Infrastructure Module Reference

This section inventories every Layer‑1 subdirectory returned by 31 discover_infrastructure_modules(repo_root). File totals use 1335 Python sources across infra + 12,564 infra tests guarding them. Documentation Duality = paired README.md + AGENTS.md; optional SKILL.md manifests feed python -m infrastructure.skills.

Alphabetical summaries

Below, ${module_*_python_file_count} placeholders expand per subdirectory at render-time.

infrastructure.autoresearch (11 files)

Readiness planner, validation CLI, and report models for AutoResearch-style project promotion (infrastructure/autoresearch/).

infrastructure.benchmark (4 files)

Template harness scoring and comparative gate helpers exercised in CI smoke paths.

infrastructure/config (non-package subdirectory)

Repository-wide YAML templates and secure manifests (.env.template, hardened defaults referenced by Docker + CLI). config/ carries no __init__.py, so it is a configuration subdirectory rather than an importable package.

infrastructure.core (201 files)

Checkpointing, logging, pipeline YAML parsing, telemetry bridges, filesystem helpers, hardened exceptions. Everything else imports logging + error taxonomy from here first.

infrastructure.doctor (14 files)

Checkout diagnose/fix/undo repairs for broken local workspace states.

infrastructure.docker (0 files)

Pinned images / compose scaffolding for reproducible CI + remote builds.

infrastructure.documentation (23 files)

Figure registries plus glossary tooling feeding manuscript automation.

infrastructure.formal_contracts (5 files)

Typed, machine-checkable manuscript contract layer: frozen block model, evidence-tier policies, monoidal composition, and a fail-closed checker with stable FORMAL.* diagnostics.

infrastructure.fonds (6 files)

Resource pool management for curated fonds (tracked reference datasets, bibliographic collections, and evidence corpora). Fonds mirror projects/templates/ with git-tracked templates/* exemplars and sidecar-linked private lifecycle folders.

infrastructure.llm (57 files)

Ollama integrations, sanitization adapters, templated reviewer flows. Literature ingestion now lives primarily in search/literature + citation helpers in reference/.

infrastructure.metadata (3 files)

Shared publication-metadata leaves: repository-URL normalization (normalized_repository_url) and ebook metadata package generation (ONIX, metadata.json, EPUB OPF). Consumed by publishing, rendering, documentation, and project layers; extracted from publishing by RENDERING-LAYERING-1 so renderers import it without an inverted publishing dependency.

infrastructure.methods (10 files)

Deterministic methods-orchestration contracts (MethodStage, MethodsOrchestrationPlan, MethodsIssue): builds and validates an ordered methods plan for a research project so the manuscript’s “Methods” track stays bound to executable stages.

infrastructure.orchestration (14 files)

python -m infrastructure.orchestration exposes interactive menus, subprocess wiring for thin shell wrappers (run.sh, secure_run.sh), and stubs used in CI for menu parsing tests.

infrastructure.project (116 files)

Canonical discovery (discover_projects) enforcing src/ + tests/, slug validation, nested WIP namespaces.

infrastructure.prose (9 files)

Readability metrics + Markdown tooling for prose-centric manuscripts / CI gates.

infrastructure.provenance (9 files)

Content-addressed provenance DAG. Records artifact lineage (which run produced which file, from which inputs) as a verifiable graph of artifact/run/source/claim nodes connected by produced/consumed/derived-from/supports/refutes edges. Includes a structured Review system with severity (blocking/major/minor/info) and verdict (refutes/supports). Features a CLI and pipeline integration hooks for automatic lineage recording after every stage.

infrastructure.publishing (85 files)

Metadata models, APA/BibTeX/MLA formatters, optional Zenodo clients.

infrastructure.reference (16 files)

Citation/BibTeX parsing + conversion utilities leveraged by manuscripts and retrieval scripts.

infrastructure.rendering (121 files)

Pandoc shim, Unicode/XeLaTeX postprocessors, combined PDF/HTML/slide exporters.

infrastructure.reporting (412 files)

Parses pytest + coverage artefacts for dashboards; pairs with Stage 01 summaries and downstream executive exports.

infrastructure.research (3 files)

Seven-stage research workflow (SCOPE → LITERATURE → REASON → DESIGN → COMPUTE → SYNTHESIZE → WRITE) defined as typed ResearchStage data classes with explicit outputs, skills, and template commands per stage. Includes a full PRISMA-adapted literature review prompt and a research workflow prompt referencing template/ infrastructure commands.

infrastructure.rules (6 files)

Governance rules layer for validating project lifecycle transitions, sidecar sync policies, and pipeline gate orchestration. Rules mirror projects/templates/ with git-tracked templates/* exemplars.

infrastructure.scientific (4 files)

Stability probing, benchmarking hooks—consumed heavily by optimization exemplars (template_code_project scripts).

infrastructure.search (77 files)

Two-tier search architecture: the literature/ client stack (client.py, backends, caches) powers literature search with arXiv, Crossref, local, and Paperclip backends. connectors/ exposes the built-in scientific database adapters through a uniform ConnectorRegistry; OpenAlex, UniProt, PDB, Semantic Scholar, European PMC, bioRxiv, and other registered adapters share list/search CLI commands with HTTP timeout, retry, and TTL caching. monid/ provides an opt-in paid gateway (discover / inspect / run) with offline USD/1k pricing reference in monid/PRICING.md. deep_research/ dispatches long-horizon provider-neutral manuscript research (PAID, opt-in). The live registry, not this prose, is authoritative for connector count.

infrastructure.sia (10 files)

Generic Self-Improving-AI loop utilities: task-layout validation, execution harness, and metric capture reused by template_sia (fixture-replay by default).

infrastructure.skills (8 files)

Discovers SKILL.md frontmatter → .agents/skill_manifest.json.

infrastructure.steganography (13 files)

Watermark overlays, hashing companions triggered by secure pipeline path.

infrastructure.tools (6 files)

Invocable tool definitions registered by resource-pool governance; tools mirror projects/templates/ with git-tracked templates/* exemplars.

infrastructure.transmission (6 files)

Rendered-release transmission leaves: LaTeX single-page bookends (transmission_bookends), page-check validation for Stage 04 (transmission_page_check), barcode strips, figure embedding, and shared models. Consumed by the publishing release workflow; regular package so the documentation module-reference guard resolves nested refs on disk.

infrastructure.validation (86 files)

Markdown + PDF + integrity CLIs underpinning Stage 04 diagnostics.

infrastructure/logrotate.d (0 files)

Operational templates for deployments (documentation-first; intentionally minimal Python footprint).

Documentation maturity: Coverage statements in Results pull from introspection—not hand-maintained denominators—so newly promoted modules automatically flow into manuscripts after generate_manuscript_metrics.py.

FAIR+RSE linkage: MCP-ready SKILL.md artefacts align with evaluator heuristics (executability + metadata richness) emphasized by FAIRsoft guidance [garijo2024fairsoft].