Skills & reviewer agents for AI-first climate science — built and used by a PhD atmospheric scientist
개요
A toolkit for AI-assisted scientific computing: Claude Code skills, domain-expert reviewer agents, and shell utilities — adopt it wholesale or grab single pieces. Skills are slash commands and mid-task capabilities for Claude Code. Type /pathfinder for a guided map of when to reach for each. Some skills are user-invoked only (you type the slash command) while others Claude may reach for mid-task — see CLAUDE.md for the invocation-control conventions. Subagent personas deploy to ~/.claude/agents/. Each adopts a domain-expert reviewer stance — adversarial, ranked concerns, no rewriting — and they can run individually or as a parallel review panel. If you use Claude Code's plugin system, add this repo as a marketplace and install the bundle: This installs every skill and reviewer agent. Updates come via /plugin marketplace update ai-science-toolkit. To cherry-pick individual pieces or register the session-naming boot hook, use the sync.sh workflow below. — it involves no shell.
README
ai-science-toolkit
A toolkit for AI-assisted scientific computing: Claude Code skills, domain-expert reviewer agents, and shell utilities — adopt it wholesale or grab single pieces.
Skills
Skills are slash commands and mid-task capabilities for Claude Code. Type /pathfinder for a guided map of when to reach for each.
| Skill | Command | Purpose |
|---|---|---|
| ai-review | /ai-review |
Comprehensive senior-engineer repo review; orchestrates a parallel fan-out that delegates to code-review/security-review/unstale/overbaked/reviewer-2 and adds gap-hunting, grounded ideation, and prioritized synthesis. Report-only by default; --fix opts into HIGH-confidence unstale repairs. |
| commit-batch | /commit-batch |
Batch the working tree into logical, single-concern commits, then commit and push if asked. Thin launcher for the model-invokable commit-batching core. |
| commit-batching | /commit-batching |
Batch a dirty working tree into logical, single-concern commits (survey → group → stage by path → commit → push if asked) — the model-invokable core behind /commit-batch. |
| create-alert | /create-alert |
Author a scheduled Slack alert: grill a “tell me when X happens” ask into a testable trigger, dry-run it live, and — after you sign off on the synthesized spec — create a claude.ai cloud routine that messages Slack when it fires. |
| evolve-claude-md | /evolve-claude-md |
Update CLAUDE.md — or the canonical AGENTS.md it redirects to — with durable knowledge from the current session. |
| figure-review | /figure-review |
Audit a scientific figure for publication-readiness: colormaps, uncertainty, axes, caption, and claim support; panel-aware, and raises likely-deliberate choices as by-design?; --style adds CC house style. |
| grill-me | /grill-me |
Interview the user relentlessly about a plan or design until reaching shared understanding, resolving each branch of the decision tree. Thin launcher for the model-invokable grilling core. By Matt Pocock. |
| grilling | /grilling |
Grill the user relentlessly about a plan or design, one decision at a time, until shared understanding — the model-invokable core behind /grill-me. Adapted from Matt Pocock. |
| handoff | /handoff |
Create or update a durable project handoff (.ai/HANDOFF.md) for the next AI agent/session. |
| lit-review | /lit-review |
Search and synthesize scientific literature from Zotero, arxiv, bioRxiv, Google Scholar, and Consensus. Zotero write support needs ZOTERO_* env vars in ~/.claude/settings.json. |
| overbaked | /overbaked |
Audit a document, plan, or code for over-engineering, verbosity, and scope creep. |
| pathfinder | /pathfinder |
Router: a navigable map of every skill and subagent and when to reach for each; resolves the reviewer-2-vs-panel review decision. |
| pickup | /pickup |
Pick up work from repo-local handoff state — the read side of the handoff pair. |
| repo-init | /repo-init |
Scaffold a new repo (or retrofit an existing one) with a standard structure via a short intake grill: research mode by default, --package for a distributable library. Never overwrites; --dry-run previews. |
| reviewer-2 | /reviewer-2 |
Adopt a critical-reviewer stance to stress-test a claim, result, or manuscript section: baseline, counterfactual, alternatives, uncertainty consistency. |
| slack-message | /slack-message |
Draft an internal Slack message grounded in current project context and recent workflow. |
| spot-ai | /spot-ai |
Audit a document, paragraph, or sentence for AI-isms: gray-list style tells (lane 1) and substance weaknesses — hollow claims, fabricated specifics, missing hedges (lane 2). Severity + confidence per finding, fix suggested or missing substance named; per-repo .ai/graylist.md can add, exempt, or re-tune thresholds. Flags only — never rewrites. |
| tab-setup | /tab-setup |
Assign a unique high-contrast color and name to the current Claude Code session; all recolors every active session. Forked from Jerald Huff. |
| unstale | /unstale |
Detect and repair staleness residue in Python library code and notebooks — dead imports, dead code, resolved TODOs, stale comments/docstrings, and HANDOFF blockers; --auto applies HIGH-confidence fixes. |
| worklog | /worklog |
Log a work entry to the Notion Work Journal + remote server cache + local .ai/ mirror — the capture core invoked by /handoff and whenever you ask to log something. |
| write-new-skill | /write-new-skill |
Create new Claude Code skills with proper structure and progressive disclosure. |
Some skills are user-invoked only (you type the slash command) while others Claude may reach for mid-task — see CLAUDE.md for the invocation-control conventions.
Agents
Subagent personas deploy to ~/.claude/agents/. Each adopts a domain-expert reviewer stance — adversarial, ranked concerns, no rewriting — and they can run individually or as a parallel review panel.
| Agent | Purpose |
|---|---|
| attribution-reviewer | Reviews climate-attribution claims for counterfactual, baseline, framing, uncertainty, model adequacy, and overclaiming |
| stats-reviewer | Reviews statistical analyses for estimator validity, causal identification, inference under dependence, model specification, multiple testing, and ML validity |
| meteo-reviewer | Reviews weather event analyses and atmospheric mechanism claims for dynamical, physical, observational, and hydrological rigor |
| scicomm-reviewer | Reviews public-facing science products for audience specificity, relevance framing, cognitive load, jargon, solutions/benefits, and uncertainty language (COMPASS principles) |
Installation
As a plugin (one line)
If you use Claude Code’s plugin system, add this repo as a marketplace and install the bundle:
/plugin marketplace add dgilford/ai-science-toolkit
/plugin install ai-science-toolkit@ai-science-toolkit
This installs every skill and reviewer agent. Updates come via /plugin marketplace update ai-science-toolkit. To cherry-pick individual pieces or register the session-naming boot hook, use the sync.sh workflow below.
On Windows, this is the route to use — it involves no shell. See Platform support.
With sync.sh (clone and deploy)
Clone the repo, then deploy everything:
git clone https://github.com/dgilford/ai-science-toolkit.git ~/ai-science-toolkit
cd ~/ai-science-toolkit
bash scripts/sync.sh push
push installs all skills to ~/.claude/skills/, all agents to ~/.claude/agents/, and registers the boot hook for session auto-naming (docs/tab-setup.md).
Just the pieces you want
Name any skills or agents and only those are installed:
bash scripts/sync.sh push figure-review reviewer-2 stats-reviewer
Names are auto-detected as skills or agents. Skills that invoke other skills bring them along automatically (e.g. handoff pulls in worklog and evolve-claude-md), and a named push never touches ~/.claude/settings.json unless tab-setup is included.
Most of the toolkit needs zero configuration; the exceptions (Zotero write access, the Notion work journal, session-name generation) are covered in docs/configuration.md.
Keeping in sync
skills/ and agents/ in the repo are the source of truth — edit there (or git pull updates), then re-run push. To go the other way and capture globally installed skills into the repo:
bash scripts/sync.sh pull # ~/.claude/skills/ → skills/; ~/.claude/agents/ → agents/
After pull, review git diff skills/ agents/ — it brings in every installed skill and agent, including ones not tracked here.
Listing running sessions (ai-sessions)
Beyond skills and agents, the toolkit ships shell utilities. scripts/ai-sessions.sh defines an ai-sessions function that lists your running Claude/Codex CLI sessions with their resume commands. Source it directly from the repo (no copy — git pull keeps it current) by adding to ~/.bashrc (or ~/.zshrc):
source ~/ai-science-toolkit/scripts/ai-sessions.sh
Run ai-sessions to list sessions. Claude’s own recap (away_summary) is shown by default for each session.
Session workflow
The handoff skills form a session lifecycle that keeps project state durable across sessions:
/pickup # start of session — loads handoff, reports state
/handoff # end of session — writes handoff, updates CLAUDE.md
/evolve-claude-md # anytime — promote new knowledge to CLAUDE.md
State lives in a repo-local .ai/ directory — add it to .gitignore in any project where you use these skills.
Platform support
Developed on macOS and Linux, where everything works. On Windows, the prompt-driven skills work untouched; the shell layer — preambles, repo scripts, hooks — does not.
| Windows | |
|---|---|
| All 4 reviewer agents | ✅ works unmodified |
commit-batch · evolve-claude-md · grill-me · grilling · overbaked · pathfinder · reviewer-2 · write-new-skill |
✅ works unmodified |
| Plugin install | ✅ recommended route — no shell involved |
| Status line | ⚠️ works once jq is installed |
worklog · lit-review |
⚠️ usable; their shell examples are Unix-only |
sync.sh and the other repo scripts |
⚠️ work under Git Bash, after setup |
Every skill with a shell preamble (incl. handoff, pickup, figure-review, repo-init) |
❌ preamble blocks don’t execute |
| Line endings | ❌ every .sh checks out CRLF; the shell lint fails |
| Session auto-naming hook | ❌ terminal integration is iTerm2/VS Code only |
The root cause is that preambles run in PowerShell rather than bash, and the repo ships no .gitattributes to normalize line endings. Windows setup steps, the per-skill matrix, and the full root-cause analysis are in docs/platform-support.md.
More documentation
- docs/platform-support.md — what works on Windows today, what breaks and why, and Windows setup steps
- docs/configuration.md — per-skill setup: env vars, connectors, and what degrades gracefully without them
- docs/tab-setup.md — session auto-naming and color: startup reminders, machine-level config, uninstall
- docs/repo-layout.md — what every file and directory in this repo is for
- docs/harness-behavior.md — observed (undocumented) Claude Code behavior, each claim tagged with its evidence tier and CLI version
- CLAUDE.md — skill-development conventions, sync internals, and repo workflow notes
Citation
If this toolkit supports your work, please cite it. GitHub’s “Cite this repository” button reads CITATION.cff and generates APA/BibTeX for the specific release, while the DOI badge above (the Zenodo concept DOI) always resolves to the latest archived version.
License
Released under the MIT License — Copyright © 2026 Daniel Gilford.
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