removing the comments that described my changes

Author: djarecka

nipype/algorithms/tests/test_mesh_ops.py

@@ -11,8 +11,6 @@
 from nipype.algorithms import mesh as m
 from ...interfaces import vtkbase as VTKInfo
 
-#NOTE_dj: I moved all tests of errors reports to a new test function
-#NOTE_dj: some tests are empty
 
 @pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed")
 def test_ident_distances(tmpdir):

nipype/interfaces/fsl/tests/test_FILMGLS.py

@@ -45,8 +45,6 @@ def test_filmgls():
                       use_pava=dict(argstr='--pava',),
                       )
     instance = FILMGLS()
-    #NOTE_dj: don't understand this test: 
-    #NOTE_dj: IMO, it should go either to IF or ELSE, instance doesn't depend on any parameters
     if isinstance(instance.inputs, FILMGLSInputSpec):
         for key, metadata in list(input_map.items()):
             for metakey, value in list(metadata.items()):

nipype/interfaces/fsl/tests/test_base.py

@@ -9,9 +9,6 @@
 
 import pytest
 
-
-#NOTE_dj: a function, e.g. "no_fsl" always gives True, shuld always change to no_fsl in pytest skipif
-#NOTE_dj: removed the IF statement, since skipif is used? 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed") 
 def test_fslversion():
     ver = fsl.Info.version()
@@ -64,7 +61,7 @@ def test_FSLCommand2():
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
 @pytest.mark.parametrize("args, desired_name", 
-                         [({},   {"file": 'foo.nii.gz'}), # just the filename #NOTE_dj: changed slightly the test to meet description "just the file" 
+                         [({},   {"file": 'foo.nii.gz'}), # just the filename 
                           ({"suffix": '_brain'}, {"file": 'foo_brain.nii.gz'}), # filename with suffix 
                           ({"suffix": '_brain', "cwd": '/data'}, 
                            {"dir": '/data', "file": 'foo_brain.nii.gz'}), # filename with suffix and working directory 

nipype/interfaces/fsl/tests/test_dti.py

@@ -19,7 +19,6 @@
 
 import pytest, pdb
 
-#NOTE_dj: this file contains not finished tests (search xfail) and function that are not used
 
 @pytest.fixture(scope="module")
 def create_files_in_directory(request):
@@ -71,33 +70,6 @@ def test_dtifit2(create_files_in_directory):
                                                                        filelist[1])
 
 
-#NOTE_dj: setup/teardown_tbss are not used! 
-#NOTE_dj: should be removed or will be used in the tests that are not finished?
-# Globals to store paths for tbss tests
-tbss_dir = None
-test_dir = None
-
-
-def setup_tbss():
-    # Setup function is called before each test.  Setup is called only
-    # once for each generator function.
-    global tbss_dir, tbss_files, test_dir
-    test_dir = os.getcwd()
-    tbss_dir = mkdtemp()
-    os.chdir(tbss_dir)
-    tbss_files = ['a.nii', 'b.nii']
-    for f in tbss_files:
-        fp = open(f, 'wt')
-        fp.write('dummy')
-        fp.close()
-
-
-def teardown_tbss():
-    # Teardown is called after each test to perform cleanup
-    os.chdir(test_dir)
-    rmtree(tbss_dir)
-
-
 @pytest.mark.xfail(reason="These tests are skipped until we clean up some of this code") 
 def test_randomise2():
 

nipype/interfaces/fsl/tests/test_maths.py

@@ -19,9 +19,6 @@
 
 import pytest
 
-#NOTE_dj: i've changed a lot in the general structure of the file (not in the test themselves)
-#NOTE_dj: set_output_type has been changed to fixture that calls  create_files_in_directory
-#NOTE_dj: used params within the fixture to recreate test_all_again, hope this is what the author had in mind...
 
 def set_output_type(fsl_output_type):
     prev_output_type = os.environ.get('FSLOUTPUTTYPE', None)
@@ -37,7 +34,6 @@ def set_output_type(fsl_output_type):
 
 @pytest.fixture(params=[None]+list(Info.ftypes))
 def create_files_in_directory(request):
-    #NOTE_dj: removed set_output_type from test functions
     func_prev_type = set_output_type(request.param)
 
     testdir = os.path.realpath(mkdtemp())

nipype/interfaces/fsl/tests/test_model.py

@@ -10,7 +10,6 @@
 import nipype.interfaces.fsl.model as fsl
 from nipype.interfaces.fsl import no_fsl
 
-# NOTE_dj: couldn't find any reason to keep setup_file (most things were not used in the test), so i removed it
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
 def test_MultipleRegressDesign(tmpdir):

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -25,8 +25,6 @@ def fsl_name(obj, fname):
     return fname + ext
 
 
-#NOTE_dj: can't find reason why the global variables are needed, removed
-
 @pytest.fixture()
 def setup_infile(request):
     ext = Info.output_type_to_ext(Info.output_type())
@@ -511,8 +509,6 @@ def test_applywarp(setup_flirt):
                                         settings[0])
         assert awarp.cmdline == realcmd
 
-    #NOTE_dj: removed a new definition of awarp, not sure why this was at the end of the test
-
 
 @pytest.fixture(scope="module")
 def setup_fugue(request):
@@ -551,7 +547,6 @@ def test_fugue(setup_fugue, attr, out_file):
         else: setattr(fugue.inputs, key, value)
     res = fugue.run()
 
-    # NOTE_dj: believe that don't have to use if, since pytest would stop here anyway  
     assert isdefined(getattr(res.outputs,out_file))
     trait_spec = fugue.inputs.trait(out_file)
     out_name = trait_spec.name_template % 'dumbfile'

nipype/interfaces/fsl/tests/test_utils.py

@@ -15,10 +15,6 @@
 
 from .test_maths import (set_output_type, create_files_in_directory)
 
-#NOTE_dj: didn't know that some functions are shared between tests files 
-#NOTE_dj: and changed create_files_in_directory to a fixture with parameters
-#NOTE_dj: I believe there's no way to use this fixture for one parameter only 
-#NOTE_dj: the test works fine for all params so can either leave it as it is or create a new fixture
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
 def test_fslroi(create_files_in_directory):

nipype/interfaces/tests/test_base.py

@@ -485,7 +485,6 @@ class InputSpec(nib.TraitedSpec):
     class DerivedInterface1(nib.BaseInterface):
         input_spec = InputSpec
     obj = DerivedInterface1()
-    #NOTE_dj: removed yield assert_not_raises, if it raises the test will fail anyway
     obj._check_version_requirements(obj.inputs)
 
     config.set('execution', 'stop_on_unknown_version', True)
@@ -511,7 +510,6 @@ class DerivedInterface1(nib.BaseInterface):
         input_spec = InputSpec
         _version = '0.10'
     obj = DerivedInterface1()
-    #NOTE_dj: removed yield assert_not_raises
     obj._check_version_requirements(obj.inputs)
 
     class InputSpec(nib.TraitedSpec):
@@ -523,7 +521,6 @@ class DerivedInterface1(nib.BaseInterface):
     obj = DerivedInterface1()
     obj.inputs.foo = 1
     not_raised = True
-    #NOTE_dj: removed yield assert_not_raises
     obj._check_version_requirements(obj.inputs)
 
     class InputSpec(nib.TraitedSpec):
@@ -545,7 +542,6 @@ class DerivedInterface1(nib.BaseInterface):
     obj = DerivedInterface1()
     obj.inputs.foo = 1
     not_raised = True
-    #NOTE_dj: removed yield assert_not_raises
     obj._check_version_requirements(obj.inputs)
 
 
@@ -712,11 +708,6 @@ def test_global_CommandLine_output(setup_file):
     res = ci.run()
     assert res.runtime.stdout == ''
 
-#NOTE_dj: not sure if this function is needed
-#NOTE_dj: if my changes are accepted, I'll remove it
-def assert_not_raises(fn, *args, **kwargs):
-    fn(*args, **kwargs)
-    return True
 
 def check_dict(ref_dict, tst_dict):
     """Compare dictionaries of inputs and and those loaded from json files"""

nipype/interfaces/tests/test_io.py

@@ -60,8 +60,6 @@ def test_s3datagrabber():
     assert dg.inputs.template_args == {'outfiles': []}
 
 
-# NOTE_dj: changed one long test for a shorter one with parametrize; for every template and set of attributes I'm checking now the same set of fields using assert
-# NOTE_dj: in io.py, an example has different syntax with a node  dg = Node(SelectFiles(templates), "selectfiles")
 templates1 = {"model": "interfaces/{package}/model.py",
              "preprocess": "interfaces/{package}/pre*.py"}
 templates2 = {"converter": "interfaces/dcm{to!s}nii.py"}
@@ -404,7 +402,7 @@ def test_freesurfersource():
     assert fss.inputs.subject_id == Undefined
     assert fss.inputs.subjects_dir == Undefined
 
-#NOTE_dj: I split the test_jsonsink, didn't find connection between two parts, could easier use parametrize for the second part
+
 def test_jsonsink_input(tmpdir):
 
     ds = nio.JSONFileSink()