waldronlab / waldronlab/agent-protocol-standard

Surface review status when the runner selects a protocol

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Dominant language
Python
Stars
3
Forks
1
Avg merge
14h 8m
Merged PRs (30d)
23

Description

With #9, every protocol publishes structured reviews in PROTOCOLS.yaml — reviewer name, optional ORCID, date, the protocol_version reviewed, and a status from a controlled vocabulary (approved, verified-with-benchmark, changes-requested, deprecated). Nothing consumes it yet.

The protocol runner should read it and surface it at selection time, alongside the trust_tier and status signals it already uses (skills/protocol-runner/SKILL.md:29,36,41,84,143 in this repository).

Specifically:

  • List reviews among the index fields the skill relies on.
  • Show review status next to trust_tier and status in match listings and in the pre-execution summary.
  • Warn when the version about to be executed is unreviewed — that is, when no reviews entry carries a protocol_version equal to the protocol's version. This is the case the format was designed to make visible: a protocol can carry several approvals of older releases while the current one has been vetted by nobody.
  • Warn on changes-requested for the version being executed.
  • Consider review status as a tiebreaker in ranking, after trust_tier and status.

Sequencing: this was waiting on the runner relocating out of bioconductor/ai-agent-skills and being renamed, so the change would land once rather than in two repos. That happened in #14 (merged 2026-09-11), so this is now unblocked and the paths above refer to its new home here.

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with skills/protocol-runner/SKILL.md at lines 29, 36, 41, 84, and 143, then inspect the runner entry point and review fields in PROTOCOLS.yaml. Trace how trust_tier and status are shown and ranked. Done means review status appears in listings and the pre-execution summary, with version-specific warnings for unreviewed and changes-requested reviews.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
ai-infra-agents, tooling
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Active
Clarity
Clearly specified
Newbie friendliness
76/100

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