Truncate BOLD to 25 volumes in integration test fixture

Copies ds000001 and truncates the BOLD timeseries before running the
pipeline, cutting functional processing time significantly while still
exercising the full code path (motion correction, nuisance regression,
metrics, QC).

Author: nx10

tests/integration/test_all.py

@@ -4,6 +4,9 @@
 individual subcommands in sequence (disk round-trip), then verifies that both
 approaches complete without errors, produce key derivative files, and yield
 identical outputs.
+
+The BOLD timeseries is truncated to a small number of volumes so that
+functional processing finishes in minutes rather than tens of minutes.
 """
 
 from __future__ import annotations
@@ -13,18 +16,24 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
+import nibabel as nib
+import numpy as np
 import pytest
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
 
-_TEST_DATASET = Path(__file__).parents[1] / "data" / "ds000001"
+_ORIG_DATASET = Path(__file__).parents[1] / "data" / "ds000001"
 
 # Subject with no session in ds000001.
 _SUB = "01"
 _TASK = "balloonanalogrisktask"
 _RUN = "01"
 
+# Number of BOLD volumes to keep. Must be enough for nuisance regression
+# (after discarding --start-tr 2) but small enough to be fast.
+_BOLD_VOLUMES = 25
+
 
 # ---------------------------------------------------------------------------
 # Helpers
@@ -73,14 +82,36 @@ def _runner(request: pytest.FixtureRequest) -> str:
 
 
 @pytest.fixture(scope="session")
-def all_output(tmp_path_factory: pytest.TempPathFactory, _runner: str) -> Path:
+def truncated_dataset(tmp_path_factory: pytest.TempPathFactory) -> Path:
+    """Copy ds000001 and truncate the BOLD to *_BOLD_VOLUMES* volumes."""
+    dest = tmp_path_factory.mktemp("ds") / "ds000001"
+    shutil.copytree(_ORIG_DATASET, dest)
+
+    bold = (
+        dest
+        / f"sub-{_SUB}"
+        / "func"
+        / f"sub-{_SUB}_task-{_TASK}_run-{_RUN}_bold.nii.gz"
+    )
+    img = nib.nifti1.load(bold)
+    data = np.asarray(img.dataobj[:, :, :, :_BOLD_VOLUMES])
+    nib.nifti1.save(nib.Nifti1Image(data, img.affine, img.header), bold)
+    return dest
+
+
+@pytest.fixture(scope="session")
+def all_output(
+    tmp_path_factory: pytest.TempPathFactory,
+    _runner: str,
+    truncated_dataset: Path,
+) -> Path:
     """Run ``rbc all`` once and return the output directory."""
     out = tmp_path_factory.mktemp("all") / "derivatives"
     out.mkdir()
     _run_rbc(
         [
             "all",
-            str(_TEST_DATASET),
+            str(truncated_dataset),
             "-o",
             str(out),
             "--runner",
@@ -92,13 +123,17 @@ def all_output(tmp_path_factory: pytest.TempPathFactory, _runner: str) -> Path:
 
 
 @pytest.fixture(scope="session")
-def sequential_output(tmp_path_factory: pytest.TempPathFactory, _runner: str) -> Path:
+def sequential_output(
+    tmp_path_factory: pytest.TempPathFactory,
+    _runner: str,
+    truncated_dataset: Path,
+) -> Path:
     """Run the four individual subcommands in order and return the output dir."""
     out = tmp_path_factory.mktemp("sequential") / "derivatives"
     out.mkdir()
 
     runner_args = ["--runner", _runner, *_COMMON_ARGS]
-    raw = str(_TEST_DATASET)
+    raw = str(truncated_dataset)
     deriv = str(out)
 
     # 1. anatomical (raw BIDS only)