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npx skills add https://github.com/WILLOSCAR/research-units-pipeline-skills --skill opener-variator
Purpose: fix a high-signal automation tell that survives structural gates:
This skill is intentionally narrow:
Required:
output/WRITER_SELFLOOP_TODO.md (Style Smells section)sections/S<sub_id>.md filesOptional (helps you stay aligned):
outline/writer_context_packs.jsonl (use opener_mode, tension_statement, thesis)Run this targeted pass immediately after style-harmonizer and before logic
polish. The deterministic script is a certification adapter: it refuses to
create the marker while the latest writer-selfloop report still names flagged
files or predates any sections/*.md file. Perform the semantic rewrite through
this Skill or the responsible upstream writer, rerun writer-selfloop, then
retry the adapter. A passing marker records the certified Section-tree SHA256.
sections/S<sub_id>.md files (still body-only; no headings)1) Open output/WRITER_SELFLOOP_TODO.md and locate ## Style Smells.
2) Treat the flagged sections/S*.md list as the *only* scope for this pass.
3) For each flagged file:
outline/writer_context_packs.jsonl and read opener_mode / tension_statement / thesis to stay aligned.subsection-writer or chapter-lead-writer; do not rely on blind local regex passes.4) Rerun writer-selfloop and confirm the Style Smells list shrinks.
You are rewriting the opening paragraph of a survey subsection.
Goal:
- replace narration/overview openers with a content-bearing framing
- vary opener cadence across subsections so the paper reads authored
Constraints:
- do not invent facts
- do not add/remove/move citation keys
- do not change the subsection’s thesis
Checklist:
- sentence 1 is content-bearing (tension/decision/failure/protocol/contrast), not “what we do in this section”
- paragraph 1 ends with a clear thesis/takeaway
- no slide navigation (“Next, we…”, “In this subsection…”, “This section provides an overview…“)
Rewrite immediately if the opener contains any of:
Pick one opener mode per H3 (the writer pack may suggest opener_mode).
Do not copy labels; write as natural prose.
Allowed opener moves (choose 1; keep it concrete):
Bad (overview narration):
This subsection provides an overview of tool interfaces for agents.Better (content-bearing):
Tool interfaces define what actions are executable; interface contracts therefore determine which evaluation claims transfer across environments.Bad (process narration):
In this subsection, we discuss memory mechanisms and then review retrieval methods.Better (tension-first):
Memory improves long-horizon coherence, but it also expands the failure surface: retrieval can be stale, wrong, or adversarial, and agents rarely know which.writer-selfloop still PASSes and Style Smells shrink.uv run python .codex/skills/opener-variator/scripts/run.py --workspace <workspace>--workspace <dir> (required)--unit-id <U###>--inputs <semicolon-separated>--outputs <semicolon-separated>--checkpoint <C#>uv run python .codex/skills/opener-variator/scripts/run.py --workspace workspaces/survey-llm-agentsIntegration 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.
Analyzes job descriptions and generates tailored resumes that highlight relevant experience, skills, and achievements to maximize interview chances
Generate Excalidraw diagrams from natural language descriptions. Use when asked to "create a diagram", "make a flowchart", "visualize a process", "draw a system architecture", "create a mind map", or "generate an Excalidraw file". Supports flowcharts, relationship diagrams, mind maps, and system architecture diagrams. Outputs .excalidraw JSON files that can be opened directly in Excalidraw.
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.
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
Take willoscar/opener-variator 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.