TST: Add test

Author: mgxd

nibabies/cli/tests/test_hbcd.py

@@ -0,0 +1,43 @@
+import pytest
+
+from ..hbcd import main
+
+
+# create a FreeSurfer / MCRIBS directory structure
+@pytest.fixture
+def freesurfer(tmp_path):
+    root = tmp_path / 'freesurfer'
+    for s in ('fsaverage', 'sub-01_ses-1', 'sub-01_ses-2'):
+        (root / s / 'mri').mkdir(parents=True, exist_ok=True)
+        (root / s / 'mri' / 'T1.mgz').touch()
+        (root / s / 'surf').mkdir(parents=True, exist_ok=True)
+        (root / s / 'surf' / 'lh.pial').touch()
+    return root
+
+
+@pytest.fixture
+def mcribs(tmp_path):
+    root = tmp_path / 'mcribs'
+    for s in ('sub-01_ses-1', 'sub-01_ses-2'):
+        (root / s / 'TissueSeg').mkdir(parents=True, exist_ok=True)
+        orig = root / s / 'TissueSeg' / f'{s}_all_labels.nii.gz'
+        orig.touch()
+        (root / s / 'TissueSeg' / f'{s}_all_labels_manedit.nii.gz').symlink_to(orig)
+    return root
+
+
+def test_hbcd_restructure(freesurfer, mcribs):
+    # running without options is fine
+    main([])
+
+    main(['--fs', str(freesurfer), '--mcribs', str(mcribs)])
+    assert sorted(x.name for x in freesurfer.iterdir()) == ['fsaverage', 'sub-01']
+    assert sorted(x.name for x in (freesurfer / 'sub-01').iterdir()) == ['ses-1', 'ses-2']
+
+    assert [x.name for x in mcribs.iterdir()] == ['sub-01']
+    linkd = mcribs / 'sub-01' / 'ses-1' / 'TissueSeg' / 'sub-01_ses-1_all_labels_manedit.nii.gz'
+    assert linkd.exists()
+    assert not linkd.is_symlink()
+
+    # and run again should not fail
+    main(['--fs', str(freesurfer), '--mcribs', str(mcribs)])