25817061370
84%

Ran 13 May 2026 06:01PM UTC

Jobs 4

Files 25

Run time 1min

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Committed 13 May 2026 06:00PM UTC coverage: 70.904% (+0.03%) from 70.878%

Build # 25817061370

Build Type

push

github

Committed by

web-flow

Commit Message

Fix #46: isolate cache in tests + defensive guard in match_clonotypes (#50)

The cmd_run integration tests were picking up the developer's
`~/.cache/tcrsift/` (added in PR #33 as a cache fallback), causing
failures when the cached IEDB v3 export had a format the loader
doesn't parse correctly — `database` ended up without a `cdr3_alpha`
column and `match_clonotypes` raised `KeyError`.

Two changes:

- `tests/conftest.py`: autouse fixture redirects `TCRSIFT_DATA_DIR`
  to an empty tmp path for every test. No more leakage from the
  developer's machine.

- `tcrsift/annotate.py`: defensive guard in `match_clonotypes`. If
  the standardized database is missing the columns we'd be indexing
  into, log a clear warning naming the database and the missing
  columns, then return the dataframe unmodified rather than crashing
  with a confusing `KeyError`.

The underlying IEDB v3 parser bug (hierarchical CSV header vs the
flat TSV the loader expects) is tracked separately in #49.

Bumps to 0.8.9.

Closes #46.

Coverage Stats

4657 of 6568 relevant lines covered (70.9%)

2.84 hits per line

Coverage Regressions

Lines	Coverage	∆	File
1	95.45	0.16%	annotate.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	python-3.11 - 25817061370.1	13 May 2026 06:01PM UTC	25	70.89	GitHub Action Run
2	python-3.12 - 25817061370.2	13 May 2026 06:01PM UTC	25	70.89	GitHub Action Run
3	python-3.10 - 25817061370.3	13 May 2026 06:01PM UTC	25	70.89	GitHub Action Run
4	python-3.9 - 25817061370.4	13 May 2026 06:01PM UTC	25	70.87	GitHub Action Run

pirl-unc / tcrsift / 25817061370
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