maint: close search.log handler + four CLI-noise warning fixes

[Jammy2211]

Overview

A /cli_noise_clean audit of the full PyAutoFit suite (1667 tests, -W all) surfaced five mechanical warning sources, all in PyAutoFit. The largest is an unclosed search.log FileHandler leaking a file descriptor per decorated search call (44 warnings/run); the rest are one deprecation each from SQLAlchemy, nautilus, scipy, and CPython's fork-in-threads check. All five are noise-only fixes with no behaviour change.

Plan

• Close the search.log FileHandler in configure_handler's finally block, beside the existing removeHandler.
• Annotate the overlapping Fit.arrays/Fit.hdus vs HDU.fit SQLAlchemy relationships with the overlaps= parameters SQLAlchemy suggests, silencing the SAWarning from configure_mappers().
• Swap the deprecated nautilus search_internal.evidence() call for the .log_z property.
• Stop forwarding the scipy-deprecated disp/iprint options to the L-BFGS-B solver (constructor keeps accepting them for API stability).
• Add a module-local filterwarnings mark to test_fork_context.py for CPython's fork-in-a-multi-threaded-process DeprecationWarning, which pytest's background thread makes unavoidable there.

Detailed implementation plan

Affected Repositories

• PyAutoFit (primary, only)

Work Classification

Library

Branch Survey

Repository	Current Branch	Dirty?
PyAutoFit	main (fresh clone @ 401e666)	clean

Branch: claude/pyautofit-cli-noise-fixes-vqs7mg (session-designated; remote web session, no local worktree — the ~/Code/PyAutoLabs-wt/ flow is not used)

Note: active.md claims PyAutoFit for stored-sample-reconstruction-guard (autofit/non_linear/samples/) and version-stamp-sync-guards (autofit/__init__.py, files/release.sh). This task is file-disjoint from both.

Implementation Steps

1. autofit/non_linear/search/abstract_search.py (configure_handler, finally block): add handler.close() after root_logger.removeHandler(handler) — the handler holds search.log open otherwise (44 ResourceWarnings per suite run).
2. autofit/database/model/array.py: Array.fit, HDU.fit, Fit.arrays and Fit.hdus all write the same array.fit_id column (HDU inherits it via joined-table inheritance), which fires SAWarning: relationship ... will copy column fit.id to column array.fit_id, which conflicts with relationship(s) ... at configure_mappers(). Add the overlaps="..." parameter with exactly the relationship names SQLAlchemy's warning lists (reproduced locally before committing).
3. autofit/non_linear/search/nest/nautilus/search.py (samples_info_from, line 535): search_internal.evidence() → search_internal.log_z (nautilus deprecated the method for the property).
4. autofit/non_linear/search/mle/bfgs/search.py: scipy 1.15 deprecated the L-BFGS-B disp/iprint options (removal slated for 1.18). Override options in LBFGS to drop both keys before the dict reaches optimize.minimize; constructor keeps accepting them (API stability; disp remains live for plain BFGS). Update test_autofit/non_linear/search/optimize/test_lbfgs.py accordingly (assert the attributes survive and the options keys are absent).
5. test_autofit/non_linear/test_fork_context.py: add pytestmark = pytest.mark.filterwarnings("ignore:This process:DeprecationWarning") — CPython 3.12+ warns on os.fork() in a multi-threaded process, and pytest's machinery keeps a thread alive; the tests exercise the fork-pinned pool deliberately.

Out of scope (noted lowest-priority in the prompt): edge-case LinAlgWarning/RuntimeWarning from tests that deliberately exercise degenerate inputs (interpolator/covariance.py, messages/normal.py, fitness.py).

Key Files

• autofit/non_linear/search/abstract_search.py — handler close
• autofit/database/model/array.py — SQLAlchemy overlaps=
• autofit/non_linear/search/nest/nautilus/search.py — .log_z
• autofit/non_linear/search/mle/bfgs/search.py + test_autofit/non_linear/search/optimize/test_lbfgs.py — L-BFGS-B options
• test_autofit/non_linear/test_fork_context.py — fork warning mark

Testing

• Reproduce each warning on main first (SAWarning via sa.orm.configure_mappers(); scipy deprecation via an af.LBFGS fit; handler leak via -W error::ResourceWarning on a search-log test), then show it gone after the fix.
• Run the affected test files: test_autofit/non_linear/search/optimize/test_lbfgs.py, test_autofit/non_linear/test_fork_context.py, test_autofit/database/, nautilus search tests, plus the non_linear/search tree.

Original Prompt

Click to expand starting prompt

PyAutoFit CLI-noise batch: unclosed search.log handler + four small warning fixes

Type: maintenance
Target: PyAutoFit
Repos:

• PyAutoFit
  Difficulty: small
  Autonomy: safe
  Priority: normal
  Status: formalised

Filed 2026-08-06 from a full /cli_noise_clean audit (full PyAutoFit suite,
1667 tests, -W all). Five mechanical fixes, all in PyAutoFit:

1. Unclosed search.log FileHandler (44 warnings/run) —
   autofit/non_linear/search/abstract_search.py:123-131 (configure_handler)
   removes the handler in finally but never calls handler.close(). Add
   handler.close() beside removeHandler at line 131.
2. SQLAlchemy SAWarning relationship overlap — Fit.arrays/Fit.hdus
   vs HDU.fit ("will copy column fit.id ... conflicts"). Add the
   overlaps="..." parameters SQLAlchemy suggests, in the DB model
   definitions (fires from configure_mappers(), not the test).
3. Nautilus deprecation — non_linear/search/nest/nautilus/search.py:535
   uses search_internal.evidence(); swap to the .log_z property.
4. scipy L-BFGS-B deprecation — non_linear/search/mle/bfgs/search.py:194
   passes deprecated disp/iprint options; drop them per scipy's migration
   note (or gate on scipy version).
5. fork() DeprecationWarning in test_fork_context.py — pytest's thread
   pool + os.fork(); add a module-local filterwarnings mark or use the
   spawn context in that test where feasible.

Edge-case numerical warnings from tests that deliberately exercise degenerate
inputs (LinAlgWarning/RuntimeWarning in interpolator/covariance.py,
messages/normal.py, fitness.py) are lowest priority — silence locally in
the triggering tests with warnings.catch_warnings(), never globally.

[Jammy2211]

Implementation pushed to claude/pyautofit-cli-noise-fixes-vqs7mg as 7d1fe19 (6 files, +42/−5). All five fixes landed as planned, each verified against its warning before/after:

• configure_handler closes the search.log handler in finally — 50 decorated calls under -W error::ResourceWarning now run clean with no handlers left on the root logger.
• Fit.arrays gets overlaps="fit", Fit.hdus gets overlaps="arrays,fit" (the exact strings SQLAlchemy 2.0.52's two SAWarnings suggest); configure_mappers() now emits zero warnings, with no follow-on overlaps.
• Nautilus samples_info_from reads .log_z; nautilus 1.0.5's deprecated evidence() is a warn-then-return self.log_z wrapper, so the swap is exactly equivalent.
• LBFGS.options drops disp/iprint (scipy 1.17.1 confirmed the DeprecationWarning fires on any L-BFGS-B call passing them); constructor still accepts both and disp stays live for plain BFGS. test_lbfgs.py updated to pin the new contract.
• test_fork_context.py carries module-local filters for both fork warnings — CPython 3.12+'s DeprecationWarning and JAX's equivalent RuntimeWarning (the latter surfaced during validation; same unavoidable-fork noise, different emitter).

Full suite on Python 3.13 / scipy 1.17.1: 1884 passed, 3 skipped. Remaining fork warnings from dynesty pool tests elsewhere in the tree are outside this prompt's scope, as are the deliberately-degenerate-input numerical warnings the prompt marks lowest priority.

No PR opened yet — branch is ready for one when wanted.

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Generated by Claude Code

[Jammy2211]

Shipped: #1496 merged as 7d4d931 with all checks green (unittest 3.12 + 3.13, docs-build), pending-release label on for the next release build. Workspace impact: none — internal changes only, no migration needed. Completion record: PyAutoMind/complete/2026/08/cli-noise-pyautofit-batch.md (landed on main via PyAutoMind#235).

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Generated by Claude Code