Merge remote-tracking branch 'upstream/master' into HEAD

Author: effigies

.circleci/config.yml

@@ -330,6 +330,19 @@ jobs:
             - /tmp/docker/cache/Dockerfile.base-pruned
           key: dockerfile-cache-v1-{{ .Branch }}-{{ checksum "/tmp/docker/cache/Dockerfile.base-pruned" }}
 
+  pypi_precheck:
+    machine: *machine_kwds
+    working_directory: /home/circleci/nipype
+    steps:
+      - checkout:
+          path: /home/circleci/nipype
+      - run:
+          name: Check pypi preconditions
+          command: |
+            pip install twine future wheel readme_renderer
+            python setup.py check -r -s
+            python setup.py sdist bdist_wheel
+
   deploy_pypi:
     machine: *machine_kwds
     working_directory: /home/circleci/nipype
@@ -339,7 +352,8 @@ jobs:
       - run:
           name: Deploy to PyPI
           command: |
-            pip install twine future wheel
+            pip install twine future wheel readme_renderer
+            python setup.py check -r -s
             python setup.py sdist bdist_wheel
             twine upload dist/*
 
@@ -422,3 +436,7 @@ 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
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,15 +1,23 @@
-Pull-request guidelines (Remove this section after reading):
+<!--
+
+Pull-request guidelines
+-----------------------
 
 1. If you would like to list yourself as a Nipype contributor and your name is not mentioned please modify .zenodo.json file.
 2. By submitting this request you acknowledge that your contributions are available under the Apache 2 license.
 3. Use a descriptive prefix for your PR: ENH (enhancement), FIX, TST, DOC, STY, REF (refactor), WIP (Work in progress)
-4. The person who accepts/merges your PR will include an update to the CHANGES file: prefix: description (URL of pull request)
-5. Run `make check-before-commit` before submitting the PR.
+4. Run `make check-before-commit` before submitting the PR.
 
------ REMOVE TILL HERE -----
+-->
+## Summary
+<!-- Please reference any related issue and use fixes/close to automatically
+close them, if pertinent -->
 
 Fixes # .
 
-Changes proposed in this pull request
--
--
+## List of changes proposed in this PR (pull-request)
+<!-- We suggest using bullets (indicated by * or -) and filled checkboxes [x] here -->
+
+## Acknowledgment
+
+- [ ] \(Mandatory\) I acknowledge that this contribution will be available under the Apache 2 license.

.travis.yml

@@ -10,10 +10,24 @@ python:
 - 3.6
 
 env:
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
-- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler" CI_SKIP_TEST=1
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,ssh" CI_SKIP_TEST=1
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler" PIP_FLAGS="--pre" CI_SKIP_TEST=1
+  global:
+    - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
+    - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
+    - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
+  matrix:
+    - INSTALL_DEB_DEPENDECIES=true
+      NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+      CI_SKIP_TEST=1
+    - INSTALL_DEB_DEPENDECIES=false
+      NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+      CI_SKIP_TEST=1
+    - INSTALL_DEB_DEPENDECIES=true
+      NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,ssh"
+      CI_SKIP_TEST=1
+    - INSTALL_DEB_DEPENDECIES=true
+      NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+      EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
+      CI_SKIP_TEST=1
 
 addons:
   apt:
@@ -39,23 +53,13 @@ before_install:
     export FSLOUTPUTTYPE=NIFTI_GZ;
   fi;
 
-# handle python operations separately to reduce timeouts
-- wget https://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
-    -O /home/travis/.cache/conda.sh
-- bash ${HOME}/.cache/conda.sh -b -p ${HOME}/conda
-- export PATH=${HOME}/conda/bin:$PATH
-- hash -r
-- conda config --set always_yes yes --set changeps1 no
-- travis_retry conda update -q conda
-- conda config --add channels conda-forge
-- travis_retry conda install -y python=${TRAVIS_PYTHON_VERSION} icu
 - 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 &&
   pip install -e ${HOME}/pybids
-- travis_retry pip install codecov
 
 install:
-- travis_retry pip install $PIP_FLAGS -e .[$NIPYPE_EXTRAS]
+- travis_retry pip install $EXTRA_PIP_FLAGS -e .[$NIPYPE_EXTRAS]
 
 script:
 - py.test -v --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype

.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",
@@ -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"
-}
+}

Makefile

@@ -3,7 +3,6 @@
 # rsync -e ssh nipype-0.1-py2.5.egg cburns,[email protected]:/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
 

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

doc/changelog/1.X.X-changelog

@@ -1,3 +1,42 @@
+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)
+=====================
+
+###### [Full changelog](https://github.com/nipy/nipype/milestone/21?closed=1)
+
+  * RF: Futures-based MultiProc (https://github.com/nipy/nipype/pull/2598)
+  * FIX: Avoid closing file descriptors on Windows (https://github.com/nipy/nipype/pull/2617)
+  * MAINT: Play nice with external logging (https://github.com/nipy/nipype/pull/2611)
+  * MAINT: Remove ignore_exception and terminal_output traits from input specs (https://github.com/nipy/nipype/pull/2618)
+  * MAINT: Converge autotest names (https://github.com/nipy/nipype/pull/2610)
+  * ENH: Add versioning metadata to crash files (https://github.com/nipy/nipype/pull/2626)
+  * ENH add -dsort option to TProject (https://github.com/nipy/nipype/pull/2623)
+  * ENH: Add Rescale interface (https://github.com/nipy/nipype/pull/2599)
+  * DOC: Improve documentation for ANTs/FSL interfaces (https://github.com/nipy/nipype/pull/2593)
+  * CI: Stop using Miniconda on Travis (https://github.com/nipy/nipype/pull/2600)
+  * CI: Add PyPI validation on rel/* branches (https://github.com/nipy/nipype/pull/2603)
+
 1.0.4 (May 29, 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 = "1.0.4"
+release = "1.1.1"
 
 # 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: `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

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
@@ -105,8 +104,8 @@
 .. _mingw: http://www.mingw.org
 .. _macports: http://www.macports.org/
 .. _Vagrant: http://www.vagrantup.com/
-.. _Docker: http://www.docker.io/
-.. _Singularity: http://singularity.lbl.gov/
+.. _Docker: http://www.docker.com/
+.. _Singularity: https://www.sylabs.io/singularity/
 .. _Virtualbox: https://www.virtualbox.org/
 
 .. Functional imaging labs