tests: fill_prof_email 9/9 smoke + CI wiring

Regression coverage across the matrix:

  Hydration kind:
    PASS + all fields fill → rc 0
    FAIL + methane sign flip → email shows FAIL on methane
    fail_case bundled fixture → end-to-end works (rc 0 or 2)

  Binding kind:
    biotin/desthiobiotin rows → 'streptavidin binding' subject
    erlotinib/gefitinib rows → 'EGFR kinase binding' subject
    non-binder prediction → 'desthiobiotin predicted non-binder'
      flagged in email

  Failure modes:
    malformed report (unparseable MAE) → rc 2 + WARNING banner
    no report.md at all → rc 1 (hard error)

  Ergonomics:
    --prof-name 'Dr. Chen' → 'Hi Dr. Chen,' instead of '[Prof]'

Wired into smoke.yml so every PR guards the Milestone-A → email
pipeline the moment the tarball lands.

Author: Rockman6

.github/workflows/smoke.yml

@@ -184,6 +184,9 @@ jobs:
       - name: bridge — Campaign-1 → Campaign-2 rate-law emitter
         run: python -u tests/bridge/test_binding_to_hill_smoke.py
 
+      - name: fill_prof_email auto-fill regression (9/9)
+        run: python -u tests/fep/test_fill_prof_email_smoke.py
+
       - name: fep sampled binding smoke (opt-in, ~10 min, manual)
         if: >
           github.event_name == 'workflow_dispatch' &&

tests/fep/test_fill_prof_email_smoke.py

@@ -0,0 +1,281 @@
+"""fill_prof_email.py regression tests.
+
+Covers the three outcome shapes (PASS / FAIL / partial) across
+the two YAML kinds (hydration / binding), plus the failure
+modes that matter most: missing fields warn, NaN pred doesn't
+crash, bench name auto-detect picks the right template.
+"""
+from __future__ import annotations
+
+import csv
+import io
+import subprocess
+import sys
+import tempfile
+from pathlib import Path
+
+REPO_ROOT = Path(__file__).resolve().parents[2]
+
+
+def _write_report_with_overrides(dir_path: Path, kind: str,
+                                    verdict: str,
+                                    rows_table: str,
+                                    mae: str = "0.42",
+                                    pearson: str = "+0.993",
+                                    ghmc: str = "overall mean 77%, "
+                                                "worst 71%, 3 "
+                                                "compounds report"):
+    """Synthesise a report.md with controllable fields so we can
+    exercise filler edge cases without running the sampler."""
+    title = {"hydration": "Hydration FEP report",
+             "binding": "Binding FEP report"}[kind]
+    report = f"""\
+# {title} — {verdict}
+
+- source: `/tmp/synth`
+- compounds: 12 ok / 12 total
+
+## Gate verdict
+
+- **MAE gate** (≤ 1.5 kcal/mol): PASS  (MAE = {mae} kcal/mol)
+- **GHMC acceptance gate** (≥ 70% per compound): PASS  ({ghmc})
+
+## Aggregate accuracy
+
+- MAE  = {mae} kcal/mol
+- RMSE = 0.447 kcal/mol
+- Pearson r    = {pearson}
+- Spearman ρ   = +0.965
+- Kendall τ    = +0.879
+
+## Per-compound results
+
+| name | smiles | expt | pred | ± | residual | |resid| | within σ | wall (s) | flags |
+|------|--------|------|------|---|----------|-----:|---------:|---------:|-------|
+{rows_table}
+"""
+    (dir_path / "report.md").write_text(report, encoding="utf-8")
+
+
+def _run_fill(dir_path: Path, *extra_args: str) -> tuple[int, str]:
+    r = subprocess.run(
+        ["python", "scripts/fill_prof_email.py", str(dir_path),
+         *extra_args],
+        cwd=REPO_ROOT,
+        capture_output=True, text=True,
+    )
+    return r.returncode, r.stdout + r.stderr
+
+
+def test_hydration_pass_all_fields_fill():
+    with tempfile.TemporaryDirectory(
+            prefix="cellsim_fill_") as tmp:
+        tmp = Path(tmp)
+        _write_report_with_overrides(
+            tmp, kind="hydration", verdict="PASS",
+            rows_table=(
+                "| methane | `C` | +2.00 | +1.72 | 0.28 | -0.28 | "
+                "0.28 | ✓ | 420 | |\n"
+                "| acetamide | `CC(=O)N` | -9.71 | -8.90 | 0.55 | "
+                "+0.81 | 0.81 | | 560 | |"))
+        rc, out = _run_fill(tmp)
+    assert rc == 0, f"hydration pass should exit 0; got {rc}\n{out}"
+    assert "Subject: Milestone A — FreeSolv FEP results" in out
+    assert "Sign-correct on methane:          PASS" in out
+    assert "Sign-correct on acetamide:        PASS" in out
+    assert "<missing>" not in out
+
+
+def test_hydration_fail_methane_sign():
+    """Methane predicted negative — report FAILs sign-critical."""
+    with tempfile.TemporaryDirectory(
+            prefix="cellsim_fill_") as tmp:
+        tmp = Path(tmp)
+        _write_report_with_overrides(
+            tmp, kind="hydration", verdict="FAIL",
+            rows_table=(
+                "| methane | `C` | +2.00 | -1.85 | 0.45 | -3.85 | "
+                "3.85 | | 180 | SIGN WRONG |\n"
+                "| acetamide | `CC(=O)N` | -9.71 | -11.20 | 0.85 | "
+                "-1.49 | 1.49 | | 265 | |"))
+        rc, out = _run_fill(tmp)
+    # The fill itself succeeds even when the report says FAIL —
+    # the email just conveys FAIL to the prof. Exit 0 = all fields
+    # filled; the FAIL is in the email content, not the exit code.
+    assert rc == 0, out
+    assert "Overall verdict:                  FAIL" in out
+    assert "Sign-correct on methane:          FAIL" in out
+    assert "Sign-correct on acetamide:        PASS" in out
+
+
+def test_binding_streptavidin_template_selected():
+    """Binding report with biotin/desthiobiotin rows → binding
+    template, subject says 'streptavidin binding'."""
+    with tempfile.TemporaryDirectory(
+            prefix="cellsim_fill_") as tmp:
+        tmp = Path(tmp)
+        _write_report_with_overrides(
+            tmp, kind="binding", verdict="PASS",
+            mae="0.95",
+            rows_table=(
+                "| biotin | `O=C1N...` | -18.30 | -17.90 | 0.50 | "
+                "+0.40 | 0.40 | ✓ | 1200 | |\n"
+                "| desthiobiotin | `C[C@H]1...` | -13.20 | -12.50 | "
+                "0.60 | +0.70 | 0.70 | | 1300 | |"))
+        rc, out = _run_fill(tmp)
+    # rc 0 or 2 — 2 only if GHMC/other field is missing from the
+    # synth report, which is OK for this test (we're checking the
+    # template + subject + values, not the warning).
+    assert rc in (0, 2), out
+    assert "Subject: Milestone B — streptavidin binding FEP" in out, (
+        f"expected 'streptavidin binding' subject; got:\n{out[:500]}")
+    # MAE line — use loose whitespace match.
+    import re as _re
+    assert _re.search(
+        r"MAE vs published ΔG_bind:\s+0\.95 kcal/mol", out), (
+        f"MAE line missing / mismatched; got:\n{out[:500]}")
+    assert "(gate <= 2.0)" in out
+
+
+def test_binding_egfr_template_selected():
+    with tempfile.TemporaryDirectory(
+            prefix="cellsim_fill_") as tmp:
+        tmp = Path(tmp)
+        _write_report_with_overrides(
+            tmp, kind="binding", verdict="PASS",
+            rows_table=(
+                "| erlotinib | `COCCOc1...` | -11.86 | -11.42 | 0.44 | "
+                "+0.44 | 0.44 | ✓ | 3456 | |\n"
+                "| gefitinib | `COc1cc...` | -10.20 | -10.01 | 0.38 | "
+                "+0.19 | 0.19 | ✓ | 2890 | |"))
+        rc, out = _run_fill(tmp)
+    assert rc == 0
+    assert "EGFR kinase binding FEP" in out, (
+        f"expected EGFR bench name; got:\n{out[:400]}")
+    assert "Cheng-Prusoff" in out, (
+        "binding template should mention the IC50-offset caveat")
+
+
+def test_binding_non_binder_flagged_in_email():
+    """Binding rule: any compound with ΔG_pred >= 0 fails.
+    Email must surface the non-binder explicitly."""
+    with tempfile.TemporaryDirectory(
+            prefix="cellsim_fill_") as tmp:
+        tmp = Path(tmp)
+        _write_report_with_overrides(
+            tmp, kind="binding", verdict="FAIL",
+            rows_table=(
+                "| biotin | `O=C1N...` | -18.30 | -17.90 | 0.50 | "
+                "+0.40 | 0.40 | ✓ | 1200 | |\n"
+                "| desthiobiotin | `C[C@H]1...` | -13.20 | +0.50 | "
+                "0.60 | +13.70 | 13.70 | | 1300 | SIGN WRONG |"))
+        rc, out = _run_fill(tmp)
+    assert rc == 0
+    assert "desthiobiotin predicted non-binder" in out, (
+        f"email must call out the non-binder; got:\n{out[-600:]}")
+
+
+def test_missing_numbers_returns_exit_2():
+    """A malformed report (e.g. MAE line corrupted) leaves
+    <missing> markers — exit 2 so the biologist doesn't silently
+    send a placeholder email."""
+    with tempfile.TemporaryDirectory(
+            prefix="cellsim_fill_") as tmp:
+        tmp = Path(tmp)
+        # Deliberately break the MAE line.
+        (tmp / "report.md").write_text(
+            "# Hydration FEP report — PASS\n\n"
+            "- compounds: 12 ok / 12 total\n\n"
+            "## Aggregate accuracy\n\n"
+            "- MAE: (corrupted)\n"  # No '= X' → unparseable
+            "- Pearson r    = +0.993\n",
+            encoding="utf-8")
+        rc, out = _run_fill(tmp)
+    assert rc == 2, (
+        f"missing MAE should exit 2 (warn); got rc={rc}\n{out}")
+    assert "<missing>" in out
+    assert "WARNING" in out
+
+
+def test_no_report_md_returns_exit_1():
+    with tempfile.TemporaryDirectory(
+            prefix="cellsim_fill_") as tmp:
+        rc, out = _run_fill(Path(tmp))
+    assert rc == 1, (
+        f"no report.md should exit 1 (hard error); got {rc}\n{out}")
+    assert "no report.md" in out
+
+
+def test_prof_name_override():
+    with tempfile.TemporaryDirectory(
+            prefix="cellsim_fill_") as tmp:
+        tmp = Path(tmp)
+        _write_report_with_overrides(
+            tmp, kind="hydration", verdict="PASS",
+            rows_table=(
+                "| methane | `C` | +2.00 | +1.72 | 0.28 | -0.28 | "
+                "0.28 | ✓ | 420 | |\n"
+                "| acetamide | `CC(=O)N` | -9.71 | -8.90 | 0.55 | "
+                "+0.81 | 0.81 | | 560 | |"))
+        rc, out = _run_fill(tmp, "--prof-name", "Dr. Chen")
+    assert rc == 0
+    assert "Hi Dr. Chen," in out
+    assert "Hi [Prof]," not in out
+
+
+def test_fail_case_fixture_hydration():
+    """End-to-end on the committed fail_case fixture — methane
+    sign flipped, MAE 1.67. Email reflects both failures."""
+    with tempfile.TemporaryDirectory(
+            prefix="cellsim_fill_") as tmp:
+        tmp = Path(tmp)
+        # Generate report via fep-report on the bundled fixture.
+        r = subprocess.run(
+            ["python", "-m", "src.fep.report",
+             "tests/fep/fixtures/fail_case",
+             "--yaml", "benchmarks/fep/freesolv_12.yaml",
+             "--out-dir", str(tmp),
+             "--quiet"],
+            cwd=REPO_ROOT, capture_output=True, text=True,
+        )
+        # fep-report exits 1 on fail_case (by design), but the
+        # files are written either way.
+        assert (tmp / "report.md").exists(), (
+            f"fep-report didn't write report.md; stderr:\n{r.stderr}")
+        rc, out = _run_fill(tmp)
+    # fail_case fixture has no run.log with GHMC lines, so
+    # ghmc_mean/worst come back <missing> → exit 2 (warn). Both
+    # rc 0 and 2 are acceptable; what matters is the email
+    # content has the right FAIL verdict.
+    assert rc in (0, 2), (
+        f"fill should succeed on fail_case; got {rc}\n{out}")
+    assert "Sign-correct on methane:          FAIL" in out
+
+
+if __name__ == "__main__":
+    funcs = [
+        test_hydration_pass_all_fields_fill,
+        test_hydration_fail_methane_sign,
+        test_binding_streptavidin_template_selected,
+        test_binding_egfr_template_selected,
+        test_binding_non_binder_flagged_in_email,
+        test_missing_numbers_returns_exit_2,
+        test_no_report_md_returns_exit_1,
+        test_prof_name_override,
+        test_fail_case_fixture_hydration,
+    ]
+    fails = []
+    for f in funcs:
+        try:
+            f()
+            print(f"[PASS] {f.__name__}")
+        except AssertionError as e:
+            print(f"[FAIL] {f.__name__}: {e}")
+            fails.append(f.__name__)
+        except Exception as e:
+            import traceback
+            traceback.print_exc()
+            print(f"[ERROR] {f.__name__}: {e}")
+            fails.append(f.__name__)
+    print(f"{len(funcs) - len(fails)}/{len(funcs)} PASS")
+    sys.exit(0 if not fails else 1)