What is hypotree copilot-instructions.md?

A set of project instructions for Hypotree, a Python application that uses SQLite to store data and includes tools for analysis and testing.

Use it when refactoring Hypotree, changing its SQLite schema, adding tests, or running its Python checks and analysis tools.

It gives coding agents clear rules for compatible database changes, code quality, testing, and support across Linux, macOS, and Windows.

How tygryso/hypotree configures GitHub Copilot

Reuse

Borrowing it

Nothing to install: this file belongs to tygryso/hypotree. 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/tygryso/hypotree/master/.github/copilot-instructions.md

Clone the repo

git clone --depth 1 https://github.com/tygryso/hypotree

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/tygryso/hypotree/copilot-instructions/github.svg)](https://agentmods.dev/instructions/tygryso/hypotree/copilot-instructions)

Your own site

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

Per session 1,749 This file is loaded in full into every session.

When invoked 1,749 The same file — it is already loaded in full.

Security scan C 1 finding. 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	$0.01749	$0.01749
Opus 5.5	$0.00700	$0.00700
Sonnet 5.5	$0.00350	$0.00350
Haiku 4.5	$0.00175	$0.00175

Measured 2mo ago against content hash cbe27eddc032, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade C, and why

hypotree copilot-instructions.md scanned grade C with 1 finding 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 2mo 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.

Recursive force deletehighDestructive command

rm -rf with a variable or a broad path is one typo away from removing the wrong tree.

- **NEVER run `rm -rf` on the belief-state database** before or after `pytest`. This wipes the belief-state and is completely unnecessary — all test fixtures create temp DBs via `tmp_path`.

.github/copilot-instructions.md · 89 lines

How it starts

The opening of the file, as written. The whole thing — 89 lines — stays where its author put it; the contents beside it link to each section on GitHub.

hypotree — Project Instructions

Platform & Environment

OS: Linux, macOS and Windows. eval.sh is bash-only (WSL or Git Bash on Windows); everything else runs natively on all three.
Languages: Python 3.10+
Frameworks/Libraries: MCP (modelcontextprotocol), Pydantic, SciPy (Beta distributions), SQLite (stdlib)
Eval/Plotting: Pandas, NumPy, Matplotlib, Seaborn
Tooling: uv, pytest, ruff, mypy
Version Control: Git (GitHub)

Refactoring & Code Quality

Migrations and backward compatibility are required. The project is open-source and entering production. SQLite schema changes must bump the version and upgrade old databases automatically. Deprecation warnings should precede removals by at least one minor version. Never break existing belief-state databases without a migration.
Prefer generalization. When implementing a feature, look for opportunities to generalize. Enhance and consolidate logic proactively rather than adding narrow one-off code.
Maintain inline comments. Keep and improve inline code comments that describe why something exists or what a non-obvious block does. Add brief logic descriptions where they aid comprehension. Never reference plan phase numbers, step numbers, or plan names in comments — comments must be self-contained, descriptive, and meaningful without any external context.

Testing & Linting Discipline

Always use uv run — never system Python or pip. This project uses uv for all environment management. Commands must be prefixed with uv run to use the correct virtual environment.
Modified code requires verification. Any modified class, function, or variable within a file requires a full pytest run on that module/file plus ruff on that file. No exceptions — the edit is not complete until both pass.
- Tests: uv run pytest <test_file> -x -q
- Linter: uv run ruff check <file>
- Format: uv run ruff format <file>
- Type check: uv run mypy src/hypotree/
New code requires new tests. Any new function, class, or method must have a corresponding new pytest test written for it before the task is considered done. The new test must pass alongside ruff on the new and changed files.
No untested code is shipped. If you add code and do not write a test for it, you have failed the task. Period.

Read the full file on GitHub · 89 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.

2mo ago First seen · 89 lines · 1,749 tokens per session scan C cbe27eddc032

Subscribe to this mod's changes

hypotree copilot-instructions.md is an instructions file published in the GitHub repository tygryso/hypotree (12 stars, last pushed 2mo ago), licensed MIT. It adds 1,749 tokens to every session, about $0.0070 per session on Opus 5.5. A static security scan graded it C with 1 finding (recursive force delete). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

agentic-memory agentic-memory-architecture ai-agents dag graph-memory hypothesis

hypotree copilot-instructions.md next to 6 instructions from other repositories
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hypotree: Instructions file for GitHub Copilot