Pytest follow-up

.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)