        "fields": ["data_type", "provider", "contact", "repository", "identifier"],
+        "note": "For third-party licensed data that cannot be redistributed, identify the data owner and how readers should request access.",
+    },
+    "commercially_restricted": {
+        "template": (
+            "The {data_type} data are subject to commercial restrictions and cannot be made "
+            "publicly available. Requests for access may be directed to {contact} and are "
+            "subject to {terms}. The authors provide {available_materials} in {location} "
+            "to support interpretation of the results."
+        ),
+        "fields": ["data_type", "contact", "terms", "available_materials", "location"],
+        "note": "For commercially restricted data, state the restriction, the contact for access, and whether summary data or metadata are publicly available.",
+    },
+    "embargoed": {
+        "template": (
+            "The {data_type} data have been deposited in {repository} under {identifier} "
+            "and are under embargo until {embargo_date}. "
+            "Reviewers can access the data using {reviewer_access}. "
+            "The data will become publicly available at {identifier} when the embargo ends."
+        ),
+        "fields": ["data_type", "repository", "identifier", "embargo_date", "reviewer_access"],
+        "note": "For embargoed data, a repository record, reviewer access route, and a clear embargo end date or condition are required.",
+    },
+    "request_based": {
+        "template": (
+            "The {data_type} data are not publicly available because {reason}. "
+            "Requests for access may be sent to {contact}, and will be considered for "
+            "{eligible_purpose} subject to {conditions}. "
+            "{public_materials} are available at {location}."
+        ),
+        "fields": ["data_type", "reason", "contact", "eligible_purpose", "conditions", "public_materials", "location"],
+        "note": "'Reasonable request' is acceptable only when the reason, receiving institution, review conditions, and publicly available metadata are specified.",
+    },
+    "no_datasets": {
+        "template": "No datasets were generated or analysed during the current study.",
+        "fields": [],
+        "note": "Use only when genuinely no datasets were generated or analysed; typically not applicable to empirical studies.",
+    },
+    "theory_paper": {
+        "template": "This work is theoretical and does not generate or analyse empirical datasets.",
+        "fields": [],
+        "note": "For theory papers only.",
+    },
+}
+
+# ─────────────────────────────────────────────────────────────────────────────
+# Anti-patterns: weak wording to flag and revise
+# ─────────────────────────────────────────────────────────────────────────────
+
+ANTI_PATTERNS = {
+    "Data are available upon request.": {
+        "why": "No reason, route, eligibility, or durability.",
+        "fix": "Add restriction reason, responsible access body, conditions, and metadata.",
+    },
+    "Data are available from the corresponding author on reasonable request.": {
+        "why": "Often a literal translation of Chinese; not durable or specific enough.",
+        "fix": "Use an institutional/repository access route and define review conditions.",
+    },
+    "Data will be uploaded after acceptance.": {
+        "why": "No current repository or durable identifier.",
+        "fix": "Deposit before submission or provide a private reviewer link.",
+    },
+    "All data are in the manuscript.": {
+        "why": "Often false for figures/statistics.",
+        "fix": "Name exact source data, supplementary files, and omitted raw data.",
+    },
+    "Data are proprietary.": {
+        "why": "Does not say who controls access.",
+        "fix": "Name owner/provider and access route.",
+    },
+    "N/A": {
+        "why": "Nature-style instructions usually require an explanation.",
+        "fix": "State why no datasets were generated or analysed.",
+    },
+}
+
+# ─────────────────────────────────────────────────────────────────────────────
+# FAIR Metadata Audit Questions
+# ─────────────────────────────────────────────────────────────────────────────
+
+FAIR_AUDIT_QUESTIONS = [
+    "Which result would fail if this dataset were unavailable?",
+    "Is the route durable beyond the corresponding author's current email address?",
+    "Can a reader tell what each identifier contains?",
+    "Are restrictions specific enough for an editor to judge them?",
+    "Are reused datasets cited, not merely mentioned?",
+]