P1: fail-closed spectrum cache (source-blind + verify exit code)#1
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lfu46 wants to merge 2 commits into
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P1: fail-closed spectrum cache (source-blind + verify exit code)#1lfu46 wants to merge 2 commits into
lfu46 wants to merge 2 commits into
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Move the spectrum cache into mzml_utils.spectrum_cache and export open_spectra / SpectrumCache / build_cache / verify_cache / cache_path_for at the package top level. open_spectra(path) returns a local SpectrumCache when a co-located spectra_cache/ exists, else MzMLReader (identical Spectrum API), so it is a drop-in single reader. Add SpectrumCache.find_best_ms1 for full MzMLReader parity. Unit test in tests/test_spectrum_cache.py (21 checks). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…fusal + exit code) is_stale()/the info CLI are source-blind by default -- they refuse a /Volumes source unless --check-source/allow_network, so a wedged SMB share can no longer hang the process in uninterruptible I/O. verify_cache refuses a network source without an explicit local --source and the CLI now exits nonzero on mismatch. lossless=True meta -> peak_dtype=float32,bit_exact=False + corrected docstrings (float32 near-lossless, not bit-exact). Added test_source_blind_safety. Commits only these 2 files; other working-tree changes are unrelated WIP. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Fixes the cache-safety hole surfaced in the skill-review round.
is_stale()and theinfoCLI are source-blind by default — they refuse to stat a/Volumessource unless--check-source/allow_network, so a wedged SMB share can't hang the process (it froze two procs on 2026-07-09).verify_cacherefuses a network source without an explicit local--source, and the CLI now exits nonzero on mismatch. Thelossless=Truemeta flag ->peak_dtype=float32, bit_exact=Falsewith corrected docstrings (float32 is near-lossless, not bit-exact). Addstest_source_blind_safety. Onlyspectrum_cache.py+ its test; other working-tree changes are unrelated WIP.