Merge branch 'master' into fix/prov

* master: (1016 commits)
  RF: Use runtime.cwd in Rename
  Add gitter and slack channels
  Update link to mailing list
  Update links to user and developer help forums
  CI: Install nipy dependencies when installing AFNI/FSL from NeuroDebian
  CI: Remove non-working Circle filters
  CI: Attempt again to ignore travis branches
  CI: Separate matrix for 3.4
  CI: Ignore branches, not tags
  CI: Move tests to Xenial
  CI: Do not run Circle tests on Travis-focused branches
  [skip ci] Install Release Drafter
  CI: Try Python 3.7 matrix entry
  CI: Test 3.7-dev, remove fmri extra from Travis
  MAINT: Bump version to 1.1.3-dev
  REL: 1.1.2
  CI: Only run PyPI pre-checks on rel/* and tags
  DOC: Update changelog
  FIX: Pybids grabbids API is going away
  importing InputMultiObject
  ...

Author: satra

.circleci/config.yml

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e NIPYPE_NUMBER_OF_CPUS=4 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py27" /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline

.circleci/test_py2_fmri_spm_nested_multiproc_l2.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py27" /usr/bin/run_pytests.sh

.circleci/test_py2_pytest.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /src/nipype/doc "${DOCKER_IMAGE}:py36" /usr/bin/run_builddocs.sh

.circleci/test_py3_docs.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline

.circleci/test_py3_fmri_fsl_feeds_linear_l1.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow

.circleci/test_py3_fmri_fsl_reuse_linear_l1.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_spm_dartel MultiProc /data/examples/ level1

.circleci/test_py3_fmri_spm_dartel_multiproc_l1.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_spm_dartel MultiProc /data/examples/ l2pipeline

.circleci/test_py3_fmri_spm_dartel_multiproc_l2.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d

.circleci/test_py3_fmri_spm_linear_3d.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d

.circleci/test_py3_fmri_spm_linear_4d.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e NIPYPE_NUMBER_OF_CPUS=4 "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1

.circleci/test_py3_fmri_spm_nested_multiproc_l1.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py36" /usr/bin/run_pytests.sh

.circleci/test_py3_pytest.sh

@@ -34,4 +34,4 @@ Vagrantfile
 .mailmap
 
 # Previous coverage results
-.coverage
+.coverage

.circleci/tests.sh

@@ -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
 

.dockerignore

@@ -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.

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,4 @@
+template: |
+  ## What's Changed
+
+  $CHANGES

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,6 +19,7 @@
 .DS_Store
 nipype/testing/data/von-ray_errmap.nii.gz
 nipype/testing/data/von_errmap.nii.gz
+nipype/testing/data/.proc*
 crash*.pklz
 .coverage
 htmlcov/
@@ -27,3 +28,4 @@ __pycache__/
 .*.swp
 .ipynb_checkpoints/
 .ruby-version
+.pytest_cache

.github/release-drafter.yml

@@ -1,5 +1,6 @@
 Aimi Watanabe <[email protected]> stymy <[email protected]>
 Aimi Watanabe <[email protected]> stymy <[email protected]>
+Alejandro de la Vega <[email protected]> adelavega <[email protected]>
 Alexander Schaefer <[email protected]> Alexander Schaefer <[email protected]>
 Alexander Schaefer <[email protected]> alexschaefer83 <[email protected]>
 Alexander Schaefer <[email protected]> aschaefer <aschaefer@aschaefer-U36SD.(none)>
@@ -13,6 +14,7 @@ Ariel Rokem <[email protected]> arokem <[email protected]>
 Arman Eshaghi <[email protected]> armaneshaghi <[email protected]>
 Ashely Gillman <[email protected]> Ashley Gillman <[email protected]>
 Ashely Gillman <[email protected]> ashgillman <[email protected]>
+Andrey Chetverikov <[email protected]> achetverikov <[email protected]>
 Basille Pinsard <[email protected]> bpinsard <[email protected]>
 Basille Pinsard <[email protected]> bpinsard <[email protected]>
 Ben Cipollini <[email protected]> Ben Cipollini <[email protected]>
@@ -56,11 +58,13 @@ Franz Liem <[email protected]> fliem <franz.liem>
 Gael Varoquaux <[email protected]> GaelVaroquaux
 Gael Varoquaux <[email protected]> GaelVaroquaux <[email protected]>
 Gavin Cooper <[email protected]> gjcooper <[email protected]>
+Gilles de Hollander <[email protected]> Gilles86 <[email protected]>
 Hans Johnson <[email protected]> Hans Johnson <[email protected]>
 Hans Johnson <[email protected]> hjmjohnson <[email protected]>
 Horea Christian <[email protected]> Horea Christian <[email protected]>
 Isaac Schwabacher <[email protected]> ischwabacher <[email protected]>
 James Kent <[email protected]> jdkent <[email protected]>
+Jakub Kaczmarzyk <[email protected]> kaczmarj <[email protected]>
 Jason Wong <[email protected]> Jason <[email protected]>
 Jason Wong <[email protected]> jason <[email protected]>
 Jason Wong <[email protected]> Jason W <[email protected]>
@@ -72,8 +76,12 @@ Joerg Stadler <[email protected]> Jörg Stadler <Stadler@lin-magdeb
 Joke Durnez <[email protected]> jokedurnez <[email protected]>
 Josh Warner <[email protected]> Josh Warner (Mac) <[email protected]>
 Kai Schlamp <[email protected]> medihack <[email protected]>Jessica Forbes <[email protected]> jessicaforbes <[email protected]>
+Kevin Sitek <[email protected]> sitek <[email protected]>
 Leonie Lampe <[email protected]> Leonie Lmape <[email protected]>
+Lukas Snoek <[email protected]> Lukas Snoek <[email protected]>
 Mathias Goncalves <[email protected]> mathiasg <[email protected]>
+Matteo Mancini <[email protected]> matteomancini <[email protected]>
+Matteo Visconti dOC <[email protected]> mvdoc <[email protected]>
 Michael Dayan <[email protected]> Michael <[email protected]>
 Michael Dayan <[email protected]> Michael <[email protected]>
 Michael Dayan <[email protected]> mick-d <mid2021@CHUCK.(none)>
@@ -102,5 +110,6 @@ Steven Giavasis <[email protected]> sgiavasis <[email protected]>
 Tristan Glatard <[email protected]> Tristan Glatard <[email protected]>
 Victor Saase <[email protected]> vsaase <[email protected]>
 William Triplett <[email protected]> William Triplett <[email protected]>
+Wolfgang Pauli <[email protected]> Wolfgang Pauli <[email protected]>
 Yaroslav Halchenko <[email protected]> Yaroslav Halchenko <[email protected]>
 pipolose <[email protected]> pipolose <[email protected]>

.gitignore

@@ -1,62 +1,100 @@
-cache:
-  apt: true
+dist: xenial
+sudo: true
 
 language: python
+# our build matrix
 python:
 - 2.7
-- 3.4
 - 3.5
 - 3.6
+- 3.7
+
+# NOTE: Any changes to the matrix section should be duplicated below for
+#       Python 3.4
 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" 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,nipy,profiler"
+      CI_SKIP_TEST=1
+    - INSTALL_DEB_DEPENDECIES=false
+      NIPYPE_EXTRAS="doc,tests,profiler"
+      CI_SKIP_TEST=1
+    - INSTALL_DEB_DEPENDECIES=true
+      NIPYPE_EXTRAS="doc,tests,nipy,profiler,duecredit,ssh"
+      CI_SKIP_TEST=1
+    - INSTALL_DEB_DEPENDECIES=true
+      NIPYPE_EXTRAS="doc,tests,nipy,profiler"
+      EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
+      CI_SKIP_TEST=1
+
+# Python 3.4 is only available on Trusty, so we need to duplicate the
+# env matrix specifically for it.
+matrix:
+  include:
+    - python: 3.4
+      dist: trusty
+      env:
+        - INSTALL_DEB_DEPENDECIES=true
+          NIPYPE_EXTRAS="doc,tests,nipy,profiler"
+          CI_SKIP_TEST=1
+    - python: 3.4
+      dist: trusty
+      env:
+        - INSTALL_DEB_DEPENDECIES=false
+          NIPYPE_EXTRAS="doc,tests,profiler"
+          CI_SKIP_TEST=1
+    - python: 3.4
+      dist: trusty
+      env:
+        - INSTALL_DEB_DEPENDECIES=true
+          NIPYPE_EXTRAS="doc,tests,nipy,profiler,duecredit,ssh"
+          CI_SKIP_TEST=1
+    - python: 3.4
+      dist: trusty
+      env:
+        - INSTALL_DEB_DEPENDECIES=true
+          NIPYPE_EXTRAS="doc,tests,nipy,profiler"
+          EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
+          CI_SKIP_TEST=1
+
+addons:
+  apt:
+    packages:
+      - xvfb
+      - fusefat
+      - graphviz
+
+cache:
+  directories:
+    - ${HOME}/.cache
+
 before_install:
-- function apt_inst {
-  if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi &&
-  if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi &&
-  bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh) &&
-  sudo apt-get -y update &&
-  sudo apt-get -y install xvfb fusefat graphviz &&
-  if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -y -qq
-  fsl afni elastix fsl-atlases; fi &&
-  if $INSTALL_DEB_DEPENDECIES; then
+- if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; sudo ln -s /run/shm /dev/shm; fi
+- travis_retry bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh);
+- if $INSTALL_DEB_DEPENDECIES; then
+    travis_retry sudo apt-get -y update &&
+    travis_retry sudo apt-get install -y -qq fsl afni elastix fsl-atlases;
+  fi;
+- if $INSTALL_DEB_DEPENDECIES; then
     source /etc/fsl/fsl.sh;
     source /etc/afni/afni.sh;
-    export FSLOUTPUTTYPE=NIFTI_GZ; fi }
-- function conda_inst {
-  export CONDA_HOME=$HOME/conda &&
-  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/travis/.cache/conda.sh -b -p ${CONDA_HOME} &&
-  export PATH=${CONDA_HOME}/bin:$PATH &&
-  hash -r &&
-  conda config --set always_yes yes --set changeps1 no &&
-  conda update -q conda &&
-  conda config --add channels conda-forge &&
-  conda install python=${TRAVIS_PYTHON_VERSION} &&
-  conda install -y icu &&
-  pip install -r requirements.txt &&
-  pushd $HOME;
-  git clone https://github.com/INCF/pybids.git;
-  cd pybids;
-  pip install -e .;
-  popd; }
-#  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi
-- travis_retry apt_inst
-- travis_retry conda_inst
+    export FSLOUTPUTTYPE=NIFTI_GZ;
+  fi;
+
+- 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
+
 install:
-- travis_retry pip install $PIP_FLAGS -e .[$NIPYPE_EXTRAS]
+- travis_retry pip install $EXTRA_PIP_FLAGS -e .[$NIPYPE_EXTRAS]
+
 script:
-- py.test -v --doctest-modules nipype
-deploy:
-  provider: pypi
-  user: satra
-  password:
-    secure: OCO0FXb4f+pH4Uw7zWCIRp3qOJ1t7rhky4K8MjNU8tyVCJgd6O/Bv8GJgceS0LktPodlAAjB8SxAhTORPAQZ1D/44PJYy3NQIisvej1zjLpaA9TEGfl6W7MqhDpRyMHW+cnSi/n84SAmdr+Z4vOxScDHdwr13EPmGyOIlHMAGnE=
-  on:
-    tags: true
-    repo: nipy/nipype
-    branch: master
-  distributions: "sdist"
+- py.test -v --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype
+
+after_script:
+- codecov --file cov.xml --flags unittests -e TRAVIS_JOB_NUMBER