Merge remote-tracking branch 'dorota/pytest_satrarev' into fix/bunchmapnode

* dorota/pytest_satrarev:
  it looks like codecov works at the end, removing COVERAGE_PROCESS_START  and COVERAGE_DATA_FILE from travis again
  trying to fix coverage (codecov doesnt report anything), restoring some lines from travis
  removing workflows from the directories that are omitted
  restore get_info in nipype/__init__.py
  Removing nosetest from nipype/__init__.py; pytest version is missing for now
  fixing the travis file
  removing coverage from travis (so the coverage is calculated from Circle CI only)
  removing fixes
  removing scripts from tools directory that are not used anymore
  changing test_auto_TCompCor.py to the output of checkspecs.py
  adding the auto test for ACompCor
  changing a simple assert to np.isclose in test_icc_anova
  cleaning:removing pdb
  restring one skipif in interfaces/tests/test_io.py
  removing one test from interfaces/tests/test_base.py; it was repeating the same assert as the previous one
  fixing one assert in test_math
  restoring 2 tests that had only import statement, changing comments

Author: satra

.coveragerc

@@ -4,6 +4,5 @@ source = nipype
 include = */nipype/*
 omit =
     */nipype/external/*
-    */nipype/workflows/*
     */nipype/fixes/*
     */setup.py

.travis.yml

@@ -36,15 +36,10 @@ install:
   conda install -y nipype &&
   rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype* &&
   pip install -r requirements.txt &&
-  pip install -e .[$NIPYPE_EXTRAS] &&
-  export COVERAGE_PROCESS_START=$(pwd)/.coveragerc &&
-  export COVERAGE_DATA_FILE=$(pwd)/.coverage &&
-  echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START}; }
+  pip install -e .[$NIPYPE_EXTRAS]; }
 - travis_retry inst
 script:
-- py.test --doctest-modules --cov=nipype nipype
-after_success:
-- bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
+- py.test --doctest-modules nipype
 deploy:
   provider: pypi
   user: satra

nipype/__init__.py

@@ -11,7 +11,6 @@
                    STATUS as __status__,
                    __version__)
 from .utils.config import NipypeConfig
-from .fixes.numpy.testing import nosetester
 from .utils.logger import Logging
 from .refs import due
 
@@ -24,48 +23,48 @@
 config = NipypeConfig()
 logging = Logging(config)
 
+#NOTE_dj: it has to be changed to python
+#class _NoseTester(nosetester.NoseTester):
+#    """ Subclass numpy's NoseTester to add doctests by default
+#    """
 
-class _NoseTester(nosetester.NoseTester):
-    """ Subclass numpy's NoseTester to add doctests by default
-    """
+#    def _get_custom_doctester(self):
+#        return None
 
-    def _get_custom_doctester(self):
-        return None
+#    def test(self, label='fast', verbose=1, extra_argv=['--exe'],
+#             doctests=True, coverage=False):
+#        """Run the full test suite
+#
+#        Examples
+#        --------
+#        This will run the test suite and stop at the first failing
+#        example
+#        >>> from nipype import test
+#        >>> test(extra_argv=['--exe', '-sx'])  # doctest: +SKIP
+#        """
+#        return super(_NoseTester, self).test(label=label,
+#                                             verbose=verbose,
+#                                             extra_argv=extra_argv,
+#                                             doctests=doctests,
+#                                             coverage=coverage)
 
-    def test(self, label='fast', verbose=1, extra_argv=['--exe'],
-             doctests=True, coverage=False):
-        """Run the full test suite
-
-        Examples
-        --------
-        This will run the test suite and stop at the first failing
-        example
-        >>> from nipype import test
-        >>> test(extra_argv=['--exe', '-sx'])  # doctest: +SKIP
-        """
-        return super(_NoseTester, self).test(label=label,
-                                             verbose=verbose,
-                                             extra_argv=extra_argv,
-                                             doctests=doctests,
-                                             coverage=coverage)
-
-try:
-    test = _NoseTester(raise_warnings="release").test
-except TypeError:
+#try:
+#    test = _NoseTester(raise_warnings="release").test
+#except TypeError:
     # Older versions of numpy do not have a raise_warnings argument
-    test = _NoseTester().test
-del nosetester
+#    test = _NoseTester().test
+#del nosetester
 
 # Set up package information function
 from .pkg_info import get_pkg_info as _get_pkg_info
 get_info = lambda: _get_pkg_info(os.path.dirname(__file__))
 
 # If this file is exec after being imported, the following lines will
 # fail
-try:
-    del Tester
-except:
-    pass
+#try:
+#    del Tester
+#except:
+#    pass
 
 
 from .pipeline import Node, MapNode, JoinNode, Workflow

nipype/algorithms/tests/test_auto_ACompCor.py

@@ -0,0 +1,36 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..confounds import ACompCor
+
+
+def test_ACompCor_inputs():
+    input_map = dict(components_file=dict(usedefault=True,
+    ),
+    header=dict(),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    mask_file=dict(),
+    num_components=dict(usedefault=True,
+    ),
+    realigned_file=dict(mandatory=True,
+    ),
+    regress_poly_degree=dict(usedefault=True,
+    ),
+    use_regress_poly=dict(usedefault=True,
+    ),
+    )
+    inputs = ACompCor.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_ACompCor_outputs():
+    output_map = dict(components_file=dict(),
+    )
+    outputs = ACompCor.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/algorithms/tests/test_auto_TCompCor.py

@@ -29,8 +29,22 @@ def test_TCompCor_inputs():
 
 
 def test_TCompCor_outputs():
-    output_map = dict(components_file=dict(),
-                      high_variance_mask=dict()
+    output_map = dict(components_file=dict(usedefault=True,
+    ),
+    header=dict(),
+    high_variance_mask=dict(),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    mask_file=dict(),
+    num_components=dict(usedefault=True,
+    ),
+    realigned_file=dict(mandatory=True,
+    ),
+    regress_poly_degree=dict(usedefault=True,
+    ),
+    use_regress_poly=dict(usedefault=True,
+    ),
     )
     outputs = TCompCor.output_spec()
 

nipype/algorithms/tests/test_icc_anova.py

@@ -19,4 +19,4 @@ def test_ICC_rep_anova():
     assert round(icc, 2) == 0.71
     assert dfc == 3
     assert dfe == 15
-    assert r_var / (r_var + e_var) == icc
+    assert np.isclose(r_var / (r_var + e_var), icc)