prompt: re-home pynufft removal to maintenance, file two follow-ups

dashboard.md

@@ -11,7 +11,7 @@ Every task the Mind is holding, on one page: what is in flight, what is parked,
 | [In flight](#in-flight) (`active/`) | 2 |
 | [Parked](#parked) (`parked.md`) | 3 |
 | [Planned](#planned) (`planned.md`) | 6 |
-| [Backlog](#backlog) (`draft/`) | 146 |
+| [Backlog](#backlog) (`draft/`) | 148 |
 
 ## Start here
 
@@ -115,7 +115,13 @@ Every task the Mind is holding, on one page: what is in flight, what is parked,
 
 **Quick wins** (small enough, and safe enough to run unattended)
 
-- _(none right now)_
+<details><summary>📋 <a href="draft/maintenance/libraries/defer_scipy_sparse_import.md">Defer the eager scipy.sparse import in derivative_util (~0.10 s of</a> — libraries · small · safe · normal</summary>
+
+```
+/start_dev draft/maintenance/libraries/defer_scipy_sparse_import.md
+```
+
+</details>
 
 ## In flight
 
@@ -229,7 +235,7 @@ Scoped but not started; some are not yet prompt files. Full detail in [`planned.
 
 ## Backlog
 
-**146** filed prompts, not started. Each section is sorted most-pickable first (priority, then size). **23** of them belong to an epic and are listed only under [Epics](#epics) below.
+**148** filed prompts, not started. Each section is sorted most-pickable first (priority, then size). **23** of them belong to an epic and are listed only under [Epics](#epics) below.
 
 <details>
 <summary><b>feature</b> — 28</summary>
@@ -730,7 +736,7 @@ Scoped but not started; some are not yet prompt files. Full detail in [`planned.
 </details>
 
 <details>
-<summary><b>research</b> — 16</summary>
+<summary><b>research</b> — 17</summary>
 
 <details><summary>📋 <a href="draft/research/autoarray/delaunay_research.md">Deep research: Can we speed up Delaunay in PyAutoArray?</a> — autoarray · too-large · supervised · high</summary>
 
@@ -804,6 +810,14 @@ Scoped but not started; some are not yet prompt files. Full detail in [`planned.
 
 </details>
 
+<details><summary>📋 <a href="draft/research/libraries/intel_macos_support_policy.md">Is Intel macOS a supported platform, and what is the</a> — libraries · medium · supervised · normal</summary>
+
+```
+/start_dev draft/research/libraries/intel_macos_support_policy.md
+```
+
+</details>
+
 <details><summary>📋 <a href="draft/research/pyautomemory/checkerboard_psf_mismatch_residual_diagnostic.md">Checkerboard PSF-mismatch residual diagnostic — research + document + ingest</a> — pyautomemory · medium · supervised · normal</summary>
 
 ```
@@ -863,7 +877,7 @@ Scoped but not started; some are not yet prompt files. Full detail in [`planned.
 </details>
 
 <details>
-<summary><b>maintenance</b> — 18</summary>
+<summary><b>maintenance</b> — 20</summary>
 
 <details><summary>📋 <a href="draft/maintenance/ci/smoke_install_stale_jax_pin.md">smoke_install.sh's stale <code>jax&lt;0.7</code> pin — CI is on the right</a> — ci · low · supervised · medium</summary>
 
@@ -881,6 +895,14 @@ Scoped but not started; some are not yet prompt files. Full detail in [`planned.
 
 </details>
 
+<details><summary>📋 <a href="draft/maintenance/libraries/defer_scipy_sparse_import.md">Defer the eager scipy.sparse import in derivative_util (~0.10 s of</a> — libraries · small · safe · normal</summary>
+
+```
+/start_dev draft/maintenance/libraries/defer_scipy_sparse_import.md
+```
+
+</details>
+
 <details><summary>📋 <a href="draft/maintenance/workspaces/config_key_mirror_drift.md">Mirror drifted library config keys into the workspace configs</a> — workspaces · small · supervised · normal</summary>
 
 ```
@@ -969,6 +991,14 @@ Scoped but not started; some are not yet prompt files. Full detail in [`planned.
 
 </details>
 
+<details><summary>📋 <a href="draft/maintenance/libraries/remove_pynufft_legacy_transformer.md">Remove pynufft + legacy TransformerNUFFTPyNUFFT</a> — libraries · low-medium · supervised · normal</summary>
+
+```
+/start_dev draft/maintenance/libraries/remove_pynufft_legacy_transformer.md
+```
+
+</details>
+
 <details><summary>📋 <a href="draft/maintenance/autolens_profiling/jwst_lw_untracked_gitignore_gap.md">dataset/imaging/jwst_lw is untracked because the gitignore was never extended for</a> — autolens_profiling · small · supervised · low</summary>
 
 ```
@@ -1129,7 +1159,7 @@ Scoped but not started; some are not yet prompt files. Full detail in [`planned.
 </details>
 
 <details>
-<summary><b>refactor</b> — 6</summary>
+<summary><b>refactor</b> — 5</summary>
 
 <details><summary>📋 <a href="draft/refactor/autogalaxy/einstein_radius_jit_native_seed_finder.md"><code>einstein_radius_jit_from</code>: replace static init_guess with a JAX-native seed finder</a> — autogalaxy · too-large · supervised · high</summary>
 
@@ -1163,14 +1193,6 @@ Scoped but not started; some are not yet prompt files. Full detail in [`planned.
 
 </details>
 
-<details><summary>📋 <a href="draft/refactor/autoarray/remove_pynufft_legacy_transformer.md">Remove pynufft + legacy TransformerNUFFTPyNUFFT (0.23s of import, one fallback</a> — autoarray · low-medium · supervised · normal</summary>
-
-```
-/start_dev draft/refactor/autoarray/remove_pynufft_legacy_transformer.md
-```
-
-</details>
-
 <details><summary>📋 <a href="draft/refactor/pyautomind/repos_sync_check_dedup.md">Deduplicate repos_sync.py's check/write pairs</a> — pyautomind · medium · safe · low</summary>
 
 ```

draft/bug/autoarray/pynufft_scipy_pinv2_dev_extra.md

@@ -7,7 +7,7 @@ Repos:
 Difficulty: small
 Autonomy: supervised
 Priority: normal
-Status: draft
+Status: superseded
 
 ## Original request
 
@@ -40,3 +40,20 @@ exists, or retire the legacy backend and its tests. Keep this separate from the
 - The PyNUFFT test either passes against the supported dependency set or is
   removed together with an explicit backend-retirement decision.
 - The standard optional-profile suite remains green.
+
+## Superseded 2026-08-22
+
+Resolved by `draft/maintenance/libraries/remove_pynufft_legacy_transformer.md`,
+which takes this prompt's third sanctioned remedy — "retire the legacy backend
+and its tests". `pynufft` is gone from PyAutoArray's `optional` and `dev`
+extras, so there is no longer a dev-extra install that can hit
+`scipy.linalg.pinv2`.
+
+Confirmed on a clean Python 3.13 install (2026-08-22): with
+`pynufft==2022.2.2` present, `hasattr(scipy.linalg, "pinv2")` is `False` under
+SciPy 1.17.1 — the drift this prompt reported is real, and pre-existing rather
+than a Python-floor regression as it said. pynufft 2022.2.2 also emits
+`SyntaxWarning: "is" with 'str' literal` on 3.13, i.e. it is unmaintained
+against the supported interpreter range.
+
+Close this out when the removal PRs merge.

draft/maintenance/libraries/defer_scipy_sparse_import.md

@@ -0,0 +1,89 @@
+# Defer the eager scipy.sparse import in derivative_util (~0.10 s of import)
+
+Type: maintenance
+Target: libraries
+Repos:
+- @PyAutoArray
+Difficulty: small
+Autonomy: safe
+Priority: normal
+Status: in-flight
+
+## Where this came from
+
+Found 2026-08-22 while measuring the pynufft removal
+(`draft/maintenance/libraries/remove_pynufft_legacy_transformer.md`). That task
+assumed removing pynufft would take ~0.23 s off `import autoarray`. It takes
+~10 ms. The reason is the real target:
+
+`autoarray/operators/derivative_util.py:30` does
+
+```python
+from scipy.sparse import csr_matrix
+```
+
+at module scope. `scipy.sparse` costs **0.106 s cumulative** and is imported on
+every `import autoarray`, whether or not anything touches a derivative
+operator. pynufft's apparent 0.19 s was ~95 % this same shared subtree —
+removing pynufft did not remove it, because `derivative_util` pulls it in
+anyway.
+
+## Evidence (Python 3.13, dev extras, median of 7 runs)
+
+| | `import autoarray` |
+|---|---|
+| main, pynufft installed | 369.8 ms |
+| pynufft removed | 359.9 ms |
+
+`python -X importtime` on the pynufft-removed branch still shows
+`scipy.sparse` at 0.106 s cumulative.
+
+## Task
+
+Defer the `csr_matrix` import into the functions that build the sparse
+operators (the same pattern `transformer.py` already uses for `nufftax` via
+`_load_nufftax()`). Check for other eager `scipy.sparse` importers before
+assuming this is the only one — the win only lands if *no* module-scope import
+of it survives on the `import autoarray` path.
+
+Note the precedent in `transformer.py`: the deferral must survive unpickling in
+multiprocessing workers, so hang it off the call sites rather than `__init__`
+alone.
+
+## Acceptance
+
+- `python -X importtime -c "import autoarray" | grep scipy.sparse` is empty.
+- Median `import autoarray` drops by ~0.10 s against the same measurement
+  method above (record the before/after numbers in the PR).
+- Full suite green; sparse-operator behaviour unchanged.
+
+## Correction + result (implemented 2026-08-22, PyAutoArray#477)
+
+**This prompt's own premise was wrong, in exactly the way the pynufft one
+was.** Deferring `derivative_util.py:30` changed nothing: `scipy.sparse` was
+never imported from there. Traced with a `sys.meta_path` hook:
+
+```
+autoarray/__init__.py:80
+  -> inversion/mesh/mesh_geometry/delaunay.py:2   import scipy.spatial
+    -> scipy/spatial/__init__.py:111              from ._kdtree import *
+      -> scipy/spatial/_kdtree.py:4               from ._ckdtree import cKDTree
+```
+
+`scipy.spatial` (134 ms) pulls `scipy.sparse` (154 ms) transitively, so the
+`csr_matrix` import was riding on a subtree already paid for. Deferring
+`scipy.spatial` as well is what removes both — and is required to satisfy this
+prompt's own acceptance criterion.
+
+The general lesson, now hit twice: **a module's `importtime` cumulative figure
+is not its exclusive cost.** Attributing a saving to a dependency requires
+checking who else pulls its subtree in.
+
+Result: `import autoarray` **464.4 ms -> 183.7 ms** (medians of 15 runs,
+Python 3.13, dev extras) — a 281 ms saving, ~2.8x this prompt's ~0.10 s
+estimate, because `scipy.spatial`'s own cost comes off too. Both greps are
+empty. Suites green: autoarray 1179, autogalaxy 1103/1 skipped,
+autolens 532/1 skipped.
+
+Note `delaunay.py` already had local `import scipy.spatial` at two of its three
+use sites — this deferral had been started and left half-done.

draft/maintenance/libraries/remove_pynufft_legacy_transformer.md

@@ -0,0 +1,138 @@
+# Remove pynufft + legacy TransformerNUFFTPyNUFFT
+
+Type: maintenance
+Target: libraries
+Repos:
+- @PyAutoArray
+- @PyAutoGalaxy
+- @PyAutoLens
+Difficulty: low-medium
+Autonomy: supervised
+Priority: normal
+Status: shipped
+
+Re-homed 2026-08-22 from `draft/refactor/autoarray/`. The Brain Refactor Agent
+refused it there (`SUSPECT-API-CHANGE`, effective autonomy `human-required`):
+deleting a public class is not behaviour-preserving, so it cannot be a
+`refactor/`. `maintenance/` ("dependency updates, hygiene, cleanup") is the
+taxonomy fit for removing a dependency.
+
+## Original request (verbatim, 2026-08-19)
+
+> do we even use pynufft? maybe we should file a follow up to remove it I think
+> its purely for one function, so make that filing remove it but also include
+> this check of import time.
+
+## Corrections to the original filing (measured 2026-08-22)
+
+The 2026-08-19 filing had two factual errors, both found during implementation:
+
+1. **pynufft was never a base dependency.** It sat in the `optional` extra
+   (`PyAutoArray/pyproject.toml:67`) and the `dev` extra (line 77). A plain
+   `pip install autoarray` never had it, so `TransformerNUFFTPyNUFFT` already
+   raised `pynufft_exception()` for most users.
+2. **The import-time saving is ~10 ms, not ~230 ms.** Measured as the median of
+   7 runs on Python 3.13 with the dev extras: `import autoarray` goes
+   369.8 ms → 359.9 ms. `pynufft`'s 0.19 s *cumulative* import is ~95 %
+   `scipy.sparse` (0.11 s), which `autoarray/operators/derivative_util.py:30`
+   pulls in eagerly for `csr_matrix` regardless of pynufft. Only ~10 modules and
+   ~10 ms are exclusive to pynufft.
+
+The removal is still worth doing — an unmaintained dependency, one dead class,
+and a `dev` extra that is broken against SciPy >= 1.17 — but **not** on
+import-time grounds. The real 0.10 s win is filed separately as
+`draft/maintenance/libraries/defer_scipy_sparse_import.md`.
+
+## The Intel-macOS decision (settled 2026-08-22)
+
+The original filing flagged one blocking question: does removing the pynufft
+fallback cost Intel-Mac users their interferometer transformer? Verified
+against PyPI:
+
+- `jaxlib`'s **last Intel-macOS (x86_64) wheel is 0.4.38**, uploaded
+  2024-12-17. Every release since (through 0.11.1) is `macosx_11_0_arm64` only.
+- `jaxlib` has **never published an sdist**, for any version — so there is no
+  pip fallback that builds from source.
+- PyAutoNerves' floor is `jax>=0.7.0`
+  (`PyAutoNerves/pyproject.toml:38`, markered
+  `sys_platform != "darwin" or platform_machine == "arm64"`).
+- `nufftax` is pure-JAX; even its `xp=np` path calls `nufftax.nufft2d2`. So no
+  JAX means no `TransformerNUFFT` either.
+
+So Intel macOS keeps **`TransformerDFT` only** for interferometry — exact, pure
+numpy, but O(N_vis x N_pix). Human decision (2026-08-22): accept this; record
+it as a release-note line, not a blocker. The broader "is Intel macOS a
+supported platform" question is filed as
+`draft/research/libraries/intel_macos_support_policy.md`.
+
+## Work done (branches pushed 2026-08-22)
+
+All three on `claude/remove-pynufft-6uwt2z`:
+
+- **@PyAutoArray** — deleted `TransformerNUFFTPyNUFFT`, the `NUFFTPlaceholder`
+  / `NUFFT_cpu` module-scope try-import and `pynufft_exception()`; dropped the
+  re-exports from `__init__.py` and `type.py` and its arm of the `Transformer`
+  union; removed the three `test__nufft_pynufft__*` tests and the `"pynufft"`
+  arm of the nufftax-absent skip filter in `conftest.py`; dropped `pynufft`
+  from `optional` and the `pynufft==2022.2.2` pin from `dev`. Rewrote
+  `nufftax_exception()` and the `use_adjoint_scaling` docstrings, which cited
+  the deleted class. **1164 passed, 1 skipped.**
+- **@PyAutoGalaxy** — dropped the `__init__.py:29` re-export and the `optional`
+  entry; updated installation docs, the feature overview and the live citation
+  surface (`files/citations.{md,tex,bib}`, `docs/index.md`) to cite `nufftax`.
+  **1103 passed, 1 skipped.**
+- **@PyAutoLens** — same, minus the citation *addition* (nufftax was already
+  cited); the PyNUFFT entry was simply dropped. **532 passed, 1 skipped.**
+
+`paper/` in both downstream repos was deliberately left untouched — published
+JOSS records of what the software used at time of publication, not live docs.
+
+## Remaining
+
+1. **Workspace tier** (not started, needs the workspace repos):
+   - `autolens_workspace_test/scripts/interferometer/nufft.py:211` — the one
+     executable use; drop or replace the PyNUFFT leg of the parity comparison.
+   - Four prose mentions in autolens_workspace (`start_here.py`, `using_jax.py`,
+     `simulator.py`, `linear_light_profiles/modeling.py`) describing it as a
+     "non-JAX fallback".
+   - Check `PyAutoHands/autohands/config/no_run.yaml` per the ship_library
+     reference.
+2. **PR bodies need the `## API Changes` breaking entry** (release-notes
+   contract): `TransformerNUFFTPyNUFFT` removed; migration is `TransformerNUFFT`
+   (nufftax), or `TransformerDFT` where JAX is unavailable.
+3. All three library PRs **must merge together** — the downstream re-exports
+   break at import the moment PyAutoArray's removal lands alone.
+4. Closes the separate bug draft
+   `draft/bug/autoarray/pynufft_scipy_pinv2_dev_extra.md`: the
+   `pynufft==2022.2.2` dev pin calls `scipy.linalg.pinv2`, absent from SciPy
+   1.17.1 (confirmed 2026-08-22 — `hasattr(scipy.linalg, "pinv2")` is `False`).
+   Retiring the backend was one of that prompt's three sanctioned remedies.
+
+## Shipped 2026-08-22
+
+Library tier merged: @PyAutoArray#475, @PyAutoGalaxy#583, @PyAutoLens#709 —
+all green on CI, including each repo's `unittest-nojax` job, which is the
+standing evidence that the no-JAX path survives without the pynufft fallback.
+Merged galaxy -> lens -> array so main was never red (dropping a re-export is
+safe against an autoarray that still has the class; the reverse is not).
+
+Workspace tier raised: @autolens_workspace#497 (prose across `scripts/`,
+`notebooks/`, `markdown/`) and @autolens_workspace_test#261 (the `nufft.py`
+parity script rewritten around `TransformerDFT` as its sole reference; verified
+by running it — all four tests pass, 3.0e-14 relative residual at 256x256).
+
+`PyAutoHands/autohands/config/no_run.yaml` checked: no nufft entries, nothing
+hidden there.
+
+Two things found along the way that are NOT closed by this task:
+
+1. `use_adjoint_scaling` is now a **no-op on both remaining transformers** — it
+   was load-bearing only for the deleted class's pynufft-internal IFFT
+   normalisation. Kept, with docstrings rewritten, rather than widening this
+   removal. Worth a separate decision.
+2. `autolens_workspace_test/scripts/interferometer/jax_likelihood/rectangular_sparse.py`
+   recorded the `apply_sparse_operator` / `TransformerNUFFT` incompatibility as
+   being caused by pynufft's kernel-deconvolved adjoint scale. That backend is
+   gone; whether the incompatibility still holds against the nufftax adjoint is
+   **unverified**. The dead attribution was removed without asserting a
+   replacement claim.