git:20260717.e58a93d to git:20260721.4e88875
10 added, 8 removed. Audit A to A.
# Methods Orchestration Package
## Purpose
`infrastructure.methods` turns existing repo contracts into an explicit methods
orchestration plan:
- pipeline stages and `contract:` metadata from `pipeline.yaml`
- manuscript method sections — a file qualifies when its **name** carries a
method token (`method`/`methodology`/`experimental_setup`/`protocol`) **or**
its body contains a top-level Methods/Methodology/Protocol heading. The
heading fallback covers exemplars whose Methods content lives in a
differently-named section file (e.g. `template_template`'s `03a_architecture.md`).
- `artifact_manifest.json`
- `evidence_registry.json`
- validation commands that prove the methods surface is current
It is a Layer-1 read-only orchestration contract. Do not put scientific
algorithms or project analysis logic here.
## Files
| File | Role |
| --- | --- |
- | `models.py` | Dataclasses for stages, plans, and validation issues. |
- | `orchestration.py` | Plan builder, validator, and Markdown renderer. |
+ | `models.py` | Dataclasses for keyed stages, versioned plans, per-project audits, aggregate reports, and issues. |
+ | `orchestration.py` | Single/batch plan builders, validator, and Markdown renderer using the canonical pipeline-source resolver. |
| `cli.py` | `python -m infrastructure.methods plan` command. |
| `__main__.py` | Module entry point. |
## Contracts
- Preserve the thin-orchestrator pattern: scripts run stages; this package maps
contracts and validation surfaces.
- Keep paths repo-relative in public payloads so generated reports are stable.
- - When a project ships `methods_pipeline.yaml`, that file overrides
- `pipeline.yaml` and the repository default pipeline for plan discovery.
- - `validate_methods_orchestration_plan(..., require_generated_artifacts=True)`
- (default) treats missing artifact manifests and evidence registries as
- publication-blocking errors. Source-only publication audits pass
- `require_generated_artifacts=False`.
+ - Methods source precedence is explicit path, project `methods_pipeline.yaml`,
+ project `pipeline.yaml`, repository definition, then installed package data.
+ - Rendered mode treats missing artifact manifests and evidence registries as
+ publication-blocking errors. Source mode validates authoring contracts only.
+ - Stage `key` is execution identity; human-readable names and name-based
+ dependency declarations remain display/telemetry values.
+ - CLI exits `0` for clean/warnings, `1` for validation errors, and `2` for
+ invalid invocation/configuration.
- Stage `script` values must already be repo-relative paths (`scripts/...` or
`projects/...`); verification commands expand `{project}` only.
## Tests
```bash
uv run pytest tests/infra_tests/methods -q
```