test: cross-pipeline smoke run for all three modalities

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

tests/pipelines/test_cross_pipeline_smoke.py

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+"""End-to-end smoke test exercising all three pipelines back-to-back.
+
+Asserts each pipeline produces a non-empty Parquet at its expected schema —
+the hackathon-judge "does the whole stack still work?" check. Each pipeline
+uses its own fixture (no cross-modality data sharing).
+"""
+from __future__ import annotations
+
+from pathlib import Path
+
+import pandas as pd
+import pytest
+
+from src.pipelines import bbb_pipeline, eeg_pipeline, mri_pipeline
+
+
+_REPO_ROOT = Path(__file__).resolve().parents[2]
+_FIXTURES = _REPO_ROOT / "tests" / "fixtures"
+
+
+def test_bbb_pipeline_smoke(tmp_path: Path) -> None:
+    """Run the BBB pipeline on the committed CSV fixture; validate fp_ column count."""
+    out = tmp_path / "bbb.parquet"
+    bbb_pipeline.run_pipeline(
+        input_path=_FIXTURES / "bbbp_sample.csv",
+        output_path=out,
+    )
+    df = pd.read_parquet(out)
+    assert len(df) == 4
+    assert sum(c.startswith("fp_") for c in df.columns) == 2048
+
+
+def test_eeg_pipeline_smoke(tmp_path: Path) -> None:
+    """Use the committed EEG fixture; build_eeg_fixture.build() takes no args."""
+    fif = _FIXTURES / "eeg_sample.fif"
+    if not fif.exists():
+        pytest.skip(f"Committed EEG fixture missing: {fif}")
+    out = tmp_path / "eeg.parquet"
+    eeg_pipeline.run_pipeline(input_path=fif, output_path=out)
+    df = pd.read_parquet(out)
+    assert len(df) == 5
+    feat_cols = [c for c in df.columns if c.startswith("feat_")]
+    assert len(feat_cols) > 0
+
+
+def test_mri_pipeline_smoke(tmp_path: Path) -> None:
+    """Use the MRI fixture builder to materialize NIfTI inputs + sites.csv."""
+    from tests.fixtures.build_mri_fixture import build as build_mri
+    fixture_dir = build_mri(out_dir=tmp_path / "mri_fixture")
+    out = tmp_path / "mri.parquet"
+    mri_pipeline.run_pipeline(
+        input_dir=fixture_dir,
+        sites_csv=fixture_dir / "sites.csv",
+        output_path=out,
+    )
+    df = pd.read_parquet(out)
+    assert len(df) == 6
+    assert "subject_id" in df.columns
+    assert "site" in df.columns
+
+
+def test_all_three_pipelines_run_in_one_process(tmp_path: Path) -> None:
+    """Sanity: nothing in pipeline A leaks state that breaks pipeline B."""
+    test_bbb_pipeline_smoke(tmp_path / "bbb")
+    test_eeg_pipeline_smoke(tmp_path / "eeg")
+    test_mri_pipeline_smoke(tmp_path / "mri")