template-methods-paper

Project-scoped skill for the in-repo exemplar at projects/templates/template_methods_paper/. Load this when working inside the project.

When to Use

• Working inside the template_methods_paper exemplar — running scripts, editing source,

or regenerating outputs.

• Forking this exemplar as the starting scaffold for a new research project.
• Validating that the exemplar's contracts (thin-orchestrator, layer boundaries,

no-mocks testing) still hold after changes.

Quick Reference

bash
# From the repository root
uv run pytest projects/templates/template_methods_paper/tests --cov=projects/templates/template_methods_paper/src --cov-fail-under=90
uv run python scripts/pipeline/stage_02_analysis.py --project templates/template_methods_paper
uv run python scripts/pipeline/stage_03_render.py --project templates/template_methods_paper
uv run python scripts/pipeline/stage_04_validate.py --project templates/template_methods_paper
uv run python scripts/pipeline/stage_05_copy.py --project templates/template_methods_paper

Pitfalls

• Keep scripts thin. Business logic belongs in src/ or shared

infrastructure/, not in scripts/.

• No mocks. All tests must use real data, real files, and real

computation.

• Outputs are disposable. Never hand-edit output/ — regenerate from

source and config.

• Figure provenance is part of analysis. methods_analysis.py validates

step_counts.png against src/figure_specs.py before writing output/figures/figure_registry.json.

• Run from the repo root. Commands assume the template monorepo root

as working directory unless the child AGENTS.md states otherwise.

Cross-refs

• Project contract: AGENTS.md
• README: README.md
• TODO: TODO.md
• Exemplar roster: projects/AGENTS.md