| Write H2 chapter lead blocks (`sections/S<sec_id>_lead.md`) that preview the chapter's comparison lens and connect its H3 subsections, without adding new facts.
npx skills add https://github.com/WILLOSCAR/research-units-pipeline-skills --skill chapter-lead-writer
This skill writes the body-only lead block that sits under an H2 heading and makes a chapter with multiple H3 subsections read like one argument.
This SKILL.md is now the package router, not the full method manual.
This package is in P0 compatibility-preserving migration:
references/ and assets/ now hold the intended knowledge and contract layers.scripts/run.py remains in compatibility mode for active generation.For now, preserve the existing output contract and treat scripts/run.py as the execution source of truth.
Required:
outline/outline.ymloutline/chapter_briefs.jsonlcitations/ref.bibOptional:
outline/writer_context_packs.jsonlFor each H2 section with H3 subsections:
sections/S<sec_id>_lead.mdKeep these file-shape rules stable:
Always read:
references/overview.mdreferences/lead_block_archetypes.mdRead by task:
references/throughline_patterns.md — when chapter briefs are thin or hard to convert into a throughlinereferences/bridge_examples.md — when the lead needs stronger H3 transitions without slide narrationreferences/bad_narration_examples.md — when removing table-of-contents narration, planner talk, count-based openersMachine-readable assets:
assets/lead_block_contract.json — stable package contract for lead-block shapeassets/lead_block_compatibility_defaults.json — fallback phrasing, item limits, joiners, sentence cadenceUse this skill in the following order:
outline/outline.ymloutline/chapter_briefs.jsonlreferences/overview.mdreferences/lead_block_archetypes.mdoutline/writer_context_packs.jsonl exists, use it for cross-cutting chapter citationscitations/ref.bibscripts/run.py in compatibility mode to preserve active behavior and output shapescripts/run.py for deterministic execution only, with the writing method and anti-pattern inventory living in references/scripts/run.py still contains active lead-generation logic.
That is temporary. For now:
assets/lead_block_compatibility_defaults.json as the primary compatibility-mode wording sourceSKILL.mdRegardless of where the detailed method lives, this skill should produce chapter leads that:
Stop and route upstream if any of these are true:
outline/chapter_briefs.jsonl is missingscripts/run.py should currently be treated as a compatibility executor.
Its long-term role after script thinning is narrower:
It is not the long-term home for lead archetypes, bridge examples, or narration anti-patterns.
uv run python .codex/skills/chapter-lead-writer/scripts/run.py --workspace <workspace>--workspace <dir>--unit-id <id>--inputs <a;b;...>--outputs <a;b;...>--checkpoint <C*>uv run python .codex/skills/chapter-lead-writer/scripts/run.py --workspace <workspace>outline/chapter_briefs.jsonl is missing or too thin, rebuild chapter briefs first.outline/writer_context_packs.jsonl is missing, the script will still run but with a thinner citation pool.Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.
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Build and distribute Expo development clients locally or via TestFlight
Use when you have a written implementation plan to execute in a separate session with review checkpoints
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
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Take willoscar/chapter-lead-writer from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.