REL: 1.0.4

.circleci/config.yml

@@ -343,6 +343,38 @@ jobs:
             python setup.py sdist bdist_wheel
             twine upload dist/*
 
+  update_feedstock:
+    machine: *machine_kwds
+    working_directory: /home/circleci/nipype
+    steps:
+      - checkout:
+          path: /home/circleci/nipype
+      - run:
+          name: Install hub
+          command: |
+            curl -sSL https://github.com/github/hub/releases/download/v2.2.9/hub-linux-amd64-2.2.9.tgz | \
+            tar zxv -C /tmp
+            sudo /tmp/hub-linux-amd64-2.2.9/install
+      - run:
+          name: Expand SSH Key
+          command: |
+            (echo "-----BEGIN OPENSSH PRIVATE KEY-----";
+             echo $GITHUB_ED25519 | fold -w 71;
+             echo "-----END OPENSSH PRIVATE KEY-----") > ~/.ssh/id_ed25519
+            chmod go-rwx ~/.ssh/id_ed25519
+            ssh-keygen -y -f ~/.ssh/id_ed25519 > ~/.ssh/id_ed25519.pub
+      - run:
+          name: Set git identity
+          command: |
+            git config --global user.name "nipybot"
+            git config --global user.email "nipybot@gmail.com"
+      - run:
+          name: Update feedstock
+          command: |
+              ssh-add -D
+              ssh-add ~/.ssh/id_ed25519
+              /home/circleci/nipype/tools/feedstock.sh
+
 workflows:
   version: 2
   build_test_deploy:
@@ -380,3 +412,10 @@ workflows:
             - test_fmri_spm_nested_fsl_feeds
             - test_py3_fmri_fsl_spm
             - test_py3_fmri_spm_dartel_multiproc
+      - update_feedstock:
+          context: nipybot
+          filters:
+            branches:
+              only: /rel\/.*/
+            tags:
+              only: /.*/

.gitignore

@@ -28,3 +28,4 @@ __pycache__/
 .*.swp
 .ipynb_checkpoints/
 .ruby-version
+.pytest_cache

.zenodo.json

@@ -10,16 +10,16 @@
       "name": "Esteban, Oscar",
       "orcid": "0000-0001-8435-6191"
     },
-    {
-      "affiliation": "Independent",
-      "name": "Ziegler, Erik",
-      "orcid": "0000-0003-1857-8129"
-    },
     {
       "affiliation": "Stanford University",
       "name": "Markiewicz, Christopher J.",
       "orcid": "0000-0002-6533-164X"
     },
+    {
+      "affiliation": "Independent",
+      "name": "Ziegler, Erik",
+      "orcid": "0000-0003-1857-8129"
+    },
     {
       "affiliation": "The University of Iowa",
       "name": "Ellis, David Gage",
@@ -65,15 +65,15 @@
       "name": "Jordan, Kesshi",
       "orcid": "0000-0001-6313-0580"
     },
-    {
-      "affiliation": "Department of Psychology, Stanford University",
-      "name": "Waskom, Michael"
-    },
     {
       "affiliation": "MIT",
       "name": "Goncalves, Mathias",
       "orcid": "0000-0002-7252-7771"
     },
+    {
+      "affiliation": "Department of Psychology, Stanford University",
+      "name": "Waskom, Michael"
+    },
     {
       "affiliation": "Developer",
       "name": "Clark, Daniel",
@@ -97,6 +97,11 @@
     {
       "name": "Madison, Cindee"
     },
+    {
+      "affiliation": "Dartmouth College",
+      "name": "Visconti di Oleggio Castello, Matteo",
+      "orcid": "0000-0001-7931-5272"
+    },
     {
       "affiliation": "National Institutes of Health",
       "name": "Clark, Michael G. "
@@ -116,11 +121,6 @@
       "name": "Keshavan, Anisha",
       "orcid": "0000-0003-3554-043X"
     },
-    {
-      "affiliation": "Dartmouth College",
-      "name": "Visconti di Oleggio Castello, Matteo",
-      "orcid": "0000-0001-7931-5272"
-    },
     {
       "name": "Pinsard, Basile"
     },
@@ -137,6 +137,10 @@
       "name": "Nielson, Dylan M.",
       "orcid": "0000-0003-4613-6643"
     },
+    {
+      "affiliation": "Molecular Imaging Research Center, CEA, France",
+      "name": "Bougacha, Salma"
+    },
     {
       "affiliation": "INRIA",
       "name": "Varoquaux, Gael",
@@ -160,10 +164,6 @@
     {
       "name": "Moloney, Brendan"
     },
-    {
-      "affiliation": "Molecular Imaging Research Center, CEA, France",
-      "name": "Bougacha, Salma"
-    },
     {
       "affiliation": "Dartmouth College: Hanover, NH, United States",
       "name": "Halchenko, Yaroslav O.",
@@ -218,11 +218,6 @@
       "name": "Pauli, Wolfgang M.",
       "orcid": "0000-0002-0966-0254"
     },
-    {
-      "affiliation": "University College London",
-      "name": "Mancini, Matteo",
-      "orcid": "0000-0001-7194-4568"
-    },
     {
       "affiliation": "Duke University",
       "name": "Iqbal, Shariq",
@@ -232,6 +227,11 @@
       "affiliation": "Nathan s Kline institute for psychiatric research",
       "name": "Sikka, Sharad"
     },
+    {
+      "affiliation": "University College London",
+      "name": "Mancini, Matteo",
+      "orcid": "0000-0001-7194-4568"
+    },
     {
       "name": "Schwartz, Yannick"
     },
@@ -381,6 +381,11 @@
     {
       "name": "Hallquist, Michael"
     },
+    {
+      "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging",
+      "name": "Chetverikov, Andrey",
+      "orcid": "0000-0003-2767-6310"
+    },
     {
       "name": "Salvatore, John"
     },
@@ -395,11 +400,6 @@
       "name": "Craddock, R. Cameron",
       "orcid": "0000-0002-4950-1303"
     },
-    {
-      "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging",
-      "name": "Chetverikov, Andrey",
-      "orcid": "0000-0003-2767-6310"
-    },
     {
       "name": "Inati, Souheil"
     },
@@ -587,4 +587,4 @@
   ],
   "license": "Apache-2.0",
   "upload_type": "software"
-}
+}

doc/changelog/1.X.X-changelog

@@ -1,3 +1,26 @@
+1.0.4 (May 29, 2018)
+====================
+
+###### [Full changelog](https://github.com/nipy/nipype/milestone/20?closed=1)
+
+  * FIX: Update logging levels in enable_debug_mode (https://github.com/nipy/nipype/pull/2595)
+  * FIX: Set default result in DistributedPluginBase._clean_queue (https://github.com/nipy/nipype/pull/2596)
+  * FIX: Correctly connect JoinNodes in nested iterables (https://github.com/nipy/nipype/pull/2597)
+  * FIX: DTITK nonlinear workflow origin reslicing (https://github.com/nipy/nipype/pull/2561)
+  * FIX: ResponseSD support for multiple b-vals (https://github.com/nipy/nipype/pull/2582)
+  * FIX: Workaround to ICA-AROMA change of directory (https://github.com/nipy/nipype/pull/2566)
+  * FIX/TEST: Gunzip cleanup and test (https://github.com/nipy/nipype/pull/2564)
+  * FIX: Print UID in crashfile if login name is unavailable (https://github.com/nipy/nipype/pull/2563)
+  * ENH: initial connectome workbench support (https://github.com/nipy/nipype/pull/2594)
+  * ENH: AFNI (3d)LocalBistat interface (https://github.com/nipy/nipype/pull/2590)
+  * ENH: Reorient interface (https://github.com/nipy/nipype/pull/2572)
+  * ENH: FSL slice interface (https://github.com/nipy/nipype/pull/2585)
+  * ENH: LabelGeometryMeasures interface (https://github.com/nipy/nipype/pull/2586)
+  * ENH: MRTrix3 dwidenoise interface (https://github.com/nipy/nipype/pull/2568)
+  * ENH: ReportCapableInterface mix-in/base interface (https://github.com/nipy/nipype/pull/2560)
+  * CI: Move PyPI deployment to Circle (https://github.com/nipy/nipype/pull/2587)
+  * CI: Submit Travis results to codecov (https://github.com/nipy/nipype/pull/2574)
+
 1.0.3 (April 30, 2018)
 ======================
 

doc/conf.py

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "1.0.3"
+release = "1.0.4"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions: `0.14.0 <http://nipype.readthedocs.io/en/v0.14.0/>`_ `0.13.1 <http://nipype.readthedocs.io/en/0.13.1/>`_
+Previous versions: `1.0.3 <http://nipype.readthedocs.io/en/1.0.3/>`_ `1.0.2 <http://nipype.readthedocs.io/en/1.0.2/>`_
 
 
 .. container:: doc2

nipype/info.py

@@ -11,7 +11,7 @@
 # full release.  '.dev' as a version_extra string means this is a development
 # version
 # Remove -dev for release
-__version__ = '1.0.4-dev'
+__version__ = '1.0.4'
 
 
 def get_nipype_gitversion():

nipype/interfaces/image.py

@@ -77,6 +77,12 @@ class Reorient(SimpleInterface):
      [ 0.  0.  1.  0.]
      [ 0.  0.  0.  1.]]
 
+    .. testcleanup::
+
+        >>> import os
+        >>> os.unlink(res.outputs.out_file)
+        >>> os.unlink(res.outputs.transform)
+
     """
     input_spec = ReorientInputSpec
     output_spec = ReorientOutputSpec

nipype/interfaces/mixins/tests/__init__.py

@@ -0,0 +1 @@
+# -*- coding: utf-8 -*-

nipype/interfaces/mixins/tests/test_auto_ReportCapableInterface.py

@@ -0,0 +1,17 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..reporting import ReportCapableInterface
+
+
+def test_ReportCapableInterface_inputs():
+    input_map = dict(
+        ignore_exception=dict(
+            deprecated='1.0.0',
+            nohash=True,
+            usedefault=True,
+        ), )
+    inputs = ReportCapableInterface.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value