What is academic-figures-mcp copilot-instructions.md?

An instruction file for GitHub Copilot and Claude Code in an academic-figures MCP project. That project turns PubMed papers into scientific figures using Google Gemini image generation.

Use it to guide changes to the project’s domain logic, application flow, external integrations, MCP interface, tests, and documentation.

It explains the project’s architecture, development practices, memory system, agents, and enforced layer boundaries.

How u9401066/academic-figures-mcp configures GitHub Copilot

Reuse

Borrowing it

Nothing to install: this file belongs to u9401066/academic-figures-mcp. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/u9401066/academic-figures-mcp/main/.github/copilot-instructions.md

Clone the repo

git clone --depth 1 https://github.com/u9401066/academic-figures-mcp

Made for: GitHub Copilot.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/instructions/u9401066/academic-figures-mcp/copilot-instructions/github.svg)](https://agentmods.dev/instructions/u9401066/academic-figures-mcp/copilot-instructions)

Your own site

<a href="https://agentmods.dev/instructions/u9401066/academic-figures-mcp/copilot-instructions"><img src="https://agentmods.dev/badge/instructions/u9401066/academic-figures-mcp/copilot-instructions/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/instructions/u9401066/academic-figures-mcp/copilot-instructions"><img src="https://agentmods.dev/badge/instructions/u9401066/academic-figures-mcp/copilot-instructions.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 2,230 This file is loaded in full into every session.

When invoked 2,230 The same file — it is already loaded in full.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.02230	$0.02230
Opus 5	$0.01115	$0.01115
Sonnet 5	$0.00446	$0.00446
Haiku 4.5	$0.00223	$0.00223

Measured 8d ago against content hash d20e60bb14c2, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-08, from the pricing page.

Security

Grade A, and why

academic-figures-mcp copilot-instructions.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.github/copilot-instructions.md · 217 lines

How it starts

The opening of the file, as written. The whole thing — 217 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Academic Figures MCP — Copilot Instructions

此文件為 VS Code GitHub Copilot 及 Claude Code 提供專案上下文與操作規範。

Project Overview

Academic Figures MCP is a Model Context Protocol server that turns PubMed papers into publication-ready scientific figures using Google Gemini image generation.

整合了：

DDD (Domain-Driven Design) 四層架構
Memory Bank 專案記憶系統
14 個 Custom Copilot Agents（含模型成本策略）
完整 Pre-commit Hooks（16+ hooks）

開發哲學 💡

「想要寫文件的時候，就更新 Memory Bank 吧！」「想要零散測試的時候，就寫測試檔案進 tests/ 資料夾吧！」

不要另開檔案寫筆記，直接寫進 Memory Bank
今天的零散測試，就是明天的回歸測試

Architecture: Domain-Driven Design (DDD)

src/
  domain/          ← Pure business logic, NO external imports
  application/     ← Use-case orchestration
  infrastructure/  ← External integrations (Gemini, PubMed, file I/O)
  presentation/    ← MCP server surface (tools, resources, prompts)

Layer Rules (STRICTLY ENFORCED)

Layer	May import from	Forbidden imports
`domain/`	stdlib, dataclasses, enum, typing, abc	Any external package
`application/`	`domain/`	Infrastructure classes directly
`infrastructure/`	`domain/` (interfaces, entities)	`application/`, `presentation/`
`presentation/`	`application/`, `infrastructure/` (for DI), `domain/`	N/A

依賴方向：Presentation → Application → Domain ← Infrastructure

Key Patterns

Dependency Injection: presentation/dependencies.py wires infrastructure into use cases.
Domain interfaces: domain/interfaces.py defines ABCs; infrastructure implements them.
Value Objects: Immutable, use @dataclass(frozen=True) or Enum.
Use Cases: One class per business operation, single execute() method.
Repository Pattern: DAL (Data Access Layer) 必須獨立。

Technology Stack

Runtime: Python 3.10+
MCP: mcp[cli]>=1.27.0 (FastMCP)
AI: google-genai (Gemini image generation)
Package manager: uv (never pip/conda)
Lint: ruff
Types: mypy --strict
Tests: pytest
Security: bandit
Pre-commit: ruff, mypy, pytest, bandit, gitleaks, conventional-commits, commit-size-guard

Read the full file on GitHub · 217 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

8d ago First seen · 217 lines · 2,230 tokens per session scan A d20e60bb14c2

Subscribe to this mod's changes

academic-figures-mcp copilot-instructions.md is an instructions file published in the GitHub repository u9401066/academic-figures-mcp (0 stars, last pushed 4mo ago), licensed Apache-2.0. It adds 2,230 tokens to every session, about $0.0112 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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academic-figures-mcp: Instructions file for GitHub Copilot