TEST: Add fixtures for testing interfaces with doctests

Author: effigies

nibabies/interfaces/conftest.py

@@ -0,0 +1,24 @@
+"""py.test configuration"""
+from pathlib import Path
+import pytest
+from tempfile import TemporaryDirectory
+
+
+@pytest.fixture(scope="package")
+def data_dir():
+    with TemporaryDirectory() as tmpdir:
+        tmp_path = Path(tmpdir)
+        for fname in (
+                'functional.nii',
+                'anatomical.nii',
+                'epi.nii',
+                'T1w.nii',
+                'func_to_struct.mat',
+                ):
+            Path.touch(tmp_path / fname)
+        yield tmp_path
+
+
+@pytest.fixture(autouse=True)
+def set_namespace(doctest_namespace, data_dir):
+    doctest_namespace["data_dir"] = data_dir

nibabies/interfaces/workbench.py

@@ -196,6 +196,36 @@ class VolumeAffineResampleOutputSpec(TraitedSpec):
 class VolumeAffineResample(WBCommand):
     """
     Resample a volume file with an affine transformation.
+
+    >>> from nibabies.interfaces.workbench import VolumeAffineResample
+    >>> resample = VolumeAffineResample()
+    >>> resample.inputs.in_file = data_dir /'functional.nii'
+    >>> resample.inputs.volume_space = data_dir /'anatomical.nii'
+    >>> resample.inputs.method = 'CUBIC'
+    >>> resample.inputs.affine = data_dir / 'func_to_struct.mat'
+    >>> resample.cmdline  #doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
+    'wb_command -volume-resample .../functional.nii .../anatomical.nii CUBIC \
+    resampled_functional.nii.gz -affine .../func_to_struct.mat'
+
+    If the affine was generated with FLIRT, this should be indicated.
+    By default, the interface will use the ``in_file`` and ``volume_space``
+    for references.
+
+    >>> resample.inputs.flirt = True
+    >>> resample.cmdline  #doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
+    'wb_command -volume-resample .../functional.nii .../anatomical.nii CUBIC \
+    resampled_functional.nii.gz -affine .../func_to_struct.mat \
+    -flirt .../functional.nii .../anatomical.nii'
+
+    However, if other volumes were used to calculate the affine, they can
+    be provided:
+
+    >>> resample.inputs.flirt_source_volume = data_dir / 'epi.nii'
+    >>> resample.inputs.flirt_target_volume = data_dir /'T1w.nii'
+    >>> resample.cmdline  #doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
+    'wb_command -volume-resample .../functional.nii .../anatomical.nii CUBIC \
+    resampled_functional.nii.gz -affine .../func_to_struct.mat \
+    -flirt .../epi.nii .../T1w.nii'
     """
 
     input_spec = VolumeAffineResampleInputSpec