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infrastructure-overview

Skill20 starsChanged 2 months agoApache-2.0View on GitHub

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 orchestrators, per-subpackage SKILL.md paths, and .cursor/skill_manifest.json (see infrastructure.skills).

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Files
SKILL.md

Infrastructure Layer

The infrastructure/ package provides generic, reusable functionality for research projects. All business logic resides here (Layer 1) or in project-specific src/ (Layer 2). Scripts are thin orchestrators that coordinate these modules.

Finding skills (Cursor and other agents)

  • Hub: This file lists every subpackage skill and a module map.
  • Manifest: .cursor/skill_manifest.json lists every discovered first-party skill (name, description, path); regenerate with uv run python -m infrastructure.skills write.
  • Search: default discovery covers infrastructure/**/SKILL.md, scripts/**/SKILL.md, public projects/templates/**/SKILL.md including .agents/skills, public resource-pool template skills under fonds/templates/, rules/templates/, and tools/templates/, plus .cursor/skills/.
  • In Cursor: @infrastructure/SKILL.md or @infrastructure/<module>/SKILL.md to load context; pair with the matching AGENTS.md for API tables.
  • Frontmatter: Each SKILL.md has YAML name and description for routing (see also the table in infrastructure/README.md).

Module Map

ModulePurposeKey Imports
autoresearch/Deterministic research plans, stage-gate readiness, artifact/evidence reportsbuild_autoresearch_plan, validate_autoresearch_plan
benchmark/Deterministic benchmark manifests and public exemplar readiness scoringrun_benchmark_manifest, score_project_against_manifest
config/Repo defaults (.env.template, secure_config.yaml)(YAML/dotenv; use core.config_loader)
core/Logging, config, exceptions, pipeline, progress, retry, securityget_logger, load_config, PipelineExecutor
docker/Dockerfile, docker-compose.yml for container runs(CLI / docs/CLOUD_DEPLOY.md)
validation/PDF/Markdown/output validation, link checking, auditsvalidate_pdf_rendering, validate_markdown, verify_output_integrity
rendering/Multi-format output (PDF, HTML, slides)RenderManager, RenderingConfig
documentation/Figure/image management, markdown integration, glossaryFigureManager, ImageManager, MarkdownIntegration
llm/Local LLM integration via OllamaLLMClient, OllamaClientConfig, detect_repetition, check_format_compliance
methods/Methods orchestration plans over DAG, manuscript methods, artifacts, and evidencebuild_methods_orchestration_plan, validate_methods_orchestration_plan
orchestration/Pipeline CLI, menu, project discovery, stage logging, secure-run wrapper (backs run.sh/secure_run.sh)build_parser, PipelineRunner, validate_project_slug, run_secure_pipeline
publishing/Academic publishing (DOI, citations, Zenodo, arXiv)publish_to_zenodo, generate_citation_bibtex
reference/BibTeX I/O (read / write / convert) matching references.bib syntaxparse_bibfile, render_database, paper_to_bibentry
search/Paperclip-style multi-source literature search (arXiv, Crossref, local, Paperclip)LiteratureClient, SearchQuery, ArxivBackend, CrossrefBackend
prose/Prose analysis (readability, structure, editorial quality, manuscript reports)analyze_manuscript, compute_metrics, analyze_structure, analyze_quality
reporting/Pipeline reports, error aggregation, dashboardsgenerate_pipeline_report, get_error_aggregator
scientific/Benchmarking, numerical stability, scientific templatesbenchmark_function, check_numerical_stability
sia/SIA harness: task layout, fixture replay loop, evaluation runnervalidate_task_dir, run_sia_loop, run_evaluation
project/Multi-project discovery and validationdiscover_projects, validate_project_structure
skills/Enumerate and parse SKILL.md; maintain Cursor manifestdiscover_skills, write_skill_manifest
steganography/Cryptographic PDF watermarking and verificationSteganographyProcessor, SteganographyConfig, embed_steganography
core/telemetry/Unified pipeline telemetry (stage resources + diagnostics, JSON/text reports)TelemetryCollector, TelemetryConfig

Import Patterns

# Convenience imports (exported on infrastructure package root)
from infrastructure import get_logger, load_config, TemplateError

# Direct submodule imports (recommended for clarity)
from infrastructure.core import CheckpointManager
from infrastructure.core.pipeline import PipelineExecutor
from infrastructure.rendering import RenderManager
from infrastructure.llm.core.client import LLMClient
from infrastructure.methods import build_methods_orchestration_plan
from infrastructure.validation import validate_markdown, validate_pdf_rendering
from infrastructure.skills import discover_skills

# In project scripts (thin orchestrator pattern)
from infrastructure.core.logging.utils import get_logger
from infrastructure.validation import validate_pdf_rendering

Architecture Principles

  1. Thin Orchestrator Pattern — Scripts import from infrastructure; never implement business logic
  2. No Mocks Policy — All tests use real data and computations
  3. Test Coverage — Infrastructure requires 60%+ coverage
  4. Exception Hierarchy — All errors extend TemplateError from infrastructure.core.exceptions
  5. Unified Logging — Always use get_logger(__name__) for consistent output

Common Workflows

Running Infrastructure Tests

uv run pytest tests/infra_tests/ --cov=infrastructure --cov-fail-under=60

Using the Pipeline

uv run python scripts/runner/execute_pipeline.py --project template_code_project --mode core

Validating Outputs

uv run python -m infrastructure.validation.cli markdown projects/templates/template_code_project/manuscript/
uv run python -m infrastructure.validation.cli pdf --project templates/template_code_project --repo-root .

Submodule Skills

Each subpackage has a SKILL.md (YAML frontmatter + body) for agent discovery—search the repo for infrastructure/**/SKILL.md or open paths below:

  • infrastructure/config/SKILL.md — Repo configuration templates and secure defaults
  • infrastructure/autoresearch/SKILL.md — Deterministic AutoResearch readiness planning
  • infrastructure/benchmark/SKILL.md — Deterministic public exemplar benchmark harnesses
  • infrastructure/core/SKILL.md — Foundation utilities
  • infrastructure/docker/SKILL.md — Container build and compose
  • infrastructure/doctor/SKILL.md — Repository diagnostics and audited repairs
  • infrastructure/documentation/SKILL.md — Figure and doc management
  • infrastructure/llm/SKILL.md — LLM integration
  • infrastructure/methods/SKILL.md — Methods orchestration plans
  • infrastructure/orchestration/SKILL.md — Pipeline CLI, menu, and runner orchestration
  • infrastructure/prose/SKILL.md — Manuscript prose quality analysis
  • infrastructure/project/SKILL.md — Project discovery and validation
  • infrastructure/publishing/SKILL.md — Academic publishing
  • infrastructure/reference/SKILL.md — Bibliographic reference workflows
  • infrastructure/reference/citation/SKILL.md — BibTeX read/write/convert subpackage
  • infrastructure/rendering/SKILL.md — Output generation
  • infrastructure/reporting/SKILL.md — Pipeline reporting
  • infrastructure/scientific/SKILL.md — Scientific computing
  • infrastructure/search/SKILL.md — Literature discovery and search workflows
  • infrastructure/search/literature/SKILL.md — Academic literature-search subpackage
  • infrastructure/sia/SKILL.md — Self-Improvement Agent harness contracts
  • infrastructure/skills/SKILL.md — Programmatic skill discovery and manifest I/O
  • infrastructure/steganography/SKILL.md — Secure PDF post-processing
  • infrastructure/core/telemetry/SKILL.md — Unified pipeline telemetry (nested under core/)
  • infrastructure/reference/verification/SKILL.md — Reference-existence verification gate
  • infrastructure/validation/SKILL.md — Quality assurance

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