25817469984
84%

Ran 13 May 2026 06:09PM UTC

Jobs 4

Files 25

Run time 1min

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Committed 13 May 2026 06:07PM UTC coverage: 70.998% (+0.09%) from 70.904%

Build # 25817469984

Build Type

push

github

Committed by

web-flow

Commit Message

Fix #49: parse IEDB v3 hierarchical-header CSV in load_iedb (#51)

The IEDB receptor_full_v3.zip export tcrsift downloads ships as a CSV
with a two-row header — top row is the section ("Receptor", "Epitope",
"Assay", "Chain 1", "Chain 2"), second row is the field. The previous
loader used sep="\t" and looked for flat headers like "Chain 2 CDR3
Curated", silently producing a dataframe without cdr3_alpha/cdr3_beta
when handed the real cached file. That was the root cause of the
KeyError #46 papered over with a defensive guard.

Now:

- Sniff the first line: if it starts "Receptor,Receptor" treat as the
  v3 hierarchical CSV; otherwise fall back to the legacy flat TSV
  parser for backward compatibility.
- v3 path filters to Receptor Type == alphabeta, then extracts
  cdr3_alpha from Chain 1 and cdr3_beta from Chain 2, preferring
  "CDR3 Curated" over "CDR3 Calculated" per chain.
- Drops rows with no CDR3 on either chain (unmatchable).

Verified end-to-end against the cached tcr_full_v3.csv (99MB,
225,664 alphabeta rows extracted, 64K with alpha, 195K with beta).

Bumps to 0.8.10.

Closes #49.

Coverage Stats

4683 of 6596 relevant lines covered (71.0%)

2.84 hits per line

Coverage Regressions

Lines	Coverage	∆	File
5	95.1	-0.36%	annotate.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	python-3.12 - 25817469984.1	13 May 2026 06:09PM UTC	25	70.99	GitHub Action Run
2	python-3.10 - 25817469984.2	13 May 2026 06:09PM UTC	25	70.99	GitHub Action Run
3	python-3.9 - 25817469984.3	13 May 2026 06:09PM UTC	25	70.96	GitHub Action Run
4	python-3.11 - 25817469984.4	13 May 2026 06:09PM UTC	25	70.99	GitHub Action Run

pirl-unc / tcrsift / 25817469984
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