feat: strip PyAutoEyes to the organ skeleton — registry, eyes/ package, pyauto-eyes, Pages (PyAutoEyes 1b)

[Jammy2211]

Overview

Phase 1b of the pyautoeyes-birth epic. Under the layered design (human decision 2026-09-28), each <lib>_visualization project repo makes, stores and tracks its figures; the organ PyAutoEyes becomes the cross-project dashboard over them. This task strips PyAutoEyes of the lens gallery content that phase 1a (#446) moved to PyAutoLabs/autolens_visualization, and builds the organ skeleton: registry.yaml, the versioned manifest contract, the eyes/ package, bin/pyauto-eyes, and the Pages dashboard workflows. The organ renders nothing, copies no figures, never judges, and never edits library plot code.

Plan

• Strip (commit 1, reviewable alone): delete producers, simulators, dataset/, tracked PNGs, GALLERY.md, instruments/, config/, gallery/, _viz_cli.py, activate.sh, lint.yml/render.yml. The history is preserved in git and on PyAutoLabs/autolens_visualization (refs/heads/main 8f3e712).
• Skeleton (commit 2): registry.yaml (lens row only), REFERENCE.md (manifest contract schema 1), the eyes/ package (registry, manifest reader, board builder), bin/pyauto-eyes (board, check, survey), organ prose stating the layering and boundary, hermetic tests, and the workflows lint.yml, pages_dashboard.yml and dashboard_refresh.yml (repository_dispatch eyes-refresh plus a daily cron, the Cortex pattern).
• Brain (one change): replace the PyAutoEyes WITNESS_EXEMPT entry in tests/test_policy_seams.py with a pyautoeyes: PyAutoEyes/tests row in the config/policy.yaml test_witness map.
• Ship order: PyAutoEyes first, then PyAutoBrain. PRs wait until PyAutoMind#447 (phase 1a) is merged. Merge stays human.

Detailed implementation plan

Affected Repositories

• PyAutoEyes (primary)
• PyAutoBrain (witness row only)

Branch Survey

Repository	Current Branch	Dirty?
./organs/PyAutoEyes	main (8f3e712 = origin)	clean
./organs/PyAutoBrain	main	clean

worktree_check_conflict: PyAutoEyes is free. PyAutoBrain is claimed by eyes-organ-order (#439) and autolens-visualization-rebirth (#446). A parallel claim was human-approved in-session on 2026-09-28. The files do not overlap: 1b touches only tests/test_policy_seams.py and config/policy.yaml, #446 touches the eyes conductor prose, docs and clean_slate, and #439 touches _pyauto_root and docs.

Suggested branch: feature/eyes-organ-skeleton

Implementation Steps

1. PyAutoEyes commit 1 (strip): git rm of scripts/, dataset/, config/, instruments/, gallery/, GALLERY.md, _viz_cli.py, activate.sh, .github/workflows/{lint,render}.yml. Keep LICENSE, AI_POLICY.md, ruff.toml, the CLAUDE.md stub, .claude/ hooks, and the repos_sync:* marker blocks in AGENTS.md.
2. PyAutoEyes commit 2 (skeleton):
   • registry.yaml: lens row with name, repo, path, github, library, import_name, manifest, images_base_url, gallery, dispatch_event.
   • REFERENCE.md: the manifest contract, schema 1 (schema, generated, rendered_with{...}, figure_count, figures[{file, producer, domain, source, bytes, sha256}]), what the organ reads, and the versioning rule.
   • eyes/registry.py, eyes/manifest.py (local path or raw GitHub URL; validates schema 1), eyes/board.py (dashboard.md + dashboard.html: per instance the figure count, rendered_with, generated date, freshness vs the latest library release with a graceful offline fallback, a thumbnail grid linking the raw PNGs, and a copyable /eyes review <instance> <figure> line per figure).
   • bin/pyauto-eyes: board [--offline] [--from <instance>=<path>], check, survey [<instance>|--all] (delegates to pyauto-brain eyes survey <instance path>).
   • AGENTS.md / README.md / CLAUDE.md: state the layering and the boundary.
   • tests/: hermetic tests for the registry, the manifest reader, the board builder and check.
   • .github/workflows/lint.yml (ruff, pytest, pyauto-eyes check, lychee), pages_dashboard.yml, dashboard_refresh.yml.
3. PyAutoBrain: move PyAutoEyes out of WITNESS_EXEMPT into the test_witness row in config/policy.yaml. Run the policy_seams and skill_seams tests.

Key Files

• PyAutoEyes/registry.yaml, PyAutoEyes/REFERENCE.md, PyAutoEyes/eyes/*.py, PyAutoEyes/bin/pyauto-eyes, PyAutoEyes/tests/, PyAutoEyes/.github/workflows/*.yml
• PyAutoBrain/config/policy.yaml (test_witness), PyAutoBrain/tests/test_policy_seams.py (WITNESS_EXEMPT)
• Read contract source: autolens_visualization/gallery/viz_manifest.yaml, gallery/gallery_build.py, .github/workflows/render.yml (fires eyes-refresh)

Feature Agent note

The Feature Agent sized this as large and suggested splitting it further. The epic's declared phasing (1a / 1b / 2) wins: the dashboard content is kept modest here, and phase 2 (eyes_p2_board_and_conductor_registry.md) expands it.

Original Prompt

Click to expand starting prompt

PyAutoEyes phase 1b — strip the organ to its dashboard skeleton

Type: feature
Target: PyAutoEyes
Repos:

• PyAutoEyes
• PyAutoBrain
  Themes:
• visualization
• infrastructure
  Difficulty: large
  Autonomy: supervised
  Priority: high
  Lane: local-dev
  Status: draft
  Consequence: judge
  Witness: pyauto-eyes check green against the lens registry row (manifest resolves, every listed PNG URL resolves); hermetic tests green (registry, manifest reader, board builder on a fabricated manifest, check); lint.yml green on the PR; pyauto-eyes board writes dashboard.md/.html with a lens row linking into PyAutoLabs/autolens_visualization
  Review-minutes: 15
  Epic: pyautoeyes-birth
  Phase: 1b
  Filed: 2026-09-28

Blocked on: phase 1a shipped (history confirmed on PyAutoLabs/autolens_visualization).

Task

PyAutoEyes becomes the cross-project dashboard of the layered design (human
decision 2026-09-28): it reads each <lib>_visualization project repo's
tracked manifest and links to its PNGs. It renders nothing, copies no
figures, never judges (the Brain Eyes conductor does), never edits library
plot code (critiques route through intake).

• Strip, in one PR. Delete from the organ everything phase 1a moved to
  autolens_visualization: scripts/ producers + simulators, dataset/,
  the tracked PNGs, GALLERY.md, instruments/, config/, gallery/,
  _viz_cli.py, activate.sh, render.yml. History stays in git and in
  the project repo.
• registry.yaml — one row per instance: name, path, github, library, import_name, manifest (tracked path in the project repo, e.g.
  gallery/viz_manifest.yaml), images_base_url (raw.githubusercontent
  base), dispatch (the library release event the project repo re-renders
  on). Lens row only.
• Manifest contract — REFERENCE.md specifies the fields the project
  repos commit (figure list + rendered stack version) and what the organ
  reads; versioned so project repos and organ can move independently.
• eyes/ package — registry.py (read + validate registry.yaml),
  manifest.py (read a manifest from a local checkout or its GitHub raw URL),
  board.py (build dashboard.md/.html from registry + manifests; phase 2
  fills the content).
• bin/pyauto-eyes — board, check (registry valid, every manifest
  reachable and parseable, every PNG URL resolves), survey (runs
  pyauto-brain eyes survey <instance root> per registered instance).
• Organ prose — AGENTS.md / README.md / REFERENCE.md / CLAUDE.md stub
  stating the layering (project repos make, store and track figures; the
  organ is where the human checks in on visualization across all projects;
  same layering as autolens_profiling / autolens_inference under the
  Brain board), repos_sync:map markers kept.
• Workflows — lint.yml (ruff, pytest, pyauto-eyes check, lychee);
  pages_dashboard.yml + dashboard_refresh.yml on repository_dispatch
  (eyes-refresh, fired by each project repo's render.yml) and a daily
  cron (Cortex pattern).
• Tests — hermetic: registry, manifest reader, board builder on a
  fabricated manifest, check. Then replace the Brain WITNESS_EXEMPT
  entry (tests/test_policy_seams.py) with a pyautoeyes: row in
  config/policy.yaml's witness map.

Ship policy

PyAutoBrain (witness row) merges after PyAutoEyes. While Heart is RED the PRs
ship only under a contemporaneous human RED override. Merge stays human.

[Jammy2211]

PRs created — phase 1b (eyes-organ-skeleton)

• PyAutoEyes organ skeleton: strip lens content + cross-project dashboard (PyAutoMind#448) PyAutoEyes#2 — strip (commit 1, reviewable alone) + organ skeleton + organism-map regen; label pending-release (label created on PyAutoEyes, mirroring Mind's)
• policy: PyAutoEyes test_witness row (PyAutoMind#448) PyAutoBrain#428 — config/policy.yaml PyAutoEyes test_witness row; label pending-release. Merge after PyAutoEyes#2.

Validation

• PyAutoEyes: pytest tests -q 48 passed; ruff check + format clean
• bin/pyauto-eyes check live against the raw GitHub URL: check: OK (registry 1 instance; lens manifest schema 1, 40 figures; all 40 raw URLs resolve; dashboard current). Dashboard freshness now reads behind (rendered 2026.8.17.1, released 2026.9.27.2).
• PyAutoBrain full suite (outside bundle env, rebased onto docs: align community policy with five discussion categories #427 831a927): 1078 passed
• Heart readiness: YELLOW — identical to today's human-acknowledged set (Memory open PR 8d; manifest drift = autolens_visualization unregistered, a stale Heart snapshot — repos_sync now reports 40/40; autolens_test multi_dataset/rectangular.py timeout cloud#36404726969). No new reasons.

The organ renders nothing, judges nothing and copies nothing; the removed lens content's history lives on PyAutoLabs/autolens_visualization (PR #1 merged).

Human steps

1. /prm — merge PyAutoEyes#2, then PyAutoBrain#428.
2. Enable GitHub Pages for PyAutoEyes (Settings → Pages → Source: GitHub Actions) so pages_dashboard.yml publishes the board after merge. dashboard_refresh.yml listens for the eyes-refresh dispatch from autolens_visualization's render.yml.

🤖 Generated with Claude Code

https://claude.ai/code/session_01CpGs8DxC5qA1MtHcmHeaBQ

[Jammy2211]

Shipped — phase 1b (eyes-organ-skeleton)

Both PRs merged by the human via /prm on 2026-09-28:

• PyAutoEyes organ skeleton: strip lens content + cross-project dashboard (PyAutoMind#448) PyAutoEyes#2 — strip + organ skeleton + cross-project dashboard (merged 20:36:47Z, b299dc7)
• policy: PyAutoEyes test_witness row (PyAutoMind#448) PyAutoBrain#428 — config/policy.yaml PyAutoEyes test_witness row (merged 20:36:51Z, 195033f)

Merge proven per repo: both branch tips (Eyes 3153793, Brain 3c443bc) are ancestors of origin/main.

Post-merge verification on PyAutoEyes main

• Tracked tree: registry.yaml, eyes/, bin/pyauto-eyes, dashboard.md/.html; no scripts/, dataset/ or GALLERY.md.
• bin/pyauto-eyes check (live):

  ok   registry: 1 instance(s) (lens)
  ok   lens: manifest schema 1, 40 figures (https://raw.githubusercontent.com/PyAutoLabs/autolens_visualization/main/gallery/viz_manifest.yaml)
  ok   lens: all 40 figures resolve (raw URLs resolve)
  ok   dashboard: current with every manifest
  check: OK
  

• lint on the merge commit: success. Pages Dashboard on the merge commit (run 36480443757): failure, as expected. actions/configure-pages got Get Pages site failed: Not Found and then Create Pages site failed: Resource not accessible by integration, because Pages is not enabled on the repo yet.

Human steps left

1. Enable GitHub Pages on PyAutoEyes (Settings → Pages → Source: GitHub Actions), then re-run pages_dashboard.yml (workflow_dispatch) so the board publishes.
2. After it publishes, open a later PR that removes the --exclude '^https://pyautolabs\.github\.io/PyAutoEyes' lychee exclusion in .github/workflows/lint.yml.
3. PAT coverage: autolens_visualization's render.yml sends the eyes-refresh dispatch with secrets.PAT_PYAUTOLABS. That PAT must be granted to autolens_visualization and must cover PyAutoLabs/PyAutoEyes. Without it the step warns and skips, and dashboard_refresh.yml only catches up on its schedule. Add both repos to the PAT's repository list.

Pending release (carried into the record): PyAutoEyes#2, PyAutoBrain#428.

Next: phase 2 (draft/feature/pyautoeyes/eyes_p2_board_and_conductor_registry.md).

🤖 Generated with Claude Code

https://claude.ai/code/session_01CpGs8DxC5qA1MtHcmHeaBQ