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
Container build and compose assets for the research template. Use when reproducing CI or cloud environments with Docker, following docs/CLOUDDEPLOY.md, or wiring Ollama sidecars via docker-compose.
Skill Claude CodeCodex
Skill for the doctor infrastructure module providing repository-level diagnostics and safe, reversible automated repair. Use when the local checkout is acting up, before opening a bug, when onboarding a fresh clone, or as a periodic health probe. Every mutation is backed up under .doctor/backups/ and journalled in…
Skill Claude CodeCodex
Skill for the documentation infrastructure module providing figure management, image handling, markdown integration, and API glossary generation. Use when managing research figures, inserting images into manuscripts, auto-numbering figures, or generating API documentation.
Skill Claude CodeCodex
Skill for the fonds module — discovery, validation, scope, and private-sidecar symlink sync for the top-level fonds/ directory (archival collection units such as bibliographies, contact registries, and dataset catalogs). Use when discovering fonds (discoverfonds), resolving a fond path (resolvefondroot), validating…
Skill Claude CodeCodex
Skill for the LLM infrastructure module providing local Large Language Model integration via Ollama. Covers client initialization, prompt templates, output validation, manuscript review generation, conversation context, and CLI usage. Use when querying LLMs, generating manuscript reviews, validating LLM outputs, or…
Skill Claude CodeCodex
Methods orchestration contract builder for template projects. Use when mapping pipeline stages, manuscript methods, artifact manifests, evidence registries, figures, claim ledgers, experiment plans, and validation commands into one reproducible methods plan.
Skill Claude CodeCodex
Python CLI and menu orchestration for pipeline runs — project slug validation, interactive picker, PipelineRunner wrapping PipelineExecutor, per-stage logs, secure pipeline wrapper. Use when extending run.sh behavior, fixing menu/CLI routing, or testing discovery helpers.
Skill Claude CodeCodex needs its repo
Skill for the project management infrastructure module providing multi-project discovery, structure validation, and metadata extraction. Use when discovering active projects, validating project directory structure, or extracting project configuration metadata.
Skill Claude CodeCodex
Prose analysis utilities for research manuscripts and prose-focused projects. Provides readability metrics (Flesch, Flesch-Kincaid, Gunning Fog), heading-outline structural analysis, editorial quality flags (passive voice, hedge words, citation density, long sentences), aggregate ManuscriptReport across a manuscript…
Skill Claude CodeCodex needs its repo
Content-addressed provenance DAG for research lineage tracking. Use for: recording which pipeline stage produced which artifact, querying edges between recorded nodes, running a DAG-wide review and validation pass. CLI: python -m infrastructure.provenance {list,record-artifact,review,validate}. Library…
Skill Claude CodeCodex
Skill for the publishing infrastructure module providing academic publishing workflows including BibTeX CLI citation generation, APA/MLA citation helper functions, DOI management, Zenodo publication, arXiv submission preparation, GitHub releases, PyPI and TestPyPI package distribution, static-site deployment to GitHub…
Skill Claude CodeCodex
Bibliographic-reference utilities for research projects. Read, write, and convert BibTeX entries that match the syntax/semantics of projects/templates/templatecodeproject/manuscript/references.bib (consumed by Pandoc with --natbib during PDF render -- see infrastructure/rendering/pdfcombinedpandoc.py). Exposes the…
Skill Claude CodeCodex
BibTeX read/write/convert that matches the syntax/semantics of projects/templates/templatecodeproject/manuscript/references.bib (consumed by Pandoc with --natbib -- see infrastructure/rendering/pdfcombinedrenderer.py). Provides BibEntry/BibDatabase models, parsebibfile/renderdatabase functions, papertobibentry…
Skill Claude CodeCodex
Deterministic anti-hallucination gate for cited references. Resolves each entry in a manuscript .bib file against Crossref, OpenAlex, and arXiv; flags fabricated (identifier resolves to nothing), mismatched (title/author/year disagree), unverifiable (no identifier), unchecked (offline cache miss — never silently OK)…
Skill Claude CodeCodex needs its repo
Skill for the rendering infrastructure module providing multi-format output generation including PDF manuscripts, HTML web pages, and Beamer/Reveal.js slides. Use when rendering research outputs, converting markdown to PDF, generating slides, or configuring LaTeX rendering.
Skill Claude CodeCodex
Skill for the reporting infrastructure module providing pipeline reporting, error aggregation, executive summaries, dashboard generation, test reporting, and multi-project reports. Use when generating build reports, aggregating errors, creating visual dashboards, or producing executive summaries across projects.
Skill Claude CodeCodex needs its repo
Seven-stage research workflow (SCOPE→LITERATURE→REASON→DESIGN→COMPUTE→SYNTHESIZE→WRITE). Use for: structuring an AI agent's research process, generating literature review prompts, scoping methodology. Usage: from infrastructure.research import ResearchWorkflow; ResearchWorkflow.describe() Config: set stage overrides…
Skill Claude CodeCodex
Skill for the rules module — discovery, validation, scope, and private-sidecar symlink sync for the top-level rules/ directory (specifications include soft markdown guidelines and strong yaml/json formal constraints). Use when discovering rules (discoverrules), resolving a rule path (resolveruleroot), validating rule…
Skill Claude CodeCodex
Skill for the scientific infrastructure module providing numerical stability checks, performance benchmarking, and independent improvement confirmation. Use when benchmarking functions, checking numerical stability, or confirming a candidate beats a baseline beyond the noise band.
Skill Claude CodeCodex
Discovery utilities. Hosts subpackages — literature for Paperclip-style multi-source academic search; exa for Exa-backed web search, contents, answers, and find-similar; monid for the Monid gateway (discover/inspect/run) plus offline USD-per-1k search API pricing; and deepresearch for provider-neutral long-running…
Skill Claude CodeCodex needs its repo
Search 8+ scientific databases through a uniform Connector interface. Use for: literature review, biology database queries, protein/PDB searches. CLI: python -m infrastructure.search.connectors {list-dbs,search}. Config: set queries in projects/{name}/manuscript/config.yaml connectorsearch: block. Orchestrator…
Skill Claude CodeCodex
Paperclip-style multi-source literature search across arXiv, Crossref, local JSON corpora, and (opt-in) the Paperclip API. Provides Paper/SearchQuery/SearchResult data models, a LiteratureClient aggregator with per-backend failure isolation, DOI/arXiv-aware deduplication via mergepapers, deterministic JSON caching via…
Skill Claude CodeCodex
Monid HTTP API client for discovering, inspecting, and running hundreds of data endpoints through one wallet (discover/inspect/run/poll/balance). Includes an offline USD-per-1k comparison table for direct search APIs (Exa, Brave, Tavily, Serper, SerpAPI) versus Monid's per-endpoint gateway pricing. Use when the user…
Skill Claude CodeCodex needs its repo
Skill for the Self-Improvement Agent (SIA) harness contract. Use when validating task public/private layouts, generation artifact trees, evaluation runners, fixture replay loops, or opt-in live Meta→Target→Feedback cycles in template projects.
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: