Merge remote-tracking branch 'upstream/master' into dev/2.0

effigies · effigies · commit f4f7865fca7e · 2018-07-30T13:20:27.000-04:00
diff --git a/.travis.yml b/.travis.yml
@@ -53,6 +53,7 @@ before_install:
     export FSLOUTPUTTYPE=NIFTI_GZ;
   fi;
 
+- travis_retry pip install --upgrade pytest>=3.4  # Work around pip failure
 - 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 &&
diff --git a/.zenodo.json b/.zenodo.json
@@ -30,16 +30,16 @@
       "name": "Notter, Michael Philipp",
       "orcid": "0000-0002-5866-047X"
     },
-    {
-      "affiliation": "MIT",
-      "name": "Jarecka, Dorota",
-      "orcid": "0000-0003-1857-8129"
-    },
     {
       "affiliation": "University of Iowa",
       "name": "Johnson, Hans",
       "orcid": "0000-0001-9513-2660"
     },
+    {
+      "affiliation": "MIT",
+      "name": "Jarecka, Dorota",
+      "orcid": "0000-0003-1857-8129"
+    },
     {
       "name": "Burns, Christopher"
     },
@@ -60,16 +60,16 @@
       "name": "Salo, Taylor",
       "orcid": "0000-0001-9813-3167"
     },
-    {
-      "affiliation": "University of California, San Francisco",
-      "name": "Jordan, Kesshi",
-      "orcid": "0000-0001-6313-0580"
-    },
     {
       "affiliation": "MIT",
       "name": "Goncalves, Mathias",
       "orcid": "0000-0002-7252-7771"
     },
+    {
+      "affiliation": "University of California, San Francisco",
+      "name": "Jordan, Kesshi",
+      "orcid": "0000-0001-6313-0580"
+    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Waskom, Michael"
@@ -151,6 +151,11 @@
       "name": "Cipollini, Ben",
       "orcid": "0000-0002-7782-0790"
     },
+    {
+      "affiliation": "Dartmouth College: Hanover, NH, United States",
+      "name": "Halchenko, Yaroslav O.",
+      "orcid": "0000-0003-3456-2493"
+    },
     {
       "affiliation": "Montreal Neurological Institute and Hospital",
       "name": "Markello, Ross",
@@ -164,11 +169,6 @@
     {
       "name": "Moloney, Brendan"
     },
-    {
-      "affiliation": "Dartmouth College: Hanover, NH, United States",
-      "name": "Halchenko, Yaroslav O.",
-      "orcid": "0000-0003-3456-2493"
-    },
     {
       "affiliation": "Athena EPI, Inria Sophia-Antipolis",
       "name": "Wassermann , Demian",
@@ -325,9 +325,6 @@
     {
       "name": "Millman, Jarrod"
     },
-    {
-      "name": "Haehn, Daniel"
-    },
     {
       "name": "Lai, Jeff"
     },
@@ -449,6 +446,9 @@
     {
       "name": "Mertz, Fred"
     },
+    {
+      "name": "Haehn, Daniel"
+    },
     {
       "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry",
       "name": "Geisler, Daniel",
diff --git a/Makefile b/Makefile
@@ -3,7 +3,6 @@
 # rsync -e ssh nipype-0.1-py2.5.egg cburns,nipy@frs.sourceforge.net:/home/frs/project/n/ni/nipy/nipype/nipype-0.1/
 
 PYTHON ?= python
-NOSETESTS=`which nosetests`
 
 .PHONY: zipdoc sdist egg upload_to_pypi trailing-spaces clean-pyc clean-so clean-build clean-ctags clean in inplace test-code test-coverage test html specs check-before-commit check gen-base-dockerfile gen-main-dockerfile gen-dockerfiles
 
diff --git a/Vagrantfile b/Vagrantfile
@@ -27,7 +27,7 @@ echo "export PATH=$HOME/miniconda3/bin:\\$PATH" >> .bashrc
 
 # install nipype dependencies
 $HOME/miniconda3/bin/conda update --yes conda
-$HOME/miniconda3/bin/conda install --yes pip scipy nose networkx lxml future simplejson
+$HOME/miniconda3/bin/conda install --yes pip scipy networkx lxml future simplejson
 $HOME/miniconda3/bin/conda install --yes python-dateutil jupyter matplotlib
 $HOME/miniconda3/bin/pip install nibabel
 $HOME/miniconda3/bin/pip install prov
diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog
@@ -1,3 +1,25 @@
+1.1.1 (July 30, 2018)
+=====================
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/22?closed=1)
+
+  * FIX: Un-set incorrect default options in TOPUP (https://github.com/nipy/nipype/pull/2637)
+  * FIX: Copy FSCommand.version to ReconAll.version (https://github.com/nipy/nipype/pull/2656)
+  * FIX: Various BIDSDataGrabber fixes (https://github.com/nipy/nipype/pull/2651)
+  * FIX: changing Node._output_dir to realpath (https://github.com/nipy/nipype/pull/2639)
+  * FIX: Typo in DWIExtract of Mrtrix3interface (https://github.com/nipy/nipype/pull/2634)
+  * FIX: Typo in FSLXCommandInputSpec (https://github.com/nipy/nipype/pull/2628)
+  * ENH: Allow transform to be saved from AFNI 3dWarp (https://github.com/nipy/nipype/pull/2642)
+  * ENH: Allow BIDS-style slice timings to be passed directly to TShift  (https://github.com/nipy/nipype/pull/2608)
+  * ENH: S3 access using instance role (https://github.com/nipy/nipype/pull/2621)
+  * ENH Minor improvements to PR template (https://github.com/nipy/nipype/pull/2636)
+  * TEST: make specs (https://github.com/nipy/nipype/pull/2653)
+  * DOC: update neurodocker tutorial for neurodocker version 0.4.0 (https://github.com/nipy/nipype/pull/2647)
+  * MAINT: Remove vestiges of nose testing library (https://github.com/nipy/nipype/pull/2662)
+  * MAINT: Make pytest-xdist a dependency (https://github.com/nipy/nipype/pull/2649)
+  * CI: Install pytest>=3.4 in Travis (https://github.com/nipy/nipype/pull/2659)
+
+
 1.1.0 (July 04, 2018)
 =====================
 
diff --git a/doc/conf.py b/doc/conf.py
@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "1.1.0"
+release = "1.1.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/doc/documentation.rst b/doc/documentation.rst
@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions: `1.0.3 <http://nipype.readthedocs.io/en/1.0.3/>`_ `1.0.2 <http://nipype.readthedocs.io/en/1.0.2/>`_
+Previous versions: `1.1.0 <http://nipype.readthedocs.io/en/1.1.0/>`_ `1.0.4 <http://nipype.readthedocs.io/en/1.0.4/>`_
 
 
 .. container:: doc2
diff --git a/doc/links_names.txt b/doc/links_names.txt
@@ -56,7 +56,6 @@
 .. _doctest-mode: http://www.cis.upenn.edu/~edloper/projects/doctestmode/
 .. _bazaar: http://bazaar-vcs.org/
 .. _subversion: http://subversion.tigris.org/
-.. _nose: http://nose.readthedocs.io/en/latest/
 .. _`python coverage tester`: http://nedbatchelder.com/code/modules/coverage.html
 
 .. Other python projects
diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py
@@ -122,7 +122,7 @@ class ANTSOutputSpec(TraitedSpec):
 
 
 class ANTS(ANTSCommand):
-    """ANTS wrapper for registration of images 
+    """ANTS wrapper for registration of images
     (old, use Registration instead)
 
     Examples
diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py
@@ -1322,6 +1322,12 @@ def _get_expert_file(self):
         with open(xopts_file, 'r') as fobj:
             return fobj.read()
 
+    @property
+    def version(self):
+        ver = Info.looseversion()
+        if ver > LooseVersion("0.0.0"):
+            return ver.vstring
+
 
 class BBRegisterInputSpec(FSTraitedSpec):
     subject_id = traits.Str(
diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py
@@ -195,16 +195,12 @@ class TOPUPInputSpec(FSLCommandInputSpec):
     # TODO: the following traits admit values separated by commas, one value
     # per registration level inside topup.
     warp_res = traits.Float(
-        10.0, usedefault=True,
         argstr='--warpres=%f',
         desc=('(approximate) resolution (in mm) of warp '
-              'basis for the different sub-sampling levels'
-              '.'))
-    subsamp = traits.Int(1, usedefault=True,
-                         argstr='--subsamp=%d', desc='sub-sampling scheme')
+              'basis for the different sub-sampling levels'))
+    subsamp = traits.Int(argstr='--subsamp=%d',
+                         desc='sub-sampling scheme')
     fwhm = traits.Float(
-        8.0,
-        usedefault=True,
         argstr='--fwhm=%f',
         desc='FWHM (in mm) of gaussian smoothing kernel')
     config = traits.String(
@@ -214,13 +210,12 @@ class TOPUPInputSpec(FSLCommandInputSpec):
         desc=('Name of config file specifying command line '
               'arguments'))
     max_iter = traits.Int(
-        5, usedefault=True,
-        argstr='--miter=%d', desc='max # of non-linear iterations')
+        argstr='--miter=%d',
+        desc='max # of non-linear iterations')
     reg_lambda = traits.Float(
-        1.0, usedefault=True,
-        argstr='--miter=%0.f',
-        desc=('lambda weighting value of the '
-              'regularisation term'))
+        argstr='--lambda=%0.f',
+        desc=('Weight of regularisation, default '
+              'depending on --ssqlambda and --regmod switches.'))
     ssqlambda = traits.Enum(
         1,
         0,
@@ -255,7 +250,6 @@ class TOPUPInputSpec(FSLCommandInputSpec):
         desc=('Minimisation method 0=Levenberg-Marquardt, '
               '1=Scaled Conjugate Gradient'))
     splineorder = traits.Int(
-        3, usedefault=True,
         argstr='--splineorder=%d',
         desc=('order of spline, 2->Qadratic spline, '
               '3->Cubic spline'))
@@ -317,11 +311,9 @@ class TOPUP(FSLCommand):
     >>> topup.inputs.output_type = "NIFTI_GZ"
     >>> topup.cmdline # doctest: +ELLIPSIS
     'topup --config=b02b0.cnf --datain=topup_encoding.txt \
---fwhm=8.000000 --imain=b0_b0rev.nii --miter=5 \
---out=b0_b0rev_base --iout=b0_b0rev_corrected.nii.gz \
+--imain=b0_b0rev.nii --out=b0_b0rev_base --iout=b0_b0rev_corrected.nii.gz \
 --fout=b0_b0rev_field.nii.gz --jacout=jac --logout=b0_b0rev_topup.log \
---rbmout=xfm --dfout=warpfield --miter=1 --splineorder=3 --subsamp=1 \
---warpres=10.000000'
+--rbmout=xfm --dfout=warpfield'
     >>> res = topup.run() # doctest: +SKIP
 
     """
diff --git a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py
@@ -25,19 +25,13 @@ def test_TOPUP_inputs():
             usedefault=True,
         ),
         estmov=dict(argstr='--estmov=%d', ),
-        fwhm=dict(
-            argstr='--fwhm=%f',
-            usedefault=True,
-        ),
+        fwhm=dict(argstr='--fwhm=%f', ),
         in_file=dict(
             argstr='--imain=%s',
             mandatory=True,
         ),
         interp=dict(argstr='--interp=%s', ),
-        max_iter=dict(
-            argstr='--miter=%d',
-            usedefault=True,
-        ),
+        max_iter=dict(argstr='--miter=%d', ),
         minmet=dict(argstr='--minmet=%d', ),
         numprec=dict(argstr='--numprec=%s', ),
         out_base=dict(
@@ -86,26 +80,14 @@ def test_TOPUP_inputs():
             requires=['encoding_direction'],
             xor=['encoding_file'],
         ),
-        reg_lambda=dict(
-            argstr='--miter=%0.f',
-            usedefault=True,
-        ),
+        reg_lambda=dict(argstr='--lambda=%0.f', ),
         regmod=dict(argstr='--regmod=%s', ),
         regrid=dict(argstr='--regrid=%d', ),
         scale=dict(argstr='--scale=%d', ),
-        splineorder=dict(
-            argstr='--splineorder=%d',
-            usedefault=True,
-        ),
+        splineorder=dict(argstr='--splineorder=%d', ),
         ssqlambda=dict(argstr='--ssqlambda=%d', ),
-        subsamp=dict(
-            argstr='--subsamp=%d',
-            usedefault=True,
-        ),
-        warp_res=dict(
-            argstr='--warpres=%f',
-            usedefault=True,
-        ),
+        subsamp=dict(argstr='--subsamp=%d', ),
+        warp_res=dict(argstr='--warpres=%f', ),
     )
     inputs = TOPUP.input_spec()
 
diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py
@@ -120,7 +120,7 @@ def add_traits(base, names, trait_type=None):
 
 
 def _get_head_bucket(s3_resource, bucket_name):
-    """ Try to get the header info of a bucket, in order to 
+    """ Try to get the header info of a bucket, in order to
     check if it exists and its permissions
     """
 
diff --git a/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py b/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py
@@ -8,6 +8,7 @@ def test_BIDSDataGrabber_inputs():
         output_query=dict(),
         raise_on_empty=dict(usedefault=True, ),
         return_type=dict(usedefault=True, ),
+        strict=dict(),
     )
     inputs = BIDSDataGrabber.input_spec()
 
diff --git a/nipype/pipeline/plugins/tests/test_base.py b/nipype/pipeline/plugins/tests/test_base.py
@@ -16,7 +16,7 @@ def test_scipy_sparse():
 
 '''
 Can use the following code to test that a mapnode crash continues successfully
-Need to put this into a nose-test with a timeout
+Need to put this into a unit-test with a timeout
 
 import nipype.interfaces.utility as niu
 import nipype.pipeline.engine as pe
diff --git a/nipype/pipeline/plugins/tests/test_tools.py b/nipype/pipeline/plugins/tests/test_tools.py
@@ -38,7 +38,7 @@ def test_report_crash():
 
 '''
 Can use the following code to test that a mapnode crash continues successfully
-Need to put this into a nose-test with a timeout
+Need to put this into a unit-test with a timeout
 
 import nipype.interfaces.utility as niu
 import nipype.pipeline.engine as pe
diff --git a/nipype/utils/tests/test_filemanip.py b/nipype/utils/tests/test_filemanip.py
@@ -544,7 +544,7 @@ class PickledBreaker:
     def __setstate__(self, d):
         raise Exception()
 
-        
+
 def test_versioned_pklization(tmpdir):
     tmpdir.chdir()
 
@@ -557,7 +557,7 @@ def test_versioned_pklization(tmpdir):
 
             loadpkl('./pickled.pkz', versioning=True)
 
-        
+
 def test_unversioned_pklization(tmpdir):
     tmpdir.chdir()
 
