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coverage: 75.408% (+0.08%) from 75.329%
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v1.30.49: extend disk cache to from_ensembl (closes #251) (#253)

* extend disk cache to ProteomeIndex.from_ensembl (closes #251)

The disk cache shipped in PR #247 (closes #246) only covered
from_fasta.  This commit extends the same caching pattern to
from_ensembl, the path tsarina hits once per patient (see
@iskandr's comment on #251 — separate processes mean the
in-memory _FASTA_INDEX_CACHE never amortizes across patients;
the disk cache does).

Refactor: extracted three helpers from the from_fasta cache flow
that both factories now share —

- _hit_in_memory_cache(cache_key, label, verbose)
- _hit_disk_cache(cache_key, label, verbose)  (also promotes into in-memory)
- _populate_caches(cache_key, idx)
- _populate_in_memory_cache(cache_key, idx)  (used by the above)

from_fasta switched to these helpers (reduces duplication, no
behavior change — verified by all 49 existing proteome tests still
passing).

from_ensembl additions:

- _resolve_ensembl_gtf_path(ensembl): tolerantly probes a small
  sequence of pyensembl attribute names (gtf_path, _gtf_path, gtf)
  for the local GTF file.  Returns None when unresolvable (synthetic
  test fakes, missing local data) → caching silently skipped, cold
  path runs unchanged.
- _build_ensembl_cache_key(ensembl, release, species, biotype, lengths):
  builds the cache-key tuple ("ensembl", release, species, biotype,
  lengths, gtf_size, gtf_mtime_ns).  Returns None when GTF
  unresolvable.
- from_ensembl: checks in-memory then disk cache before the gene
  iteration, populates both after the cold _build.

_disk_cache_filename now handles two cache-key shapes via the first-
element discriminant:

- ("ensembl", ...) → v{V}_ensembl_{species}_r{release}_{biotype}_L{n}_{hash}.pkl
- (path_str, ...) → v{V}_{fasta_basename}_L{n}_{hash}.pkl  (legacy)

Format version unchanged (v1) — both shapes serialize the same
ProteomeIndex object via pickle.

Tests added (5 new in test_proteome.py):

- test_from_ensembl_disk_cache_persis... (continued)

4394 of 5827 relevant lines covered (75.41%)

0.75 hits per line

Coverage Regressions

Lines Coverage ∆ File
41
88.28
 -0.74% proteome.py
Jobs
ID Job ID Ran Files Coverage
1 25711341345.1 28
75.41
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Source Files on build 25711341345