Merge master

Author: adelavega

.travis.yml

@@ -87,8 +87,7 @@ before_install:
 
 - travis_retry pip install -r requirements.txt
 - travis_retry pip install grabbit==0.1.2
-- travis_retry git clone https://github.com/INCF/pybids.git ${HOME}/pybids && git checkout 0.6.5
-  pip install -e ${HOME}/pybids
+- travis_retry git clone -b 0.6.5 https://github.com/INCF/pybids.git ${HOME}/pybids && pip install -e ${HOME}/pybids
 
 install:
 - travis_retry pip install $EXTRA_PIP_FLAGS -e .[$NIPYPE_EXTRAS]

doc/conf.py

@@ -50,7 +50,7 @@
               'sphinx.ext.autosummary',
               'numpydoc',
               'matplotlib.sphinxext.plot_directive',
-              'matplotlib.sphinxext.only_directives',
+              #'matplotlib.sphinxext.only_directives',
               'nipype.sphinxext.plot_workflow',
               #'IPython.sphinxext.ipython_directive',
               #'IPython.sphinxext.ipython_console_highlighting'

nipype/info.py

@@ -154,7 +154,7 @@ def get_nipype_gitversion():
 if sys.version_info <= (3, 4):
     REQUIRES.append('configparser')
 
-TESTS_REQUIRES = ['pytest-cov', 'codecov', 'pytest-env']
+TESTS_REQUIRES = ['pytest-cov', 'codecov', 'pytest-env', 'coverage<5']
 
 EXTRA_REQUIRES = {
     'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],
@@ -164,7 +164,7 @@ def get_nipype_gitversion():
     'profiler': ['psutil>=5.0'],
     'duecredit': ['duecredit'],
     'xvfbwrapper': ['xvfbwrapper'],
-    'pybids': ['pybids'],
+    'pybids': ['pybids==0.6.5'],
     'ssh': ['paramiko'],
     # 'mesh': ['mayavi']  # Enable when it works
 }

nipype/interfaces/base/tests/test_resource_monitor.py

@@ -18,10 +18,16 @@
 from ... import utility as niu
 
 # Try to enable the resource monitor
-config.enable_resource_monitor()
 run_profile = config.resource_monitor
 
 
+@pytest.fixture(scope="module")
+def use_resource_monitor():
+    config.enable_resource_monitor()
+    yield
+    config.disable_resource_monitor()
+
+
 class UseResourcesInputSpec(CommandLineInputSpec):
     mem_gb = traits.Float(
         desc='Number of GB of RAM to use', argstr='-g %f', mandatory=True)
@@ -51,7 +57,7 @@ class UseResources(CommandLine):
     os.getenv('CI_SKIP_TEST', False), reason='disabled in CI tests')
 @pytest.mark.parametrize("mem_gb,n_procs", [(0.5, 3), (2.2, 8), (0.8, 4),
                                             (1.5, 1)])
-def test_cmdline_profiling(tmpdir, mem_gb, n_procs):
+def test_cmdline_profiling(tmpdir, mem_gb, n_procs, use_resource_monitor):
     """
     Test runtime profiler correctly records workflow RAM/CPUs consumption
     of a CommandLine-derived interface
@@ -73,7 +79,7 @@ def test_cmdline_profiling(tmpdir, mem_gb, n_procs):
     True, reason='test disabled temporarily, until funcion profiling works')
 @pytest.mark.parametrize("mem_gb,n_procs", [(0.5, 3), (2.2, 8), (0.8, 4),
                                             (1.5, 1)])
-def test_function_profiling(tmpdir, mem_gb, n_procs):
+def test_function_profiling(tmpdir, mem_gb, n_procs, use_resource_monitor):
     """
     Test runtime profiler correctly records workflow RAM/CPUs consumption
     of a Function interface

nipype/interfaces/mrtrix3/base.py

@@ -4,11 +4,39 @@
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)
 
-from ... import logging
-from ..base import (CommandLineInputSpec, CommandLine, traits, File, isdefined)
+from ... import logging, LooseVersion
+from ...utils.filemanip import which
+from ..base import (CommandLineInputSpec, CommandLine, traits, File, isdefined, PackageInfo)
 iflogger = logging.getLogger('nipype.interface')
 
 
+class Info(PackageInfo):
+    version_cmd = 'mrconvert --version'
+
+    @staticmethod
+    def parse_version(raw_info):
+        # info is like: "== mrconvert 0.3.15-githash"
+        for line in raw_info.splitlines():
+            if line.startswith('== mrconvert '):
+                v_string = line.split()[2]
+                break
+        else:
+            return None
+
+        # -githash may or may not be appended
+        v_string = v_string.split('-')[0]
+
+        return '.'.join(v_string.split('.')[:3])
+
+    @classmethod
+    def looseversion(cls):
+        """ Return a comparable version object
+
+        If no version found, use LooseVersion('0.0.0')
+        """
+        return LooseVersion(cls.version() or '0.0.0')
+
+
 class MRTrix3BaseInputSpec(CommandLineInputSpec):
     nthreads = traits.Int(
         argstr='-nthreads %d',
@@ -78,3 +106,7 @@ def _parse_inputs(self, skip=None):
             pass
 
         return super(MRTrix3Base, self)._parse_inputs(skip=skip)
+
+    @property
+    def version(self):
+        return Info.version()

nipype/interfaces/mrtrix3/reconst.py

@@ -39,8 +39,8 @@ class FitTensorInputSpec(MRTrix3BaseInputSpec):
         argstr='-method %s',
         desc=('select method used to perform the fitting'))
     reg_term = traits.Float(
-        5.e3, usedefault=True,
         argstr='-regularisation %f',
+        max_ver='0.3.13',
         desc=('specify the strength of the regularisation term on the '
               'magnitude of the tensor elements (default = 5000). This '
               'only applies to the non-linear methods'))
@@ -64,8 +64,7 @@ class FitTensor(MRTrix3Base):
     >>> tsr.inputs.in_mask = 'mask.nii.gz'
     >>> tsr.inputs.grad_fsl = ('bvecs', 'bvals')
     >>> tsr.cmdline                               # doctest: +ELLIPSIS
-    'dwi2tensor -fslgrad bvecs bvals -mask mask.nii.gz \
--regularisation 5000.000000 dwi.mif dti.mif'
+    'dwi2tensor -fslgrad bvecs bvals -mask mask.nii.gz dwi.mif dti.mif'
     >>> tsr.run()                                 # doctest: +SKIP
     """
 

nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py

@@ -34,7 +34,7 @@ def test_FitTensor_inputs():
         ),
         reg_term=dict(
             argstr='-regularisation %f',
-            usedefault=True,
+            max_ver='0.3.13',
         ),
     )
     inputs = FitTensor.input_spec()

nipype/pipeline/engine/tests/test_engine.py

@@ -484,9 +484,12 @@ def test_deep_nested_write_graph_runs(tmpdir):
             except OSError:
                 pass
 
+import networkx
+# Format of the graph has slightly changed
+graph_str = '""' if int(networkx.__version__.split('.')[0]) == 1 else ''
 
 # examples of dot files used in the following test
-dotfile_orig = ['strict digraph  {\n',
+dotfile_orig = ['strict digraph ' + graph_str + ' {\n',
                 '"mod1 (engine)";\n',
                 '"mod2 (engine)";\n',
                 '"mod1 (engine)" -> "mod2 (engine)";\n',

nipype/pipeline/engine/utils.py

@@ -1473,7 +1473,8 @@ def clean_working_directory(outputs,
         needed_files += [path for path, type in input_files if type == 'f']
     for extra in [
             '_0x*.json', 'provenance.*', 'pyscript*.m', 'pyjobs*.mat',
-            'command.txt', 'result*.pklz', '_inputs.pklz', '_node.pklz'
+            'command.txt', 'result*.pklz', '_inputs.pklz', '_node.pklz',
+            '.proc-*',
     ]:
         needed_files.extend(glob(os.path.join(cwd, extra)))
     if files2keep:

nipype/utils/config.py

@@ -291,6 +291,10 @@ def enable_resource_monitor(self):
         """Sets the resource monitor on"""
         self.resource_monitor = True
 
+    def disable_resource_monitor(self):
+        """Sets the resource monitor off"""
+        self.resource_monitor = False
+
     def get_display(self):
         """Returns the first display available"""