changing str(tmpdir) to tmpdir.strpath in tests

Author: djarecka

nipype/algorithms/tests/test_compcor.py

@@ -21,7 +21,7 @@ class TestCompCor():
     @pytest.fixture(autouse=True)
     def setup_class(self, tmpdir):
         # setup
-        self.temp_dir = str(tmpdir)
+        self.temp_dir = tmpdir.strpath
         os.chdir(self.temp_dir)
         noise = np.fromfunction(self.fake_noise_fun, self.fake_data.shape)
         self.realigned_file = utils.save_toy_nii(self.fake_data + noise,

nipype/algorithms/tests/test_confounds.py

@@ -20,7 +20,7 @@
 
 
 def test_fd(tmpdir):
-    tempdir = str(tmpdir)
+    tempdir = tmpdir.strpath
     ground_truth = np.loadtxt(example_data('fsl_motion_outliers_fd.txt'))
     fdisplacement = FramewiseDisplacement(in_file=example_data('fsl_mcflirt_movpar.txt'),
                                           out_file=tempdir + '/fd.txt',
@@ -43,7 +43,7 @@ def test_dvars(tmpdir):
                          in_mask=example_data('ds003_sub-01_mc_brainmask.nii.gz'),
                          save_all=True,
                          intensity_normalization=0)
-    os.chdir(str(tmpdir))
+    os.chdir(tmpdir.strpath)
     res = dvars.run()
 
     dv1 = np.loadtxt(res.outputs.out_all, skiprows=1)

nipype/algorithms/tests/test_errormap.py

@@ -11,7 +11,7 @@
 
 def test_errormap(tmpdir):
 
-    tempdir = str(tmpdir)
+    tempdir = tmpdir.strpath
     # Single-Spectual
     # Make two fake 2*2*2 voxel volumes
     volume1 = np.array([[[2.0, 8.0], [1.0, 2.0]], [[1.0, 9.0], [0.0, 3.0]]])  # John von Neumann's birthday

nipype/algorithms/tests/test_mesh_ops.py

@@ -15,7 +15,7 @@
 
 @pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed")
 def test_ident_distances(tmpdir):
-    tempdir = str(tmpdir)
+    tempdir = tmpdir.strpath
     os.chdir(tempdir)
 
     in_surf = example_data('surf01.vtk')
@@ -33,7 +33,7 @@ def test_ident_distances(tmpdir):
 
 @pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed")
 def test_trans_distances(tmpdir):
-    tempdir = str(tmpdir)
+    tempdir = tmpdir.strpath
     from ...interfaces.vtkbase import tvtk
 
     in_surf = example_data('surf01.vtk')
@@ -63,14 +63,14 @@ def test_trans_distances(tmpdir):
 
 @pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed")
 def test_warppoints(tmpdir):
-    os.chdir(str(tmpdir))
+    os.chdir(tmpdir.strpath)
 
     # TODO: include regression tests for when tvtk is installed
 
 
 @pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed")
 def test_meshwarpmaths(tmpdir):
-    os.chdir(str(tmpdir))
+    os.chdir(tmpdir.strpath)
 
     # TODO: include regression tests for when tvtk is installed
 

nipype/algorithms/tests/test_modelgen.py

@@ -17,7 +17,7 @@
 
 
 def test_modelgen1(tmpdir):
-    tempdir = str(tmpdir)
+    tempdir = tmpdir.strpath
     filename1 = os.path.join(tempdir, 'test1.nii')
     filename2 = os.path.join(tempdir, 'test2.nii')
     Nifti1Image(np.random.rand(10, 10, 10, 200), np.eye(4)).to_filename(filename1)
@@ -56,7 +56,7 @@ def test_modelgen1(tmpdir):
 
 
 def test_modelgen_spm_concat(tmpdir):
-    tempdir = str(tmpdir)
+    tempdir = tmpdir.strpath
     filename1 = os.path.join(tempdir, 'test1.nii')
     filename2 = os.path.join(tempdir, 'test2.nii')
     Nifti1Image(np.random.rand(10, 10, 10, 30), np.eye(4)).to_filename(filename1)
@@ -122,7 +122,7 @@ def test_modelgen_spm_concat(tmpdir):
 
 
 def test_modelgen_sparse(tmpdir):
-    tempdir = str(tmpdir)
+    tempdir = tmpdir.strpath
     filename1 = os.path.join(tempdir, 'test1.nii')
     filename2 = os.path.join(tempdir, 'test2.nii')
     Nifti1Image(np.random.rand(10, 10, 10, 50), np.eye(4)).to_filename(filename1)

nipype/algorithms/tests/test_normalize_tpms.py

@@ -18,7 +18,7 @@
 
 
 def test_normalize_tpms(tmpdir):
-    tempdir = str(tmpdir)
+    tempdir = tmpdir.strpath
 
     in_mask = example_data('tpms_msk.nii.gz')
     mskdata = nb.load(in_mask, mmap=NUMPY_MMAP).get_data()

nipype/algorithms/tests/test_overlap.py

@@ -20,7 +20,7 @@ def check_close(val1, val2):
     in1 = example_data('segmentation0.nii.gz')
     in2 = example_data('segmentation1.nii.gz')
 
-    os.chdir(str(tmpdir))
+    os.chdir(tmpdir.strpath)
     overlap = Overlap()
     overlap.inputs.volume1 = in1
     overlap.inputs.volume2 = in1

nipype/algorithms/tests/test_splitmerge.py

@@ -14,13 +14,13 @@ def test_split_and_merge(tmpdir):
     from nipype.algorithms.misc import split_rois, merge_rois
 
     in_mask = example_data('tpms_msk.nii.gz')
-    dwfile = op.join(str(tmpdir), 'dwi.nii.gz')
+    dwfile = op.join(tmpdir.strpath, 'dwi.nii.gz')
     mskdata = nb.load(in_mask, mmap=NUMPY_MMAP).get_data()
     aff = nb.load(in_mask, mmap=NUMPY_MMAP).affine
 
     dwshape = (mskdata.shape[0], mskdata.shape[1], mskdata.shape[2], 6)
     dwdata = np.random.normal(size=dwshape)
-    os.chdir(str(tmpdir))
+    os.chdir(tmpdir.strpath)
     nb.Nifti1Image(dwdata.astype(np.float32),
                    aff, None).to_filename(dwfile)
 

nipype/algorithms/tests/test_tsnr.py

@@ -30,7 +30,7 @@ class TestTSNR():
     @pytest.fixture(autouse=True)
     def setup_class(self, tmpdir):
         # setup temp folder
-        self.temp_dir = str(tmpdir)
+        self.temp_dir = tmpdir.strpath
         os.chdir(self.temp_dir)
 
         utils.save_toy_nii(self.fake_data, self.in_filenames['in_file'])

nipype/caching/tests/test_memory.py

@@ -25,7 +25,7 @@ def test_caching(tmpdir):
     try:
         # Prevent rerun to check that evaluation is computed only once
         config.set('execution', 'stop_on_first_rerun', 'true')
-        mem = Memory(str(tmpdir))
+        mem = Memory(tmpdir.strpath)
         first_nb_run = nb_runs
         results = mem.cache(SideEffectInterface)(input1=2, input2=1)
         assert nb_runs == first_nb_run + 1

nipype/interfaces/cmtk/tests/test_nbs.py

@@ -18,7 +18,7 @@ def creating_graphs(tmpdir):
     for idx, name in enumerate(graphnames):
         graph = np.random.rand(10,10)
         G = nx.from_numpy_matrix(graph)
-        out_file = str(tmpdir) + graphnames[idx] + '.pck'
+        out_file = tmpdir.strpath + graphnames[idx] + '.pck'
         # Save as pck file
         nx.write_gpickle(G, out_file)
         graphlist.append(out_file)

nipype/interfaces/freesurfer/tests/test_model.py

@@ -15,7 +15,7 @@
 
 @pytest.mark.skipif(no_freesurfer(), reason="freesurfer is not installed")
 def test_concatenate(tmpdir):
-    tempdir = str(tmpdir)
+    tempdir = tmpdir.strpath
     os.chdir(tempdir)
     in1 = os.path.join(tempdir, 'cont1.nii')
     in2 = os.path.join(tempdir, 'cont2.nii')

nipype/interfaces/fsl/tests/test_model.py

@@ -13,7 +13,7 @@
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
 def test_MultipleRegressDesign(tmpdir):
-    os.chdir(str(tmpdir))
+    os.chdir(tmpdir.strpath)
     foo = fsl.MultipleRegressDesign()
     foo.inputs.regressors = dict(voice_stenght=[1, 1, 1], age=[0.2, 0.4, 0.5], BMI=[1, -1, 2])
     con1 = ['voice_and_age', 'T', ['age', 'voice_stenght'], [0.5, 0.5]]

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -27,7 +27,7 @@ def fsl_name(obj, fname):
 @pytest.fixture()
 def setup_infile(tmpdir):
     ext = Info.output_type_to_ext(Info.output_type())
-    tmp_dir = str(tmpdir)
+    tmp_dir = tmpdir.strpath
     tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
     open(tmp_infile, 'w')
 
@@ -183,7 +183,7 @@ def _run_and_test(opts, output_base):
 @pytest.fixture()
 def setup_flirt(tmpdir):
     ext = Info.output_type_to_ext(Info.output_type())
-    tmp_dir = str(tmpdir)
+    tmp_dir = tmpdir.strpath
     _, infile = tempfile.mkstemp(suffix=ext, dir=tmp_dir)
     _, reffile = tempfile.mkstemp(suffix=ext, dir=tmp_dir)
 
@@ -549,7 +549,7 @@ def setup_fugue(tmpdir):
     import os.path as op
 
     d = np.ones((80, 80, 80))
-    tmp_dir = str(tmpdir)
+    tmp_dir = tmpdir.strpath
     infile = op.join(tmp_dir, 'dumbfile.nii.gz')
     nb.Nifti1Image(d, None, None).to_filename(infile)
 

nipype/interfaces/tests/test_base.py

@@ -70,7 +70,7 @@ def test_bunch_hash():
 
 @pytest.fixture(scope="module")
 def setup_file(request, tmpdir_factory):
-    tmp_dir = str(tmpdir_factory.mktemp('files'))
+    tmp_dir = tmpdir_factory.mktemp('files').strpath
     tmp_infile = os.path.join(tmp_dir, 'foo.txt')
     with open(tmp_infile, 'w') as fp:
         fp.writelines([u'123456789'])
@@ -412,7 +412,7 @@ def _run_interface(self, runtime):
 
 
 def test_BaseInterface_load_save_inputs(tmpdir):
-    tmp_json = os.path.join(str(tmpdir), 'settings.json')
+    tmp_json = os.path.join(tmpdir.strpath, 'settings.json')
 
     class InputSpec(nib.TraitedSpec):
         input1 = nib.traits.Int()

nipype/interfaces/tests/test_io.py

@@ -117,7 +117,7 @@ def test_s3datagrabber_communication(tmpdir):
     dg.inputs.anon = True
     dg.inputs.bucket = 'openfmri'
     dg.inputs.bucket_path = 'ds001/'
-    dg.inputs.local_directory = str(tmpdir)
+    dg.inputs.local_directory = tmpdir.strpath
     dg.inputs.sort_filelist = True
     dg.inputs.template = '*'
     dg.inputs.field_template = dict(func='%s/BOLD/task001_%s/bold.nii.gz',
@@ -147,7 +147,7 @@ def test_datagrabber_order(tmpdir):
         tmpdir.join(file_name).open('a').close()
 
     dg = nio.DataGrabber(infields=['sid'])
-    dg.inputs.base_directory = str(tmpdir)
+    dg.inputs.base_directory = tmpdir.strpath
     dg.inputs.template = '%s_L%d_R*.q*'
     dg.inputs.template_args = {'outfiles': [['sid', 1], ['sid', 2],
                                             ['sid', 3]]}
@@ -208,7 +208,7 @@ def test_datasink_to_s3(dummy_input, tmpdir):
     attr_folder = 'text_file'
     output_dir = 's3://' + bucket_name
     # Local temporary filepaths for testing
-    fakes3_dir = str(tmpdir)
+    fakes3_dir = tmpdir.strpath
     input_path = dummy_input
 
     # Start up fake-S3 server
@@ -280,7 +280,7 @@ def test_datasink_localcopy(dummy_input, tmpdir):
     '''
 
     # Init variables
-    local_dir = str(tmpdir)
+    local_dir = tmpdir.strpath
     container = 'outputs'
     attr_folder = 'text_file'
 
@@ -370,7 +370,7 @@ def test_datasink_copydir():
 
 
 def test_datafinder_depth(tmpdir):
-    outdir = str(tmpdir)
+    outdir = tmpdir.strpath
     os.makedirs(os.path.join(outdir, '0', '1', '2', '3'))
 
     df = nio.DataFinder()
@@ -387,7 +387,7 @@ def test_datafinder_depth(tmpdir):
 
 
 def test_datafinder_unpack(tmpdir):
-    outdir = str(tmpdir)
+    outdir = tmpdir.strpath
     single_res = os.path.join(outdir, "findme.txt")
     open(single_res, 'a').close()
     open(os.path.join(outdir, "dontfindme"), 'a').close()
@@ -425,7 +425,7 @@ def test_jsonsink_input(tmpdir):
         {'new_entry' : 'someValue', 'test' : 'testInfields'}
 ])
 def test_jsonsink(tmpdir, inputs_attributes):
-    os.chdir(str(tmpdir))
+    os.chdir(tmpdir.strpath)
     js = nio.JSONFileSink(infields=['test'], in_dict={'foo': 'var'})
     setattr(js.inputs, 'contrasts.alt', 'someNestedValue')
     expected_data = {"contrasts": {"alt": "someNestedValue"}, "foo": "var"}

nipype/interfaces/utility/tests/test_base.py

@@ -11,13 +11,13 @@
 
 
 def test_rename(tmpdir):
-    os.chdir(str(tmpdir))
+    os.chdir(tmpdir.strpath)
 
     # Test very simple rename
     _ = open("file.txt", "w").close()
     rn = utility.Rename(in_file="file.txt", format_string="test_file1.txt")
     res = rn.run()
-    outfile = str(tmpdir.join("test_file1.txt"))
+    outfile = tmpdir.join("test_file1.txt").strpath
     assert res.outputs.out_file == outfile
     assert os.path.exists(outfile)
 
@@ -31,7 +31,7 @@ def test_rename(tmpdir):
     rn.inputs.field1 = "test"
     rn.inputs.field2 = 2
     res = rn.run()
-    outfile = str(tmpdir.join("test_file2.txt"))
+    outfile = tmpdir.join("test_file2.txt").strpath
     assert res.outputs.out_file == outfile
     assert os.path.exists(outfile)
 
@@ -41,7 +41,7 @@ def test_rename(tmpdir):
         ({"squeeze" : True},  (0  , [1,2,3]))
         ])
 def test_split(tmpdir, args, expected):
-    os.chdir(str(tmpdir))
+    os.chdir(tmpdir.strpath)
 
     node = pe.Node(utility.Split(inlist=list(range(4)),
                                  splits=[1, 3],
@@ -64,7 +64,7 @@ def test_split(tmpdir, args, expected):
          [[0, 2, 4], [1, 3, 5]]),
         ])
 def test_merge(tmpdir, args, kwargs, in_lists, expected):
-    os.chdir(str(tmpdir))
+    os.chdir(tmpdir.strpath)
 
     node = pe.Node(utility.Merge(*args, **kwargs), name='merge')
 

nipype/interfaces/utility/tests/test_csv.py

@@ -12,7 +12,7 @@ def test_csvReader(tmpdir):
              "bar,world,5\n",
              "baz,goodbye,0.3\n"]
     for x in range(2):
-        name = str(tmpdir.join("testfile.csv"))
+        name = tmpdir.join("testfile.csv").strpath
         with open(name, 'w') as fid:
             reader = utility.CSVReader()
             if x % 2 == 0:

nipype/interfaces/utility/tests/test_wrappers.py

@@ -16,7 +16,7 @@ def concat_sort(in_arrays):
 """
 
 def test_function(tmpdir):
-    os.chdir(str(tmpdir))
+    os.chdir(tmpdir.strpath)
 
     def gen_random_array(size):
         import numpy as np
@@ -59,11 +59,11 @@ def should_fail(tmpdir):
 
 def test_should_fail(tmpdir):
     with pytest.raises(NameError):
-        should_fail(str(tmpdir))
+        should_fail(tmpdir.strpath)
 
 
 def test_function_with_imports(tmpdir):
-    os.chdir(str(tmpdir))
+    os.chdir(tmpdir.strpath)
 
     node = pe.Node(utility.Function(input_names=["size"],
                                     output_names=["random_array"],
@@ -79,7 +79,7 @@ def test_aux_connect_function(tmpdir):
     """ This tests excution nodes with multiple inputs and auxiliary
     function inside the Workflow connect function.
     """
-    os.chdir(str(tmpdir))
+    os.chdir(tmpdir.strpath)
 
     wf = pe.Workflow(name="test_workflow")
 

nipype/pipeline/engine/tests/test_engine.py

@@ -661,7 +661,7 @@ def test_parameterize_dirs_false(tmpdir):
     n2 = pe.Node(IdentityInterface(fields='in1'), name='Node2')
 
     wf = pe.Workflow(name='Test')
-    wf.base_dir = str(tmpdir)
+    wf.base_dir = tmpdir.strpath
     wf.config['execution']['parameterize_dirs'] = False
     wf.connect([(n1, n2, [('output1', 'in1')])])