waldronlab / waldronlab/agent-protocol-standard
Add a `create-protocol` skill
Nobody has claimed this yet.
- 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_citationand required; who invented the method ismethod_origin_citation, optional, and omitted rather than guessed at when the protocol originates no method - write
## Materialsand## Stepswith at least one### Step, since CI rejects a protocol without them - open
## History & Reviewswith a first version entry, a#### Changeslist, and*No reviews yet.* - scaffold the optional parts too, each marked
Optional, delete if unneeded.— the## Notessection, 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.Rbefore 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
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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