FIX: Avoid cluttering directories with test files

Author: mgxd

nibabies/conftest.py

@@ -2,44 +2,36 @@
 
 import json
 from pathlib import Path
-from tempfile import TemporaryDirectory
+from shutil import copytree
 
 import nibabel as nb
 import numpy as np
 import pytest
 
 from nibabies.data import load as load_data
 
-FILES = (
-    'functional.nii',
-    'anatomical.nii',
-    'func.dlabel.nii',
-    'func.dtseries.nii',
-    'epi.nii',
-    'T1w.nii',
-    'func_to_struct.mat',
-    'atlas.nii',
-    'label_list.txt',
-    'sub-01_run-01_echo-1_bold.nii.gz',
-    'sub-01_run-01_echo-2_bold.nii.gz',
-    'sub-01_run-01_echo-3_bold.nii.gz',
-)
-
-
-@pytest.fixture(scope='package')
-def data_dir():
-    with TemporaryDirectory() as tmpdir:
-        tmp_path = Path(tmpdir)
-        for fname in FILES:
-            Path.touch(tmp_path / fname)
-        yield tmp_path
+try:
+    from importlib.resources import files as ir_files
+except ImportError:  # PY<3.9
+    from importlib_resources import files as ir_files
+
+
+def copytree_or_skip(source, target):
+    data_dir = ir_files('nibabies') / source
+    if not data_dir.exists():
+        pytest.skip(f'Cannot chdir into {data_dir!r}. Probably in a zipped distribution.')
+
+    try:
+        copytree(data_dir, target / data_dir.name)
+    except Exception:  # noqa: BLE001
+        pytest.skip(f'Cannot copy {data_dir!r} into {target / data_dir.name}. Probably in a zip.')
 
 
 @pytest.fixture(autouse=True)
-def _populate_namespace(doctest_namespace, data_dir):
-    doctest_namespace['data_dir'] = data_dir
-    doctest_namespace['test_data'] = load_data.cached('../tests/data')
-    doctest_namespace['Path'] = Path
+def _populate_namespace(doctest_namespace, tmp_path):
+    doctest_namespace['copytree_or_skip'] = copytree_or_skip
+    doctest_namespace['testdir'] = tmp_path
+    doctest_namespace['datadir'] = load_data()
 
 
 @pytest.fixture

nibabies/data/sub-01_run-01_echo-1_bold.nii.gz

@@ -1,5 +1,6 @@
 from pathlib import Path
 from shutil import copytree
+from tempfile import TemporaryDirectory
 
 import pytest
 
@@ -19,17 +20,37 @@ def _chdir(path):
             os.chdir(cwd)
 
 
-@pytest.fixture(scope='module')
+DATA_FILES = (
+    'functional.nii',
+    'anatomical.nii',
+    'func.dlabel.nii',
+    'func.dtseries.nii',
+    'epi.nii',
+    'T1w.nii',
+    'func_to_struct.mat',
+    'atlas.nii',
+    'label_list.txt',
+    'sub-01_run-01_echo-1_bold.nii.gz',
+    'sub-01_run-01_echo-2_bold.nii.gz',
+    'sub-01_run-01_echo-3_bold.nii.gz',
+)
+
+
+@pytest.fixture(scope='package')
 def data_dir():
-    return Path(__file__).parent / 'tests' / 'data'
+    with TemporaryDirectory() as tmpdir:
+        tmp_path = Path(tmpdir)
+        for fname in DATA_FILES:
+            Path.touch(tmp_path / fname)
+        yield tmp_path
 
 
 @pytest.fixture(autouse=True)
-def _docdir(request, tmp_path):
+def _docdir(data_dir, request, tmp_path):
     # Trigger ONLY for the doctests.
     doctest_plugin = request.config.pluginmanager.getplugin('doctest')
     if isinstance(request.node, doctest_plugin.DoctestItem):
-        copytree(Path(__file__).parent / 'tests' / 'data', tmp_path, dirs_exist_ok=True)
+        copytree(data_dir, tmp_path, dirs_exist_ok=True)
 
         # Chdir only for the duration of the test.
         with _chdir(tmp_path):

nibabies/data/sub-01_run-01_echo-2_bold.nii.gz

@@ -164,16 +164,16 @@ class CiftiCreateDenseFromTemplate(WBCommand):
 
     >>> from nibabies.interfaces import workbench as wb
     >>> frmtpl = wb.CiftiCreateDenseFromTemplate()
-    >>> frmtpl.inputs.in_file = data_dir / "func.dtseries.nii"
+    >>> frmtpl.inputs.in_file = testdir / "func.dtseries.nii"
     >>> frmtpl.inputs.series = True
     >>> frmtpl.inputs.series_step = 0.8
     >>> frmtpl.inputs.series_start = 0
     >>> frmtpl.cmdline  # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
     'wb_command -cifti-create-dense-from-template .../func.dtseries.nii \
     template_func.dtseries.nii -series 0.8 0.0'
 
-    >>> frmtpl.inputs.volume = [("OTHER", data_dir / 'functional.nii', True), \
-        ("PUTAMEN_LEFT", data_dir / 'functional.nii')]
+    >>> frmtpl.inputs.volume = [("OTHER", testdir / 'functional.nii', True), \
+        ("PUTAMEN_LEFT", testdir / 'functional.nii')]
     >>> frmtpl.cmdline  # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
     'wb_command -cifti-create-dense-from-template .../func.dtseries.nii \
     template_func.dtseries.nii -series 0.8 0.0 \
@@ -330,8 +330,8 @@ class CiftiCreateDenseTimeseries(WBCommand):
 
     >>> from nibabies.interfaces.workbench import CiftiCreateDenseTimeseries
     >>> createdts = CiftiCreateDenseTimeseries()
-    >>> createdts.inputs.volume_data = data_dir /'functional.nii'
-    >>> createdts.inputs.volume_structure_labels = data_dir / 'atlas.nii'
+    >>> createdts.inputs.volume_data = testdir /'functional.nii'
+    >>> createdts.inputs.volume_structure_labels = testdir / 'atlas.nii'
     >>> createdts.cmdline  # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
     'wb_command -cifti-create-dense-timeseries out.dtseries.nii \
     -volume .../functional.nii .../atlas.nii'
@@ -467,8 +467,8 @@ class CiftiCreateLabel(WBCommand):
 
     >>> from nibabies.interfaces import workbench as wb
     >>> lab = wb.CiftiCreateLabel()
-    >>> lab.inputs.volume_label = data_dir / "functional.nii"
-    >>> lab.inputs.structure_label_volume = data_dir / "functional.nii"
+    >>> lab.inputs.volume_label = testdir / "functional.nii"
+    >>> lab.inputs.structure_label_volume = testdir / "functional.nii"
     >>> lab.cmdline # doctest: +ELLIPSIS
     'wb_command -cifti-create-label out.dlabel.nii -volume .../functional.nii .../functional.nii'
     """
@@ -940,9 +940,9 @@ class CiftiResample(WBCommand):
 
     >>> from nibabies.interfaces import workbench as wb
     >>> res = wb.CiftiResample()
-    >>> res.inputs.in_file = data_dir / "func.dtseries.nii"
+    >>> res.inputs.in_file = testdir / "func.dtseries.nii"
     >>> res.inputs.direction = "COLUMN"
-    >>> res.inputs.template = data_dir / "func.dlabel.nii"
+    >>> res.inputs.template = testdir / "func.dlabel.nii"
     >>> res.inputs.template_direction = "COLUMN"
     >>> res.inputs.surface_method = "ADAP_BARY_AREA"
     >>> res.inputs.volume_method = "CUBIC"
@@ -1051,7 +1051,7 @@ class CiftiSeparate(WBCommand):
     dimension, columns for .dtseries.
 
     >>> separate = CiftiSeparate()
-    >>> separate.inputs.in_file = data_dir / "func.dtseries.nii"
+    >>> separate.inputs.in_file = testdir / "func.dtseries.nii"
     >>> separate.inputs.direction = "COLUMN"
     >>> separate.inputs.volume_all_file = "volume_all.nii.gz"
     >>> separate.cmdline  # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
@@ -1216,10 +1216,10 @@ class VolumeAffineResample(WBCommand):
 
     >>> 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.in_file = testdir /'functional.nii'
+    >>> resample.inputs.volume_space = testdir /'anatomical.nii'
     >>> resample.inputs.method = 'CUBIC'
-    >>> resample.inputs.affine = data_dir / 'func_to_struct.mat'
+    >>> resample.inputs.affine = testdir / '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'
@@ -1237,8 +1237,8 @@ class VolumeAffineResample(WBCommand):
     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.inputs.flirt_source_volume = testdir / 'epi.nii'
+    >>> resample.inputs.flirt_target_volume = testdir /'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 \
@@ -1297,7 +1297,7 @@ class VolumeAllLabelsToROIs(WBCommand):
 
     >>> from nibabies.interfaces.workbench import VolumeAllLabelsToROIs
     >>> rois = VolumeAllLabelsToROIs()
-    >>> rois.inputs.in_file = data_dir / 'atlas.nii'
+    >>> rois.inputs.in_file = testdir / 'atlas.nii'
     >>> rois.inputs.label_map = 1
     >>> rois.cmdline  # doctest: +ELLIPSIS
     'wb_command -volume-all-labels-to-rois .../atlas.nii 1 atlas_rois.nii.gz'
@@ -1346,7 +1346,7 @@ class VolumeLabelExportTable(WBCommand):
 
     >>> from nibabies.interfaces.workbench import VolumeLabelExportTable
     >>> label_export = VolumeLabelExportTable()
-    >>> label_export.inputs.in_file = data_dir / 'atlas.nii'
+    >>> label_export.inputs.in_file = testdir / 'atlas.nii'
     >>> label_export.inputs.label_map = 1
     >>> label_export.cmdline  # doctest: +ELLIPSIS
     'wb_command -volume-label-export-table .../atlas.nii 1 atlas_labels.txt'
@@ -1434,8 +1434,8 @@ class VolumeLabelImport(WBCommand):
 
     >>> from nibabies.interfaces.workbench import VolumeLabelImport
     >>> label_import = VolumeLabelImport()
-    >>> label_import.inputs.in_file = data_dir / 'atlas.nii'
-    >>> label_import.inputs.label_list_file = data_dir / 'label_list.txt'
+    >>> label_import.inputs.in_file = testdir / 'atlas.nii'
+    >>> label_import.inputs.label_list_file = testdir / 'label_list.txt'
     >>> label_import.cmdline  # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
     'wb_command -volume-label-import .../atlas.nii .../label_list.txt \
     atlas_labels.nii.gz'

nibabies/data/sub-01_run-01_echo-3_bold.nii.gz

@@ -321,11 +321,11 @@ def parse_roi_labels(label_file: str):
 
     Return a list of structure names and label keys.
 
-    >>> structs, ids = parse_roi_labels(test_data / "labelfile.txt")
+    >>> structs, ids = parse_roi_labels(datadir / "FreeSurferSubcorticalLabelTableLut.txt")
     >>> structs
-    ['CEREBELLUM_LEFT', 'THALAMUS_LEFT', 'CAUDATE_LEFT']
+    ['ACCUMBENS_LEFT', 'ACCUMBENS_RIGHT', 'AMYGDALA_LEFT', ...]
     >>> ids
-    [8, 10, 11]
+    [26, 58, 18, ...]
     """
 
     with open(label_file) as fp: