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Ran 13 May 2026 07:47PM UTC

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Build # 25822228984

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push

github

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web-flow

Commit Message

Rename PhaseAmbiguousEffect -> PhaseCandidateSet (#376)

* Rename PhaseAmbiguousEffect -> PhaseCandidateSet (bump 4.23.0)

The class wraps a set of phase-hypothesis candidates, so a plural-
flavored name reads better at call sites:

    if isinstance(eff, PhaseCandidateSet):
        for c in eff.candidates:
            ...

Hard rename (no alias). The class is only exported via
varcode.effects.effect_classes, so this affects only callers that
imported the name directly.

docs/germline.md rewritten to lead with three concrete scenarios:
1. no germline (reference-relative)
2. germline + unknown phase -> PhaseCandidateSet
3. germline + phase_resolver -> single MutationEffect

Capturing real CFTR test-fixture output throughout.

* test.sh: memory-aware pytest-xdist worker count

Mirror the worker-cap logic from trufflepig/hitlist/tsarina/vaxrank
so concurrent test runs across sibling repos can't fork-bomb the
laptop. Picks min(cpu_reserve, available_RAM / PER_WORKER_GB),
reserves 1-2 cores, falls back to serial pytest when xdist isn't
installed, logs inputs so the chosen worker count is auditable.

* Address review nits: rename test method, CHANGELOG entry, resolver-stub caveat

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