Revert BOLD truncation, use full test dataset for now

Remove the volume truncation optimization so we can shake out all bugs
with the real data first. Can revisit truncation once the pipeline
passes end-to-end.

Author: nx10

tests/integration/test_all.py

@@ -4,9 +4,6 @@
 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
@@ -16,25 +13,18 @@
 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
 
-_ORIG_DATASET = Path(__file__).parents[1] / "data" / "ds000001"
+_TEST_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. The 36-parameter regressor model needs
-# more timepoints than regressors (~36 columns + derivatives). After
-# discarding --start-tr 2, we need at least ~45 usable volumes.
-_BOLD_VOLUMES = 50
-
 
 # ---------------------------------------------------------------------------
 # Helpers
@@ -83,36 +73,14 @@ def _runner(request: pytest.FixtureRequest) -> str:
 
 
 @pytest.fixture(scope="session")
-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:
+def all_output(tmp_path_factory: pytest.TempPathFactory, _runner: str) -> Path:
     """Run ``rbc all`` once and return the output directory."""
     out = tmp_path_factory.mktemp("all") / "derivatives"
     out.mkdir()
     _run_rbc(
         [
             "all",
-            str(truncated_dataset),
+            str(_TEST_DATASET),
             "-o",
             str(out),
             "--runner",
@@ -124,17 +92,13 @@ def all_output(
 
 
 @pytest.fixture(scope="session")
-def sequential_output(
-    tmp_path_factory: pytest.TempPathFactory,
-    _runner: str,
-    truncated_dataset: Path,
-) -> Path:
+def sequential_output(tmp_path_factory: pytest.TempPathFactory, _runner: str) -> 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(truncated_dataset)
+    raw = str(_TEST_DATASET)
     deriv = str(out)
 
     # 1. anatomical (raw BIDS only)