Harden CLI information architecture, protocol semantics, and maintainer workflows

[e-south]

Summary

• harden the CLI preflight and execution surfaces so inspect, validate, explain, dry-run, and records flows stay explicit and less drift-prone
• add reader-owned SFXI plot surfaces for setpoint scatter and the triptych sequence review bundle while keeping dnadesign behind public optional APIs
• add a neutral dual-reporter triptych notebook/template surface so assay visualization can be reused without coupling it to SFXI-specific semantics
• refresh maintainer docs/specs and keep the repo format/doc/test gates green

What changed

• added plot/sfxi_setpoint_scatter and plot/sfxi_triptych_sequence, with protocol exposure through logic/sfxi_screen
• split the triptych implementation into reader domain assembly, a narrow dnadesign/BaseRender/USR adapter, and artifact publication helpers
• added atomic bundle staging for poster/PDF/index/manifest/movie/frame outputs and canonical records support
• added dry-run dependency preflight so missing/incompatible dnadesign APIs fail before execution with actionable messages
• added dual_reporter_triptych notebook assets and refactored sfxi_eda to use the shared notebook primitive
• isolated the formatter cleanup for tools/audit_repo_skills.py after the repo format gate exposed it

Validation

• uv run pytest -q src/reader/tests/domains/logic/sfxi/test_setpoint_scatter.py src/reader/tests/plugins/plot/test_sfxi_setpoint_scatter.py src/reader/tests/plugins/plot/test_sfxi_triptych_sequence.py src/reader/tests/notebooks/test_dual_reporter_triptych.py src/reader/tests/notebooks/test_templates.py src/reader/tests/workbench/test_assets.py src/reader/tests/cli/test_plot_export.py src/reader/tests/cli/test_ux.py (125 passed)
• uv run ruff check .
• uv run ruff format . --check
• uv run python tools/check_docs.py
• git diff --check
• uv run pytest -q (386 passed, 24 deselected)

Audit notes

• implementation imports only public dnadesign surfaces; the only dnadesign.*.src.* matches are docs/spec text forbidding private imports
• SFXI persisted columns keep the canonical objective names logic_fidelity and effect_scaled, without compatibility alias columns
• ignored experiment preview outputs were left untracked; the commit set contains source, tests, and docs only

[codecov]

Codecov Report

❌ Patch coverage is 75.25662% with 458 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
...ader/workbench/notebooks/dual_reporter_triptych.py	56.21%	75 Missing and 13 partials ⚠️
src/reader/domains/logic/sfxi/triptych_sequence.py	77.38%	48 Missing and 28 partials ⚠️
.../domains/logic/sfxi/triptych_sequence_dnadesign.py	48.78%	39 Missing and 3 partials ⚠️
...er/domains/logic/sfxi/triptych_sequence_outputs.py	53.48%	33 Missing and 7 partials ⚠️
src/reader/workbench/dop/model.py	70.17%	24 Missing and 10 partials ⚠️
src/reader/domains/logic/sfxi/setpoint_scatter.py	73.55%	18 Missing and 14 partials ⚠️
src/reader/workbench/cli/_surface_execution.py	81.65%	22 Missing and 9 partials ⚠️
src/reader/workbench/notebooks/_launch_registry.py	70.58%	11 Missing and 9 partials ⚠️
src/reader/workbench/inspection/dop.py	39.28%	17 Missing ⚠️
...reader/domains/plate_reader/analysis/timepoints.py	11.11%	16 Missing ⚠️
... and 13 more

📢 Thoughts on this report? Let us know!