test: regression suite for the predict.py rule/computed packs

.github/workflows/ci.yml

@@ -21,6 +21,8 @@ jobs:
         run: pip install ruff pytest
       - name: Ruff lint
         run: ruff check .
+      - name: Install runtime deps
+        run: pip install -r requirements.txt
       - name: Pytest
         run: |
           if git ls-files '*test_*.py' '*_test.py' 'tests/**/*.py' | grep -q .; then

requirements.txt

@@ -0,0 +1,9 @@
+# Core runtime for the prediction pipeline (training/predict.py) + the test suite.
+# Demo/export extras (skl2onnx, onnxruntime, pubchempy, umap-learn, fastapi,
+# openpyxl) are listed in training/SETUP.md and installed as needed.
+rdkit
+numpy
+pandas
+scikit-learn
+joblib
+pyarrow

tests/conftest.py

@@ -0,0 +1,5 @@
+"""Make the training/ modules importable from the test suite."""
+import os
+import sys
+
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), "..", "training"))

tests/test_physchem.py

@@ -0,0 +1,32 @@
+"""Physicochemical / stability / chemesthesis packs — exact-from-structure, model-independent."""
+from rdkit import Chem
+
+import predict
+
+
+def test_physchem_benzene_mw():
+    out = predict.physchem(Chem.MolFromSmiles("c1ccccc1"))
+    assert abs(out["computed"]["mol_weight"] - 78.11) < 0.5
+    assert "logP" in out["computed"]
+    assert "water_solubility_logS" in out["estimate"]
+
+
+def test_stability_flags_vanillin_motifs():
+    out = predict.stability(Chem.MolFromSmiles("O=Cc1ccc(O)c(OC)c1"))  # vanillin
+    assert "aldehyde" in out["oxidation_watch"]
+    assert "phenol/catechol" in out["oxidation_watch"]
+
+
+def test_chemesthesis_astringent_polyphenol():
+    out = predict.chemesthesis(Chem.MolFromSmiles("Oc1cccc(O)c1O"))  # pyrogallol, 3 phenols
+    assert any("astringent" in c for c in out["classes"])
+
+
+def test_chemesthesis_pungent_isothiocyanate():
+    out = predict.chemesthesis(Chem.MolFromSmiles("C=CCN=C=S"))  # allyl isothiocyanate
+    assert any("pungent" in c for c in out["classes"])
+
+
+def test_chemesthesis_silent_on_plain_molecule():
+    out = predict.chemesthesis(Chem.MolFromSmiles("CCO"))  # ethanol
+    assert out["classes"] == []

tests/test_predict.py

@@ -0,0 +1,24 @@
+"""End-to-end predict() — must run and stay well-formed even with NO trained models
+(as in CI). The trained taste heads sharpen the output; their absence must never crash it.
+"""
+import predict
+
+
+def test_predict_wellformed_without_models():
+    out = predict.predict("OC(=O)CC(O)(CC(=O)O)C(=O)O")  # citric acid
+    for key in ("smiles", "physchem", "stability", "chemesthesis",
+                "analytical", "labeling", "safety", "taste_profile"):
+        assert key in out
+    assert out["safety"]["review_required"] is True
+    assert out["sour"] is True  # the rule fires regardless of trained heads
+
+
+def test_predict_rejects_bad_smiles():
+    out = predict.predict("not-a-molecule")
+    assert "error" in out
+
+
+def test_predict_aroma_is_honest_placeholder():
+    out = predict.predict_aroma("CCO")
+    assert out["available"] is False
+    assert "AROMA.md" in out["note"]

tests/test_rules.py

@@ -0,0 +1,62 @@
+"""Deterministic rule / lookup logic — no trained models or data files required.
+
+These cover the rule layer the .NET product (M2) will port: sour/salty calls,
+allergen labeling, and the documented dangerous-mixture screen.
+"""
+from rdkit import Chem
+
+import predict
+
+
+def _mol(smiles):
+    return Chem.MolFromSmiles(smiles)
+
+
+def test_sour_fires_on_acid():
+    out = predict._sour(_mol("CC(=O)O"))  # acetic acid
+    assert out["sour"] is True
+    assert out["sour_reason"]
+
+
+def test_sour_silent_on_nonacid():
+    out = predict._sour(_mol("c1ccccc1"))  # benzene
+    assert out["sour"] is False
+    assert out["sour_reason"] == []
+
+
+def test_salty_inorganic_salt():
+    out = predict._salty(_mol("[Na+].[Cl-]"))  # NaCl
+    assert out["salty"] is True
+    assert "inorganic" in out["salty_reason"]
+
+
+def test_salty_defers_to_organic_anion():
+    # monosodium glutamate — cation present, but the organic anion owns the taste
+    out = predict._salty(_mol("C(CC(=O)[O-])C(C(=O)O)N.[Na+]"))
+    assert out["salty"] is False
+    assert "organic anion" in out["salty_reason"]
+
+
+def test_salty_silent_on_single_fragment():
+    out = predict._salty(_mol("OC1OC(CO)C(O)C(O)C1O"))  # glucose
+    assert out["salty"] is False
+
+
+def test_labeling_shape_and_negative():
+    out = predict.labeling(_mol("O=Cc1ccc(O)c(OC)c1"))  # vanillin — not declarable
+    assert out["eu_declarable_allergen"] is False
+    assert out["allergen_name"] is None
+
+
+def test_check_mixture_empty_is_wellformed():
+    out = predict.check_mixture([])
+    assert out["active_hazards"] == []
+    assert out["conditional_hazards"] == []
+    assert "disclaimer" in out
+
+
+def test_check_mixture_flags_nitrosamine():
+    # sodium nitrite + a secondary amine -> documented nitrosamine hazard
+    out = predict.check_mixture(["[Na+].[O-]N=O", "CNC"])
+    hazards = out["active_hazards"] + out["conditional_hazards"]
+    assert any("nitrosamine" in h["possible_product"].lower() for h in hazards)

tests/test_substitute.py

@@ -0,0 +1,39 @@
+"""Substitution search — graceful without a reference set, correct ranking with one.
+
+The ranking logic is tested against a hand-built in-memory index so it needs no data
+files; the .NET product (M6) mirrors this as a pgvector ANN query.
+"""
+from rdkit import Chem
+
+import predict
+
+
+def _canon(s):
+    return Chem.MolToSmiles(Chem.MolFromSmiles(s))
+
+
+def test_substitute_rejects_bad_smiles():
+    assert "error" in predict.substitute("nope")
+
+
+def test_substitute_graceful_without_data(monkeypatch):
+    monkeypatch.setattr(predict, "_SUB_INDEX", ([], [], []))
+    out = predict.substitute("CCO")
+    assert out["neighbors"] == []
+    assert "note" in out
+
+
+def test_substitute_ranks_by_similarity(monkeypatch):
+    mols = ["CCO", "CCCO", "c1ccccc1"]  # ethanol, propanol, benzene
+    fps = [predict._MORGAN.GetFingerprint(Chem.MolFromSmiles(s)) for s in mols]
+    canon = [_canon(s) for s in mols]
+    monkeypatch.setattr(predict, "_SUB_INDEX", (fps, canon, [[], [], []]))
+    out = predict.substitute("CCO", k=2)
+    neighbors = out["neighbors"]
+    # the query itself is excluded
+    assert all(n["smiles"] != _canon("CCO") for n in neighbors)
+    # propanol (closer to ethanol) ranks above benzene
+    assert neighbors[0]["smiles"] == _canon("CCCO")
+    # similarities come back sorted descending
+    sims = [n["similarity"] for n in neighbors]
+    assert sims == sorted(sims, reverse=True)