prompt: re-home pynufft removal to maintenance, file two follow-ups - #265
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The Brain Refactor Agent refused the removal prompt under `refactor/` (SUSPECT-API-CHANGE, human-required): deleting a public class is not behaviour-preserving. Re-homed to `draft/maintenance/libraries/`, the taxonomy fit for a dependency removal, and rewritten against what was actually measured while implementing it. Two corrections to the original filing: - pynufft was never a base dependency; it sat in the `optional` and `dev` extras only. - the import-time saving is ~10 ms, not ~230 ms. pynufft's 0.19 s cumulative import is ~95% `scipy.sparse`, which `derivative_util.py:30` imports eagerly regardless. The Intel-macOS question the prompt flagged as blocking is settled and recorded: jaxlib's last x86_64 macOS wheel is 0.4.38 (2024-12-17), there has never been a jaxlib sdist, and nufftax is pure-JAX, so Intel Macs keep TransformerDFT only. Accepted as a release-note line. New prompts: - `draft/research/libraries/intel_macos_support_policy.md` — the general platform question, since one "NumPy-only path" turned out to be a JAX path in disguise. - `draft/maintenance/libraries/defer_scipy_sparse_import.md` — the real ~0.10 s import win the pynufft measurement uncovered. Marks `draft/bug/autoarray/pynufft_scipy_pinv2_dev_extra.md` superseded: retiring the backend was one of its three sanctioned remedies.
The pynufft removal's library tier is merged (PyAutoArray#475, PyAutoGalaxy#583, PyAutoLens#709) and the workspace tier is raised (autolens_workspace#497, autolens_workspace_test#261). Records the merge order and the two open items the work surfaced but does not close: `use_adjoint_scaling` is now a no-op on both remaining transformers, and the `apply_sparse_operator` incompatibility's recorded cause was pynufft-specific and is now unverified. The scipy.sparse deferral prompt gets the same treatment its predecessor needed: its own premise was wrong. `scipy.sparse` was never imported from `derivative_util.py` — `scipy.spatial` pulls it in transitively, so deferring csr_matrix alone achieved nothing. Deferring both gives 464.4 ms -> 183.7 ms, ~2.8x the estimate. Implemented in PyAutoArray#477. The lesson, now hit twice and written down: a module's importtime cumulative figure is not its exclusive cost.
This was referenced Aug 24, 2026
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Conflicts were the three generated files plus one genuine collision. The collision: `delaunay_nan_probe_ell_comps_validator.md` was retired on both sides — by this sweep as `delaunay-nan-probe-ell-comps-validator`, and on main by the session that actually shipped the fix, as `delaunay-nan-probe-fix`. Theirs is kept and mine is dropped: it is the owning session's ship record, with the CI validation, the "the validator was right" finding and the probe's new shape. The sweep's version only pointed at the evidence from outside. The generated files (`complete/index.md`, `dashboard.md`, `dashboard.html`) were resolved by regenerating from the merged source of truth, not by hand: python3 scripts/lifecycle.py index --apply pyauto-brain intake --apply dashboard Rendered against PyAutoBrain main at 9063997 (#265 merged), so `intake dashboard --check` agrees with what CI will produce. Main had also retired `jax_point_source_point_smoke_sentinel.md` and `point_jax_vmap_parity_nondeterministic.md` — both merged cleanly, and both were prompts this sweep had inspected and deliberately left in the backlog. Backlog 144 -> 142. lifecycle check / index --check / orphans and registry_toc --check all OK. Co-Authored-By: Claude <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NcL3NFXVPW4xipE8wJfjSx
Jammy2211
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The Dashboard Refresh check failed on the merge commit even though the pages had just been regenerated. Cause: this session's PyAutoBrain checkout was 37 commits behind origin/main, so every render used a stale renderer AND a stale config/policy.yaml. The dashboard census classifies prompts through repo_aliases, which PyAutoBrain#268/#271 changed, and the renderer itself gained the freshness banner and refresh block in #265 -- so CI, which runs the renderer from PyAutoBrain main, correctly saw the committed pages as stale. Fast-forwarded the Brain checkout to origin/main and re-ran `intake dashboard --apply`. `dashboard --check` now reports the pages current against the same renderer CI uses. lifecycle check OK, index --check OK, repos_sync --check 0 mismatches. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01MPhEXMoPYa7H1sNHWR2GNW
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Summary
Mind-state changes for the pynufft removal shipped in PyAutoArray#475, PyAutoGalaxy#583 and PyAutoLens#709.
Re-homed
remove_pynufft_legacy_transformer.mdfromdraft/refactor/autoarray/todraft/maintenance/libraries/. The Brain Refactor Agent refused it underrefactor/—SUSPECT-API-CHANGE, effective autonomyhuman-required, "re-route: file under feature/ (API change implied); a refactor must be behaviour-preserving". Deleting a public class is not behaviour-preserving.maintenance/("dependency updates, hygiene, cleanup, small technical debt", perROUTING.md) is the taxonomy fit for a dependency removal, better than the agent's suggestedfeature/, which is for new capability.Rewrote it against what was actually measured, correcting two errors in the 2026-08-19 filing:
optionalanddevextras only.scipy.sparse, whichderivative_util.py:30imports eagerly forcsr_matrixregardless.Settled the blocking Intel-macOS decision the prompt flagged: jaxlib's last x86_64 macOS wheel is 0.4.38 (2024-12-17), jaxlib has never shipped an sdist, and nufftax is pure-JAX — so Intel Macs keep
TransformerDFTonly. Accepted as a release-note line rather than a blocker.Two new prompts:
draft/research/libraries/intel_macos_support_policy.md— the general platform question. One documented "NumPy-only path" turned out to be a JAX path in disguise, so others may be too; the current de-facto answer is "installs fine, fails at analysis time", which is the worst one.draft/maintenance/libraries/defer_scipy_sparse_import.md— the real ~0.10 s import win the measurement uncovered, 10× the pynufft one.Superseded
draft/bug/autoarray/pynufft_scipy_pinv2_dev_extra.md— retiring the backend was one of its three sanctioned remedies. Confirmed its report on a clean Python 3.13 install:hasattr(scipy.linalg, "pinv2")isFalseunder SciPy 1.17.1.Dashboard regenerated via
pyauto-brain intake --apply dashboard(148 prompts).Test Plan
python3 scripts/lifecycle.py check→lifecycle check: OKdashboard.md/dashboard.htmlregenerated, not hand-editedGenerated by Claude Code