GitHub template for reproducible research repos — two-layer Python 3.10+/uv monorepo splitting generic infrastructure from per-project code, with pytest coverage gates (60% infra, 90% projects), a 17-stage build pipeline, markdown-to-PDF rendering via pandoc/LaTeX, and 24 canonical exemplars.
This repository also configures its own agents. See what template tells them →
Skill Claude CodeCodex
Standards-compliant code for the Research Project Template — infrastructure or project src/, thin orchestrators, type hints, no mocks. USE WHEN implementing an algorithm, utility, analysis method, optimizer, new module in projects//src or infrastructure/, or user says add code following template architecture — even…
Skill Claude CodeCodex needs its repo
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…
Skill Claude CodeCodex
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.
Skill Claude CodeCodex needs its repo
Author or refresh AGENTS.md and README.md for template directories — accurate commands, Mermaid where helpful, link generated/activeprojects.md. USE WHEN folder needs AGENTS, README audit, doc contract fix, or signposting after code change — even without documentationcreation prompt.
Skill Claude CodeCodex needs its repo
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 featureaddition prompt.
Skill Claude CodeCodex
Add or extend generic infrastructure/ packages — Layer 1 modules with SKILL.md, AGENTS.md, tests in tests/infratests/, 60% coverage. USE WHEN new reusable package under infrastructure/, extending validation/rendering/llm, or skill manifest entry — even without infrastructuremodule prompt.
Skill Claude CodeCodex
LLM prompt blocks for per-paper and corpus literature synthesis after a search pipeline. USE WHEN synthesizing arXiv/Crossref results, writing per-paper notes, thematic clusters, gap analysis from a literature corpus, or wiring templatesearchproject synthesis — even without naming infrastructure.llm templates.
Skill Claude CodeCodex needs its repo
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…
Skill Claude CodeCodex needs its repo
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 templatecodeproject exemplar — even without copy-paste prompts.
Skill Claude CodeCodex
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.
Skill Claude CodeCodex needs its repo
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.
Skill Claude CodeCodex needs its repo
Systematic pipeline DAG failure triage for the Research Project Template. USE WHEN ./run.sh or executepipeline.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…
Skill Claude CodeCodex
End-to-end publication-readiness audit for public template exemplars — tests, no-mocks, methods contracts, claims, evidence, figures, references, rendered outputs, and deterministic regeneration. USE WHEN preparing a template or project for release, DOI deposit, peer review, or a publication sign-off.
Skill Claude CodeCodex needs its repo
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.
Skill Claude CodeCodex needs its repo
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.
Skill Claude CodeCodex needs its repo
Full installation and validation workflow for a fresh clone of the Research Project Template. Installs dependencies, runs pre-commit hooks, executes the core pipeline against templatecodeproject, validates outputs, and reports a structured PASS / FAIL for each checkpoint. USE WHEN the user says "start", "set up the…
Skill Claude CodeCodex
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.
Skill Claude CodeCodex
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 validationquality prompt.
Skill Claude CodeCodex needs its repo
Top-level skill for the research template infrastructure layer. Use in Cursor, Claude Code, or similar agents when editing or importing anything under infrastructure/, understanding the two-layer architecture, or wiring build/validation/rendering/publishing. Covers module discovery, import patterns, thin…
Skill Claude CodeCodex
Skill for deterministic AutoResearch readiness planning. Use when adding, validating, or documenting opt-in autoresearch.yaml controls, stage-gate readiness, evidence-grounded claims, artifact readiness reports, or AutoResearchClaw-inspired workflow checks in template projects.
Skill Claude CodeCodex
Deterministic benchmark harnesses for public template exemplars. Use when scoring generated project outputs against benchmark manifests, refreshing the default template smoke manifest, checking publication-readiness rubrics, or adding bounded no-network readiness checks for public template outputs.
Skill Claude CodeCodex
Repository-scoped configuration for the template—environment variable templates and default secure/steganography YAML. Use when editing .env patterns, secureconfig defaults, or cross-referencing project manuscript config overrides.
Skill Claude CodeCodex
Skill for the core infrastructure module providing logging, configuration, exception handling, progress tracking, checkpoints, retry logic, pipeline execution, performance monitoring, security, file operations, and multi-project orchestration. Use when setting up logging, loading config, handling errors, running…
Skill Claude CodeCodex
Unified pipeline telemetry — collects per-stage performance metrics (CPU, memory, I/O) and diagnostic events into structured reports (JSON, text).
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: