TEST: Add smoke tests for full workflow and most branching flags (#3155)

Add more smoke tests that build the whole workflow, setting most flags
that affect workflow shape.

Added a regression test for #3154.

Fixes #3154.

fmriprep/workflows/bold/fit.py

@@ -83,7 +83,8 @@ def get_sbrefs(
     """
     entities = extract_entities(bold_files)
     entities.pop("echo", None)
-    entities.update(suffix="sbref", extension=[".nii", ".nii.gz"], **entity_overrides)
+    entities.update(suffix="sbref", extension=[".nii", ".nii.gz"])
+    entities.update(entity_overrides)
 
     return sorted(
         layout.get(return_type="file", **entities),

fmriprep/workflows/tests/test_base.py

@@ -1,11 +1,19 @@
 from copy import deepcopy
+from pathlib import Path
+from unittest.mock import patch
 
 import bids
+import nibabel as nb
+import numpy as np
+import pytest
+from nipype.pipeline.engine.utils import generate_expanded_graph
 from niworkflows.utils.testing import generate_bids_skeleton
 from sdcflows.fieldmaps import clear_registry
 from sdcflows.utils.wrangler import find_estimators
 
-from ..base import get_estimator
+from ... import config
+from ..base import get_estimator, init_fmriprep_wf
+from ..tests import mock_config
 
 BASE_LAYOUT = {
     "01": {
@@ -19,7 +27,7 @@
                 {
                     "task": "rest",
                     "run": i,
-                    "suffix": "bold",
+                    "suffix": suffix,
                     "metadata": {
                         "RepetitionTime": 2.0,
                         "PhaseEncodingDirection": "j",
@@ -28,6 +36,7 @@
                         "SliceTiming": [0.0, 0.2, 0.4, 0.6, 0.8, 1.0, 1.2, 1.4, 1.6, 1.8],
                     },
                 }
+                for suffix in ("bold", "sbref")
                 for i in range(1, 3)
             ),
             *(
@@ -64,6 +73,163 @@
 }
 
 
+@pytest.fixture(scope="module", autouse=True)
+def _quiet_logger():
+    import logging
+
+    logger = logging.getLogger("nipype.workflow")
+    old_level = logger.getEffectiveLevel()
+    logger.setLevel(logging.ERROR)
+    yield
+    logger.setLevel(old_level)
+
+
+@pytest.fixture(autouse=True)
+def _reset_sdcflows_registry():
+    yield
+    clear_registry()
+
+
+@pytest.fixture(scope="module")
+def bids_root(tmp_path_factory):
+    base = tmp_path_factory.mktemp("base")
+    bids_dir = base / "bids"
+    generate_bids_skeleton(bids_dir, BASE_LAYOUT)
+
+    img = nb.Nifti1Image(np.zeros((10, 10, 10, 10)), np.eye(4))
+
+    for bold_path in bids_dir.glob('sub-01/*/*.nii.gz'):
+        img.to_filename(bold_path)
+
+    yield bids_dir
+
+
+def _make_params(
+    bold2t1w_init: str = "register",
+    use_bbr: bool | None = None,
+    dummy_scans: int | None = None,
+    me_output_echos: bool = False,
+    medial_surface_nan: bool = False,
+    project_goodvoxels: bool = False,
+    cifti_output: bool | str = False,
+    run_msmsulc: bool = True,
+    skull_strip_t1w: str = "auto",
+    use_syn_sdc: str | bool = False,
+    force_syn: bool = False,
+    freesurfer: bool = True,
+    ignore: list[str] = None,
+    bids_filters: dict = None,
+):
+    if ignore is None:
+        ignore = []
+    if bids_filters is None:
+        bids_filters = {}
+    return (
+        bold2t1w_init,
+        use_bbr,
+        dummy_scans,
+        me_output_echos,
+        medial_surface_nan,
+        project_goodvoxels,
+        cifti_output,
+        run_msmsulc,
+        skull_strip_t1w,
+        use_syn_sdc,
+        force_syn,
+        freesurfer,
+        ignore,
+        bids_filters,
+    )
+
+
+@pytest.mark.parametrize("level", ["minimal", "resampling", "full"])
+@pytest.mark.parametrize("anat_only", [False, True])
+@pytest.mark.parametrize(
+    (
+        "bold2t1w_init",
+        "use_bbr",
+        "dummy_scans",
+        "me_output_echos",
+        "medial_surface_nan",
+        "project_goodvoxels",
+        "cifti_output",
+        "run_msmsulc",
+        "skull_strip_t1w",
+        "use_syn_sdc",
+        "force_syn",
+        "freesurfer",
+        "ignore",
+        "bids_filters",
+    ),
+    [
+        _make_params(),
+        _make_params(bold2t1w_init="header"),
+        _make_params(use_bbr=True),
+        _make_params(use_bbr=False),
+        _make_params(bold2t1w_init="header", use_bbr=True),
+        # Currently disabled
+        # _make_params(bold2t1w_init="header", use_bbr=False),
+        _make_params(dummy_scans=2),
+        _make_params(me_output_echos=True),
+        _make_params(medial_surface_nan=True),
+        _make_params(cifti_output='91k'),
+        _make_params(cifti_output='91k', project_goodvoxels=True),
+        _make_params(cifti_output='91k', project_goodvoxels=True, run_msmsulc=False),
+        _make_params(cifti_output='91k', run_msmsulc=False),
+        _make_params(skull_strip_t1w='force'),
+        _make_params(skull_strip_t1w='skip'),
+        _make_params(use_syn_sdc='warn', force_syn=True, ignore=['fieldmaps']),
+        _make_params(freesurfer=False),
+        _make_params(freesurfer=False, use_bbr=True),
+        _make_params(freesurfer=False, use_bbr=False),
+        # Currently unsupported:
+        # _make_params(freesurfer=False, bold2t1w_init="header"),
+        # _make_params(freesurfer=False, bold2t1w_init="header", use_bbr=True),
+        # _make_params(freesurfer=False, bold2t1w_init="header", use_bbr=False),
+        # Regression test for gh-3154:
+        _make_params(bids_filters={'sbref': {'suffix': 'sbref'}}),
+    ],
+)
+def test_init_fmriprep_wf(
+    bids_root: Path,
+    tmp_path: Path,
+    level: str,
+    anat_only: bool,
+    bold2t1w_init: str,
+    use_bbr: bool | None,
+    dummy_scans: int | None,
+    me_output_echos: bool,
+    medial_surface_nan: bool,
+    project_goodvoxels: bool,
+    cifti_output: bool | str,
+    run_msmsulc: bool,
+    skull_strip_t1w: str,
+    use_syn_sdc: str | bool,
+    force_syn: bool,
+    freesurfer: bool,
+    ignore: list[str],
+    bids_filters: dict,
+):
+    with mock_config(bids_dir=bids_root):
+        config.workflow.level = level
+        config.workflow.anat_only = anat_only
+        config.workflow.bold2t1w_init = bold2t1w_init
+        config.workflow.use_bbr = use_bbr
+        config.workflow.dummy_scans = dummy_scans
+        config.execution.me_output_echos = me_output_echos
+        config.workflow.medial_surface_nan = medial_surface_nan
+        config.workflow.project_goodvoxels = project_goodvoxels
+        config.workflow.run_msmsulc = run_msmsulc
+        config.workflow.skull_strip_t1w = skull_strip_t1w
+        config.workflow.cifti_output = cifti_output
+        config.workflow.run_reconall = freesurfer
+        config.workflow.ignore = ignore
+        with patch.dict('fmriprep.config.execution.bids_filters', bids_filters):
+            wf = init_fmriprep_wf()
+
+    generate_expanded_graph(wf._create_flat_graph())
+
+
 def test_get_estimator_none(tmp_path):
     bids_dir = tmp_path / "bids"
 
@@ -100,7 +266,6 @@ def test_get_estimator_b0field_and_intendedfor(tmp_path):
 
     assert get_estimator(layout, bold_files[0]) == ('epi',)
     assert get_estimator(layout, bold_files[1]) == ('auto_00000',)
-    clear_registry()
 
 
 def test_get_estimator_overlapping_specs(tmp_path):
@@ -130,7 +295,6 @@ def test_get_estimator_overlapping_specs(tmp_path):
     # B0Fields take precedence
     assert get_estimator(layout, bold_files[0]) == ('epi',)
     assert get_estimator(layout, bold_files[1]) == ('epi',)
-    clear_registry()
 
 
 def test_get_estimator_multiple_b0fields(tmp_path):
@@ -156,4 +320,3 @@ def test_get_estimator_multiple_b0fields(tmp_path):
     # Always get an iterable; don't care if it's a list or tuple
     assert get_estimator(layout, bold_files[0]) == ['epi', 'phasediff']
     assert get_estimator(layout, bold_files[1]) == ('epi',)
-    clear_registry()