fix doctests

Author: josephmje

dmriprep/conftest.py

@@ -5,7 +5,6 @@
 import numpy as np
 import nibabel as nb
 import pytest
-from bids.layout import BIDSLayout
 from dipy.data.fetcher import _make_fetcher, UW_RW_URL
 
 _dipy_datadir_root = os.getenv('DMRIPREP_TESTS_DATA') or Path.home()
@@ -29,20 +28,6 @@
     'bvals': np.loadtxt(dipy_datadir / "HARDI193.bval"),
 }
 
-test_data_env = os.getenv('TEST_DATA_HOME', '/tmp/data')
-test_output_dir = os.getenv('TEST_OUTPUT_DIR')
-test_workdir = os.getenv('TEST_WORK_DIR')
-
-layouts = {p.name: BIDSLayout(str(p), validate=False, derivatives=True)
-           for p in Path(test_data_env).glob('*') if p.is_dir()}
-
-
-def pytest_report_header(config):
-    msg = "Datasets found: %s" % ', '.join([v.root for v in layouts.values()])
-    if test_output_dir is not None:
-        msg += '\nOutput folder: %s' % Path(test_output_dir).resolve()
-    return msg
-
 
 @pytest.fixture(autouse=True)
 def doctest_autoimport(doctest_namespace):
@@ -63,18 +48,3 @@ def doctest_autoimport(doctest_namespace):
 def dipy_test_data(scope='session'):
     """Create a temporal directory shared across tests to pull data in."""
     return _sherbrooke_data
-
-
-@pytest.fixture
-def workdir():
-    return None if test_workdir is None else Path(test_workdir)
-
-
-@pytest.fixture
-def output_path():
-    return None if test_output_dir is None else Path(test_output_dir)
-
-
-@pytest.fixture
-def bids_layouts():
-    return layouts

dmriprep/workflows/dwi/base.py

@@ -2,7 +2,6 @@
 Orchestrating the dMRI-preprocessing workflow.
 
 .. autofunction:: init_dwi_preproc_wf
-.. autofunction:: init_dwi_derivatives_wf
 
 """
 

dmriprep/workflows/dwi/util.py

@@ -33,7 +33,7 @@ def init_dwi_reference_wf(omp_nthreads, dwi_file=None,
 
             from dmriprep.workflows.dwi.util import init_dwi_reference_wf
             wf = init_dwi_reference_wf(omp_nthreads=1)
-            wf.inputnode.inputs.b0_ixs=[0]
+            wf.inputs.inputnode.b0_ixs=[0]
 
     Parameters
     ----------