test: Make datadir a fixture that can skip a test

Author: effigies

niworkflows/tests/conftest.py

@@ -30,9 +30,16 @@
 from templateflow.api import get as get_template
 
 from niworkflows.testing import data_env_canary, test_data_env
-from niworkflows.tests.data import load_test_data
 
-datadir = load_test_data()
+
+@pytest.fixture
+def datadir():
+    try:
+        from niworkflows.tests.data import load_test_data
+    except ImportError:
+        pytest.skip('niworkflows installed as wheel, data excluded')
+
+    return load_test_data()
 
 
 def _run_interface_mock(objekt, runtime):

niworkflows/tests/test_confounds.py

@@ -31,7 +31,6 @@
 
 from ..interfaces.confounds import ExpandModel, SpikeRegressors
 from ..interfaces.plotting import CompCorVariancePlot, ConfoundsCorrelationPlot
-from .conftest import datadir
 
 
 def _smoke_test_report(report_interface, artifact_name):
@@ -43,7 +42,7 @@ def _smoke_test_report(report_interface, artifact_name):
     assert os.path.isfile(out_report), f'Report "{out_report}" does not exist'
 
 
-def _expand_test(model_formula):
+def _expand_test(model_formula, datadir):
     orig_data_file = os.path.join(datadir, 'confounds_test.tsv')
     exp_data_file = (
         pe.Node(
@@ -56,7 +55,7 @@ def _expand_test(model_formula):
     return pd.read_csv(exp_data_file, sep='\t')
 
 
-def _spikes_test(lags=None, mincontig=None, fmt='mask'):
+def _spikes_test(lags=None, mincontig=None, fmt='mask', *, datadir):
     orig_data_file = os.path.join(datadir, 'spikes_test.tsv')
     lags = lags or [0]
     spk_data_file = (
@@ -78,7 +77,7 @@ def _spikes_test(lags=None, mincontig=None, fmt='mask'):
     return pd.read_csv(spk_data_file, sep='\t')
 
 
-def test_expansion_variable_selection():
+def test_expansion_variable_selection(datadir):
     """Test model expansion: simple variable selection"""
     model_formula = 'a + b + c + d'
     expected_data = pd.DataFrame(
@@ -89,11 +88,11 @@ def test_expansion_variable_selection():
             'd': [9, 7, 5, 3, 1],
         }
     )
-    exp_data = _expand_test(model_formula)
+    exp_data = _expand_test(model_formula, datadir)
     pd.testing.assert_frame_equal(exp_data, expected_data)
 
 
-def test_expansion_derivatives_and_powers():
+def test_expansion_derivatives_and_powers(datadir):
     """Temporal derivatives and quadratics"""
     model_formula = '(dd1(a) + d1(b))^^2 + d1-2((c)^2) + d + others'
     # b_derivative1_power2 is dropped as an exact duplicate of b_derivative1
@@ -112,13 +111,13 @@ def test_expansion_derivatives_and_powers():
             'f': [np.nan, 6, 4, 2, 0],
         }
     )
-    exp_data = _expand_test(model_formula)
+    exp_data = _expand_test(model_formula, datadir)
     assert set(exp_data.columns) == set(expected_data.columns)
     for col in expected_data.columns:
         pd.testing.assert_series_equal(expected_data[col], exp_data[col], check_dtype=False)
 
 
-def test_expansion_na_robustness():
+def test_expansion_na_robustness(datadir):
     """NA robustness"""
     model_formula = '(dd1(f))^^2'
     expected_data = pd.DataFrame(
@@ -129,16 +128,16 @@ def test_expansion_na_robustness():
             'f_derivative1_power2': [np.nan, np.nan, 4, 4, 4],
         }
     )
-    exp_data = _expand_test(model_formula)
+    exp_data = _expand_test(model_formula, datadir)
     assert set(exp_data.columns) == set(expected_data.columns)
     for col in expected_data.columns:
         pd.testing.assert_series_equal(expected_data[col], exp_data[col], check_dtype=False)
 
 
-def test_spikes():
+def test_spikes(datadir):
     """Test outlier flagging"""
     outliers = [1, 1, 0, 0, 1]
-    spk_data = _spikes_test()
+    spk_data = _spikes_test(datadir=datadir)
     assert np.all(np.isclose(outliers, spk_data['motion_outlier']))
 
     outliers_spikes = pd.DataFrame(
@@ -148,30 +147,30 @@ def test_spikes():
             'motion_outlier02': [0, 0, 0, 0, 1],
         }
     )
-    spk_data = _spikes_test(fmt='spikes')
+    spk_data = _spikes_test(fmt='spikes', datadir=datadir)
     assert set(spk_data.columns) == set(outliers_spikes.columns)
     for col in outliers_spikes.columns:
         assert np.all(np.isclose(outliers_spikes[col], spk_data[col]))
 
     lags = [0, 1]
     outliers_lags = [1, 1, 1, 0, 1]
-    spk_data = _spikes_test(lags=lags)
+    spk_data = _spikes_test(lags=lags, datadir=datadir)
     assert np.all(np.isclose(outliers_lags, spk_data['motion_outlier']))
 
     mincontig = 2
     outliers_mc = [1, 1, 1, 1, 1]
-    spk_data = _spikes_test(lags=lags, mincontig=mincontig)
+    spk_data = _spikes_test(lags=lags, mincontig=mincontig, datadir=datadir)
     assert np.all(np.isclose(outliers_mc, spk_data['motion_outlier']))
 
 
-def test_CompCorVariancePlot():
+def test_CompCorVariancePlot(datadir):
     """CompCor variance report test"""
     metadata_file = os.path.join(datadir, 'confounds_metadata_test.tsv')
     cc_rpt = CompCorVariancePlot(metadata_files=[metadata_file], metadata_sources=['aCompCor'])
     _smoke_test_report(cc_rpt, 'compcor_variance.svg')
 
 
-def test_ConfoundsCorrelationPlot():
+def test_ConfoundsCorrelationPlot(datadir):
     """confounds correlation report test"""
     confounds_file = os.path.join(datadir, 'confounds_test.tsv')
     cc_rpt = ConfoundsCorrelationPlot(
@@ -182,7 +181,7 @@ def test_ConfoundsCorrelationPlot():
     _smoke_test_report(cc_rpt, 'confounds_correlation.svg')
 
 
-def test_ConfoundsCorrelationPlotColumns():
+def test_ConfoundsCorrelationPlotColumns(datadir):
     """confounds correlation report test"""
     confounds_file = os.path.join(datadir, 'confounds_test.tsv')
     cc_rpt = ConfoundsCorrelationPlot(

niworkflows/tests/test_registration.py

@@ -39,7 +39,7 @@
     SpatialNormalizationRPT,
 )
 from ..testing import has_freesurfer, has_fsl
-from .conftest import _run_interface_mock, datadir
+from .conftest import _run_interface_mock
 
 
 def _smoke_test_report(report_interface, artifact_name):
@@ -61,7 +61,7 @@ def test_FLIRTRPT(reference, moving):
 
 
 @pytest.mark.skipif(not has_freesurfer, reason='No FreeSurfer')
-def test_MRICoregRPT(monkeypatch, reference, moving, nthreads):
+def test_MRICoregRPT(monkeypatch, reference, moving, nthreads, datadir):
     """the MRICoreg report capable test"""
 
     def _agg(objekt, runtime):
@@ -120,7 +120,7 @@ def test_FLIRTRPT_w_BBR(reference, reference_mask, moving):
 
 
 @pytest.mark.skipif(not has_freesurfer, reason='No FreeSurfer')
-def test_BBRegisterRPT(monkeypatch, moving):
+def test_BBRegisterRPT(monkeypatch, moving, datadir):
     """the BBRegister report capable test"""
 
     def _agg(objekt, runtime):
@@ -145,7 +145,7 @@ def _agg(objekt, runtime):
     _smoke_test_report(bbregister_rpt, 'testBBRegister.svg')
 
 
-def test_SpatialNormalizationRPT(monkeypatch, moving):
+def test_SpatialNormalizationRPT(monkeypatch, moving, datadir):
     """the SpatialNormalizationRPT report capable test"""
 
     def _agg(objekt, runtime):
@@ -164,7 +164,7 @@ def _agg(objekt, runtime):
     _smoke_test_report(ants_rpt, 'testSpatialNormalizationRPT.svg')
 
 
-def test_SpatialNormalizationRPT_masked(monkeypatch, moving, reference_mask):
+def test_SpatialNormalizationRPT_masked(monkeypatch, moving, reference_mask, datadir):
     """the SpatialNormalizationRPT report capable test with masking"""
 
     def _agg(objekt, runtime):
@@ -188,7 +188,7 @@ def _agg(objekt, runtime):
     _smoke_test_report(ants_rpt, 'testSpatialNormalizationRPT_masked.svg')
 
 
-def test_ANTSRegistrationRPT(monkeypatch, reference, moving):
+def test_ANTSRegistrationRPT(monkeypatch, reference, moving, datadir):
     """the SpatialNormalizationRPT report capable test"""
     from niworkflows import data
 

niworkflows/tests/test_segmentation.py

@@ -38,7 +38,7 @@
 )
 from ..interfaces.reportlets.segmentation import FASTRPT, ReconAllRPT
 from ..testing import has_freesurfer, has_fsl
-from .conftest import _run_interface_mock, datadir
+from .conftest import _run_interface_mock
 
 
 def _smoke_test_report(report_interface, artifact_name):
@@ -160,7 +160,7 @@ def test_SimpleShowMaskRPT():
     _smoke_test_report(msk_rpt, 'testSimpleMask.svg')
 
 
-def test_BrainExtractionRPT(monkeypatch, moving, nthreads):
+def test_BrainExtractionRPT(monkeypatch, moving, nthreads, datadir):
     """test antsBrainExtraction with reports"""
 
     def _agg(objekt, runtime):
@@ -201,7 +201,7 @@ def _agg(objekt, runtime):
 
 @pytest.mark.skipif(not has_fsl, reason='No FSL')
 @pytest.mark.parametrize('segments', [True, False])
-def test_FASTRPT(monkeypatch, segments, reference, reference_mask):
+def test_FASTRPT(monkeypatch, segments, reference, reference_mask, datadir):
     """test FAST with the two options for segments"""
     from nipype.interfaces.fsl.maths import ApplyMask
 

niworkflows/tests/test_viz.py

@@ -35,7 +35,6 @@
 from niworkflows.viz.plots import fMRIPlot
 
 from .. import viz
-from .conftest import datadir
 from .generate_data import _create_dtseries_cifti
 
 
@@ -135,7 +134,7 @@ def test_carpetplot(tr, sorting):
         ),
     ],
 )
-def test_fmriplot(input_files):
+def test_fmriplot(input_files, datadir):
     """Exercise the fMRIPlot class."""
     save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS')
     rng = np.random.default_rng(2010)
@@ -249,7 +248,7 @@ def test_plot_melodic_components(tmp_path):
     )
 
 
-def test_compcor_variance_plot(tmp_path):
+def test_compcor_variance_plot(tmp_path, datadir):
     """Test plotting CompCor variance"""
     out_dir = Path(os.getenv('SAVE_CIRCLE_ARTIFACTS', str(tmp_path)))
     out_file = str(out_dir / 'variance_plot_short.svg')