Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/tests/test_figure4_sources.py

@@ -0,0 +1,52 @@
+"""Legacy contrast files must not silently stand in for corrected Figure 4 data."""
+import importlib.util
+import json
+import os
+from pathlib import Path
+
+os.environ["CUDA_VISIBLE_DEVICES"] = ""
+import pytest
+
+PATH = Path(__file__).resolve().parents[1] / "tools/build_results_figures.py"
+spec = importlib.util.spec_from_file_location("figure4_sources", PATH)
+figures = importlib.util.module_from_spec(spec)
+spec.loader.exec_module(figures)
+
+
+def test_missing_corrected_signal_renders_pending_even_if_legacy_headline_exists(tmp_path, monkeypatch):
+    monkeypatch.setattr(figures, "ROOT", tmp_path)
+    old = tmp_path / "source_data/fig4_strict_contrast.csv"
+    old.parent.mkdir()
+    old.write_text("cohort,arm,partial_r\nye2026_sepsis,lora,0.99\n")
+    saved = []
+    def save(fig, name):
+        saved.append(name)
+        figures.plt.close(fig)
+    monkeypatch.setattr(figures, "save", save)
+    rows, reasons = figures.donor_signal_panels({c: [] for c in figures.COHORTS})
+    assert not rows and reasons
+    assert len(saved) == 4
+    assert "fig4_disease_signal_strict" in saved
+
+
+def test_corrected_provenance_must_cover_all_twenty_canonical_supports(tmp_path, monkeypatch):
+    monkeypatch.setattr(figures, "ROOT", tmp_path)
+    path = tmp_path / "source_data/fig4_donor_aware_provenance.json"
+    path.parent.mkdir()
+    path.write_text(json.dumps({"schema": "pbisc.fig4.donor-aware-signal.v1", "status": "complete", "units": {}}))
+    with pytest.raises(ValueError, match="support differs"):
+        figures.donor_signal_panels({c: [] for c in figures.COHORTS})
+
+
+def test_actual_historical_comparison_uses_real_bulk_lora_and_scsemi_and_excludes_giroux_sex_genes():
+    rows, gaps = figures.historical_fivefold_rows()
+    assert not gaps
+    assert len(rows) == 16
+    for cohort in figures.COHORTS:
+        sub = [r for r in rows if r["cohort"] == cohort]
+        pair = {r["arm"]: r for r in sub}
+        assert pair["lora"]["source_arm"] == "real_lora__raw"
+        assert pair["scsemi"]["source_arm"] == "scsemi__raw"
+        assert pair["lora"]["reference_sha256"] == pair["scsemi"]["reference_sha256"]
+        if cohort == "giroux2022":
+            assert all("scores_nosex" in r["source"] and r["gene_exclusion_sha256"] for r in sub)

paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/tests/test_figure5_details.py

@@ -0,0 +1,26 @@
+from pathlib import Path
+import sys
+import pandas as pd
+import pytest
+
+sys.path.insert(0, str(Path(__file__).resolve().parents[1] / 'tools'))
+from figure5_details import all_state_metrics
+
+
+def test_zero_states_remain_detection_outcomes_not_abundance_auc():
+    base = dict(cohort='a',unit='draw0',arm='lora',state='rare')
+    donor = pd.DataFrame([{**base,'donor_id':'A','obs_state':2,'gen_state':0},
+                          {**base,'donor_id':'B','obs_state':0,'gen_state':1},
+                          {**base,'donor_id':'C','obs_state':1,'gen_state':1}])
+    summary = pd.DataFrame([{**base,'high_low_abundance_auroc':.7}])
+    row = all_state_metrics(donor,summary).iloc[0]
+    assert row.missed_observed_fraction == .5
+    assert row.generated_in_observed_zero_fraction == 1
+    assert row.high_low_abundance_auroc == .7
+    assert row.n_evaluable_donors == 3
+
+
+def test_visits_cannot_be_counted_as_donors():
+    base = dict(cohort='a',unit='draw0',arm='lora',state='rare',donor_id='A',obs_state=1,gen_state=0)
+    with pytest.raises(ValueError,match='repeated visits'):
+        all_state_metrics(pd.DataFrame([base,base]),pd.DataFrame())

paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/tests/test_import_scsemi_legacy.py

@@ -0,0 +1,103 @@
+"""Regression gates for adopting a prior five-pair scSemi sepsis run."""
+from __future__ import annotations
+
+import importlib.util
+import json
+from pathlib import Path
+
+import pytest
+
+ROOT = Path(__file__).resolve().parents[1]
+SPEC = importlib.util.spec_from_file_location("import_scsemi_legacy", ROOT / "tools/import_scsemi_legacy.py")
+assert SPEC and SPEC.loader
+I = importlib.util.module_from_spec(SPEC)
+SPEC.loader.exec_module(I)
+SUPPORT = ROOT / "protocol/splits/ye2026_sepsis/disease/draw0/support.json"
+
+
+def test_only_canonical_sepsis_disease_draw_is_accepted(tmp_path: Path) -> None:
+    assert I.paths(SUPPORT)[0]["unit"] == "draw0_n5"
+    copied = tmp_path / "support.json"
+    copied.write_text(SUPPORT.read_text())
+    with pytest.raises(ValueError, match="noncanonical"):
+        I.paths(copied)
+    other = ROOT / "protocol/splits/ji2025_chili/disease/draw0/support.json"
+    with pytest.raises(ValueError, match="limited to five sepsis"):
+        I.paths(other)
+
+
+def test_draw0_exact_five_own_hvg_and_source_receipts() -> None:
+    proof = I.verify(SUPPORT)
+    assert proof["status"] == "verified_source_not_native_strict_run"
+    assert len(proof["model_sha256"]) == 10
+    assert len(proof["target_shard_sha256"]) == 77
+    assert len(proof["prepared_assets_equal"]) == 15
+    assert "hvset.npy" in proof["prepared_assets_equal"]
+    assert len(proof["source_sample_sc_cleaned_after_training"]) == 5
+    assert proof["source_provenance"]["approved_migration"] is not None
+
+
+def test_reuse_cv_metadata_fails_closed(monkeypatch) -> None:
+    original = I.read
+    old = I.paths(SUPPORT)[1]
+    source_inputs = old / "inputs/inputs_manifest.json"
+
+    def altered(path: Path) -> dict:
+        value = original(path)
+        if path == source_inputs:
+            return {**value, "reuse_cv": "/larger/reference"}
+        return value
+
+    monkeypatch.setattr(I, "read", altered)
+    with pytest.raises(ValueError, match="reused another run"):
+        I.verify(SUPPORT)
+
+
+def test_all_five_exports_are_source_bound_and_independently_validated() -> None:
+    for draw in range(5):
+        support = ROOT / f"protocol/splits/ye2026_sepsis/disease/draw{draw}/support.json"
+        s, source_work, strict_work, source_output = I.paths(support)
+        adoption_path = strict_work / "adopted_legacy/ADOPTION.json"
+        adoption = json.loads(adoption_path.read_text())
+        output = ROOT / f"generated/ye2026_sepsis/disease/draw{draw}/scsemi.npz"
+        receipt = json.loads(output.with_suffix(".log").read_text())
+        validation = json.loads(output.with_suffix(".validation.json").read_text())
+        assert output.samefile(source_output)
+        assert adoption["status"] == "verified_source_not_native_strict_run"
+        assert adoption["support_sha256"] == s["sha256"]
+        assert len(adoption["model_sha256"]) == 10
+        assert len(adoption["target_shard_sha256"]) == len(s["test_sample_ids"]) == 77
+        assert receipt["schema"] == "pbisc.scsemi.adopted-output.v1"
+        assert receipt["source_work"] == str(source_work)
+        assert receipt["source_output"] == str(source_output)
+        assert receipt["output_sha256"] == I.sha(output)
+        assert validation["passed"] is True
+        assert validation["npz_sha256"] == receipt["output_sha256"]
+
+
+def test_adopted_generation_returns_strict_scorer_binding() -> None:
+    support = json.loads(SUPPORT.read_text())
+    output = ROOT / "generated/ye2026_sepsis/disease/draw0/scsemi.npz"
+    binding = I.validate_adopted_generation(output, support)
+    assert binding["arm"] == "scsemi"
+    assert binding["source_kind"] == "verified_legacy_scsemi_adoption"
+    assert binding["support_sha256"] == support["sha256"]
+    assert binding["source_binding"].endswith("/adopted_legacy/ADOPTION.json")
+
+
+def test_adopted_generation_rejects_wrong_path_or_receipt(monkeypatch) -> None:
+    support = json.loads(SUPPORT.read_text())
+    output = ROOT / "generated/ye2026_sepsis/disease/draw0/scsemi.npz"
+    with pytest.raises(ValueError, match="canonical adopted output"):
+        I.validate_adopted_generation(ROOT / "generated/ye2026_sepsis/disease/draw1/scsemi.npz", support)
+    original = I.read
+
+    def altered(path: Path) -> dict:
+        record = original(path)
+        if path == output.with_suffix(".log"):
+            return {**record, "condition_sha256": "0" * 64}
+        return record
+
+    monkeypatch.setattr(I, "read", altered)
+    with pytest.raises(ValueError, match="adopted output receipt differs"):
+        I.validate_adopted_generation(output, support)

paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/tests/test_legacy_export_dispatch.py

@@ -0,0 +1,37 @@
+import importlib.util
+import os
+from pathlib import Path
+import unittest
+
+os.environ["CUDA_VISIBLE_DEVICES"] = ""
+ROOT = Path(__file__).resolve().parents[1]
+LEGACY = ROOT.parent / "paired_finetune_intradataset_20260927/scsemi/tools/export_npz.py"
+
+
+class DispatchTests(unittest.TestCase):
+    def module(self):
+        spec = importlib.util.spec_from_file_location("legacy_export_dispatch", LEGACY)
+        mod = importlib.util.module_from_spec(spec)
+        spec.loader.exec_module(mod)
+        self.assertTrue(hasattr(mod, "strict_export_arguments"), "strict mode has no safe exporter dispatch")
+        return mod
+
+    def test_legacy_modes_stay_on_original_exporter(self):
+        mod = self.module()
+        for mode in ("fewshot", "cv", "budget"):
+            self.assertIsNone(mod.strict_export_arguments({"mode": mode}, Path("work"), Path("out.npz")))
+
+    def test_strict_support_path_comes_from_bound_condition_location(self):
+        mod = self.module()
+        cond = ROOT / "data/immicro/healthy/fold0/n5/test_raw.npz"
+        args = mod.strict_export_arguments({"mode": "strict", "condition_npz": str(cond)}, ROOT / "scsemi/x", ROOT / "g.npz")
+        self.assertEqual(args[-1], str(ROOT / "protocol/splits/immicro/healthy/fold0/n5/support.json"))
+
+    def test_unrelated_condition_cannot_dispatch_to_strict_plan(self):
+        mod = self.module()
+        with self.assertRaises(ValueError):
+            mod.strict_export_arguments({"mode": "strict", "condition_npz": "/tmp/unbound.npz"}, Path("work"), Path("out"))
+
+
+if __name__ == "__main__":
+    unittest.main()