27153087900
77%

Ran 08 Jun 2026 04:51PM UTC

Jobs 1

Files 37

Run time 1min

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Committed 08 Jun 2026 04:50PM UTC coverage: 73.986% (+0.06%) from 73.929%

Build # 27153087900

Build Type

push

github

Committed by

web-flow

Commit Message

reference_data: delegate cache dir + download to datacache (like pyensembl) (#106)

Per the "why not datacache?" question. hitlist and tsarina each hand-rolled
cache-dir resolution + download, while pyensembl (same openvax ecosystem)
already uses datacache for exactly this. reference_data now does too:

- cache_dir() -> datacache.get_data_dir(subdir="tsarina",
  envkey="TSARINA_DATA_DIR") + ensure_dir. Platform-appropriate via appdirs
  (e.g. ~/Library/Caches/tsarina) when the env var is unset, instead of the
  bespoke repo-.cache / ~/.cache fallback.
- download() -> datacache.download._download_and_decompress_if_necessary
  (the same private helper pyensembl's download_cache calls), replacing the
  hand-rolled urllib fetch + zipfile/_extract_to. Handles .zip and .gz.

The value-add layer datacache does NOT provide stays here: the dataset
registry, HPA version pinning, and the sha256/version/timestamp manifest.

datacache added as a direct dependency (it was only transitive via the
optional pyensembl extra). Verified end-to-end: `reference fetch
hpa_rna_consensus` downloads + decompresses to the identical 37,949,495-byte
TSV. Cache location moves to the appdirs dir (behavior change, intended).

Tests rewritten to stub datacache's downloader instead of urllib. 424 pass.

Coverage Stats

2682 of 3625 relevant lines covered (73.99%)

0.74 hits per line

Coverage Regressions

Lines	Coverage	∆	File
4	94.81	5.67%	reference_data.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	27153087900.1	08 Jun 2026 04:51PM UTC	37	73.99	GitHub Action Run

pirl-unc / tsarina / 27153087900
77%

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