sdrf-skills: Instructions file for Claude Code

CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

What this repo is

A skills-first repo: the product is skills/*/SKILL.md — markdown workflows that teach an AI assistant to annotate proteomics SDRF files. Supporting Python lives in tools/. Specification data is not stored here; it is read at runtime from the spec/ git submodule.

Skills are auto-discovered — .claude-plugin/plugin.json carries no skills key, so Claude Code scans the skills/ directory automatically. Each SKILL.md declares its own name and routing description in frontmatter. Currently 4: sdrf-annotate, sdrf-contribute, sdrf-campaign (invoked as /sdrf-skills:sdrf-annotate etc. once installed as a marketplace plugin) plus sdrf-adversarial-review, which sdrf-annotate dispatches into a fresh context at Step 9.5 and which is never typed. sdrf-annotate is the one entry point for everything about one SDRF - create (review always included), review/validate/check/score/fix an existing file, look up cell lines and terms, verify technical metadata from raw files, plan, explain. Its references/ hold what used to be separate skills (setup, knowledge, templates, validate, fix, techrefine, cellline, review, design). Run ls skills/ for the current set — do not trust a hardcoded skill count anywhere in this repo; README.md alone carries three contradictory numbers, and commit d5c4c70 exists only to repair drift.

Commands

# Tests (126, ~2s, no network). CI runs: python -m pytest tests/ -v --tb=short
python -m pytest tests/ -q
python -m pytest tests/test_parser.py -q                                # single file
python -m pytest tests/test_services.py::TestPRIDEClient::test_get_project_mock -q  # single test (tests use classes)
python -m pytest tests/ -q -k unimod                                    # by keyword

# Lint — NOT in CI, and currently RED: 32 errors (28 F401, 4 F541), all auto-fixable.
# tools/review_gate.py is clean; the rest predates it. Run `ruff check --fix` before gating on it.
ruff check tools/ tests/

# Submodule: TWO levels deep (spec/ -> spec/sdrf-proteomics/sdrf-templates).
# `--recursive` is mandatory or templates.yaml is silently MISSING.
git submodule update --init --recursive     # restore pinned state (what you usually want)
git submodule update --remote --recursive   # advance to upstream tip; leaves a dirty gitlink

# tools CLI: `sdrf-tools` console script after `pip install -e .`; `python -m tools` also works from the repo root
sdrf-tools --help   # check, structure, contract, build, score, fix, benchmark, massive-files,
                         # verify, cellline, review-gate, reconcile, audit-existing, curated,
                         # bruker-dia, search-params