26967851842
80%

Ran 04 Jun 2026 05:22PM UTC

Jobs 1

Files 29

Run time 1min

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Committed 04 Jun 2026 05:19PM UTC coverage: 76.754% (+0.3%) from 76.466%

Build # 26967851842

Build Type

push

github

Committed by

web-flow

Commit Message

v1.30.55: download timeout + retries (closes #255) (#266)

* v1.30.55: download timeout + retries (closes #255)

Replace urllib.request.urlretrieve (no timeout) with a shared
_download_to_file helper that uses urlopen(timeout=...) +
shutil.copyfileobj, so a stalled TCP connection raises socket.timeout
instead of blocking forever.

- Per-attempt timeout default 300s, override via HITLIST_DOWNLOAD_TIMEOUT
- 2 retries with 5s/30s backoff for transient blips
- Atomic .tmp -> dest move; partial downloads never clobber a good cache
- Applied to all three download sites: fetch_species_proteome,
  fetch_proteome_by_upid, and fetch (IEDB/HPA datasets)

Surfaced in the v3 review of #254 (parallel mapping pre-fetch makes a
single hung download stall every worker).

* Address review: Python 3.9 with-syntax + fail fast on 4xx

- Use comma-form 'with' (parenthesized context managers are a
  SyntaxError on Python 3.9, our declared minimum; CI only runs 3.11
  so it would have shipped broken)
- Don't retry permanent 4xx HTTP errors — fail fast instead of burning
  the 35s backoff window on a bad/withdrawn proteome ID
- Tests for the 404-no-retry and 503-retry paths

Coverage Stats

4705 of 6130 relevant lines covered (76.75%)

0.77 hits per line

Coverage Regressions

Lines	Coverage	∆	File
113	46.95	8.62%	downloads.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	26967851842.1	04 Jun 2026 05:21PM UTC	29	76.75	GitHub Action Run

pirl-unc / hitlist / 26967851842
80%

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