Initialize the Atlas Research Graph

Overview

An Atlas project is this repo's research graph — the root that hypotheses, experiments, training/eval runs, evidence, and decisions hang off. Creating (or linking to an existing) graph is a one-command, dedupe-safe operation. It is keyed off the git repo, not the opened folder, so a subfolder or a fresh clone at a different path resolves to the same graph.

Run this skill when:

• The canvas shows "no graph for this project" / the folder isn't linked yet.
• The user asks to "initialize", "set up Atlas", or "start tracking" research.
• You are about to begin research work that should be recorded.

Steps

1. (Optional) Confirm the CLI is authenticated.

   atlas doctor --format=json

   If it reports unavailable/unauthenticated, tell the user to run openscience login — the graph cannot be created without a session.

2. Create or link the graph (idempotent — safe to re-run; returns the existing graph if one already exists):

   openscience project init --format=json

   On success this prints {"project_id":"<id>"} and writes .openscience/project.json at the repo root so the canvas links to it immediately.

   On failure it prints project_id: null plus an error kind (and host, status, message when known). Relay the fix that matches the kind — do NOT guess or tell the user to re-login for a network problem:

   • "unauthenticated" — no session, or the backend rejected the saved key. Tell the user to run openscience login.
   • "unreachable" — the Atlas backend at the printed host could not be reached (network/DNS error or 5xx). The user IS logged in; suggest checking connectivity and any OPENSCIENCE_API_BASE/SYNSC_API_BASE override, then retrying — not re-authenticating.
   • "plan" — authenticated, but the account has no active Atlas plan. Point the user at https://app.syntheticsciences.ai/billing; include the backend message if present.
   • "backend" — anything else; show the backend's status/message verbatim.

3. Confirm to the user. Report the project_id and tell them the graph now shows in the canvas (Atlas pane). From here, milestones are recorded against this graph as the work progresses.

Notes

• Idempotent & dedupe-safe: re-running never creates a duplicate; it returns the same graph for the same repo.
• Repo-rooted: run it from anywhere inside the repo — it resolves to the git top-level.
• Do not hand-edit .openscience/project.json; let openscience project init manage it (use openscience project merge to pick a canonical root if duplicates exist).