"""Tests for the coefficient registry.""" from __future__ import annotations from pathlib import Path import numpy as np import pytest from icg_cast.coefficients import ( EVIDENCE_LEVELS, PRIOR_DISTRIBUTIONS, CoefficientCard, load_registry, prior_sigma_for_evidence, registry, sampled_registry, save_registry, ) from icg_cast.constants import ARCHETYPE_KCC, ARCHETYPE_ORDER, ARCHETYPE_SIGNATURE def test_registry_loads_default_yaml() -> None: r = registry() assert len(r) > 100 assert r.schema_version == "0.2" def test_registry_cards_include_prior_metadata() -> None: r = registry() for card in r: assert card.prior_distribution in PRIOR_DISTRIBUTIONS assert isinstance(card.prior_params, dict) assert card.effect_direction in (None, -1, 0, 1) def test_registry_exposes_load_bearing_effect_directions() -> None: r = registry() assert r.card("dynamics.latent_risk.dna_coupling").effect_direction == 1 assert r.card("dynamics.latent_risk.immune_coupling").effect_direction == -1 assert r.card("dynamics.mutation_rate.scale").effect_direction == 1 def test_registry_returns_correct_types() -> None: r = registry() # scalar assert r.get("dynamics.dna_adducts.decay") == pytest.approx(0.68) # vector kcc = r.get_vector("archetypes.pah_tobacco_like.kcc") assert isinstance(kcc, tuple) and len(kcc) == 10 # string assert r.get_str("archetypes.pah_tobacco_like.signature") == "SBS4_like" def test_registry_get_rejects_wrong_kind() -> None: r = registry() with pytest.raises(TypeError): r.get("archetypes.pah_tobacco_like.kcc") # is a vector with pytest.raises(TypeError): r.get_vector("dynamics.dna_adducts.decay") # is a scalar with pytest.raises(TypeError): r.get_str("dynamics.dna_adducts.decay") # is a scalar with pytest.raises(KeyError): r.get("does.not.exist") def test_registry_filter_by_evidence_and_prefix() -> None: r = registry() e5 = r.filter(evidence_level="E5") e4 = r.filter(evidence_level="E4") assert len(e5) > 0 assert len(e4) > 0 assert len(e5) + len(e4) <= len(r) dyn = r.filter(prefix="dynamics.") assert all(c.name.startswith("dynamics.") for c in dyn) # invalid evidence level with pytest.raises(ValueError): r.filter(evidence_level="X9") def test_evidence_level_validation_in_cards() -> None: with pytest.raises(ValueError, match="invalid evidence_level"): CoefficientCard(name="x", default_value=1.0, evidence_level="X1") for level in EVIDENCE_LEVELS: CoefficientCard(name=f"x.{level}", default_value=1.0, evidence_level=level) def test_prior_spread_tracks_evidence_level() -> None: assert prior_sigma_for_evidence("E1") < prior_sigma_for_evidence("E5") with pytest.raises(ValueError): prior_sigma_for_evidence("X9") def test_sampled_registry_is_seedable_and_bounded() -> None: base = registry() first = sampled_registry(base, seed=123) second = sampled_registry(base, seed=123) third = sampled_registry(base, seed=124) assert first.get("dynamics.dna_adducts.decay") == pytest.approx( second.get("dynamics.dna_adducts.decay") ) assert first.get_vector("archetypes.pah_tobacco_like.kcc") == pytest.approx( second.get_vector("archetypes.pah_tobacco_like.kcc") ) assert first.get("dynamics.dna_adducts.decay") != pytest.approx( third.get("dynamics.dna_adducts.decay") ) assert first.get_str("archetypes.pah_tobacco_like.signature") == base.get_str( "archetypes.pah_tobacco_like.signature" ) assert first.get("signatures.background.seed") == base.get("signatures.background.seed") prior = np.asarray(first.get_vector("archetypes.sample_prior"), dtype=float) assert prior.sum() == pytest.approx(1.0) assert np.all(prior > 0.0) kcc = np.asarray(first.get_vector("archetypes.pah_tobacco_like.kcc"), dtype=float) assert np.all((0.0 <= kcc) & (kcc <= 1.0)) def test_constants_archetype_tables_are_built_from_registry() -> None: """ARCHETYPE_KCC / ARCHETYPE_SIGNATURE must mirror the registry exactly.""" r = registry() for name in ARCHETYPE_ORDER: assert ARCHETYPE_KCC[name] == r.get_vector(f"archetypes.{name}.kcc") assert ARCHETYPE_SIGNATURE[name] == r.get_str(f"archetypes.{name}.signature") def test_load_registry_accepts_override_yaml(tmp_path: Path) -> None: yaml_text = """ schema_version: "0.2" defaults: evidence_level: "E5" source: "test fixture" cards: - name: test.alpha default_value: 0.42 - name: test.vec default_value: [1.0, 2.0, 3.0] - name: test.label default_value: "hello" """ p = tmp_path / "custom.yaml" p.write_text(yaml_text, encoding="utf-8") r = load_registry(p) assert r.get("test.alpha") == pytest.approx(0.42) assert r.get_vector("test.vec") == (1.0, 2.0, 3.0) assert r.get_str("test.label") == "hello" def test_load_registry_rejects_duplicate_names(tmp_path: Path) -> None: yaml_text = """ schema_version: "0.2" cards: - name: dup default_value: 1.0 - name: dup default_value: 2.0 """ p = tmp_path / "dup.yaml" p.write_text(yaml_text, encoding="utf-8") with pytest.raises(ValueError, match="duplicate coefficient"): load_registry(p) def test_save_registry_roundtrip(tmp_path: Path) -> None: r = registry() path = save_registry(r.replace_card("dynamics.dna_adducts.decay", default_value=0.77), tmp_path / "cards.yaml") loaded = load_registry(path) assert loaded.get("dynamics.dna_adducts.decay") == pytest.approx(0.77) assert loaded.schema_version == r.schema_version def test_load_registry_rejects_missing_required_fields(tmp_path: Path) -> None: yaml_text = """ schema_version: "0.2" cards: - name: missing_value """ p = tmp_path / "bad.yaml" p.write_text(yaml_text, encoding="utf-8") with pytest.raises(ValueError, match="missing required field"): load_registry(p) def test_registry_is_singleton() -> None: a = registry() b = registry() assert a is b def test_no_inline_numeric_literals_in_covered_sites() -> None: """Spot-check that every covered file reads its coefficients from the registry.""" import inspect from icg_cast import omics, signatures, simulator for module, sentinels in ( (simulator, ("0.68 *", "0.36 *", "-7.5", "4.50 * clone_fraction")), (omics, ("0.8 * dna + 1.2 * k1", "0.45 * signature_profiles", "0.40 * k2")), (signatures, ("default_rng(123)", "shape=1.0, scale=0.2", "+= 2.0")), ): src = inspect.getsource(module) assert "from .coefficients import registry" in src, ( f"{module.__name__} no longer imports the registry" ) for sentinel in sentinels: assert sentinel not in src, ( f"{module.__name__} still contains inline literal: {sentinel!r}" ) def test_registry_acceptance_check_sources_present() -> None: """Audit signal: every card has a non-empty source field.""" r = registry() unsourced = [c for c in r if not c.source.strip()] assert unsourced == [], ( f"{len(unsourced)} coefficient cards have empty source fields; " "this is allowed during draft work but should fail PRs that try to " "ship without provenance." )