Journal-quality hydrology manuscripts, drafted and reviewed by Claude.
Drafts, reviews, revises, proofreads, audits, and submission-formats scientific manuscripts.
Calibrated for hydrology ( Hydrogeology Journal • Journal of Hydrology: Regional Studies • Journal of Hydrology • Water Resources Research • HESS • Groundwater ), with profiles for Engineering Geology , IEEE Transactions on Instrumentation and Measurement , JMBE and Physiological Measurement , plus a generic profile for any other quantitative-science journal — extensible via a single reference file.
Most LLM writing tools are general-purpose and produce text that reviewers immediately recognise as AI-generated. paper-agent is purpose-built for hydrology and water-resources peer review: it enforces journal-specific structure, refuses to fabricate citations, and surfaces consistency failures — gap-vs-conclusions mismatches, sample-size drift, terminology inconsistency — that authors and reviewers routinely miss.
paper-agent runs in your local Claude Code session and produces journal-submission-quality output. It is not a writing assistant in the usual sense — it follows strict mode boundaries, refuses to invent values or fabricate citations, and pauses for confirmation after every section.
Use it when you have:
- A workspace of project data (CSVs, source code, metadata) and need a complete first manuscript draft.
- An existing
.docxmanuscript and need reviewer-style feedback, section-by-section revision suggestions, or a language-level polish. - Reviewer comments from a journal decision letter and need help producing a point-by-point response and revised text.
Two bundled, synthetic demos let you try the skill in ~60 seconds with no data of your own — see examples/.
Audit mode reads a manuscript and surfaces inconsistencies authors miss. Given this (synthetic) draft:
Abstract: "We analysed six years of monitoring data (January 2018–December 2022)… a network of 33 wells…" Results: "Across all 35 wells, the model reproduced the seasonal cycle (Figure 1)… the spatial pattern is shown in Figure 3… the correlation with the tidal signal was not significant (rho = 0.02, p = 0.94)."
Audit flags, among others:
- 🔴 Temporal error — "six years" but January 2018–December 2022 is five years.
- 🔴 Sample-size drift — 33 wells in the Abstract/Methods, 35 in the Results.
- 🔴 Argument-honesty conflict — the Abstract calls the tidal correlation "strong", but the Results report it as not significant.
- 🟠 Broken cross-reference — the text cites Figure 3, but only Figures 1–2 are captioned.
The full demo (with answer key) and a Draft-mode demo that turns synthetic CSVs into manuscript prose are in examples/.
| Mode | Input | Output | |
|---|---|---|---|
| ✍️ | Draft | Project data files (CSVs, source code, metadata) | Complete manuscript sections with inline citations, plus a .docx export |
| 👀 | Review | Existing .docx manuscript |
Structured reviewer report in chat (no file edits) |
| 🔄 | Revise | Existing .docx + optional reviewer comments |
Section-by-section BEFORE / AFTER / RATIONALE suggestions in chat (you apply them), plus a response-to-reviewers letter when reviewer comments are provided |
| 🔍 | Proofread | Existing .docx manuscript |
Revised .docx with language-level fixes only — no scientific changes, no restructuring, no new citations |
| 🧭 | Audit | Existing .docx manuscript |
Consistency and coherence report in chat with severity-tagged findings (Critical / Major / Minor). Catches gap-vs-conclusions mismatches, sample-size inconsistencies, broken cross-references, terminology drift, argument honesty conflicts |
| 📐 | Format | Existing .docx + target journal |
Submission-ready .docx (continuous line numbers, page numbers, double spacing, single column) plus the separate files the portal needs (e.g. highlights), and a two-layer compliance report. Changes presentation only, never a word of text |
The user selects one mode at session start. Each mode has its own reference file under references/ with the exact protocol, allowed/forbidden operations, and output format.
paper-agent is a Claude Code skill. Install it as a plugin (recommended) or clone it into your skills directory.
Option A — Install as a plugin (recommended, one command each):
/plugin marketplace add Rekin226/paper-agent
/plugin install paper-agent@paper-agentThis registers the repo as a marketplace and installs the skill. The bundled .mcp.json also wires up the Semantic Scholar MCP server automatically (see Setup).
Option B — Clone directly into the skills directory:
git clone https://github.com/Rekin226/paper-agent.git ~/.claude/skills/paper-agentOption C — Clone anywhere and symlink:
git clone https://github.com/Rekin226/paper-agent.git ~/code/paper-agent
ln -s ~/code/paper-agent ~/.claude/skills/paper-agentWith Option B or C, restart your Claude Code session (or open a new one) so it picks up the skill.
Option D — Upload to claude.ai or Claude Desktop: run ./package_for_claude_ai.sh from a clone. It writes paper-agent.zip (to ~/Downloads by default) with the frontmatter adjusted for claude.ai's skill validator. Upload that zip through the Skills section of your claude.ai settings. Requires Python with PyYAML.
In any Claude Code session, invoke the skill explicitly:
/paper-agent
…or trigger it implicitly by phrasing the task naturally:
I want to draft a manuscript for Hydrogeology Journal from the CSVs in ./workspace.
Please review my manuscript at ~/papers/my-paper.docx and tell me what a JHRS reviewer would say.
Proofread ~/papers/my-paper.docx for language only — no scientific changes.
Is ~/papers/my-paper.docx ready to submit to Engineering Geology?
The skill will run a short startup interview to pick the mode, the target journal, and the data sources, then proceed section-by-section with a pause-and-confirm protocol.
Requires Claude Code, uv for the bundled Semantic Scholar server, and pandoc for .docx round-trips. No API keys needed.
Dependencies, project presets, MCP configuration, and how to add a profile for your own journal or field are in docs/SETUP.md. New journal profiles are the easiest way to contribute.
See CONTRIBUTING.md for issue and PR guidelines, plus instructions for testing the skill locally.
MIT — see the LICENSE file for the full text.
Built by Ouédraogo Abdoul Rachid, Postdoctoral Researcher at National Central University and Adjunct Lecturer at Feng Chia University. Designed alongside research on gray-box groundwater modeling for the Zhuoshui Alluvial Fan, Taiwan (accepted, Hydrogeology Journal).
Built for researchers who want Claude as a rigorous co-author, not a stylish ghostwriter.