"""Tests for PPI results collection (scripts_ppi/collect_results.py).""" from __future__ import annotations import json import sys from pathlib import Path import numpy as np import pandas as pd import pytest ROOT = Path(__file__).parent.parent sys.path.insert(0, str(ROOT / "scripts_ppi")) from collect_results import ( MODEL_ORDER, NEG_ORDER, SPLIT_ORDER, TABLE_METRICS, aggregate_over_seeds, build_table1, filter_results, format_markdown, load_results, summarize_exp1, ) # --------------------------------------------------------------------------- # Fixtures # --------------------------------------------------------------------------- def _make_result_json( run_dir: Path, model: str = "siamese_cnn", split: str = "random", negative: str = "negbiodb", dataset: str = "balanced", seed: int = 42, log_auc: float = 0.300, ) -> Path: """Create a fake results.json in a run directory.""" run_name = f"{model}_{dataset}_{split}_{negative}_seed{seed}" d = run_dir / run_name d.mkdir(parents=True, exist_ok=True) payload = { "run_name": run_name, "model": model, "split": split, "negative": negative, "dataset": dataset, "seed": seed, "best_val_log_auc": log_auc, "n_train": 1000, "n_val": 100, "n_test": 200, "test_metrics": { "log_auc": log_auc, "auprc": log_auc * 0.8, "bedroc": log_auc * 0.9, "ef_1pct": 5.0, "ef_5pct": 3.0, "mcc": log_auc * 0.5, "auroc": log_auc + 0.5, }, } path = d / "results.json" with open(path, "w") as f: json.dump(payload, f) return path @pytest.fixture def results_dir(tmp_path: Path) -> Path: """Create a results directory with 18 runs (3 models x 6 configs).""" rd = tmp_path / "ppi_baselines" for model in MODEL_ORDER: # B1-B3: 3 splits x negbiodb for split in ["random", "cold_protein", "cold_both"]: _make_result_json(rd, model=model, split=split, negative="negbiodb", log_auc=0.300) # E1: 2 controls x random _make_result_json(rd, model=model, split="random", negative="uniform_random", log_auc=0.450) _make_result_json(rd, model=model, split="random", negative="degree_matched", log_auc=0.400) # E4: DDB _make_result_json(rd, model=model, split="ddb", negative="negbiodb", log_auc=0.280) return rd # --------------------------------------------------------------------------- # Tests # --------------------------------------------------------------------------- class TestLoadResults: def test_loads_all(self, results_dir: Path): df = load_results(results_dir) assert len(df) == 18 # 3 models x 6 configs def test_empty_dir(self, tmp_path: Path): df = load_results(tmp_path / "nonexistent") assert df.empty def test_has_expected_columns(self, results_dir: Path): df = load_results(results_dir) for col in ["model", "split", "negative", "dataset", "seed"] + TABLE_METRICS: assert col in df.columns def test_deduplication(self, results_dir: Path): # Create a duplicate run _make_result_json(results_dir, model="siamese_cnn", split="random", negative="negbiodb", log_auc=0.350) df = load_results(results_dir) mask = (df["model"] == "siamese_cnn") & (df["split"] == "random") & (df["negative"] == "negbiodb") assert mask.sum() == 1 class TestFilterResults: def test_filter_by_model(self, results_dir: Path): df = load_results(results_dir) filtered = filter_results(df, models=["siamese_cnn"]) assert len(filtered) == 6 assert (filtered["model"] == "siamese_cnn").all() def test_filter_by_split(self, results_dir: Path): df = load_results(results_dir) filtered = filter_results(df, splits=["random"]) assert len(filtered) == 9 # 3 models x 3 negatives def test_filter_by_negative(self, results_dir: Path): df = load_results(results_dir) filtered = filter_results(df, negatives=["negbiodb"]) assert len(filtered) == 12 # 3 models x 4 splits class TestBuildTable1: def test_ordered_output(self, results_dir: Path): df = load_results(results_dir) table = build_table1(df) assert len(table) == 18 # First row should be siamese_cnn (first in MODEL_ORDER) assert table.iloc[0]["model"] == "siamese_cnn" def test_has_metrics(self, results_dir: Path): df = load_results(results_dir) table = build_table1(df) for m in TABLE_METRICS: assert m in table.columns class TestAggregateOverSeeds: def test_single_seed(self, results_dir: Path): df = load_results(results_dir) agg = aggregate_over_seeds(df) assert len(agg) == 18 # same as unique configs (1 seed each) assert (agg["n_seeds"] == 1).all() def test_multi_seed(self, results_dir: Path): # Add seed=43 runs for model in MODEL_ORDER: _make_result_json(results_dir, model=model, split="random", negative="negbiodb", seed=43, log_auc=0.320) df = load_results(results_dir) agg = aggregate_over_seeds(df) mask = (agg["split"] == "random") & (agg["negative"] == "negbiodb") assert (agg.loc[mask, "n_seeds"] == 2).all() def test_empty(self): agg = aggregate_over_seeds(pd.DataFrame()) assert agg.empty class TestFormatMarkdown: def test_produces_table(self, results_dir: Path): df = load_results(results_dir) table = build_table1(df) md = format_markdown(table) assert "| **Model**" in md assert "siamese_cnn" in md assert len(md.split("\n")) == 20 # header + separator + 18 rows class TestSummarizeExp1: def test_inflation_computed(self, results_dir: Path): df = load_results(results_dir) exp1_df = df[df["split"] == "random"] summary = summarize_exp1(exp1_df) assert "NegBioDB=" in summary assert "uniform_random=" in summary assert "degree_matched=" in summary def test_empty_df(self): summary = summarize_exp1(pd.DataFrame()) assert "No Exp 1" in summary class TestMainCLI: def test_main_success(self, results_dir: Path, tmp_path: Path): from collect_results import main out_dir = tmp_path / "out" ret = main([ "--results-dir", str(results_dir), "--out", str(out_dir), ]) assert ret == 0 assert (out_dir / "table1.csv").exists() assert (out_dir / "table1.md").exists() def test_main_aggregate(self, results_dir: Path, tmp_path: Path): from collect_results import main out_dir = tmp_path / "out" ret = main([ "--results-dir", str(results_dir), "--out", str(out_dir), "--aggregate-seeds", ]) assert ret == 0 assert (out_dir / "table1_aggregated.csv").exists() def test_main_no_results(self, tmp_path: Path): from collect_results import main ret = main([ "--results-dir", str(tmp_path / "empty"), "--out", str(tmp_path / "out"), ]) assert ret == 1