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fix: install finufft in Array-based Colab bootstraps #204
Description
Overview
The TestPyPI candidate 2026.10.25.1.dev83701 fails install verification F because finufft, now an AutoArray dependency, is absent after the Nerves Colab --no-deps bootstrap. Repair the package list rather than relaxing Heart's gate.
Exact published Heart RED reason: install verification FAILED (testpypi; checks F).
Evidence: Release Integrate, verify-install job 121108376734. The second RED reason, release validation FAILED (stage integrate), remains until fresh candidate integration succeeds.
Plan
- Install
finufft>=2.4.0for Galaxy/Lens and their HowTo notebook setups, matching AutoArray's Linux floor. - Keep Fit-only setup unchanged.
- Exercise the actual setup-generated pip command for all six projects.
- Validate Nerves and existing AutoArray CPU NUFFT parity.
- Obtain incident-specific corrective-PR authorization before source commit/push/PR; then request separate merge approval. No release or rehearsal is authorized by this issue.
Tier: judge — merge mode: human /prm.
Detailed implementation plan
Affected repository and branch
PyAutoNerves only. Fresh session clone; main was clean before creating local proposal branch feature/colab-finufft-bootstrap. No active Mind repo claim for PyAutoNerves was found.
Files
autonerves/setup_colab.py: add the package to the Array-based stack.test_autonerves/test_setup_colab.py: exercise setup with a mocked Colab shell and intercept the pip command. Assert the required package and floor, and that Fit-only projects do not gain it.
Validation already obtained
- New witness before source patch: 4 failed, 2 passed; failures exactly the Array-based projects.
- Patched Nerves suite: 258 passed, 1 skipped. Existing skipped specifier-comparison test requires absent Fit/Galaxy sibling checkouts.
- Existing AutoArray
test_nufft_cpu.py: 7 passed, finufft 2.5.1 / nufftax 0.6.1. - No accepted-missing exceptions, test waivers, threshold changes or scoring changes.
Remaining evidence
The full Colab simulation and candidate-wheel integration have not been rerun. After a separately approved merge, build fresh wheels, run verify_install and integration, and reconcile verify_install:F:, the verify-install coverage records, and the linked release/validation records.
Execution location
/workspace/scratch/f77499d15f98/PyAutoNerves; source changes remain uncommitted. Mind prompt: draft/bug/pyautonerves/colab_finufft_bootstrap.md (moves to active on issue filing).
Original authorization
On 2026-10-25 the maintainer replied “Yep do all that” to the health checklist. This authorizes the investigation and repair preparation. It is not represented here as the separate named-issue Heart RED shipping exception, merge authority or release approval.
Activity
Jammy2211 commentedon Oct 25, 2026
Live corrective-PR authorization — 2026-10-25
James replied “I approve” in this session to the explicit request: “Approve committing, pushing, and opening one corrective PR for Nerves #204 against ‘install verification FAILED (testpypi; checks F)’?” This comment records that human authorization; it is not an autonomous approval.
Re-read published Heart board at ship time: timestamp
2026-10-25T09:34:29.845384+00:00, RED. The named reason remains exactly install verification FAILED (testpypi; checks F). Sibling reason release validation FAILED (stage integrate) remains open.Causal mapping: missing finufft under Colab
--no-deps→ #204 → addfinufft>=2.4.0to Array-based bootstrap stacks → six-project pip-command witness. Scope: commit, push, and one pending-release PR only. No merge, issue close, release or rehearsal authorized.Verification: witness before fix 4 failed/2 passed; patched Nerves suite 258 passed/1 existing skip; existing Array CPU NUFFT parity 7 passed. Source/base unchanged since those tests. Full Colab/candidate-wheel integration remains unrun. After separate human merge, obtain fresh wheels and rerun install verification and integration, reconciling the same Heart finding IDs.
Jammy2211 commentedon Oct 25, 2026
Shipped — source merged
James authorized the merge with “Prm I authorize”. PR #205 merged unchanged as
ec8b5c1e5f17ac03ac5246b5fbc322624a6cd3f6after verifying all four jobs on head90bd238356203233ab766976306865999a247ad6: Python 3.12, Python 3.13, no-JAX and Colab gate all completed successfully across both workflow runs. The only claimed source branch is merged.The Array-based Colab bootstrap now explicitly installs finufft>=2.4.0. No notebook migration is needed. Closing the source repair task;
pending-releaseremains on #205. This is not release publication or clearance of Heart’s install/integrate findings: fresh candidate wheels and install/release validation remain required. No release or rehearsal was performed.