PyAutoLabs · Jammy2211 · Aug 18, 2026 · Aug 18, 2026 · Aug 18, 2026 · Aug 18, 2026
diff --git a/complete/2026/08/howto-setup-notebook-audit.md b/complete/2026/08/howto-setup-notebook-audit.md
@@ -0,0 +1,134 @@
+- issue: (none — run end-to-end from a cloud session; the six PRs are the record)
+- completed: 2026-08-18
+- prs: HowToFit#45, HowToGalaxy#66, HowToLens#70, autofit_workspace#138,
+  autogalaxy_workspace#211, autolens_workspace#485 — all squash-merged 2026-08-18,
+  every check green on each.
+- merge-commits: HowToFit `1a4e7132`, HowToGalaxy `d973bc57`, HowToLens `e0fbdf61`,
+  autofit_workspace `fa55c438`, autogalaxy_workspace `47227c79`, autolens_workspace `c5960f69`.
+- summary: Full audit of the `# from auto* import setup_notebook; setup_notebook()` boilerplate
+  across every notebook-generating repo. 39 scripts were missing it — HowToFit 3, HowToGalaxy 2,
+  HowToLens 6, autofit_workspace 1, autogalaxy_workspace 5, autolens_workspace 22 — and all 39
+  were fixed with their generated notebooks updated to the uncommented form PyAutoHands emits.
+  autocti_workspace was already clean (79 scripts, 0 missing). The line chdir's to the workspace
+  root and enables inline plotting; without it a notebook that loads data by a relative path
+  fails under nbconvert, which runs with CWD set to the notebook's own directory.
+- the only live breakage: `HowToLens/scripts/simulator/lens_x{2,3}.py`, which resolve
+  `dataset_path = Path("dataset", ...)` against CWD and write FITS output there. Everything else
+  in the sweep is prose-only or import-only and passed today for exactly the reason the original
+  report predicted — they never load data by relative path.
+- the omissions were not policy: they sit alongside siblings in the SAME directory that do carry
+  the line (`autolens_workspace/scripts/cluster/` has 6 without and 5 with). Anyone re-auditing
+  should not read a missing line as a deliberate per-subtree exemption.
+- placement rule (two forms, both in the tree already): after the module docstring, OR after the
+  `from auto* import jax_wrapper` line where a script has one — jax_wrapper must set the JAX
+  environment before anything else. One outlier,
+  `autolens_workspace/scripts/guides/units/mass_to_light_ratio_units.py`, opens on imports rather
+  than a docstring; the line went at the top of the file, still ahead of every import.
+- SCOPE BOUNDARY worth keeping: `autoreduce_workspace` has 30 scripts and NONE carry the line,
+  which looks alarming until you notice it has no `notebooks/` directory — nothing generates
+  notebooks there, so the convention does not apply yet. Same for every `*_workspace_test` and
+  `*_workspace_developer` repo (verified by tree listing, not assumption). If autoreduce_workspace
+  ever starts generating notebooks, those 30 scripts need this sweep.
+- notebooks were NOT regenerated by PyAutoHands: it is not available in a cloud session, so the
+  `.ipynb` files were patched directly to the exact shape the generator emits. Verified three ways
+  before pushing — the edit reproduces already-correct sibling pairs byte-for-byte,
+  `json.dumps(nb, indent=1)` round-trips every touched file unchanged, and every `.py` still
+  parses. A real `generate.py` run should be a no-op on these; if it is not, that is the thing to
+  look at first.
+- CRLF trap: `HowToFit/scripts/chapter_1_introduction/tutorial_1_models.py` is committed with CRLF
+  line endings while everything around it is LF. A naive read/split/write rewrote all 547 lines as
+  a whitespace-only diff. The fix preserves the file's existing terminator. Anything doing a
+  mechanical sweep across these repos will hit this file.
+- pre-existing drift found, deliberately NOT touched: nine `start_here.ipynb` files in
+  autolens_workspace and six in autogalaxy_workspace are stored with a JSON formatting that
+  differs from the generator's `indent=1` output. Flagged in both PR bodies. Unrelated to this
+  task, real, and unclaimed.
+- no pending-release gate applied to the three workspace legs: `setup_notebook` is long-shipped in
+  the released libraries and is already called by every other example script in those repos, so
+  there is no unreleased API for the library-first merge gate to guard.
+- adjacent but distinct: `draft/maintenance/workspaces/notebook_setup_notebook_drift_siblings.md`
+  covers notebooks that carry the COMMENTED form and need regenerating. Different failure, still
+  open, untouched here.
+- `HowToGalaxy/chapter_1_introduction/tutorial_4_methods.py`, named in the original report as
+  missing, already carried the line — fixed before this audit ran.
+
+## Original prompt
+
+# Audit HowTo tutorials for missing setup_notebook() line
+
+Type: bug
+Target: HowToFit
+Repos:
+- @HowToFit
+- @HowToGalaxy
+- @HowToLens
+- @autofit_workspace
+- @autogalaxy_workspace
+- @autolens_workspace
+Difficulty: small
+Autonomy: safe
+Priority: normal
+Status: formalised
+
+Discovered during the batch-2b markdown rollout ([[markdown-example-renderings]]).
+Several HowTo tutorials are missing the standard
+`# from autoconf import setup_notebook; setup_notebook()` line that every other
+workspace/tutorial script carries (it chdir's to the workspace root + enables
+inline plotting). Without it, a tutorial that loads data via a relative path
+(or runs a simulator subprocess) FAILS when executed by nbconvert (which runs
+with CWD = the notebook's own directory), and only works interactively if the
+user happens to launch jupyter from the repo root.
+
+Confirmed missing in chapter_1_introduction alone: HowToFit start_here.py +
+tutorial_1_models.py; HowToGalaxy tutorial_4_methods.py; (HowToGalaxy
+tutorial_3_fitting.py + HowToLens tutorial_7_fitting.py were fixed in batch 2b's
+PRs since they blocked rendering). The 3 still-missing pass today only because
+they don't load data by relative path.
+
+Fix: audit ALL chapters of all three HowTo repos (and re-check the workspaces)
+for scripts lacking the setup_notebook line; add it right after the opening
+docstring, matching the sibling convention; regenerate the affected notebooks.
+Low-risk boilerplate consistency fix.
+
+## Audit result (2026-08-18)
+
+Every `.py` under `scripts/` — plus each HowTo repo's root `start_here.py` — was checked in the
+three HowTo repos and all five user-facing workspaces. 39 scripts were missing the line:
+
+| Repo | Missing | Notes |
+|---|---|---|
+| HowToFit | 3 | `chapter_1_introduction/{start_here,tutorial_1_models}.py`, root `start_here.py` |
+| HowToGalaxy | 2 | `chapter_2_modeling/tutorial_8_need_for_speed.py`, root `start_here.py` |
+| HowToLens | 6 | `chapter_2_lens_modeling/{tutorial_8_need_for_speed,tutorial_11_slam}.py`, `chapter_3_pixelizations/tutorial_9_model_fit.py`, `simulator/{lens_x2,lens_x3}.py`, root `start_here.py` |
+| autofit_workspace | 1 | `overview/overview_3_statistical_methods.py` |
+| autogalaxy_workspace | 5 | under `guides/`, `imaging/data_preparation/`, `interferometer/` |
+| autolens_workspace | 22 | mostly `cluster/*`, `guides/*` and feature `simulator.py` scripts |
+| autocti_workspace | 0 | clean |
+
+`tutorial_4_methods.py` in HowToGalaxy, named in the original report, already carries the line —
+it was fixed before this audit ran.
+
+The omissions are not a deliberate per-subtree policy: they sit alongside siblings in the same
+directory that do carry the line (e.g. `autolens_workspace/scripts/cluster/` has 6 without and 5
+with).
+
+The two genuinely load-bearing cases are `HowToLens/scripts/simulator/lens_x{2,3}.py`, which write
+to a relative `dataset/` path; the rest are prose-only or import-only scripts that pass today for
+the reason the report gives.
+
+**Out of scope, deliberately:** `autoreduce_workspace` has 30 scripts and none carry the line, but
+it has no `notebooks/` directory — the convention does not apply there yet. Same for every
+`*_workspace_test` and `*_workspace_developer` repo (checked by tree listing; none generates
+notebooks).
+
+**Placement:** after the module docstring, or after the `from auto* import jax_wrapper` line where
+a script has one. One outlier — `autolens_workspace/scripts/guides/units/mass_to_light_ratio_units.py`
+opens on imports rather than a docstring, so the line went at the top of the file.
+
+**Notebooks:** patched by hand to the exact shape PyAutoHands emits (uncommented, same cell,
+`json.dumps(nb, indent=1)` round-trips byte-identically), because the generator is not available in
+a cloud session. A real `generate.py` run should be a no-op on these — confirm before merging.
+
+Branch `claude/howto-setup-notebook-audit-dm2j9e` in all six repos, one commit each:
+HowToFit#45, HowToGalaxy#66, HowToLens#70, autofit_workspace#138, autogalaxy_workspace#211,
+autolens_workspace#485.
diff --git a/complete/index.md b/complete/index.md
@@ -6,7 +6,7 @@ Token-light navigation over the finished-work records (schema:
 only then grep a dated bucket. Curators: edit the band between the CURATED
 markers; everything below GENERATED is rebuilt.
 
-1005 records across 7 buckets.
+1006 records across 7 buckets.
 
 <!-- CURATED:START -->
 ## Highlights
@@ -59,6 +59,7 @@ _(curate hard-won records here — survives regeneration.)_
 - [hazard-profiling-likelihood-tier](2026/08/hazard-profiling-likelihood-tier.md) — Tier-2 likelihood profiling landed with five persistent findings and corrected NNLS continuity semantics.
 - [health-conductor-stale-verdict](2026/08/health-conductor-stale-verdict.md)
 - [heart-red-guarded-sample-escape](2026/08/heart-red-guarded-sample-escape.md) — Closed the escape path that kept release validation RED after
+- [howto-setup-notebook-audit](2026/08/howto-setup-notebook-audit.md) — none — run end-to-end from a cloud session; the six PRs are the record
 - [howto-smoke-all-tutorials](2026/08/howto-smoke-all-tutorials.md)
 - [howtofit-stub-fork-cleanup](2026/08/howtofit-stub-fork-cleanup.md)
 - [hpc-sync-first-push-race](2026/08/hpc-sync-first-push-race.md) — `hpc/sync push()` fired the `CODE_DIRS` rsyncs in parallel before

diff --git a/dashboard.md b/dashboard.md
@@ -11,7 +11,7 @@ Tasks only — the organism's health lives with the Heart (`/health`), not here.
 | [In flight](#in-flight) (`active/`) | 4 |
 | [Parked](#parked) (`parked.md`) | 1 |
 | [Planned](#planned) (`planned.md`) | 7 |
-| [Backlog](#backlog) (`draft/`) | 139 |
+| [Backlog](#backlog) (`draft/`) | 138 |
 
 Live on GitHub: [open issues](https://github.com/search?q=org%3APyAutoLabs+is%3Aissue+is%3Aopen&type=issues) · [open pull requests](https://github.com/search?q=org%3APyAutoLabs+is%3Apr+is%3Aopen&type=prs)
 
@@ -34,7 +34,6 @@ Live on GitHub: [open issues](https://github.com/search?q=org%3APyAutoLabs+is%3A
 
 **Quick wins** (small enough, and safe enough to run unattended)
 
-- [Audit HowTo tutorials for missing setup_notebook() line](draft/bug/howto/missing_setup_notebook_audit.md) — howto · small · safe · normal
 - [PyAutoFit CLI-noise batch: unclosed search.log handler + four small warning](draft/maintenance/pyautofit/cli_noise_pyautofit_batch.md) — pyautofit · small · safe · normal
 - [Tenant firewall: release_run.py carries an unlisted 'PyAutoLabs' instance fact](draft/bug/pyautoheart/tenant_firewall_release_run_instance_fact.md) — pyautoheart · small · safe · normal
 - [Silence the three autonerves-rooted CLI-noise sources (fits leak, pytest collection,](draft/maintenance/pyautonerves/cli_noise_autonerves_batch.md) — pyautonerves · small · safe · normal
@@ -83,10 +82,10 @@ Scoped but not started; some are not yet prompt files. Full detail in [`planned.
 
 ## Backlog
 
-**139** filed prompts, not started. Each section is sorted most-pickable first (priority, then size).
+**138** filed prompts, not started. Each section is sorted most-pickable first (priority, then size).
 
 <details>
-<summary><b>bug</b> — 40</summary>
+<summary><b>bug</b> — 39</summary>
 
 - [pre_build stages untracked files, publishing uncommitted human work](draft/bug/pyautohands/pre_build_stages_untracked_wip.md) — pyautohands · small · supervised · high
 - [UniformPrior bounds are not enforced in the objective on the](draft/bug/autofit/uniform_prior_bounds_unenforced_on_numpy_path.md) — autofit · medium · human-required · high
@@ -109,7 +108,6 @@ Scoped but not started; some are not yet prompt files. Full detail in [`planned.
 - [TEST_MODE bypass crashes on ordered-parameter assertion ties](draft/bug/autofit/test_mode_bypass_ordered_assertion_ties.md) — autofit · small · supervised · normal
 - [point.py JAX-vmap parity assert is non-deterministic under the smoke env](draft/bug/autolens/point_jax_vmap_parity_nondeterministic.md) — autolens · small · supervised · normal
 - [Scripts derive geometry from a hardcoded pixel_scale while the dataset](draft/bug/autolens_workspace/script_local_pixel_scale_vs_dataset_pixel_scales.md) — autolens_workspace · small · supervised · normal
-- [Audit HowTo tutorials for missing setup_notebook() line](draft/bug/howto/missing_setup_notebook_audit.md) — howto · small · safe · normal
 - [HowToGalaxy small API drifts: ellipse kwargs + plot_grid_lines (parked NEEDS_FIX)](draft/bug/howtogalaxy/small_api_drift_ellipse_and_plot_grid_lines.md) — howtogalaxy · small · supervised · normal
 - [`generate.py` deletes notebooks/ before rejecting an unknown project](draft/bug/pyautohands/generate_rejects_autocti_after_deleting_notebooks.md) — pyautohands · small · supervised · normal
 - [Tenant firewall: release_run.py carries an unlisted 'PyAutoLabs' instance fact](draft/bug/pyautoheart/tenant_firewall_release_run_instance_fact.md) — pyautoheart · small · safe · normal

diff --git a/draft/bug/howto/missing_setup_notebook_audit.md b/draft/bug/howto/missing_setup_notebook_audit.md