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Ran 13 May 2026 06:01PM UTC

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Committed 13 May 2026 06:00PM UTC coverage: 70.894% (+0.03%) from 70.867%

Job # 25817061370.3

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.

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