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research-proposal

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Use when the user has a research proposal (problem + proposed methodology + planned experiments) and wants it iteratively strengthened until it clears a passing grade. ScholarEval grades the proposal against the literature (Soundness + Contribution), a Judge scores that feedback 0-100 on a fixed rubric, and a Reviser rewrites the proposal to fix the worst points without diluting the research question; loops until the grade passes or the budget is hit. Not for generating a proposal from scratch, and not for running a literature survey on its own.

التثبيت

التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.

تشغيل في Manus

المصدر

gaasher

gaasher/Agent-Loop-Skills

فتح مستودع GitHub عرض مستودعات المنشئ

تنزيل

تشغيل في Manus

المهن ذات الصلةSOC

استنادا إلى تصنيف SOC المهني

علماء الطب (باستثناء علماء الأوبئة)علوم الحياة والطبيعة والاجتماع·SOC 19-1042

مستكشف الملفات

8 ملفات

SKILL.md

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المزيد من هذا المستودع

نفس المستودع

swe-loop

gaasher/Agent-Loop-Skills

Use when the user has a coding prompt — a feature, bug fix, or refactor — and wants it implemented end to end by a self-checking software loop, not a single pass. It refines the prompt into an executable plan (running the plan-loop internally), then executes the plan task by task: an Engineer subagent implements each PR-sized task editing only source, a separate QA subagent authors the tests that prove the task's acceptance criteria (or grades quality only when tests already cover them), runs the task's tests plus the full accumulated regression suite, and grades the code against a strict conciseness/readability/style-match rubric; the Engineer and QA loop on each task until the tests pass and the quality gate holds, then it commits and opens a pull request for the task — stacked PRs (one per task, each based on the prior) by default, or one combined PR — and moves to the next task. Author and critic have disjoint write scopes (Engineer owns source, QA owns tests) so neither can game the gate. Not for produci

2026-06-30133

plan-loop

gaasher/Agent-Loop-Skills

Use when the user has a coding or engineering prompt and wants it refined into a detailed, executable plan before any code is written — the planning stage of a prompt → plan → execute → debug pipeline. It decomposes the prompt from first principles (objective, end state, environment, building blocks, tools, packages), breaks the work into PR-sized tasks each tied to a component with its files, tests, and dependencies, orders them topologically, splits each into atomic subtasks, then a separate principal-engineer agent critiques the plan for alignment, coverage, sizing, and executability; it revises until the critique passes, emitting a plan.md layout and a structured tasks.json that a junior engineer or a smaller model can execute correctly. Not for executing, scaffolding, or debugging the plan (those are downstream loops), and not for research proposals or experiment plans.

2026-06-29133

blue-team

gaasher/Agent-Loop-Skills

Use when the user has concrete failing cases in code or a guardrail/classifier/filter/prompt/API they own — a red-team failure catalogue OR a CI/CD test-failure report (failing pytest/JUnit tests) — and wants the target patched until those failures are closed without breaking what already works. It points straight at the failed cases (normalize any source with tools/ingest.py), fixes one root-cause class per iteration, and re-checks with tools/verify.py — oracle mode against a red-team oracle, or tests mode against the test suite — keeping a patch only if it closes a class while nothing that passed before regresses, else reverting; loops until every class is closed (dry) or the budget runs out, then opens a pull request with the patch set. The defensive fixer half of a find→fix setup. Not for discovering new failures (that is red-team), and not for editing the oracle, tests, or holdout that define ground truth.

2026-06-28133

purple-team

gaasher/Agent-Loop-Skills

Use when the user wants to automatically harden a guardrail, classifier, content filter, prompt, or API they own by running attack and defense together as a closed loop, not just one or the other. It orchestrates the red-team and blue-team loops as independent agents: red finds distinct failure classes against the frozen target, blue patches the target to close them under a regression gate, then a fresh red pass re-verifies — confirming each class is closed and surfacing any new ones the fix introduced. The find→fix→re-verify cycle repeats until a fresh attack pass stays dry (the target is hardened) or a cycle budget is hit, then it opens a pull request with the patch set. Not for attacking a system the user is not authorized to test, and not for a one-shot scan — use red-team alone to only find, or blue-team alone to only fix.

2026-06-28133

scientific-figure

gaasher/Agent-Loop-Skills

Use when the user has scientific data (or a prompt alluding to scientific data) and wants a publication-quality figure made from it. A generator drafts and renders a figure that lands a frozen communication goal; an adversarial critic critiques it hard and grades it 1-5 per axis against a fixed rubric (message, aesthetic, clarity, integrity, and a conditional domain-completeness axis), aggregates to 0-100, and decides pass; the generator revises against the critic's findings until the grade clears a threshold or the budget is hit. Both roles may consult the literature (Semantic Scholar + arXiv) to verify domain content (e.g. a pathway figure's gene set, or a benchmark's reported numbers), and conform to / grade against a named journal's figure spec fetched via web search. Not for writing a paper or analyzing a dataset, and not for editing an existing finished image — this renders a figure from data/brief and iterates on it.

2026-06-23133

ml-autoresearch

gaasher/Agent-Loop-Skills

Use when the user wants an autonomous ML research loop that does more than blindly try changes. After every training run the agent analyses what actually happened inside the model — gradients, activations, embeddings, errors, data — and grounds the next change in that evidence. A `<literature>` on/off dial adds scientific-literature grounding: off behaves as a pure analysis-first loop; on searches papers, grades the evidence, and implements only what prior work supports. One change per run; loops forever until interrupted. Not for one-off training runs or hyperparameter sweeps.

2026-06-22133

name	research-proposal
description	Use when the user has a research proposal (problem + proposed methodology + planned experiments) and wants it iteratively strengthened until it clears a passing grade. ScholarEval grades the proposal against the literature (Soundness + Contribution), a Judge scores that feedback 0-100 on a fixed rubric, and a Reviser rewrites the proposal to fix the worst points without diluting the research question; loops until the grade passes or the budget is hit. Not for generating a proposal from scratch, and not for running a literature survey on its own.
compatibility	Requires Python 3.9+
metadata	{"version":"0.1.0"}

Research Proposal Loop

The artifact is a research proposal; the feedback signal is ScholarEval (literature-grounded Soundness + Contribution) turned into a 0-100 grade by a Judge against the fixed rubric.md. Each iteration evaluates → grades → revises until the grade clears <pass_threshold> or the budget runs out.

North star. Clearing the threshold is the stopping condition, not the goal. The goal is the strongest, most novel, genuinely publishable version the proposal can honestly become — every revision should ask "does this make the work more significant and more novel?", not just "does this patch a flaw?". This is grounded ambition: the lift comes from better-justified methods, a sharper-but-defensible novelty claim, and stronger baselines, all backed by real retrieved evidence. Overclaiming lowers the grade (evidence gate + Contribution axis); it never raises it.

The cast (all in this folder):

roles/ScholarEval.md — the two-module literature-grounded evaluator; emits scholareval.json.
roles/Judge.md — grades the feedback → 0-100 + ranked fixes; emits verdict.json (decides pass).
roles/Reviser.md — rewrites the proposal to address the fixes (guards the research intent).
rubrics/rubric.md — the fixed grading rubric (the Judge never edits it).
schemas/scholareval.schema.json, schemas/verdict.schema.json — the two validated outputs.

Spawn-or-degrade. On Claude Code, spawn ScholarEval / Reviser as real Agent subagents; otherwise adopt each role inline. You are the orchestrator and the Judge.

When to use

Use when a written proposal exists and the user wants it pushed past a quality bar with literature-grounded critique. Default: run the full evaluate→grade→revise loop below. Escape hatch: if the user only wants the critique (no rewriting), run one ScholarEval + Judge pass and stop. Not for writing a proposal from a blank page, and not for a standalone literature survey.

Setup

Resolve bindings interactively. If loop.run.yaml exists in the working dir, load it and skip to the loop. Otherwise: on Claude Code (the AskUserQuestion tool is available) infer a likely value for each binding and present it as the recommended option; on other hosts ask each as a quoted plain-text prompt. Then write loop.run.yaml (format: examples/run.example.yaml) and confirm every value, <intent>, and the live/degraded literature tier before creating any other files.

binding	meaning	default	how to infer
`<proposal_path>`	file with problem + methodology + planned experiments	—	scan for a likely `.md`/`.txt`/`.pdf`; if only prose is pasted, save it to `<sandbox_root>/iter1/proposal.md`
`<intent>`	core research question + headline contribution, 2-3 sentences — frozen; the Reviser may never change it	—	read the proposal, extract it, have the user confirm
`<pass_threshold>`	grade (0-100) the proposal must reach to pass	75	a solid, well-grounded proposal without demanding perfection
`<budget>`	max iterations	6	—
`<patience>`	stop after this many consecutive no-improvement iterations	2	—
`<eval_scale>`	how much literature ScholarEval pulls per iteration (`low`/`medium`/`high`, see below)	`medium`	—
`grade_weights`	`soundness · contribution · evidence_quality` (must sum to 1; frozen for the run)	`0.45 · 0.35 · 0.20`	`rubric.md`; recommend default
`<sandbox_root>`	where snapshots, ledger, and lit cache live	`./sandbox`	—

Evaluation depth dial (<eval_scale> caps per iteration — methods · dimensions examined · queries each · papers read full-text):

preset	methods · dims	queries each	fulltext reads	effort
low	2 · 2	1	0 (snippet/abstract only)	low
medium (recommended)	4 · 3	2	2	medium
high	6 · 5	3	5	high

Literature toolchain. Paper search goes through the sibling literature-search skill — resolve <lit_skill_dir> (it installs as a sibling, e.g. ~/.claude/skills/literature-search/), <lit_py> = python3, and <lit> = <lit_skill_dir>/tools/lit_search.py; append --cache-dir <sandbox_root>/literature/.cache after a subcommand to reuse the cache. Confirm <lit> --help works at setup; if the skill is absent, tell the user and either install it (copy the repo's loops/literature-search folder into ~/.claude/skills/) or degrade all retrieval to WebSearch/WebFetch (no ranked snippets or citation-graph expansion). The keyless S2 + arXiv core (search/snippet/cite/fulltext) needs no setup; a free S2_API_KEY makes snippet+cite (ScholarEval's two defining moves) reliable.

API key (optional, never block). The literature-search skill owns the key convention: run <lit> keys --init, then have the user fill the printed keys.env themselves and never paste secrets into chat. Re-run <lit> keys to confirm presence and record the tier in loop.run.yaml (literature_tiers, presence only). A missing key just degrades to the keyless pool → WebSearch.

Initialise the sandbox once bindings are confirmed:

<sandbox_root>/
├── loop.run.yaml        ← resolved bindings + <intent> + grade_weights + literature_tiers
├── ledger.tsv           ← header only (see Ledger)
├── literature/.cache/   ← lit_search on-disk cache
└── iter1/proposal.md    ← the input proposal (the baseline)

The loop

<N> starts at 1; iteration 1 evaluates the unmodified proposal (the baseline grade — no revision before it). Re-evaluate fresh every iteration: the grade comes only from a new ScholarEval pass on the revised proposal, never carried over.

Copy this checklist and tick items off:

Evaluate — run roles/ScholarEval.md (spawn-or-degrade) on iter<N>/proposal.md with the <eval_scale> caps and <lit>; it writes iter<N>/scholareval.json (validates against schemas/scholareval.schema.json).
Grade — as the Judge (roles/Judge.md) apply rubrics/rubric.md to scholareval.json: evidence gate → 0-5 per axis → weighted grade → hard gates → pass + ranked fixes; write iter<N>/verdict.json (validates against schemas/verdict.schema.json).
Log — append one ledger.tsv row (see Ledger).
Stop check — verdict.pass == true, or N == <budget>, or grade flat for <patience> iterations → stop (see Stops).
Revise — run roles/Reviser.md (spawn-or-degrade) with verdict.json, scholareval.json, <intent>, <lit>, and a small revision search budget (≈<eval_scale> searches + a couple of reads); it applies one focused fix batch and writes iter<N+1>/proposal.md + iter<N+1>/revision_notes.md.
N = N + 1 and repeat.

Every cited snippet must come from a real retrieval that iteration — never fabricated. When a lit tool returns {"error","fallback"}, fall back to WebSearch/WebFetch; never invent a paper.

Ledger

<sandbox_root>/ledger.tsv, tab-separated, never commas in free text:

iter	grade	pass	soundness	contribution	evidence_quality	top_fix	revision_summary
1	58.0	no	3	2	4	add MM-GBSA re-scoring	baseline (no revision)
2	71.0	no	4	3	4	add head-to-head vs [C2] pipeline	added re-scoring + scoped affinity claim
3	82.0	yes	4	4	4	-	reframed contribution around integration + new benchmark

The matching scholareval.json and verdict.json for each iteration live in iter<N>/. Report the best-grade iteration when stopping on budget/plateau, not necessarily the last. Leave ledger.tsv, iter*/, and literature/ untracked.

Constraints

Never fabricate citations or snippets — every evidence entry comes from a real <lit>/WebFetch result retrieved that iteration, verbatim; the evidence gate exists to catch fabrication.
The rubric is fixed — the Judge never edits rubrics/rubric.md, so the passing threshold stays meaningful across iterations.
Protect <intent> — the Reviser may strengthen but never replace the core research question or headline contribution, and never gut a central method just to lift the grade.
Grade through evidence, not prose — eloquence earns nothing; grounded support and surviving novelty earn the score.
One focused revision batch per iteration, so each grade move is attributable.
No installs — the sibling literature-search skill is stdlib-only; never print or commit API keys (keys.env stays gitignored at the project root). The sandbox is self-contained — no ../ escapes.

Stops

The loop stops on the first of:

Pass — verdict.pass == true. Report the final proposal (iter<N>/proposal.md), its grade, and the grade trajectory.
Budget — N == <budget>. Report the best-grade iteration as the deliverable.
Plateau — grade hasn't improved for <patience> consecutive iterations. Report the best iteration and the standing priority-1 fixes.

Always end with the deliverable proposal path, its grade and pass/fail, the grade trajectory from ledger.tsv, and — if it did not pass — the standing blockers between this proposal and the bar.