fix: preserve_in_zip replaces a stale archive member (#1414)

[Jammy2211]

Summary

Closes #1414.

AbstractPaths.preserve_in_zip added a file to a completed search's .zip only when that member was absent, so a post-completion artifact rewritten on disk left the stale bytes in the archive. Because restore() deletes the output directory and re-extracts the zip, the stale copy came back on the next resume — the case PyAutoGalaxy#516 creates, where a changed dataset mask invalidates files/galaxy_images_snr.fits and the images are recomputed. Correctness was never at risk (the stale cache is rejected on load), but such a search missed its cache on every run instead of once, repaying the max-log-likelihood-fit rebuild each time.

An existing member is now compared against the file on disk and replaced when it differs:

• Comparison uses the file_size and CRC already in the zip's central directory, with a chunk-streamed zlib.crc32 over the file — the archived bytes are never decompressed and a large .fits cache is never read fully into memory.
• Replacement streams every other member into a temporary archive beside the original (same directory, so the final os.replace is atomic) and swaps it in only once complete; a failure part-way leaves the original archive untouched. The replaced member's compress_type is carried over.
• Byte-identical content stays a no-op, so the common resume path — re-preserving an unchanged cache — never pays for a rewrite. The no-zip and member-absent paths are unchanged.

Rebuilding the whole archive from the output directory (what the search itself does at completion via zip_directory) is not usable here: with remove_files: true the completed search's directory is deleted after zipping, so a later post-completion write recreates only files/<cache> and a full re-zip would truncate the archive to that one file.

The issue's other-callers check: autolens/analysis/result.py writes its multiple-image-positions cache only when the loose file is absent, so it never depended on replacement — no change needed. The related config knobs force_pickle_overwrite / force_visualize_overwrite do not overlap: they act on the search whose fit() is re-invoked, which always brackets the run with paths.restore() (which deletes the zip) and post_fit_output → zip_remove() (which rebuilds it wholesale). preserve_in_zip exists for the opposite seam — a write into an upstream completed search that is not fitted this run, whose zip is never rebuilt.

API Changes

None — no signature changes. AbstractPaths.preserve_in_zip gains behaviour: it now replaces an archived member whose content differs from the file on disk, where it previously left the archive untouched. Callers that write a changed artifact into a completed search's files/ folder get the refreshed copy after restore().
See full details below.

Test Plan

• pytest test_autofit/non_linear/paths/test_paths.py — 18 passed
• pytest test_autofit — 1559 passed, 1 skipped
• New test__preserve_in_zip__replaces_stale_member fails on the pre-fix source (regression pinned), passes after
• PyAutoGalaxy suite unaffected — 1009 passed (docstring follow-up on the same branch)

Full API Changes (for automation & release notes)

Changed Behaviour

• autofit.non_linear.paths.abstract.AbstractPaths.preserve_in_zip(file_path) — an existing archive member whose content differs from file_path is now replaced (archive rewritten atomically) instead of being silently skipped. Unchanged: no-op when the zip does not exist, plain append when the member is absent, and no-op when the member is byte-identical.

Added (private)

• autofit.non_linear.paths.abstract._matches_archived(info, file_path) — size + CRC comparison against the central directory.
• autofit.non_linear.paths.abstract._replace_zip_member(zip_path, arcname, file_path) — atomic member replacement via a temporary archive.

Migration

• None — no caller changes required.

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