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Agent Quickstart

This repo is designed to be pointed at by a coding agent. The agent should use the skills, docs, schemas, and validators to turn open-ended cryo-EM requests into concrete map/model reviews, figure workflows, state-comparison plans, provider plans, run reviews, and tracker-ready issue waves.

CryoCore agent loop

Harness compatibility

Best First Prompt

This is the canonical CryoCore agent prompt. The README's Agent Prompt section uses the same text.

Use the CryoCore skill pack in this repo. Stay local. Read AGENTS.md,
README.md, docs/goal-orchestration.md, docs/workflows.md, docs/use-cases.md,
and the relevant skill under skills/. Build a useful cryo-EM map/model review,
figure workflow, state comparison, provider plan, or artifact package. Keep
private data, secrets, raw or heavy artifacts, provider logs, model weights,
and license files out of git and public outputs. Run the smallest relevant
checks first, then `make release-check` when the task is release-readiness.
Report exact artifacts, claim levels, check results, and remaining issues.

What The Agent Should Read

Task Skill
General CryoCore work skills/cryocore/SKILL.md
Public release, privacy, or secrets skills/cryocore-public-safety/SKILL.md
Map/model review skills/cryocore-map-model-dossier/SKILL.md
Provider run review skills/cryocore-run-closeout/SKILL.md
Tool/license audit skills/cryocore-toolwatch/SKILL.md
Heterogeneity/state review skills/cryocore-heterogeneity-jury/SKILL.md
Figure workflow skills/cryocore-figure-dossier/SKILL.md

What The Agent Should Produce

  • A declared input boundary.
  • A goal brief when the request is broad enough to need orchestration.
  • A claim ceiling using docs/claim-levels.md.
  • Artifacts or templates under the right repo directory.
  • Check commands and results.
  • Data, license, and provider notes.
  • A final outcome block shaped like templates/final-outcome-block.md.

Minimum Acceptable Agent Run

For a public release or release-readiness review, an agent should at least:

  1. Read AGENTS.md, README.md, this guide, and the relevant skill.

  2. State whether the task is local-only, networked public metadata, or operator-gated provider work.

  3. Run:

    make docs-link-check
make skill-check
make goal-brief-check
make public-snapshot-check

  4. For release readiness, also run:

    make release-check

  5. Report blockers first, then changed files, check results, claim ceiling, and remaining issues.

An answer that only says a provider is running, a command exited, or a demo looks good is incomplete.

Starter Tasks

Use fixtures under examples/agent-tasks/:

  • public-safety-review.prompt.md
  • map-model-dossier.prompt.md
  • cloud-provider-prep.prompt.md
  • linear-wave-planning.prompt.md
  • goal-to-campaign.prompt.md

Local Validation Ladder

make doctor
make goal-brief-check
make skill-check
make runpod-scope-check
make provider-closeout-check
make release-check

See docs/validation-command-matrix.md for side effects and network behavior.