Merge tag '1.1.3' into debian

Nipype 1.1.3

* tag '1.1.3': (34 commits)
  MAINT: Update Zenodo with latest line counts
  DOC: Update changelog
  MAINT: A few more .mailmap entries
  FIX: Return afni.Qwarp outputs as absolute paths
  DOC: .mailmap (low-hanging fruit)
  DOC: Update version strings
  DOC: Changelog 1.1.3
  MAINT: Bump version string to 1.1.3
  FIX: MCFLIRT output paths are relative to out_file, not cwd
  FIX: Drop Bunch.keys, use existing dictcopy method
  TEST: Check RuntimeErrors raised for missing/broken runtimes
  FIX: Check for runtime attributes
  Reorganized exception catching in _strip_header() for better code clarity
  FIX: make exception explicit
  Change in normalize_mc_params
  fix/enh: added the colorfa as an output in DTI
  FIX: catch exception if jobid not found in squeue call
  FIX: Provide informative error for interfaces that fail to return runtime object
  Fixed: Missing substring should raise ValueError not KeyError
  RF: Use runtime.cwd in Rename
  ...

Author: yarikoptic

.github/release-drafter.yml

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

.mailmap

@@ -1,20 +1,23 @@
 Aimi Watanabe <[email protected]> stymy <[email protected]>
 Aimi Watanabe <[email protected]> stymy <[email protected]>
+Alejandro Tabas <[email protected]> qTabs <[email protected]>
+Alejandro Tabas <[email protected]> qtabs <[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)>
 Alexandre M. Savio <[email protected]> Alexandre M. S <[email protected]>
 Alexandre M. Savio <[email protected]> Alexandre M. S <[email protected]>
 Alexandre M. Savio <[email protected]> Alexandre Manhaes Savio <[email protected]>
+Andrey Chetverikov <[email protected]> Andrey Chetverikov <[email protected]>
+Andrey Chetverikov <[email protected]> achetverikov <[email protected]>
 Anisha Keshavan <[email protected]> Anisha Keshavan <[email protected]>
 Anisha Keshavan <[email protected]> akeshavan <[email protected]>
 Ariel Rokem <[email protected]> arokem <[email protected]>
 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]>
@@ -24,6 +27,7 @@ Blake Dewey <[email protected]> Blake Dewey <[email protected]>
 Blake Dewey <[email protected]> blakedewey <[email protected]>
 Blake Dewey <[email protected]> blakedewey <[email protected]>
 Brendan Moloney <[email protected]> moloney <[email protected]>
+Caroline Froehlich <[email protected]> carolFrohlich <[email protected]>
 Chris Filo Gorgolewski <[email protected]> Chris Filo Gorgolewski <filo@filo-Precision-M6500.(none)>
 Chris Filo Gorgolewski <[email protected]> Chris Filo Gorgolewski <[email protected]>
 Chris Filo Gorgolewski <[email protected]> Chris Filo Gorgolewski <[email protected]>
@@ -40,21 +44,28 @@ Cindee Madison <[email protected]> cindeem
 Cindee Madison <[email protected]> cindeem <>
 Colin Buchanan <[email protected]> Colin Buchanan <cbuchanan@cray4.(none)>
 Colin Buchanan <[email protected]> colinbuchanan <[email protected]>
+Daniel Brenner <[email protected]> brennerd <[email protected]>
+Daniel Brenner <[email protected]> brennerd11 <[email protected]>
 Daniel Clark <[email protected]> dclark87 <[email protected]>
+Daniel Geisler <[email protected]> daniel-ge <[email protected]>
 Daniel Ginsburg <[email protected]> danginsburg <[email protected]>
 Daniel McNamee <[email protected]> danmc <[email protected]>
 David Ellis <[email protected]> David Ellis <[email protected]>
 David Ellis <[email protected]> David Ellis <[email protected]>
 David Welch <[email protected]> David Welch <[email protected]>
+Dimitri Papadopoulos Orfanos <[email protected]> Dimitri Papadopoulos <[email protected]>
 Dmytro <[email protected]> belevtsoff <[email protected]>
+Dylan Nielson <[email protected]> Dylan <[email protected]>
+Elizabeth DuPre <[email protected]> emdupre <[email protected]>
 Erik Ziegler <[email protected]> Erik <[email protected]>
 Erik Ziegler <[email protected]> Erik Ziegler <[email protected]>
 Erik Ziegler <[email protected]> erik <erik@erik-ubuntu.(none)>
 Erik Ziegler <[email protected]> erikz <[email protected]>
 Erik Ziegler <[email protected]> swederik <[email protected]>
 Fernando Pérez-García <[email protected]> Fernando <[email protected]>
-Franz Liem <[email protected]> fliem <[email protected]>
 Franz Liem <[email protected]> fliem <franz.liem>
+Franz Liem <[email protected]> fliem <[email protected]>
+Fred Loney <[email protected]> FredLoney <[email protected]>
 Gael Varoquaux <[email protected]> GaelVaroquaux
 Gael Varoquaux <[email protected]> GaelVaroquaux <[email protected]>
 Gavin Cooper <[email protected]> gjcooper <[email protected]>
@@ -63,40 +74,70 @@ 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 <james-kent@uiowa.edu> jdkent <james-kent@uiowa.edu>
+Jakub Kaczmarzyk <jakubk@mit.edu> jakubk <jakubk@mit.edu>
 Jakub Kaczmarzyk <[email protected]> kaczmarj <[email protected]>
+James Kent <[email protected]> jdkent <[email protected]>
+Janosch Linkersdörfer <[email protected]> Januzz <[email protected]>
 Jason Wong <[email protected]> Jason <[email protected]>
-Jason Wong <[email protected]> jason <[email protected]>
-Jason Wong <[email protected]> Jason W <[email protected]>
 Jason Wong <[email protected]> Jason W <[email protected]>
+Jason Wong <[email protected]> Jason W <[email protected]>
+Jason Wong <[email protected]> jason <[email protected]>
 Jason Wong <[email protected]> jason-wg <[email protected]>
 Jens Kleesiek <[email protected]> JensNRAD <[email protected]>
+Jessica Forbes <[email protected]> jessicaforbes <[email protected]>
+Jérémy Guillon <[email protected]> GUILLON Jeremy <[email protected]>
 Joerg Stadler <[email protected]> Joerg Stadler <[email protected]>
 Joerg Stadler <[email protected]> Jörg Stadler <[email protected]>
 Joke Durnez <[email protected]> jokedurnez <[email protected]>
+Josh Warner <[email protected]> JDWarner <[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]>
+Katie Bottenhorn <[email protected]> 62442katieb <[email protected]>
+Kesshi Jordan <[email protected]> Kesshi Jordan <[email protected]> 
+Kesshi Jordan <[email protected]> Kesshi Jordan <[email protected]>
+Kesshi Jordan <[email protected]> Kesshi Jordan <[email protected]>
+Kesshi Jordan <[email protected]> Kesshi Jordan <[email protected]>
+Kesshi Jordan <[email protected]> Kesshi Jordan <[email protected]>
+Kesshi Jordan <[email protected]> Kesshi jordan <[email protected]>
+Kesshi Jordan <[email protected]> kesshijordan <[email protected]>
 Kevin Sitek <[email protected]> sitek <[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]>
+Marcel Falkiewicz <[email protected]> Marcel Falkiewicz <[email protected]>
+Mathias Goncalves <[email protected]> Mathias Goncalves <[email protected]>
 Mathias Goncalves <[email protected]> mathiasg <[email protected]>
+Mathieu Dubois <[email protected]> Mathieu Dubois <[email protected]>
+Mathieu Dubois <[email protected]> duboism <[email protected]>
 Matteo Mancini <[email protected]> matteomancini <[email protected]>
+Matteo Visconti dOC <[email protected]> Matteo Visconti dOC <[email protected]>
 Matteo Visconti dOC <[email protected]> mvdoc <[email protected]>
-Michael Dayan <mdayan.research@gmail.com> Michael <[email protected]>
+Michael Clark <michael.clark195@gmail.com> Clark <[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)>
-Michael Clark <[email protected]> Clark <[email protected]>
 Michael Notter <[email protected]> miykael <[email protected]>
 Michael Waskom <[email protected]> Michael Waskom <[email protected]>
+Michael Waskom <[email protected]> Michael Waskom <[email protected]>
 Michael Waskom <[email protected]> Michael Waskom <[email protected]>
 Michael Waskom <[email protected]> mwaskom <[email protected]>
-Michael Waskom <[email protected]> mwaskom <[email protected]>
 Michael Waskom <[email protected]> mwaskom <[email protected]>
+Michael Waskom <[email protected]> mwaskom <[email protected]>
+Oliver Contier <[email protected]> oliver-contier <[email protected]>
 Oscar Esteban <[email protected]> Oscar Esteban <code@oscaresteban>
 Oscar Esteban <[email protected]> oesteban <[email protected]>
+Pablo Polosecki <[email protected]> pipolose <[email protected]>
+Pablo Polosecki <[email protected]> pipolose <[email protected]>
+Ranjit Khanuja <[email protected]> RanjitK <[email protected]>
+Ross Markello <[email protected]> Ross Markello <[email protected]>
 Russell Poldrack <[email protected]> Russ Poldrack <[email protected]>
 Russell Poldrack <[email protected]> poldrack <[email protected]>
+Salma Bougacha <[email protected]> Salma BOUGACHA <[email protected]>
+Salma Bougacha <[email protected]> salma <[email protected]>
+Salma Bougacha <[email protected]> salma1601 <[email protected]>
 Satrajit Ghosh <[email protected]> Satrajit Ghosh <[email protected]>
+Sebastian Urchs <[email protected]> sebastian <[email protected]>
+Sharad Sikka <[email protected]> ssikka <[email protected]>
 Shariq Iqbal <[email protected]> shariqiqbal2810 <[email protected]>
 Shariq Iqbal <[email protected]> shariqiqbal2810 <[email protected]>
 Shoshana Berleant <[email protected]> Shoshana Berleant <nope>
@@ -111,5 +152,5 @@ Tristan Glatard <[email protected]> Tristan Glatard <tristan.glatard@cre
 Victor Saase <[email protected]> vsaase <[email protected]>
 William Triplett <[email protected]> William Triplett <[email protected]>
 Wolfgang Pauli <[email protected]> Wolfgang Pauli <[email protected]>
+Xiangzhen Kong <[email protected]> bnucon <[email protected]>
 Yaroslav Halchenko <[email protected]> Yaroslav Halchenko <[email protected]>
-pipolose <[email protected]> pipolose <[email protected]>

.travis.yml

@@ -1,34 +1,66 @@
-dist: trusty
-sudo: required
+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:
   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"
+      NIPYPE_EXTRAS="doc,tests,nipy,profiler"
       CI_SKIP_TEST=1
     - INSTALL_DEB_DEPENDECIES=false
-      NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+      NIPYPE_EXTRAS="doc,tests,profiler"
       CI_SKIP_TEST=1
     - INSTALL_DEB_DEPENDECIES=true
-      NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,ssh"
+      NIPYPE_EXTRAS="doc,tests,nipy,profiler,duecredit,ssh"
       CI_SKIP_TEST=1
     - INSTALL_DEB_DEPENDECIES=true
-      NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+      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: