Align longitudinal integration test with test_all.py style, add -vv

- Mirror test_all.py: shared _rbc_exe / _run_rbc helpers, session-scoped
  fixtures own the subprocess invocations, the test itself only asserts
  on the resulting BIDS tree. Adds a longitudinal_template_output
  fixture so Stages 3-6 can reuse the template run without paying the
  cost again.
- Pass -vv to every rbc subprocess so the styx runner logger runs at
  DEBUG and container stdout/stderr reach the captured subprocess
  streams. Without this, a tool that exits non-zero with its own error
  output leaves only a bare returncode to diagnose from (styxcache
  discards the staging stderr.gz on exception, so the post-hoc cache
  dump approach can't recover it either).
- Keep the 7200s per-call timeout; bump the stderr capture window from
  2000 to 4000 chars to accommodate DEBUG-level logs.

Author: nx10

tests/integration/longitudinal/conftest.py

@@ -1,26 +1,61 @@
 """Fixtures for longitudinal integration tests.
 
-These fixtures own the ds000114 test dataset lifecycle (download + reuse)
-and run the cross-sectional anatomical stage once so that each
-longitudinal test can build on ``desc-brain`` T1w derivatives without
-paying the preprocessing cost per test.
+Mirrors the subprocess-driven style in ``tests/integration/test_all.py``:
+session-scoped fixtures run each ``rbc`` invocation once and return the
+output directory; tests just assert on the resulting BIDS tree.
 """
 
 from __future__ import annotations
 
 import shutil
 import subprocess
 from pathlib import Path
+from typing import TYPE_CHECKING
 
 import pytest
 
+if TYPE_CHECKING:
+    from collections.abc import Sequence
+
 _REPO_ROOT = Path(__file__).resolve().parents[3]
 _DOWNLOAD_SCRIPT = _REPO_ROOT / "scripts" / "download_ds000114.py"
 _DATASET_DIR = _REPO_ROOT / "tests" / "data" / "ds000114"
 _DATASET_SENTINEL = (
     _DATASET_DIR / "sub-01" / "ses-test" / "anat" / "sub-01_ses-test_T1w.nii.gz"
 )
 
+_SUB = "01"
+
+
+def _rbc_exe() -> str:
+    exe = shutil.which("rbc")
+    assert exe is not None, "rbc CLI not found on PATH"
+    return exe
+
+
+def _run_rbc(
+    args: Sequence[str], *, timeout: int = 7200
+) -> subprocess.CompletedProcess[str]:
+    """Invoke ``rbc`` with ``-vv`` so container output reaches the subprocess.
+
+    Without ``-vv`` the styx runner logger stays at WARNING and
+    container-side failure output (e.g. lta_convert exiting non-zero with
+    its own error text) never makes it into the captured stderr, which
+    leaves the test with only a bare ``returncode=1`` to diagnose from.
+    """
+    result = subprocess.run(  # noqa: S603
+        [_rbc_exe(), *args, "-vv"],
+        capture_output=True,
+        text=True,
+        timeout=timeout,
+    )
+    assert result.returncode == 0, (
+        f"rbc {args[0]} exited with code {result.returncode}\n"
+        f"--- stdout ---\n{result.stdout[-4000:]}\n"
+        f"--- stderr ---\n{result.stderr[-4000:]}"
+    )
+    return result
+
 
 @pytest.fixture(scope="session")
 def ds000114_dataset() -> Path:
@@ -56,16 +91,15 @@ def ds000114_dataset() -> Path:
 
 
 @pytest.fixture(scope="session")
-def runner_backend(request: pytest.FixtureRequest) -> str:
-    """Styx runner backend selected via ``--runner`` on the pytest CLI."""
+def _runner(request: pytest.FixtureRequest) -> str:
     return request.config.getoption("--runner")
 
 
 @pytest.fixture(scope="session")
 def ds000114_anat_derivatives(
     ds000114_dataset: Path,
     tmp_path_factory: pytest.TempPathFactory,
-    runner_backend: str,
+    _runner: str,
 ) -> Path:
     """Run ``rbc anatomical`` once against ds000114 sub-01 (both sessions).
 
@@ -74,33 +108,44 @@ def ds000114_anat_derivatives(
     scope ensures we only pay the registration + brain extraction cost
     once across all longitudinal integration tests.
     """
-    rbc = shutil.which("rbc")
-    if rbc is None:
-        pytest.skip("rbc CLI not found on PATH")
-
     out = tmp_path_factory.mktemp("ds000114_derivatives")
-    result = subprocess.run(  # noqa: S603
+    _run_rbc(
         [
-            rbc,
             "anatomical",
             str(ds000114_dataset),
             "-o",
             str(out),
             "--runner",
-            runner_backend,
+            _runner,
             "--participant-label",
-            "01",
+            _SUB,
         ],
-        capture_output=True,
-        text=True,
-        # Two-session anat (brain extraction + registration, twice) under
-        # xdist contention on the self-hosted runner can push past an hour;
-        # match the 7200s budget used by tests/integration/test_all.py.
-        timeout=7200,
-    )
-    assert result.returncode == 0, (
-        f"rbc anatomical exited with code {result.returncode}\n"
-        f"--- stdout ---\n{result.stdout[-2000:]}\n"
-        f"--- stderr ---\n{result.stderr[-2000:]}"
     )
     return out
+
+
+@pytest.fixture(scope="session")
+def longitudinal_template_output(
+    ds000114_anat_derivatives: Path,
+    _runner: str,
+) -> Path:
+    """Run ``rbc longitudinal template`` once and return the derivatives dir.
+
+    Writes the ``ses-longitudinal`` tree alongside the per-session
+    cross-sectional anat outputs, the same layout downstream longitudinal
+    stages will consume.
+    """
+    _run_rbc(
+        [
+            "longitudinal",
+            "template",
+            str(ds000114_anat_derivatives),
+            "-o",
+            str(ds000114_anat_derivatives),
+            "--runner",
+            _runner,
+            "--participant-label",
+            _SUB,
+        ],
+    )
+    return ds000114_anat_derivatives

tests/integration/longitudinal/test_template.py

@@ -1,16 +1,13 @@
 """Integration test for ``rbc longitudinal template``.
 
 Deferred from Stage 2 of the longitudinal refactor (tracker #301,
-Stage 2 landed in PR #306). Depends on the ds000114 multi-session test
-fixture; cross-sectional anatomical derivatives are produced by the
-session-scoped ``ds000114_anat_derivatives`` fixture so the template
-stage has ``desc-brain`` T1w volumes to consume.
+Stage 2 landed in PR #306). Depends on the ds000114 multi-session
+fixture and the cross-sectional anatomical pre-run that produces the
+``desc-brain`` T1w derivatives the template stage consumes.
 """
 
 from __future__ import annotations
 
-import shutil
-import subprocess
 from typing import TYPE_CHECKING
 
 import pytest
@@ -21,37 +18,10 @@
 
 @pytest.mark.slow
 def test_rbc_longitudinal_template_builds_bids_tree(
-    ds000114_anat_derivatives: Path,
-    runner_backend: str,
+    longitudinal_template_output: Path,
 ) -> None:
-    """Run ``rbc longitudinal template`` and verify the BIDS output tree."""
-    rbc = shutil.which("rbc")
-    assert rbc is not None, "rbc CLI not found on PATH"
-
-    result = subprocess.run(  # noqa: S603
-        [
-            rbc,
-            "longitudinal",
-            "template",
-            str(ds000114_anat_derivatives),
-            "-o",
-            str(ds000114_anat_derivatives),
-            "--runner",
-            runner_backend,
-            "--participant-label",
-            "01",
-        ],
-        capture_output=True,
-        text=True,
-        timeout=7200,
-    )
-    assert result.returncode == 0, (
-        f"rbc longitudinal template exited with code {result.returncode}\n"
-        f"--- stdout ---\n{result.stdout[-2000:]}\n"
-        f"--- stderr ---\n{result.stderr[-2000:]}"
-    )
-
-    ses_long = ds000114_anat_derivatives / "sub-01" / "ses-longitudinal" / "anat"
+    """The ``ses-longitudinal`` BIDS tree contains the expected files."""
+    ses_long = longitudinal_template_output / "sub-01" / "ses-longitudinal" / "anat"
     expected = [
         "sub-01_ses-longitudinal_T1w.nii.gz",
         "sub-01_ses-longitudinal_from-test_to-longitudinal_mode-image_xfm.txt",
@@ -60,8 +30,8 @@ def test_rbc_longitudinal_template_builds_bids_tree(
     missing = [name for name in expected if not (ses_long / name).is_file()]
     if missing:
         tree = sorted(
-            str(p.relative_to(ds000114_anat_derivatives))
-            for p in ds000114_anat_derivatives.rglob("*")
+            str(p.relative_to(longitudinal_template_output))
+            for p in longitudinal_template_output.rglob("*")
             if p.is_file()
         )
         pytest.fail(