TEST: Skip tests when test data is missing

Author: effigies

docs/conf.py

@@ -225,7 +225,7 @@
 
 apidoc_module_dir = "../niworkflows"
 apidoc_output_dir = "api"
-apidoc_excluded_paths = ["conftest.py", "*/tests/*", "tests/*", "data/*"]
+apidoc_excluded_paths = ["conftest.py", "*/tests/*", "tests/*", "data/*", "testing.py"]
 apidoc_separate_modules = True
 apidoc_extra_args = ["--module-first", "-d 1", "-T"]
 

niworkflows/conftest.py

@@ -32,14 +32,10 @@
 import pkg_resources
 
 from .utils.bids import collect_data
-
-test_data_env = os.getenv(
-    "TEST_DATA_HOME", str(Path.home() / ".cache" / "stanford-crn")
+from .testing import (
+    test_data_env, test_output_dir, test_workdir, data_dir,
+    data_env_canary, data_dir_canary
 )
-test_output_dir = os.getenv("TEST_OUTPUT_DIR")
-test_workdir = os.getenv("TEST_WORK_DIR")
-
-data_dir = Path(test_data_env) / "BIDS-examples-1-enh-ds054"
 
 
 @pytest.fixture(autouse=True)
@@ -52,6 +48,7 @@ def add_np(doctest_namespace):
     doctest_namespace["pytest"] = pytest
     doctest_namespace["Path"] = Path
     doctest_namespace["datadir"] = data_dir
+    doctest_namespace["data_dir_canary"] = data_dir_canary
     doctest_namespace["bids_collect_data"] = collect_data
     doctest_namespace["test_data"] = pkg_resources.resource_filename(
         "niworkflows", "tests/data"
@@ -82,6 +79,7 @@ def testdata_dir():
 
 @pytest.fixture
 def ds000030_dir():
+    data_env_canary()
     return Path(test_data_env) / "ds000030"
 
 

niworkflows/interfaces/bids.py

@@ -105,6 +105,10 @@ class BIDSInfo(SimpleInterface):
     This interface uses only the basename, not the path, to determine the
     subject, session, task, run, acquisition or reconstruction.
 
+    .. testsetup::
+
+        >>> data_dir_canary()
+
     >>> bids_info = BIDSInfo(bids_dir=str(datadir / 'ds054'), bids_validate=False)
     >>> bids_info.inputs.in_file = '''\
 sub-01/func/ses-retest/sub-01_ses-retest_task-covertverbgeneration_bold.nii.gz'''
@@ -224,6 +228,10 @@ class BIDSDataGrabber(SimpleInterface):
     """
     Collect files from a BIDS directory structure.
 
+    .. testsetup::
+
+        >>> data_dir_canary()
+
     >>> bids_src = BIDSDataGrabber(anat_only=False)
     >>> bids_src.inputs.subject_data = bids_collect_data(
     ...     str(datadir / 'ds114'), '01', bids_validate=False)[0]
@@ -320,6 +328,10 @@ class DerivativesDataSink(SimpleInterface):
     Saves the ``in_file`` into a BIDS-Derivatives folder provided
     by ``base_directory``, given the input reference ``source_file``.
 
+    .. testsetup::
+
+        >>> data_dir_canary()
+
     >>> import tempfile
     >>> tmpdir = Path(tempfile.mkdtemp())
     >>> tmpfile = tmpdir / 'a_temp_file.nii.gz'
@@ -732,6 +744,10 @@ class ReadSidecarJSON(SimpleInterface):
     """
     Read JSON sidecar files of a BIDS tree.
 
+    .. testsetup::
+
+        >>> data_dir_canary()
+
     >>> fmap = str(datadir / 'ds054' / 'sub-100185' / 'fmap' /
     ...            'sub-100185_phasediff.nii.gz')
 

niworkflows/interfaces/freesurfer.py

@@ -48,6 +48,10 @@ class StructuralReference(fs.RobustTemplate):
     """
     Shortcut RobustTemplate with a copy of the source if a single volume is provided.
 
+    .. testsetup::
+
+        >>> data_dir_canary()
+
     Examples
     --------
     >>> t1w = bids_collect_data(

niworkflows/interfaces/tests/test_bids.py

@@ -32,6 +32,7 @@
 from nipype.interfaces.base import Undefined
 
 from .. import bids as bintfs
+from niworkflows.testing import needs_data_dir
 
 
 XFORM_CODES = {
@@ -608,6 +609,7 @@ def test_DerivativesDataSink_values(tmp_path, dtype):
     assert sha1(out_file.read_bytes()).hexdigest() == checksum
 
 
+@needs_data_dir
 @pytest.mark.parametrize("field", ["RepetitionTime", "UndefinedField"])
 def test_ReadSidecarJSON_connection(testdata_dir, field):
     """

niworkflows/interfaces/tests/test_images.py

@@ -29,6 +29,7 @@
 import pytest
 
 from .. import images as im
+from niworkflows.testing import has_afni
 
 
 @pytest.mark.parametrize(
@@ -153,6 +154,7 @@ def test_conform_set_zooms(tmpdir):
     assert np.allclose(out_img.header.get_zooms(), conform.inputs.target_zooms)
 
 
+@pytest.mark.skipif(not has_afni, reason="Needs AFNI")
 @pytest.mark.parametrize("shape", [
     (10, 10, 10),
     (10, 10, 10, 1),

niworkflows/testing.py

@@ -0,0 +1,43 @@
+import pytest
+from functools import wraps
+import os
+from pathlib import Path
+from nipype.interfaces import fsl, freesurfer as fs, afni
+
+test_data_env = os.getenv(
+    "TEST_DATA_HOME", str(Path.home() / ".cache" / "stanford-crn")
+)
+test_output_dir = os.getenv("TEST_OUTPUT_DIR")
+test_workdir = os.getenv("TEST_WORK_DIR")
+
+data_dir = Path(test_data_env) / "BIDS-examples-1-enh-ds054"
+
+
+def create_canary(predicate, message):
+    def canary():
+        if predicate:
+            pytest.skip(message)
+
+    def decorator(f):
+        @wraps(f)
+        def wrapper(*args, **kwargs):
+            canary()
+            return f(*args, **kwargs)
+        return wrapper
+
+    return canary, decorator
+
+
+data_env_canary, needs_data_env = create_canary(
+    not os.path.isdir(test_data_env),
+    "Test data must be made available in ~/.cache/stanford-crn or in a "
+    "directory referenced by the TEST_DATA_HOME environment variable.")
+
+data_dir_canary, needs_data_dir = create_canary(
+    not os.path.isdir(data_dir),
+    "Test data must be made available in ~/.cache/stanford-crn or in a "
+    "directory referenced by the TEST_DATA_HOME environment variable.")
+
+has_fsl = fsl.Info.version() is not None
+has_freesurfer = fs.Info.version() is not None
+has_afni = afni.Info.version() is not None

niworkflows/tests/conftest.py

@@ -26,20 +26,11 @@
 from datetime import datetime as dt
 import pytest
 from templateflow.api import get as get_template
-from nipype.interfaces.fsl import Info as FSLInfo
-from nipype.interfaces.freesurfer import Info as FreeSurferInfo
+from niworkflows.testing import test_data_env, data_env_canary
 
 filepath = os.path.dirname(os.path.realpath(__file__))
 datadir = os.path.realpath(os.path.join(filepath, "data"))
 
-test_data_env = os.getenv(
-    "TEST_DATA_HOME", str(Path.home() / ".cache" / "nipreps-data")
-)
-data_dir = Path(test_data_env) / "ds000003"
-
-has_fsl = FSLInfo.version() is not None
-has_freesurfer = FreeSurferInfo.version() is not None
-
 
 def _run_interface_mock(objekt, runtime):
     runtime.returncode = 0
@@ -63,7 +54,8 @@ def reference_mask():
 
 @pytest.fixture
 def moving():
-    return str(data_dir / "sub-01/anat/sub-01_T1w.nii.gz")
+    data_env_canary()
+    return str(Path(test_data_env) / "ds000003/sub-01/anat/sub-01_T1w.nii.gz")
 
 
 @pytest.fixture

niworkflows/tests/test_registration.py

@@ -36,7 +36,8 @@
     ApplyXFMRPT,
     SimpleBeforeAfterRPT,
 )
-from .conftest import _run_interface_mock, datadir, has_fsl, has_freesurfer
+from ..testing import has_fsl, has_freesurfer
+from .conftest import _run_interface_mock, datadir
 
 
 def _smoke_test_report(report_interface, artifact_name):

niworkflows/tests/test_segmentation.py

@@ -35,7 +35,8 @@
     SimpleShowMaskRPT,
     ROIsPlot,
 )
-from .conftest import _run_interface_mock, datadir, has_fsl, has_freesurfer
+from ..testing import has_fsl, has_freesurfer
+from .conftest import _run_interface_mock, datadir
 
 
 def _smoke_test_report(report_interface, artifact_name):