feat: bootstrap PyAutoLabs/HowToGalaxy from autogalaxy_workspace

[Jammy2211]

Overview

Extract the howtogalaxy Jupyter notebook lecture series from autogalaxy_workspace into its own standalone repository at PyAutoLabs/HowToGalaxy, following the exact pattern used for PyAutoLabs/HowToLens (shipped via autolens_workspace#78, HowToLens#1, autolens_workspace#80, PyAutoLens#468). This is sub-task 1 of 3 — workspace cleanup and PyAutoGalaxy docs updates follow in separate issues once HowToGalaxy ships with tag 2026.4.13.6.

Plan

• Transfer the existing placeholder Jammy2211/HowToGalaxy (LICENSE only) to the PyAutoLabs org, matching HowToLens's ownership.
• Populate the repo with the howtogalaxy content currently living under autogalaxy_workspace/{scripts,notebooks}/howtogalaxy/ — chapters 1-4, optional chapter, and simulators — following the workspace folder layout (config / dataset / notebooks / output / scripts).
• Copy CI scaffolding (smoke_tests.yml, url_check.yml), top-level dotfiles (CITATIONS.rst, CONTRIBUTING.md, CODE_OF_CONDUCT.md, requirements.txt, runtime.txt, smoke_tests.txt, start_here.py, welcome.py, version.txt) from HowToLens as a template, swapping PyAutoLens references for PyAutoGalaxy.
• Tag 2026.4.13.6 — matches the current autogalaxy_workspace version and the URLs already baked into PyAutoGalaxy docs, giving Colab links a stable snapshot to point at.
• Smoke-test the chapter-1 tutorials to confirm they still run after the move. Any tutorial depending on pre-simulated datasets shipped only by the workspace (same situation as HowToLens tutorials 0 and 7) gets excluded from the smoke list and tracked as a follow-up content-alignment pass.

Detailed implementation plan

Affected Repositories

• PyAutoLabs/HowToGalaxy (new, primary)
• PyAutoLabs/autogalaxy_workspace (source — read-only during bootstrap; cleanup comes in sub-task 2)

Work Classification

Workspace

Branch Survey

Repository	Current Branch	Dirty?
./autogalaxy_workspace	main	untracked: path/ only
PyAutoLabs/HowToGalaxy	(transfer pending)	—

Suggested branch: feature/howtogalaxy-bootstrap
Worktree root: ~/Code/PyAutoLabs-wt/howtogalaxy-bootstrap/ (created later by /start_workspace)

Implementation Steps

1. Transfer Jammy2211/HowToGalaxy → PyAutoLabs/HowToGalaxy via gh api. Clone it locally into ~/Code/PyAutoLabs/HowToGalaxy.
2. Populate the repo skeleton by copying autogalaxy_workspace/{scripts,notebooks,config,dataset}/howtogalaxy/ trees to the new repo's top level (dropping the howtogalaxy/ prefix), alongside simulators/. Preserve per-chapter README files.
3. Scaffold CI and top-level files from HowToLens:
   • .github/workflows/smoke_tests.yml and .github/workflows/url_check.yml (update search strings PyAutoLens → PyAutoGalaxy, al → ag, etc.)
   • .github/scripts/run_smoke.py (identical between the two repos)
   • CITATIONS.rst, CODE_OF_CONDUCT.md, CONTRIBUTING.md, requirements.txt (swap autolens → autogalaxy), runtime.txt
   • start_here.py, welcome.py (rewrite prose for galaxy modeling)
   • smoke_tests.txt (chapter-1 tutorials only; exclude any that rely on external datasets — mirror of HowToLens tutorial 0 / 7 exclusions)
   • README.rst based on HowToLens's, rewritten for HowToGalaxy
   • version.txt with 2026.4.13.6
4. Push main, tag 2026.4.13.6, push the tag. This gives us the URL pattern https://colab.research.google.com/github/PyAutoLabs/HowToGalaxy/blob/2026.4.13.6/notebooks/<chapter>/<tutorial>.ipynb that sub-task 3's PyAutoGalaxy doc migration will point at.
5. Smoke-test via /smoke_test on the chapter-1 tutorials. Resolve regressions by either fixing the tutorial (if it's a trivial import path issue) or excluding it from smoke_tests.txt and filing a follow-up (if the fix needs scientific judgement).
6. Follow-up notes: register HowToGalaxy in PyAutoBuild (tracked in complete.md from sub-task 1 of HowToLens — same gap applies here).

Key Files

• HowToGalaxy/scripts/chapter_1_introduction/*.py — extracted from autogalaxy_workspace/scripts/howtogalaxy/chapter_1_introduction/
• HowToGalaxy/notebooks/chapter_1_introduction/*.ipynb — extracted equivalents
• HowToGalaxy/smoke_tests.txt — chapter-1 smoke list
• HowToGalaxy/.github/workflows/smoke_tests.yml — CI workflow
• HowToGalaxy/README.rst, start_here.py, welcome.py — top-level reader-facing content

Original Prompt

Click to expand starting prompt

Extract the HowToGalaxy Jupyter notebook lectures from @autogalaxy_workspace into their own standalone GitHub repo, following the exact same pattern we just used for HowToLens.

Starting state mirrors HowToLens pre-extraction:

• autogalaxy_workspace/scripts/howtogalaxy/ and autogalaxy_workspace/notebooks/howtogalaxy/ hold the content.
• Structure: chapter_1_introduction, chapter_2_modeling, chapter_3_search_chaining, chapter_4_pixelizations, chapter_optional, simulators.
• Jammy2211/HowToGalaxy exists but is empty (LICENSE only). It needs to be transferred to PyAutoLabs/HowToGalaxy (same "forgot to put it in the org" situation as HowToLens).
• @PyAutoGalaxy docs reference HowToGalaxy under Colab URLs pointing at autogalaxy_workspace/.../howtogalaxy/... — these need to migrate to the new repo.

Do this as three sub-tasks, with three separate GitHub issues:

1. Bootstrap PyAutoLabs/HowToGalaxy (current scope).

   • Transfer Jammy2211/HowToGalaxy → PyAutoLabs/HowToGalaxy.
   • Populate it from the existing autogalaxy_workspace/howtogalaxy/ content, following the same folder layout as every other workspace (config / dataset / notebooks / output / scripts).
   • Copy CI workflows, pre-commit configs, and release automation from HowToLens as a template.
   • Tag 2026.4.13.6 — same tag as HowToLens, matches the current autogalaxy_workspace version, lets Colab URLs reference a stable snapshot.
   • Smoke-test the chapter-1 tutorials to confirm they still run after the move.

2. Workspace cleanup (autogalaxy_workspace).

   • Remove scripts/howtogalaxy/ and notebooks/howtogalaxy/.
   • Rewrite internal references (READMEs, modeling.py prose mentioning howtogalaxy, build configs like env_vars.yaml and no_run.yaml).
   • Add a pointer to PyAutoLabs/HowToGalaxy wherever the old folder was referenced.

3. PyAutoGalaxy docs update.

   • Migrate every HowToGalaxy Colab URL from autogalaxy_workspace/.../notebooks/howtogalaxy/... to PyAutoLabs/HowToGalaxy/blob/2026.4.13.6/notebooks/....
   • Rewrite README, docs/index.rst, docs/general/workspace.rst, docs/overview/, per-chapter docs/howtogalaxy/ pages, and paper/paper.md prose to frame HowToGalaxy as a standalone repo alongside the workspace (not a sub-folder inside it).

Reference: the HowToLens trio is complete and shipped as:

• HowToLens bootstrap: feat: bootstrap HowToLens from autolens_workspace tutorials HowToLens#1
• autolens_workspace cleanup: Remove howtolens/ from workspace (extracted to PyAutoLabs/HowToLens) autolens_workspace#80
• PyAutoLens docs update: docs: update HowToLens references after extraction to standalone repo PyAutoLens#468

HowToFit is the third and final extraction, but it is out of scope for this task — handle it in its own follow-up.