pirl-unc / hitlist / 24700099692
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coverage: 48.311% (+0.2%) from 48.105%
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v1.13.2: cache ProteomeIndex.from_fasta by resolved (path, size, mtime) (#86) (#101)

`_add_flanking` in the build pipeline groups peptides by canonical
species and calls `ProteomeIndex.from_fasta(path, ...)` once per
species. When multiple canonical names fall back to the same shared
FASTA (e.g. "LCMV Armstrong", "LCMV Pasteur", "LCMV Traub", "LCMV WE"
all resolve to one cached UniProt proteome), the indexer was rebuilt
from scratch each time. For a typical IEDB build with ~300 small-
genome species that's ~15 minutes of redundant work.

Adds a process-level cache in `hitlist.proteome` keyed on

    (resolved_path, size, mtime_ns, lengths, gene_name, gene_id)

so repeated calls with the same inputs return the SAME ProteomeIndex
instance. The (size, mtime_ns) part of the key auto-invalidates when
`fetch_species_proteome` refreshes a FASTA on disk — no manual
clear-cache needed.

Also exports `clear_fasta_index_cache()` for test isolation when
multiple tests reuse the same temp filename in one process.

Three new tests:
- test_from_fasta_caches_by_path — same inputs return same instance
- test_from_fasta_cache_invalidates_on_mtime — mtime change rebuilds
- test_from_fasta_cache_keyed_on_lengths — different lengths rebuild

Scope: this is the (a) proposal from #86 — simplest diff, biggest
ROI for the common case. The larger (b)/(c)/(d) proposals (regroup by
FASTA path in _add_flanking, canonical-name collapse via UPID, per-
FASTA ProcessPool) are left as follow-ups if more is needed.

Closes #86.

1487 of 3078 relevant lines covered (48.31%)

0.48 hits per line

Coverage Regressions

Lines Coverage ∆ File
31
73.08
 1.34% proteome.py
Jobs
ID Job ID Ran Files Coverage
1 24700099692.1 21
48.31
 GitHub Action Run
Source Files on build 24700099692