Junior B.
b731478f5d
Set up the project skeleton per PLAN.md §4: - src/ package: identifiers, disease, drugs, scoring, provenance with pydantic schemas and confidence-tier logic (working); data-pull/compute functions stubbed per their build week - 5 starter notebooks (01-05) with PLAN-referenced steps - tests/test_scoring.py: tier-assignment tests pass; scoring reference test xfail until Week 3 - docs/: recovery_test_report, data_sources, known_limitations skeletons - pyproject.toml (requires-python >=3.11,<3.14), .gitignore, README - data/ tree preserved via .gitkeep; raw/processed/results gitignored Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
66 lines
2.3 KiB
Python
66 lines
2.3 KiB
Python
"""Tests for the matching engine and provenance logic.
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The headline test (PLAN.md §6, Week 3 task 4) verifies connectivity scoring against a known
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reference within tolerance; it is marked xfail until the scorer is implemented in Week 3.
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The tier-assignment tests run today — they pin the rules from PLAN.md §3 so the most
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commercially important design decision can't silently drift.
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"""
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from __future__ import annotations
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import pytest
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from src.provenance import ConfidenceTier, assign_tier
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class TestAssignTier:
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"""Tier rules from PLAN.md §3."""
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def test_measured_large_n_peer_reviewed_multi_source_is_tier_a(self):
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assert (
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assign_tier(
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is_measured=True,
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n_per_group=27,
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peer_reviewed=True,
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single_source=False,
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)
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== ConfidenceTier.A
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)
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def test_inferred_is_always_tier_c(self):
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assert (
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assign_tier(
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is_measured=False,
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n_per_group=1000,
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peer_reviewed=True,
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single_source=False,
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)
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== ConfidenceTier.C
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)
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@pytest.mark.parametrize(
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"kwargs",
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[
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dict(is_measured=True, n_per_group=6, peer_reviewed=True, single_source=False),
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dict(is_measured=True, n_per_group=27, peer_reviewed=False, single_source=False),
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dict(is_measured=True, n_per_group=27, peer_reviewed=True, single_source=True),
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dict(is_measured=True, n_per_group=None, peer_reviewed=True, single_source=False),
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],
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)
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def test_measured_but_weak_evidence_is_tier_b(self, kwargs):
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assert assign_tier(**kwargs) == ConfidenceTier.B
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@pytest.mark.xfail(reason="Connectivity scoring implemented in Week 3 (notebook 04).", strict=True)
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def test_connectivity_score_matches_reference():
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"""Verify connectivity scoring against a CMap/cmapPy reference within tolerance.
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PLAN.md §6, Week 3 task 4. Replace this body with a known reference example
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(disease up/down sets + drug signature -> expected score) once the scorer exists.
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"""
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from src.scoring import connectivity_score
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score = connectivity_score(up_genes=[], down_genes=[], drug_signature=None) # noqa
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assert score == pytest.approx(0.0, abs=1e-6)
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