feat: require Python 3.12 in PyAutoNerves

[Jammy2211]

Overview

Adopt Python 3.12 as PyAutoNerves' minimum supported version, beginning the
dependency-ordered PyAuto ecosystem migration. Remove obsolete dependency
markers while preserving behavior-driven caps, and retain a clear warning for
experimental Python 3.14 use.

Plan

• Require Python 3.12 and advertise support for 3.12/3.13.
• Simplify JAX requirements without changing their version constraints.
• Retarget the import-time warning for unsupported/experimental versions.
• Add focused warning tests and update the contributor contract.
• Validate tests and built package metadata on Python 3.12 and 3.13.

Detailed implementation plan

Affected Repositories

• PyAutoNerves (primary)

Branch Survey

Repository	Current Branch	Dirty?
PyAutoNerves	main	clean

Suggested branch: feature/python-312-floor

Implementation Steps

1. Update pyproject.toml:

   • Set requires-python = ">=3.12".
   • Remove Python 3.9-3.11 classifiers.
   • Remove the now-tautological Python markers from jax, jaxlib, and
     jaxnnls.
   • Preserve jax>=0.7.0,<0.11.0, jaxlib>=0.7.0,<0.11.0, and
     jaxnnls==1.0.1.

2. Update autonerves/__init__.py:

   • Keep the version-warning mechanism and configuration bypass.
   • Remove the unreachable Python <3.11 JAX guidance.
   • Distinguish unsupported Python <3.12 from experimental Python >3.13.
   • Keep version.python_version_check and the containing version: block.

3. Add test_autonerves/test_python_version.py:

   • Verify 3.12/3.13 produce no warning.
   • Verify 3.11 reports the unsupported floor.
   • Verify 3.14 reports experimental status.
   • Verify the YAML bypass remains effective.

4. Update AGENTS.md to state requires-python >=3.12.

5. Validate:

   • Full PyAutoNerves suite on Python 3.12 and 3.13.
   • Built metadata contains Requires-Python: >=3.12.
   • JAX requirements are unmarked but retain their existing caps.

Key Files

• pyproject.toml
• autonerves/__init__.py
• test_autonerves/test_python_version.py
• AGENTS.md

Out of Scope

JAX 0.11, Python 3.14 support, downstream manifests, Hands/Heart matrices,
release execution, workspaces, and archival documentation.

Original Prompt

Click to expand starting prompt

Ok, lets remove support for anything below python3.12, do a census to make sure
we simplify requriements, build server, testing, etc. Also make sure all docs
are updated.

[Jammy2211]

Autonomous ship checkpoint — smoke gate failed

The Python 3.12 floor implementation is complete and locally committed on feature/python-312-floor, but the autonomous four-leg ship gate cannot publish it because the required smoke leg is not green.

Passing evidence

• PyAutoNerves Python 3.12: 154 passed
• PyAutoNerves Python 3.13 isolated environment: 154 passed
• PyAutoFit downstream: 1,559 passed, 1 skipped
• PyAutoArray downstream: 930 passed
• PyAutoGalaxy downstream: 1,009 passed
• PyAutoLens downstream: 488 passed
• Independent review: CLEAN
• Heart: YELLOW with the exact launch-acknowledged reason set; no new reason and no RED

Smoke evidence

Curated six-workspace run with the task worktree sourced:

• 51 passed
• 11 failed
• 3 intentionally skipped
• 65 total

A targeted control run against unmodified main reproduced the same 11 failures with the same signatures, so the PyAutoNerves diff introduced no new smoke regression. An apparent initial twelfth failure in autolens_workspace/multi_galaxy/start_here.py was a parallel dataset-generation race and passed on retry.

The 11 baseline failures are all in autolens_workspace_test:

• imaging/jax_likelihood/rectangular.py
• imaging/jax_likelihood/mge.py
• imaging/jax_likelihood/lp.py
• interferometer/jax_likelihood/rectangular.py
• point_source/jax_likelihood/point.py
• interferometer/jax_likelihood/potential_correction.py
• multi/jax_likelihood/mge.py
• interferometer/subhalo_recovery_interferometer.py
• multi_galaxy/composition_mge.py
• imaging/subhalo_recovery.py
• multi_galaxy/jax_likelihood/lp.py

Per PyAutoBrain/AUTONOMY.md, a failed leg must park at a human checkpoint: nothing is force-pushed and code must not be changed merely to make the gate pass.

Checkpoint question: should the organism's existing smoke failures be repaired as prerequisite tasks, then this Python-floor task resumed?

[Jammy2211]

Correction — smoke gate is green; task resumed

The previous autonomous checkpoint comment was based on an invalid local smoke-wrapper invocation and is superseded.

Root cause: the wrapper called PyAutoHands build_env_for_script() with script-relative paths while its own current working directory was the PyAutoLabs parent. PyAutoHands resolves each script's in-file ENV: declaration from the supplied path and caller cwd, so the wrapper silently missed every ENV: jax full_datasets / ENV: full_datasets declaration. It therefore forced NumPy and/or 15x15 datasets into scripts whose assertions require JAX and full-resolution data. The identical control failures on main reflected the same wrapper defect, not an ecosystem baseline defect.

Corrected run:

• Passed: 62
• Failed: 0
• Intentionally skipped by no_run.yaml: 3
• Workspaces: all six required smoke surfaces
• Environment: task worktree sourced, absolute script paths passed to the canonical PyAutoHands resolver

Two scripts initially hit dataset bootstrap races because the diagnostic wrapper launched scripts sharing a dataset directory concurrently:

• autolens_workspace/multi_galaxy/start_here.py
• autolens_workspace_test/imaging/jax_likelihood/lp.py

Both passed sequentially after their canonical simulator/bootstrap completed. Every previously reported JAX, MGE, potential-correction, point-source, and subhalo signature cleared without a source change.

No ecosystem bug fix is needed. The Python 3.12 floor task is resumed at the publish gate.

[Jammy2211]

Library PR created

• PR: feat: require Python 3.12 in PyAutoNerves #143
• Branch: feature/python-312-floor
• Final local test rerun: 154 passed
• Label: pending-release
• Autonomous gate: tests PASS · smoke PASS (62 runnable scripts, 3 intentional skips) · review CLEAN · Heart YELLOW within the exact launch acknowledgement

Workspace impact

Recommendation: (iii) no workspace migration required for Phase 1A.

No public Python symbols or signatures changed. The user-visible change is the distribution's Python floor and version-warning semantics. The six-workspace smoke surface passed against the branch, so no workspace script changes are indicated.

The autonomous run ends at PR-open for this phase. Merge remains human. The dependency-ordered Python-floor campaign can continue with Phase 1B (PyAutoArray) on its own pending-release PR.

[Jammy2211]

Autonomous queue checkpoint — 2026-07-29

The Python 3.12-floor campaign has completed every currently independent package slice and stopped at the next dependency/ownership barrier.

Open pending-release PRs

• PyAutoNerves: feat: require Python 3.12 in PyAutoNerves #143 — CI 3.12/3.13 green
• PyAutoCTI: feat: require Python 3.12 in PyAutoCTI PyAutoCTI#101 — CI 3.12/3.13 green
• PyAutoReduce: feat: require Python 3.12 in PyAutoReduce PyAutoReduce#60 — local 3.12/3.13 suites green (repo has no PR checks)
• PyAutoHeart: feat: require Python 3.12 in PyAutoHeart PyAutoHeart#114 — CI 3.12/3.13 green
• euclid_assistant: https://github.com/Jammy2211/euclid_assistant/pull/11 — CI 3.12/3.13 green

All five remain open and unmerged. Independent Phase 4 is complete at PR-open.

Next queue item and blockers

Phase 1B targets PyAutoArray, but it cannot safely begin yet:

1. its upstream dependency, PyAutoNerves PR feat: require Python 3.12 in PyAutoNerves #143, is still unmerged; and
2. PyAutoMind's active api-validation-and-crash-fixes task currently claims PyAutoArray.

Phases 2–3 depend on the complete core stack, and phases 5–7 depend on the coordinated core release. The queue is therefore durably parked without overlapping another task or bypassing the human merge gate.

[Jammy2211]

Shipped — 2026-07-29

PR

• feat: require Python 3.12 in PyAutoNerves #143
• Reviewed head: a3ed651c7a52f0832ce70b34e6b174a38758a90d
• Merge commit: a9bf45612ecdf53abb586def7e5635ac7d84872d

Review and validation

Claude Opus 5 independently returned CLEAN after inspecting the full diff, rerunning 154 tests, exercising the real version-warning path on Python 3.11/3.12/3.13/3.14, and checking dependency caps and metadata. Existing ecosystem smoke and downstream suites were also green.

Follow-up

The remaining core manifests must be raised before release, and Heart's legacy install/banner checks remain Phase 2 work. These are release-sequencing requirements, not defects in this merged PR.

[Jammy2211]

python-312-floor complete across all phases (1A–5B): five core library floors, build/health machinery, live release 2026.7.29.2 (Requires-Python >=3.12), independent repos, and the full selector census. Completion record: PyAutoMind/complete/2026/07/python-312-floor.md. Closing the parent on explicit human cleanup authorization (2026-07-30).