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
Programmatic discovery of agent SKILL.md files under configured public repo roots (infrastructure, scripts, projects/templates, resource-pool templates, docs/prompts, .agents/skills, and .cursor/skills). Use when enumerating skills, validating .cursor/skillmanifest.json, writing docs/generated/skillsindex.md, checking…
Skill Claude CodeCodex needs its repo
Skill for the steganography infrastructure module providing QR code generation with dynamic mailto links, hash manifests, metadata payloads, and document-wide overlay processing. Use this module to insert opt-in cryptographic and steganographic provenance data onto PDFs.
Skill Claude CodeCodex
Skill for the tools module — discovery, validation, scope, and private-sidecar symlink sync for the top-level tools/ directory (executable entry points such as scripts, skills, and agents stored as passive manifests with scripts/ directories). Use when discovering tools (discovertools), resolving a tool path…
Skill Claude CodeCodex needs its repo
Skill for the validation infrastructure module providing PDF validation, markdown validation, output integrity checks, link verification, documentation audits, issue categorization, and repository scanning. Use when validating research outputs, checking document quality, running audits, or verifying cross-references.
Skill Claude CodeCodex
Use when auditing public research exemplars for deterministic publication readiness across tests, methods, evidence, artifacts, figures, manuscript sources, and generated outputs.
Skill Claude CodeCodex needs its repo
Active Inference multi-track exemplar — analytical formulas, pymdp simulation, sheaf manuscript composition, GNN, ontology, Lean gates, roadmap tracks.
Skill Claude CodeCodex needs its repo
Multi-phase literature-review exemplar with phase-aware retrieval, filtering, provenance, and cross-phase validation.
Skill Claude CodeCodex
Phase-aware tooling for injecting advanced-review evidence and statistics into Markdown manuscript templates.
Skill Claude CodeCodex
Combinatoric grammar that deterministically generates whole runnable child projects (src/, tests/, scripts/, manuscript/) from a seed — recompute-based provenance verification and a falsifiable honesty manifest against green-by-construction test theater.
Skill Claude CodeCodex needs its repo
AutoResearch loop exemplar — deterministic ML candidate evaluation, evidence registries, claim ledgers, artifact manifests, readiness gates.
Skill Claude CodeCodex needs its repo
AutoScientists coordination-mechanism testbed — dead-end registry, noise-band confirmation, effect-size ranking, stagnation-driven reorganization, honest null reporting.
Skill Claude CodeCodex needs its repo
Code-centric optimization research exemplar — gradient descent, convergence analysis, automated figures, dashboard, and publication-quality PDF.
Skill Claude CodeCodex needs its repo
FAIR data descriptor exemplar for schema, provenance, license, and dataset release-readiness validation.
Skill Claude CodeCodex needs its repo
Exploratory data analysis notebook exemplar — notebook-to-src extraction workflow, tested EDA library, deterministic dataset, diagnostic figures.
Skill Claude CodeCodex needs its repo
Strongly-typed multiagent ant-robot colony exemplar — ADTs, session-typed protocols, affine-discipline resource handles, storage-as-functor framing, Active-Inference-flavored decision loop, mypy-as-oracle negative controls.
Skill Claude CodeCodex needs its repo
Metallurgical gold-refining analogy for manuscript composition — ore/smelting/assaying/cupellation/certification with mega-madlib token injection.
Skill Claude CodeCodex needs its repo
Literature meta-analysis exemplar — multi-engine retrieval, dedup, full-text, bibliometrics, embeddings, optional knowledge graph. Default term: modafinil.
Skill Claude CodeCodex
Core orchestration guidelines and MCP interactions for the src/ library.
Skill Claude CodeCodex
Orchestration for bibliometrics, topological network analysis, and hypothesis scoring.
Skill Claude CodeCodex
Core inference logic, prompt construction, and RDF/Nanopublication serialization.
Skill Claude CodeCodex
LLM-based extraction of per-paper workflow graphs and content/structural reproducibility scoring.
Skill Claude CodeCodex
Orchestrates matplotlib and seaborn pipelines for rendering figures.
Skill Claude CodeCodex needs its repo
Deterministic token-injection manuscript generator — config-owned lexicon, conditional IMRAD, QA probes, authoring contract, and token provenance.
Skill Claude CodeCodex needs its repo
Methods-paper exemplar — controlled-method specification DSL with staged validation, deterministic compilation, informed by BPL.
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: