moving to temporary directories, so tests can be run in readonly; adding conftest.py with datadir variable and some basic libraries (so you dont have to import them in doctests)

Author: djarecka

conftest.py

@@ -0,0 +1,12 @@
+import pytest
+import numpy, os
+
+@pytest.fixture(autouse=True)
+def add_np(doctest_namespace):
+    doctest_namespace['np'] = numpy
+    doctest_namespace['os'] = os
+
+
+    filepath = os.path.dirname(os.path.realpath(__file__))
+    datadir = os.path.realpath(os.path.join(filepath, 'nipype/testing/data'))
+    doctest_namespace["datadir"] = datadir

nipype/interfaces/dcm2nii.py

@@ -70,13 +70,16 @@ class Dcm2nii(CommandLine):
     Examples
     ========
 
+    >>> tmp = getfixture('tmpdir')
+    >>> old = tmp.chdir() # changing to a temporary directory
     >>> from nipype.interfaces.dcm2nii import Dcm2nii
     >>> converter = Dcm2nii()
-    >>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
+    >>> converter.inputs.source_names = [os.path.join(datadir, 'functional_1.dcm'), os.path.join(datadir, 'functional_2.dcm')]
     >>> converter.inputs.gzip_output = True
     >>> converter.inputs.output_dir = '.'
-    >>> converter.cmdline
-    'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm'
+    >>> converter.cmdline #doctest: +ELLIPSIS
+    'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n ...functional_1.dcm'
+    >>> os.chdir(old.strpath)
     """
 
     input_spec = Dcm2niiInputSpec

nipype/interfaces/fsl/tests/test_Level1Design_functions.py

@@ -4,7 +4,8 @@
 from ..model import Level1Design
 
 
-def test_level1design():
+def test_level1design(tmpdir):
+    old = tmpdir.chdir()
     l = Level1Design()
     runinfo = dict(cond=[{'name': 'test_condition', 'onset': [0, 10],
                           'duration':[10, 10]}],regress=[])
@@ -29,3 +30,5 @@ def test_level1design():
                                                                do_tempfilter,
                                                                key)
         assert "set fmri(convolve1) {0}".format(val) in output_txt
+
+    os.chdir(old.strpath)

nipype/interfaces/io.py

@@ -2476,19 +2476,20 @@ class JSONFileGrabber(IOBase):
 
     Example
     -------
-
+    >>> tmp = getfixture('tmpdir')
+    >>> old = tmp.chdir() # changing to a temporary directory
     >>> import pprint
     >>> from nipype.interfaces.io import JSONFileGrabber
     >>> jsonSource = JSONFileGrabber()
     >>> jsonSource.inputs.defaults = {'param1': 'overrideMe', 'param3': 1.0}
     >>> res = jsonSource.run()
     >>> pprint.pprint(res.outputs.get())
     {'param1': 'overrideMe', 'param3': 1.0}
-    >>> jsonSource.inputs.in_file = 'jsongrabber.txt'
+    >>> jsonSource.inputs.in_file = os.path.join(datadir, 'jsongrabber.txt')
     >>> res = jsonSource.run()
     >>> pprint.pprint(res.outputs.get())  # doctest:, +ELLIPSIS
     {'param1': 'exampleStr', 'param2': 4, 'param3': 1.0}
-
+    >>> os.chdir(old.strpath)
 
     """
     input_spec = JSONFileGrabberInputSpec

nipype/interfaces/niftyreg/regutils.py

@@ -391,6 +391,8 @@ class RegAverage(NiftyRegCommand):
 
     Examples
     --------
+    >>> tmp = getfixture('tmpdir')
+    >>> old = tmp.chdir() # changing to temporary file
     >>> from nipype.interfaces import niftyreg
     >>> node = niftyreg.RegAverage()
     >>> one_file = 'im1.nii'
@@ -399,6 +401,7 @@ class RegAverage(NiftyRegCommand):
     >>> node.inputs.avg_files = [one_file, two_file, three_file]
     >>> node.cmdline  # doctest: +ELLIPSIS
     'reg_average --cmd_file .../reg_average_cmd'
+    >>> os.chdir(old.strpath)
 
     """
     _cmd = get_custom_path('reg_average')

nipype/interfaces/utility/base.py

@@ -2,15 +2,9 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
-Various utilities
-
-    Change directory to provide relative paths for doctests
-    >>> import os
-    >>> filepath = os.path.dirname(os.path.realpath(__file__))
-    >>> datadir = os.path.realpath(os.path.join(filepath,
-    ...                            '../../testing/data'))
-    >>> os.chdir(datadir)
-
+    # changing to temporary directories
+    >>> tmp = getfixture('tmpdir')
+    >>> old = tmp.chdir()
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
 from builtins import range
@@ -231,14 +225,14 @@ class Rename(IOBase):
 
     >>> from nipype.interfaces.utility import Rename
     >>> rename1 = Rename()
-    >>> rename1.inputs.in_file = "zstat1.nii.gz"
+    >>> rename1.inputs.in_file = os.path.join(datadir, "zstat1.nii.gz") # datadir is a directory with exemplary files, defined in conftest.py
     >>> rename1.inputs.format_string = "Faces-Scenes.nii.gz"
     >>> res = rename1.run()          # doctest: +SKIP
     >>> res.outputs.out_file         # doctest: +SKIP
     'Faces-Scenes.nii.gz"            # doctest: +SKIP
 
     >>> rename2 = Rename(format_string="%(subject_id)s_func_run%(run)02d")
-    >>> rename2.inputs.in_file = "functional.nii"
+    >>> rename2.inputs.in_file = os.path.join(datadir, "functional.nii")
     >>> rename2.inputs.keep_ext = True
     >>> rename2.inputs.subject_id = "subj_201"
     >>> rename2.inputs.run = 2
@@ -247,7 +241,7 @@ class Rename(IOBase):
     'subj_201_func_run02.nii'        # doctest: +SKIP
 
     >>> rename3 = Rename(format_string="%(subject_id)s_%(seq)s_run%(run)02d.nii")
-    >>> rename3.inputs.in_file = "func_epi_1_1.nii"
+    >>> rename3.inputs.in_file = os.path.join(datadir, "func_epi_1_1.nii")
     >>> rename3.inputs.parse_string = "func_(?P<seq>\w*)_.*"
     >>> rename3.inputs.subject_id = "subj_201"
     >>> rename3.inputs.run = 2

nipype/interfaces/utility/wrappers.py

@@ -1,17 +1,12 @@
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Various utilities
-
-    Change directory to provide relative paths for doctests
-    >>> import os
-    >>> filepath = os.path.dirname(os.path.realpath(__file__))
-    >>> datadir = os.path.realpath(os.path.join(filepath,
-    ...                            '../../testing/data'))
-    >>> os.chdir(datadir)
-
-
 """
+# changing to temporary directories
+    >>> tmp = getfixture('tmpdir')
+    >>> old = tmp.chdir()
+"""
+
 from __future__ import print_function, division, unicode_literals, absolute_import
 
 from future import standard_library

nipype/pipeline/engine/tests/test_utils.py

@@ -18,27 +18,29 @@
 from ..utils import merge_dict, clean_working_directory, write_workflow_prov
 
 
-def test_identitynode_removal():
+def test_identitynode_removal(tmpdir):
 
     def test_function(arg1, arg2, arg3):
         import numpy as np
         return (np.array(arg1) + arg2 + arg3).tolist()
+    
+    out_dir = tmpdir.strpath
 
-    wf = pe.Workflow(name="testidentity")
+    wf = pe.Workflow(name="testidentity", base_dir=out_dir)
 
-    n1 = pe.Node(niu.IdentityInterface(fields=['a', 'b']), name='src')
+    n1 = pe.Node(niu.IdentityInterface(fields=['a', 'b']), name='src', base_dir=out_dir,)
     n1.iterables = ('b', [0, 1, 2, 3])
     n1.inputs.a = [0, 1, 2, 3]
 
-    n2 = pe.Node(niu.Select(), name='selector')
+    n2 = pe.Node(niu.Select(), name='selector', base_dir=out_dir,)
     wf.connect(n1, ('a', test_function, 1, -1), n2, 'inlist')
     wf.connect(n1, 'b', n2, 'index')
 
-    n3 = pe.Node(niu.IdentityInterface(fields=['c', 'd']), name='passer')
+    n3 = pe.Node(niu.IdentityInterface(fields=['c', 'd']), name='passer', base_dir=out_dir,)
     n3.inputs.c = [1, 2, 3, 4]
     wf.connect(n2, 'out', n3, 'd')
 
-    n4 = pe.Node(niu.Select(), name='selector2')
+    n4 = pe.Node(niu.Select(), name='selector2', base_dir=out_dir,)
     wf.connect(n3, ('c', test_function, 1, -1), n4, 'inlist')
     wf.connect(n3, 'd', n4, 'index')
 
@@ -216,19 +218,19 @@ def test_function3(arg):
         n1 = pe.Node(niu.Function(input_names=['arg1'],
                                   output_names=['out_file1', 'out_file2', 'dir'],
                                   function=test_function),
-                     name='n1')
+                     name='n1', base_dir=out_dir)
         n1.inputs.arg1 = 1
 
         n2 = pe.Node(niu.Function(input_names=['in_file', 'arg'],
                                   output_names=['out_file1', 'out_file2', 'n'],
                                   function=test_function2),
-                     name='n2')
+                     name='n2', base_dir=out_dir)
         n2.inputs.arg = 2
 
         n3 = pe.Node(niu.Function(input_names=['arg'],
                                   output_names=['n'],
                                   function=test_function3),
-                     name='n3')
+                     name='n3', base_dir=out_dir)
 
         wf = pe.Workflow(name="node_rem_test" + plugin, base_dir=out_dir)
         wf.connect(n1, "out_file1", n2, "in_file")
@@ -271,7 +273,7 @@ def test_function3(arg):
                                                n2.name,
                                                'file3.txt')) != remove_unnecessary_outputs
 
-        n4 = pe.Node(UtilsTestInterface(), name='n4')
+        n4 = pe.Node(UtilsTestInterface(), name='n4', base_dir=out_dir)
         wf.connect(n2, "out_file1", n4, "in_file")
 
         def pick_first(l):