fix: Colab link rot — pin/repoint chapter README URLs, purge allowlists (phase 2)

[Jammy2211]

Overview

Phase 2 of the Colab maturity work (tracker: PyAutoLabs/PyAutoHands#124). Phase 1 (merged 2026-07-09: PyAutoLabs/PyAutoNerves#120, PyAutoLabs/PyAutoHands#125, PyAutoLabs/PyAutoHeart#44) made every generated notebook Colab-runnable by construction and added forbidden-URL guards that now flag the accumulated link rot. This phase fixes the rot so the Monday central url-check sweep can go green.

--auto run (effective level: safe — mechanical, well-specified link repair; header safe, difficulty medium). Plan below per the autonomy contract; ship goes through the four-leg autonomous gate and ends at PR-open. Note: the Brain Feature Agent recommended re-homing as research; overridden inline — the task has an explicit repo list, concrete edits, and a verifiable done-condition (url_check.sh green per repo).

Scope split at launch: PyAutoLens + PyAutoGalaxy are claimed by release-docs-polish-learn-paths (awaiting-input, uncommitted). Their docs/howto* dead-link fixes + allowlist purges are deferred to a follow-up leg registered in planned.md, blocked on that task. This run covers HowToFit, HowToGalaxy, HowToLens, euclid_strong_lens_modeling_pipeline.

Plan

• HowToLens — pin the 71 unpinned blob/main Colab URLs in scripts/*/README.md (mirrored in notebooks/*/README.md) to the current release tag 2026.7.6.649; fix dead filenames (tutorial_11_adapt_regularization.py.ipynb → tutorial_11_adaptive_regularization.ipynb, etc.); verify every link target exists in the repo; purge the now-fixed Colab entries from .url_check_allowlist.txt.
• HowToGalaxy — repoint the 28 wrong-repo chapter README Colab URLs (autogalaxy_workspace/... → HowToGalaxy/... at the current tag); verify targets; purge fixed allowlist Colab entries.
• HowToFit — verify every chapter README Colab link target exists at the pinned tag; fix the two moved/renamed tutorials frozen in the allowlist; purge fixed entries.
• euclid_strong_lens_modeling_pipeline — replace the forbidden Jammy2211 Colab URL in README.md with the PyAutoLabs form.
• Verify — run the merged Heart url_check.sh (offline guard, now including the new patterns) over each repo: must exit clean.

Detailed implementation plan

Affected Repositories

• HowToLens (primary)
• HowToGalaxy
• HowToFit
• euclid_strong_lens_modeling_pipeline

Branch Survey

Repository	Current Branch	Dirty?
./HowToLens	main	20 modified (regenerated dataset FITS/JSON — unrelated churn)
./HowToGalaxy	main	13 modified (same)
./HowToFit	main	315 modified (same)
./euclid_strong_lens_modeling_pipeline	main	1 modified (test_report.md)

Dirty files are local dataset-regeneration churn, none overlapping this task's files; worktrees branch from origin/main.

Suggested branch: feature/colab-link-rot
Work Classification: Workspace
Worktree root: ~/Code/PyAutoLabs-wt/colab-link-rot/

Implementation Steps

1. Script an audit: extract every colab.research.google.com URL from chapter READMEs in the three HowTo repos, map to the expected local notebooks/... path, report missing targets.
2. Fix systematically: right repo (HowToGalaxy), pinned tag (HowToLens), corrected filenames (all three); mirror scripts/ README edits into notebooks/ READMEs.
3. euclid README: Jammy2211 → PyAutoLabs owner (verify the target notebook exists; otherwise repoint to the imaging start_here).
4. Purge fixed Colab entries from each repo's .url_check_allowlist.txt (leave non-Colab entries).
5. Gate: bash PyAutoHeart/heart/checks/url_check.sh <repo> clean per repo; four-leg autonomous-ship gate; PRs with pending-release.

Key Files

• HowTo*/scripts/*/README.md + HowTo*/notebooks/*/README.md — Colab link lists
• HowTo*/.url_check_allowlist.txt — grandfathered rot to purge
• euclid_strong_lens_modeling_pipeline/README.md

Original Prompt

Click to expand starting prompt

See PyAutoMind/issued/colab_link_rot.md (line-rot inventory from the 2026-07-09 census in issued/colab_maturity.md).

[Jammy2211]

Shipped to PR-open (--auto, effective level: safe)

Four PRs are open with pending-release, all gates passed:

Repo	PR	What
HowToLens	#22	71 blob/main links → pinned 2026.7.6.649; 3 dead filenames fixed; 3 allowlist entries purged
HowToGalaxy	PyAutoLabs/HowToGalaxy#16	28 wrong-repo links repointed at HowToGalaxy; chapter 3/4 entries aligned with the tutorials that actually exist; 28 allowlist entries purged
HowToFit	PyAutoLabs/HowToFit#13	2 dead links fixed (incl. retitled tutorial_4_why_modeling_is_hard); 2 allowlist entries purged. Note: tutorial_4_hierachical_models filename typo left as-is (tiny follow-up)
euclid_strong_lens_modeling_pipeline	PyAutoLabs/euclid_strong_lens_modeling_pipeline#24	Colab intro link → canonical notebooks/imaging/start_here.ipynb at current tag

Gate: tests n/a (no test dirs) · smoke n/a (README/allowlist-only) · review CLEAN · Heart YELLOW within the launch-acknowledged reason set. Every Colab URL in the four repos was machine-verified (canonical owner, current tag, target exists) and the hardened offline guard exits clean on all four.

Remaining before the Monday sweep can go fully green: the deferred PyAutoLens/PyAutoGalaxy leg (docs dead links + allowlist purges), registered in planned.md blocked on release-docs-polish-learn-paths. Merge of these four PRs is a human act per the autonomy contract.

[Jammy2211]

All four PRs merged 2026-07-09 (HowToLens#22, PyAutoLabs/HowToGalaxy#16, PyAutoLabs/HowToFit#13, PyAutoLabs/euclid_strong_lens_modeling_pipeline#24) — merged-unchanged, logged in the calibration log. Closing; the deferred PyAutoLens/PyAutoGalaxy docs leg is tracked in PyAutoMind planned.md and the phase tracker PyAutoLabs/PyAutoHands#124 stays open until the Monday sweep is green.