template-manuscript-creation
Scaffold a research manuscript and project layout from a research brief — sections, config.yaml, src/, scripts/, tests. USE WHEN starting a new paper, new projects/ tree, manuscript from topic description, or aligning with template_code_project exemplar — even without copy-paste prompts.
Best use case
template-manuscript-creation is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
Scaffold a research manuscript and project layout from a research brief — sections, config.yaml, src/, scripts/, tests. USE WHEN starting a new paper, new projects/ tree, manuscript from topic description, or aligning with template_code_project exemplar — even without copy-paste prompts.
Teams using template-manuscript-creation should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/manuscript-creation/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How template-manuscript-creation Compares
| Feature / Agent | template-manuscript-creation | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
Scaffold a research manuscript and project layout from a research brief — sections, config.yaml, src/, scripts/, tests. USE WHEN starting a new paper, new projects/ tree, manuscript from topic description, or aligning with template_code_project exemplar — even without copy-paste prompts.
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
Related Guides
SKILL.md Source
# Manuscript creation ## Natural invoke - "Create a new optimization research project and manuscript from this brief" - "Scaffold projects/my_topic/ like template_code_project" - "I have a research idea — set up manuscript + src + tests" ## Inputs to confirm - **Research topic** — objectives, methods, expected contributions (user provides). - **Exemplar** — default [`projects/templates/template_code_project/`](../../../projects/templates/template_code_project/); Active Inference multi-track → `template_active_inference`; prose → `template_prose_project`; AutoResearch/readiness loop → `template_autoresearch_project`; meta-template / infrastructure introspection → `template_template`; search → local `template_search_project` from archive. Roster: [`projects/AGENTS.md`](../../../projects/AGENTS.md#permanent-canonical-exemplars-and-optional-search-add-on). - **Cross-ref style** — Pandoc-crossref vs registry tokens (pick one; see [manuscript-cross-references](../manuscript-cross-references/SKILL.md)). ## Workflow 1. **Copy exemplar shape** — match section numbering (`01_*` vs `00_*`), not generic skeleton if exemplar differs. 2. **Manuscript files** — `config.yaml`, `preamble.md`, `references.bib`, ordered `*.md` sections, glossary/references as exemplar does. 3. **Cross-refs** — Pandoc: `@fig:`, `@eq:`, `@sec:`, `[@key]` per [`docs/guides/manuscript-semantics.md`](../../guides/manuscript-semantics.md). Registry: `refs/labels.yaml` + `[[FIG:]]` tokens. 4. **`src/`** — typed public APIs, `get_logger`, fixed seeds, custom exceptions where needed. 5. **`scripts/`** — thin orchestrators only; `MPLBACKEND=Agg`; print output paths. 6. **`tests/`** — no mocks; ≥90% on `projects/<name>/src`. 7. **Docs** — project AGENTS.md + README.md; link active_projects doc, do not hard-code roster. 8. **One-shot alternative** — for LLM scaffold of entire tree, see [`docs/guides/new-project-one-shot-prompt.md`](../../guides/new-project-one-shot-prompt.md). ## Deliverables - Full `projects/<name>/` tree or delta from brief - How to run: `uv run pytest projects/<name>/tests/ --cov=...` and `uv run python scripts/01_run_tests.py --project <name>` ## Verification commands ```bash uv sync uv run python scripts/01_run_tests.py --project <name> uv run python -m infrastructure.validation.cli markdown projects/<name>/manuscript/ ``` ## When NOT to use - **Existing manuscript claim audit** → [manuscript-claim-verification](../manuscript-claim-verification/SKILL.md) - **Cross-ref-only fixes** → [manuscript-cross-references](../manuscript-cross-references/SKILL.md) ## References Section checklist and legacy examples: [references/structure-checklist.md](references/structure-checklist.md)
Related Skills
template-validation-quality
Run validation CLI, prerender, markdown/PDF/integrity gates, and QA workflows for the Research Project Template. USE WHEN validate manuscript, check PDF for ?? refs, prerender gate, link checker, output integrity, or pre-commit validation — even without validation_quality prompt.
template-test-creation
Create pytest suites under the no-mocks policy — real data, temp files, subprocess, pytest-httpserver. USE WHEN adding tests, raising coverage, testing new src/ module, or user forbids mocks.
template-reproducibility-audit
Deterministic reproducibility audit — fixed seeds, regenerate-from-clean, double-run diff before Zenodo/arXiv/release. USE WHEN outputs drift between runs, "worked on my machine", need regenerate-from-clean proof, or pre-release reproducibility check — even without naming docs/prompts.
template-refactoring
Clean-break refactors with migration for the Research Project Template — move logic to src/, split modules, rename APIs with test updates. USE WHEN restructuring code, extracting modules, removing duplication, or migration without behavior change.
template-pipeline-debugging
Systematic pipeline DAG failure triage for the Research Project Template. USE WHEN ./run.sh or execute_pipeline.py fails, a stage stalls (setup, tests, analysis, render, validate, LLM, copy), pytest/coverage gate fails mid-pipeline, PDF render or validate breaks, Project Analysis finishes too fast with no figures, or user says pipeline debug, stage failed, resume checkpoint, core-only triage — even without naming this skill or docs/prompts.
template-methods-orchestration
Repo-wide methods orchestration workflow for the Research Project Template. USE WHEN the user asks to add, audit, improve, or validate methods, methodology, method contracts, stage-to-method wiring, artifact/evidence provenance, or orchestration across template projects.
template-manuscript-cross-references
Audit or author registry-driven manuscript cross-refs — labels.yaml, [[FIG:]], [[THMREF:]], [[VAR:]] tokens. USE WHEN fixing figure/equation/theorem numbering, orphan registry keys, hard-coded "Theorem 7.3" in prose, or [[MISSING:]] injection failures — even for Pandoc projects that also use a YAML registry.
template-manuscript-claim-verification
Triple-pass verification of every manuscript claim against code, data, refs, and renderer; repair prose while staying renderable. USE WHEN pre-submission, pre-Zenodo, pre-arXiv, abstract numbers disagree with CSV, citations do not support sentences, or user asks to triple-check / verify every claim — even without docs/prompts. Not for casual PDF summary.
template-feature-addition
End-to-end feature work across src/, scripts/, tests/, manuscript, and docs for the Research Project Template. USE WHEN adding a pipeline-visible feature, new analysis stage, manuscript-facing output, or cross-layer integration — even without feature_addition prompt.
template-documentation-creation
Author or refresh AGENTS.md and README.md for template directories — accurate commands, Mermaid where helpful, link _generated/active_projects.md. USE WHEN folder needs AGENTS, README audit, doc contract fix, or signposting after code change — even without documentation_creation prompt.
template-deep-research
Template-native research intake, literature search, source verification, synthesis, fact-checking, and systematic-review planning. USE WHEN the user asks to research a topic, build a literature corpus, fact-check claims, prepare a PRISMA-style review, or clarify a research question before manuscript work.
template-comprehensive-assessment
Full checkout audit for the Research Project Template — tests, architecture, docs, manuscript, pipeline. USE WHEN user asks for comprehensive assessment, full repo review, health check across projects, audit everything, or pre-merge sanity sweep for template exemplars — even without naming docs/prompts or a skill. Not for single failing stage only.