refactor: remove obsolete notebook bootstrap

[Jammy2211]

Overview

Remove the obsolete %matplotlib inline plus pyprojroot notebook bootstrap from maintained AutoCTI workspace material. The public workspace's authored scripts move to the current autonerves.setup_notebook() convention and its paired notebooks are regenerated; non-legacy workspace-test scripts lose the inert bootstrap, while archived Euclid heritage remains verbatim.

This is a behavior-preserving workspace cleanup with no library or public API changes. It follows the completed standalone-comment cleanup in AutoGalaxy and AutoLens.

Plan

• Replace the old five-line bootstrap in all 79 authored AutoCTI workspace scripts with the current one-line notebook setup convention.
• Regenerate all 79 paired notebooks through PyAutoHands conversion tooling; never hand-edit notebook JSON.
• Remove the old bootstrap from the 26 non-legacy autocti_workspace_test/imaging_ci/ scripts.
• Preserve all 13 occurrences under autocti_workspace_test/legacy/ verbatim.
• Validate notebook JSON, exact file scope, literal absence in non-legacy material, and the maintained CTI smoke surface.

Detailed implementation plan

Work Classification

Workspace

Affected Repositories

• autocti_workspace (primary)
• autocti_workspace_test

Branch Survey

Repository	Current Branch	Dirty?
./autocti_workspace	main	clean
./autocti_workspace_test	main	clean

No active worktree claims overlap either repository.

Suggested branch: feature/autocti-notebook-bootstrap

Worktree root: ~/Code/PyAutoLabs-wt/autocti-notebook-bootstrap/

Implementation Steps

1. In the 79 matching autocti_workspace/scripts/**/*.py files, replace exactly:

   • # %matplotlib inline
   • the commented pyprojroot import/path setup
   • commented %cd and working-directory print

   with # from autonerves import setup_notebook; setup_notebook().

2. Regenerate the corresponding 79 notebooks/**/*.ipynb files from the scripts with PyAutoHands. If the full generate.py autocti entry remains gated by the separately tracked Colab/release registry, use PyAutoHands' build_util.py_to_notebook conversion path for the exact pairs; do not modify release wiring or notebook JSON by hand.

3. In the 26 matching non-legacy autocti_workspace_test/imaging_ci/**/*.py files, remove the obsolete five-line block. These integration/profiling scripts run from the repository root and do not need a notebook setup replacement.

4. Do not edit autocti_workspace_test/legacy/; its 13 occurrences are preserved historical material.

5. Validate all regenerated notebooks with a JSON parser and git diff --check; assert zero %matplotlib inline and zero pyprojroot references in non-legacy tracked .py/.ipynb files.

6. Run the maintained autocti_workspace_test smoke runner and representative AutoCTI workspace script/notebook checks under the configured test-mode/cache environment.

Key Files

• autocti_workspace/scripts/**/*.py — 79 authored workspace scripts.
• autocti_workspace/notebooks/**/*.ipynb — 79 generated notebook counterparts.
• autocti_workspace_test/imaging_ci/**/*.py — 26 non-legacy scripts.
• autocti_workspace_test/legacy/** — explicitly excluded, unchanged archive.

Original Prompt

Click to expand starting prompt

ok, lets get rid of the five standalones and then tackle all the CTI stuff

[Jammy2211]

CTI notebook-bootstrap cleanup is implemented and validated.

Commits and draft PRs:

• autocti_workspace 065b04d — refactor: replace legacy notebook bootstrap #8
• autocti_workspace_test c04b88a — refactor: remove legacy notebook bootstrap autocti_workspace_test#10

Scope:

• Replaced the obsolete bootstrap in 79 maintained public scripts.
• Regenerated all 79 paired notebooks through PyAutoHands.
• Removed the obsolete block from 26 maintained workspace-test scripts.
• Preserved all 13 legacy occurrences and files unchanged.

Validation:

• No %matplotlib inline or pyprojroot remains in maintained CTI scripts/notebooks.
• All changed Python files parse; all generated notebooks are valid JSON/nbformat 4.
• Representative public script and regenerated notebook both execute successfully.
• Local CTI smoke suite passed 3/3.
• Line-ending-aware diff checks pass.

Both PRs carry pending-release. The public workspace reports no CI checks; Python 3.12/3.13 smoke checks are currently running on the workspace-test PR. Remaining gate: CI completion and human merge authorization.

[Jammy2211]

CI gate is green:

• autocti_workspace refactor: replace legacy notebook bootstrap #8 is mergeable/clean; this repository reports no configured PR checks.
• autocti_workspace_test docs: fix all 29 dead internal references (hygiene refs tier) #10 is mergeable/clean; all Python 3.12 and 3.13 smoke jobs passed.

Both PRs remain draft and carry pending-release, awaiting explicit human merge authorization.

[Jammy2211]

Shipped and completed.

Merged PRs:

• autocti_workspace refactor: replace legacy notebook bootstrap #8 → 79a0e7df60f1aad6a7bad85338d5a489ffd584c5
• autocti_workspace_test docs: fix all 29 dead internal references (hygiene refs tier) #10 → 0a1e73bfdc2653bd3f2c1b39e281d6fc89ae141a

Post-merge verification on main confirms:

• 79 maintained scripts and 79 paired notebooks use autonerves.setup_notebook().
• No %matplotlib inline or pyprojroot remains in maintained public CTI scripts/notebooks.
• No obsolete block remains under maintained workspace-test imaging_ci/**.
• Exactly 13 legacy occurrences remain intentionally preserved.

PyAutoMind completion record: 78aa3a1. The task worktree and both merged feature branches were removed.