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

Author: effigies

.circleci/config.yml

@@ -316,9 +316,18 @@ jobs:
       - run:
           name: Check pypi preconditions
           command: |
-            pip install twine future wheel readme_renderer
+            pip install --upgrade twine future wheel readme_renderer setuptools
             python setup.py check -r -s
             python setup.py sdist bdist_wheel
+      - run:
+          name: Validate Python 3 installation
+          command: |
+            pyenv local 3.5.2
+            pip install dist/nipype-*-py2.py3-none-any.whl
+            # Futures should not install in Python 3
+            test $(pip show futures 2>/dev/null | wc -l) = "0"
+      - store_artifacts:
+          path: /home/circleci/nipype/dist
 
   deploy_pypi:
     machine: *machine_kwds
@@ -329,7 +338,7 @@ jobs:
       - run:
           name: Deploy to PyPI
           command: |
-            pip install twine future wheel readme_renderer
+            pip install --upgrade twine future wheel readme_renderer setuptools
             python setup.py check -r -s
             python setup.py sdist bdist_wheel
             twine upload dist/*
@@ -370,6 +379,12 @@ workflows:
   version: 2
   build_test_deploy:
     jobs:
+      - pypi_precheck:
+          filters:
+            branches:
+              only: /rel\/.*/
+            tags:
+              only: /.*/
       - compare_base_dockerfiles:
           filters:
             tags:
@@ -405,6 +420,7 @@ workflows:
             tags:
               only: /.*/
           requires:
+            - pypi_precheck
             - test_pytest
       - update_feedstock:
           context: nipybot
@@ -413,7 +429,3 @@ workflows:
               only: /rel\/.*/
             tags:
               only: /.*/
-      - pypi_precheck:
-          filters:
-            branches:
-              only: /rel\/.*/

.github/ISSUE_TEMPLATE.md

@@ -12,7 +12,13 @@ Please put URL to code or code here (if not too long).
 
 ### Platform details:
 
-Please paste the output of: `python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"`
+<!-- Please run the following code from your shell and place the output between the triple ticks, below.
+python -c "import nipype; from pprint import pprint; pprint(nipype.get_info())"
+-->
+
+```
+
+```
 
 ### Execution environment
 

.travis.yml

@@ -53,7 +53,6 @@ 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 &&

.zenodo.json

@@ -574,6 +574,10 @@
     {
       "name": "McDermottroe, Conor"
     },
+    {
+      "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
+      "name": "Weninger, Leon"
+    },
     {
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
@@ -587,4 +591,4 @@
   ],
   "license": "Apache-2.0",
   "upload_type": "software"
-}
+}

doc/changelog/1.X.X-changelog

@@ -1,3 +1,20 @@
+1.1.2 (August 11, 2018)
+=======================
+
+Hot-fix release, resolving incorrect dependencies in 1.1.1 wheel.
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/23?closed=1)
+
+  * FIX: Read BIDS config.json under grabbids or layout (https://github.com/nipy/nipype/pull/2679)
+  * FIX: Node __repr__ and detailed graph expansion (https://github.com/nipy/nipype/pull/2669)
+  * FIX: Prevent double-collapsing of nested lists by OutputMultiObject (https://github.com/nipy/nipype/pull/2673)
+  * ENH: Add interface to SPM realign_unwarp  (https://github.com/nipy/nipype/pull/2635)
+  * MAINT: Fix wheel build to ensure futures is only required in Python 2 (https://github.com/nipy/nipype/pull/2678)
+  * MAINT: ensure interface _cmd only includes executable (https://github.com/nipy/nipype/pull/2674)
+  * MAINT: Issue template: Pretty print platform details (https://github.com/nipy/nipype/pull/2671)
+  * CI: removing travis_retry for pip install pytest xdist 1.22.5 (https://github.com/nipy/nipype/pull/2664)
+
+
 1.1.1 (July 30, 2018)
 =====================
 

nipype/interfaces/afni/preprocess.py

@@ -2949,107 +2949,6 @@ def _list_outputs(self):
         return outputs
 
 
-class QwarpPlusMinusInputSpec(CommandLineInputSpec):
-    source_file = File(
-        desc=
-        'Source image (opposite phase encoding direction than base image).',
-        argstr='-source %s',
-        mandatory=True,
-        exists=True,
-        copyfile=False)
-    base_file = File(
-        desc=
-        'Base image (opposite phase encoding direction than source image).',
-        argstr='-base %s',
-        mandatory=True,
-        exists=True,
-        copyfile=False)
-    pblur = traits.List(
-        traits.Float(),
-        desc='The fraction of the patch size that'
-        'is used for the progressive blur by providing a '
-        'value between 0 and 0.25.  If you provide TWO '
-        'values, the first fraction is used for '
-        'progressively blurring the base image and the '
-        'second for the source image.',
-        argstr='-pblur %s',
-        minlen=1,
-        maxlen=2)
-    blur = traits.List(
-        traits.Float(),
-        desc="Gaussian blur the input images by (FWHM) voxels "
-        "before doing the alignment (the output dataset "
-        "will not be blurred). The default is 2.345 (for "
-        "no good reason). Optionally, you can provide 2 "
-        "values, and then the first one is applied to the "
-        "base volume, the second to the source volume. A "
-        "negative blur radius means to use 3D median "
-        "filtering, rather than Gaussian blurring.  This "
-        "type of filtering will better preserve edges, "
-        "which can be important in alignment.",
-        argstr='-blur %s',
-        minlen=1,
-        maxlen=2)
-    noweight = traits.Bool(
-        desc='If you want a binary weight (the old default), use this option.'
-        'That is, each voxel in the base volume automask will be'
-        'weighted the same in the computation of the cost functional.',
-        argstr='-noweight')
-    minpatch = traits.Int(
-        desc="Set the minimum patch size for warp searching to 'mm' voxels.",
-        argstr='-minpatch %d')
-    nopadWARP = traits.Bool(
-        desc='If for some reason you require the warp volume to'
-        'match the base volume, then use this option to have the output'
-        'WARP dataset(s) truncated.',
-        argstr='-nopadWARP')
-
-
-class QwarpPlusMinusOutputSpec(TraitedSpec):
-    warped_source = File(desc='Undistorted source file.', exists=True)
-    warped_base = File(desc='Undistorted base file.', exists=True)
-    source_warp = File(
-        desc="Field suceptibility correction warp (in 'mm') for source image.",
-        exists=True)
-    base_warp = File(
-        desc="Field suceptibility correction warp (in 'mm') for base image.",
-        exists=True)
-
-
-class QwarpPlusMinus(CommandLine):
-    """A version of 3dQwarp for performing field susceptibility correction
-    using two images with opposing phase encoding directions.
-
-    For complete details, see the `3dQwarp Documentation.
-    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dQwarp.html>`_
-
-    Examples
-    ========
-
-    >>> from nipype.interfaces import afni
-    >>> qwarp = afni.QwarpPlusMinus()
-    >>> qwarp.inputs.source_file = 'sub-01_dir-LR_epi.nii.gz'
-    >>> qwarp.inputs.nopadWARP = True
-    >>> qwarp.inputs.base_file = 'sub-01_dir-RL_epi.nii.gz'
-    >>> qwarp.cmdline
-    '3dQwarp -prefix Qwarp.nii.gz -plusminus -base sub-01_dir-RL_epi.nii.gz -nopadWARP -source sub-01_dir-LR_epi.nii.gz'
-    >>> res = warp.run()  # doctest: +SKIP
-
-    """
-    _cmd = '3dQwarp -prefix Qwarp.nii.gz -plusminus'
-    input_spec = QwarpPlusMinusInputSpec
-    output_spec = QwarpPlusMinusOutputSpec
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['warped_source'] = os.path.abspath("Qwarp_PLUS.nii.gz")
-        outputs['warped_base'] = os.path.abspath("Qwarp_MINUS.nii.gz")
-        outputs['source_warp'] = os.path.abspath("Qwarp_PLUS_WARP.nii.gz")
-        outputs['base_warp'] = os.path.abspath("Qwarp_MINUS_WARP.nii.gz")
-
-        return outputs
-
-
 class QwarpInputSpec(AFNICommandInputSpec):
     in_file = File(
         desc=
@@ -3718,3 +3617,54 @@ def _list_outputs(self):
     def _gen_filename(self, name):
         if name == 'out_file':
             return self._gen_fname(self.inputs.source_file, suffix='_QW')
+
+
+class QwarpPlusMinusInputSpec(QwarpInputSpec):
+    source_file = File(
+        desc='Source image (opposite phase encoding direction than base image)',
+        argstr='-source %s',
+        exists=True,
+        deprecated='1.1.2',
+        new_name='in_file',
+        copyfile=False)
+    out_file = File(
+        argstr='-prefix %s',
+        value='Qwarp.nii.gz',
+        position=0,
+        usedefault=True,
+        desc="Output file")
+    plusminus = traits.Bool(
+        True,
+        usedefault=True,
+        position=1,
+        desc='Normally, the warp displacements dis(x) are defined to match'
+        'base(x) to source(x+dis(x)).  With this option, the match'
+        'is between base(x-dis(x)) and source(x+dis(x)) -- the two'
+        'images \'meet in the middle\'. For more info, view Qwarp` interface',
+        argstr='-plusminus',
+        xor=['duplo', 'allsave', 'iwarp'])
+
+
+class QwarpPlusMinus(Qwarp):
+    """A version of 3dQwarp for performing field susceptibility correction
+    using two images with opposing phase encoding directions.
+
+    For complete details, see the `3dQwarp Documentation.
+    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dQwarp.html>`_
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni
+    >>> qwarp = afni.QwarpPlusMinus()
+    >>> qwarp.inputs.in_file = 'sub-01_dir-LR_epi.nii.gz'
+    >>> qwarp.inputs.nopadWARP = True
+    >>> qwarp.inputs.base_file = 'sub-01_dir-RL_epi.nii.gz'
+    >>> qwarp.cmdline
+    '3dQwarp -prefix Qwarp.nii.gz -plusminus -base sub-01_dir-RL_epi.nii.gz \
+    -source sub-01_dir-LR_epi.nii.gz -nopadWARP'
+    >>> res = warp.run()  # doctest: +SKIP
+
+    """
+
+    input_spec = QwarpPlusMinusInputSpec