[TST] Improve py.test configuration of doctests

This PR ensures that doctests are run OUTSIDE nipype's source directory
in all the cases. Previously, doctests would chdir into the testing/data
folder and some interfaces would generate results.

Also, deletes ``nipype/testing/data/slice_timing.1D``, which seems to
have seaked into the tree for these very reasons in some past PR.

Author: oesteban

nipype/conftest.py

@@ -1,21 +1,43 @@
+import os
+import shutil
+from tempfile import mkdtemp
 import pytest
 import numpy
-import os
+import py.path as pp
 
-DATADIR = os.path.realpath(
+NIPYPE_DATADIR = os.path.realpath(
     os.path.join(os.path.dirname(__file__), 'testing/data'))
+temp_folder = mkdtemp()
+data_dir = os.path.join(temp_folder, 'data')
+shutil.copytree(NIPYPE_DATADIR, data_dir)
 
 
 @pytest.fixture(autouse=True)
 def add_np(doctest_namespace):
     doctest_namespace['np'] = numpy
     doctest_namespace['os'] = os
-
-    doctest_namespace["datadir"] = DATADIR
+    doctest_namespace["datadir"] = data_dir
 
 
 @pytest.fixture(autouse=True)
-def in_testing(request):
-    # This seems to be a reliable way to distinguish tests from doctests
-    if request.function is None:
-        os.chdir(DATADIR)
+def _docdir(request):
+    """Grabbed from https://stackoverflow.com/a/46991331"""
+    # Trigger ONLY for the doctests.
+    doctest_plugin = request.config.pluginmanager.getplugin("doctest")
+    if isinstance(request.node, doctest_plugin.DoctestItem):
+
+        # Get the fixture dynamically by its name.
+        tmpdir = pp.local(data_dir)
+
+        # Chdir only for the duration of the test.
+        with tmpdir.as_cwd():
+            yield
+
+    else:
+        # For normal tests, we have to yield, since this is a yield-fixture.
+        yield
+
+
+def pytest_unconfigure(config):
+    # Delete temp folder after session is finished
+    shutil.rmtree(temp_folder)

nipype/interfaces/ants/registration.py

@@ -736,17 +736,17 @@ class Registration(ANTSCommand):
     >>> reg4.inputs.collapse_output_transforms = True
     >>> outputs = reg4._list_outputs()
     >>> pprint.pprint(outputs)  # doctest: +ELLIPSIS,
-    {'composite_transform': '.../nipype/testing/data/output_Composite.h5',
+    {'composite_transform': '...data/output_Composite.h5',
      'elapsed_time': <undefined>,
      'forward_invert_flags': [],
      'forward_transforms': [],
-     'inverse_composite_transform': '.../nipype/testing/data/output_InverseComposite.h5',
+     'inverse_composite_transform': '...data/output_InverseComposite.h5',
      'inverse_warped_image': <undefined>,
      'metric_value': <undefined>,
      'reverse_invert_flags': [],
      'reverse_transforms': [],
-     'save_state': '.../nipype/testing/data/trans.mat',
-     'warped_image': '.../nipype/testing/data/output_warped_image.nii.gz'}
+     'save_state': '...data/trans.mat',
+     'warped_image': '...data/output_warped_image.nii.gz'}
     >>> reg4.cmdline
     'antsRegistration --collapse-output-transforms 1 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] \
 --initialize-transforms-per-stage 1 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \
@@ -767,16 +767,16 @@ class Registration(ANTSCommand):
     {'composite_transform': <undefined>,
      'elapsed_time': <undefined>,
      'forward_invert_flags': [False, False],
-     'forward_transforms': ['.../nipype/testing/data/output_0GenericAffine.mat',
-     '.../nipype/testing/data/output_1Warp.nii.gz'],
+     'forward_transforms': ['...data/output_0GenericAffine.mat',
+     '...data/output_1Warp.nii.gz'],
      'inverse_composite_transform': <undefined>,
      'inverse_warped_image': <undefined>,
      'metric_value': <undefined>,
      'reverse_invert_flags': [True, False],
-     'reverse_transforms': ['.../nipype/testing/data/output_0GenericAffine.mat', \
-    '.../nipype/testing/data/output_1InverseWarp.nii.gz'],
-     'save_state': '.../nipype/testing/data/trans.mat',
-     'warped_image': '.../nipype/testing/data/output_warped_image.nii.gz'}
+     'reverse_transforms': ['...data/output_0GenericAffine.mat', \
+    '...data/output_1InverseWarp.nii.gz'],
+     'save_state': '...data/trans.mat',
+     'warped_image': '...data/output_warped_image.nii.gz'}
     >>> reg4b.aggregate_outputs()  # doctest: +SKIP
     >>> reg4b.cmdline
     'antsRegistration --collapse-output-transforms 1 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] \

nipype/interfaces/bru2nii.py

@@ -47,7 +47,7 @@ class Bru2(CommandLine):
     >>> converter = Bru2()
     >>> converter.inputs.input_dir = "brukerdir"
     >>> converter.cmdline  # doctest: +ELLIPSIS
-    'Bru2 -o .../nipype/testing/data/brukerdir brukerdir'
+    'Bru2 -o .../data/brukerdir brukerdir'
     """
     input_spec = Bru2InputSpec
     output_spec = Bru2OutputSpec

nipype/pipeline/plugins/lsf.py

@@ -113,7 +113,7 @@ def _submit_batchtask(self, scriptfile, node):
                 break
         iflogger.setLevel(oldlevel)
         # retrieve lsf taskid
-        match = re.search('<(\d*)>', result.runtime.stdout)
+        match = re.search(r'<(\d*)>', result.runtime.stdout)
         if match:
             taskid = int(match.groups()[0])
         else: