waldronlab / waldronlab/agent-protocol-standard

Add a `create-protocol` skill

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

Description

Authoring a conforming protocol currently means reading PROTOCOL_STANDARD.md end to end, and the failure modes are all in the metadata rather than in the science. A skill should do that reading.

It should:

  • fill the frontmatter from the standard's current schema, not from a copied example that may have drifted
  • ask the two citation questions separately, per ADR 0014 — who published these instructions is protocol_citation and required; who invented the method is method_origin_citation, optional, and omitted rather than guessed at when the protocol originates no method
  • write ## Materials and ## Steps with at least one ### Step, since CI rejects a protocol without them
  • open ## History & Reviews with a first version entry, a #### Changes list, and *No reviews yet.*
  • scaffold the optional parts too, each marked Optional, delete if unneeded. — the ## Notes section, and the optional frontmatter fields: category, tags, upstream_repositories, database_urls, method_origin_citation, artifact_doi, collection_doi. An author who can see a field can decide about it; one who can't discovers it in review, or never
  • run scripts/validate-protocol.R before reporting that it's done

The marker has to be literal and uniform, so deleting the unused ones is a search rather than a judgement each time. The same reason the template carries them commented rather than absent.

Lives at skills/create-protocol, beside protocol-runner, on ADR 0007's argument: what a conforming protocol looks like is federation-wide semantics defined by this standard, not something Bioconductor defines.

Worth testing against a summarized-experiment protocol locally before the first PR — writing the skill against the spec alone will miss whatever the spec leaves implicit.

Pairs with #36 (version bumps) and #37 (fixing what the validator reports).

Contributor guide

No contributing guide indexed for this repository

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 PROTOCOL_STANDARD.md, ADR 0007 and ADR 0014, then inspect the neighboring skills/create-protocol and protocol-runner directories. Use a summarized-experiment protocol as a local example and run scripts/validate-protocol.R. Done means the new skill scaffolds the required and optional sections and fields with the specified marker, and the validator accepts its output.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, r
Domain
documentation, tooling
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Active
Clarity
Clearly specified
Newbie friendliness
72/100

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