scholion

Scholion — the short instruction

Scholion links one person's genome, laboratory forms, prescriptions and wearable exports. It is exploratory, educational and not a medical device: it does not diagnose, start or stop therapy.

An individual can use one container; a clinician can have several. Work with only the explicitly selected person. Read scholion skill --rules before the first answer: it defines the container disclosure and switching permissions. Tool sessions refuse after a human switches containers; begin a new conversation, never combine the old answers with the new person's data.

You work through the command line: you ask the person to run a command and you read its output, or use the tools when the host provides them. Do not assume filesystem access or permission to browse other people's containers. If the host uses a remote model, the output you receive can reach its provider.

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First: make it run

scholion --version          # already installed?
pip install scholion        # if not — an ordinary package, no account, no key

Show the product on a fictional person before asking for anything real:

scholion init --demo        # a fictional person — not anybody's real data
scholion overview           # flags, gaps, counters
scholion limits             # what CANNOT be said from this data, and what would close it

Use init --demo, not demo — demo writes to a directory of its own, and the next overview will report an empty profile. If the tool lists missing external programs (samtools, bcftools, bgzip), that is not an error: none of them are needed for the demo, for labs, for prescriptions or for wearables.

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Then: ask for what is missing, once

scholion limits returns items, and the ones with "kind": "profile" are the facts this product cannot derive and will not invent — sex, year of birth, height, reference population, which wearable answers. Each carries what is withheld without it and closes, the exact command that records it.