pirl-unc / tsarina / 25684806806
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Stub MHCflurry predictor in pytest conftest to prevent ~55 GB OOM (#70)

* Stub MHCflurry presentation predictor in pytest conftest (#68)

Adds tests/conftest.py with an autouse fixture that installs a tiny
in-memory stand-in for Class1PresentationPredictor into the cached
singleton at tsarina.scoring._MHCFLURRY_PRESENTATION_PREDICTOR. The
real predictor loads ~140 Keras models and consumes 3-6 GB resident
per process, and the test suite had no shared guard preventing it
from being instantiated. Combined with pytest-cov subprocess
collection this manifested as a ~55 GB OOM on a developer machine.

Existing per-test monkeypatches (tsarina.scoring.score_presentation,
tsarina.scoring._load_mhcflurry_presentation_predictor) continue to
override the conftest stub; test_mhcflurry_import_error resets the
singleton to None and still exercises the real loader path.

Also extends .gitignore with .coverage.* so pytest-cov parallel-mode
data files stop showing up as untracked.

Closes #68.

* Use raise-sentinel instead of dummy values in MHCflurry conftest stub

The original stub returned deterministic dummy presentation/affinity
values, which (a) no test currently asserts on and (b) risks silently
passing a future test that forgets its per-call stub but accidentally
hits this code path.

Swap to a sentinel that raises AssertionError with an actionable
message if its `predict` is ever called. Test runs confirm zero tests
depend on the dummy values: all 312 still pass under both sequential
and `pytest -n auto` xdist modes, with peak RSS ~85 MB under xdist
(vs. ~55 GB without any stub).

2383 of 3386 relevant lines covered (70.38%)

0.7 hits per line

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