Merge branch 'master' into dev/2.0

Author: effigies

.mailmap

@@ -93,8 +93,8 @@ Jérémy Guillon <jeremy.guillon@inria.fr> GUILLON Jeremy <jeremy.guillon@etu.
 Joerg Stadler <Joerg.Stadler@lin-magdeburg.de> Joerg Stadler <joerg.stadler@lin-magdeburg.de>
 Joerg Stadler <Joerg.Stadler@lin-magdeburg.de> Joerg Stadler <jstadler@ilin-magdeburg.de>
 Joerg Stadler <Joerg.Stadler@lin-magdeburg.de> Jörg Stadler <Stadler@lin-magdeburg.de>
-John Lee <johnleenimh@gmail.com> john anthony lee <johnleenimh@gmail.com>
-John Lee <johnleenimh@gmail.com> leej3 <johnleenimh@gmail.com>
+John A. Lee <johnleenimh@gmail.com> john anthony lee <johnleenimh@gmail.com>
+John A. Lee <johnleenimh@gmail.com> leej3 <johnleenimh@gmail.com>
 Joke Durnez <joke.durnez@gmail.com> jokedurnez <joke.durnez@gmail.com>
 Josh Warner <silvertrumpet999+github@gmail.com> JDWarner <warner.joshua@mayo.edu>
 Josh Warner <silvertrumpet999+github@gmail.com> Josh Warner (Mac) <warner.joshua@mayo.edu>
@@ -133,6 +133,7 @@ Matteo Mancini <ingmatteomancini@gmail.com> matteomancini <ingmatteomancini@gmai
 Matteo Visconti di Oleggio Castello <matteo.visconti.gr@dartmouth.edu> Matteo Visconti dOC <matteo.visconti.gr@dartmouth.edu>
 Matteo Visconti di Oleggio Castello <matteo.visconti.gr@dartmouth.edu> Matteo Visconti dOC <mvdoc.gr@dartmouth.edu>
 Matteo Visconti di Oleggio Castello <matteo.visconti.gr@dartmouth.edu> mvdoc <matteo.visconti.gr@dartmouth.edu>
+Matthew Cieslak <mattcieslak@gmail.com> Matt Cieslak <mattcieslak@gmail.com>
 Michael Clark <michael.clark195@gmail.com> Clark <clarkmg@nih.gov>
 Michael Dayan <mdayan.research@gmail.com> Michael <mdayan.comp@gmail.com>
 Michael Dayan <mdayan.research@gmail.com> Michael <mdayan.research@gmail.com>
@@ -153,6 +154,8 @@ Pablo Polosecki <pipolose@us.ibm.com> pipolose <pipolose@pipoloses-MacBook-Air.l
 Pablo Polosecki <pipolose@us.ibm.com> pipolose <pipolose@pipoloses-air.watson.ibm.com>
 Paul Sharp <psharp1289@gmail.com> psharp1289 <psharp1289@gmail.com>
 Ranjit Khanuja <ranjit.jhu@gmail.com> RanjitK <ranjit.jhu@gmail.com>
+Rastko Ćirić <rc042010@mymail.pomona.edu> rciric <rc042010@mymail.pomona.edu>
+Rastko Ćirić <rc042010@mymail.pomona.edu> Rastko Ćirić <rciric@users.noreply.github.com>
 Ross Markello <rossmarkello@gmail.com> Ross Markello <rdm222@cornell.edu>
 Russell Poldrack <poldrack@gmail.com> Russ Poldrack <poldrack@gmail.com>
 Russell Poldrack <poldrack@gmail.com> poldrack <poldrack@gmail.com>
@@ -162,6 +165,7 @@ Salma Bougacha <salmabougacha@hotmail.com> salma1601 <salmabougacha@hotmail.com>
 Sami Kristian Andberg <sami.andberg@gmail.com> Sami Andberg <sami.andberg@gmail.com>
 Satrajit Ghosh <satrajit.ghosh@gmail.com> Satrajit Ghosh <satra@mit.edu>
 Sebastian Urchs <sebastian.urchs@gmail.com> sebastian <sebastian.urchs@gmail.com>
+Serge Koudoro <skab12@gmail.com> skoudoro <skab12@gmail.com>
 Sharad Sikka <ssikka25@gmail.com> ssikka <ssikka25@gmail.com>
 Shariq Iqbal <shariqiqbal2810@gmail.com> shariqiqbal2810 <shariqiqbal2810@gmail.com>
 Shariq Iqbal <shariqiqbal2810@gmail.com> shariqiqbal2810 <shariqiqbal2810@users.noreply.github.com>
@@ -176,6 +180,7 @@ Steven Giavasis <sgiava77@gmail.com> sgiavasis <sgiava77@gmail.com>
 Steven Giavasis <sgiava77@gmail.com> sgiavasis <sgiavasis@ieee.org>
 Tristan Glatard <tristan.glatard@mcgill.ca> Tristan Glatard <tristan.glatard@creatis.insa-lyon.fr>
 Victor Saase <victor@saase.net> vsaase <victor@saase.net>
+Weijie Huang <hwjbupt@gmail.com> forwho <hwjbupt@gmail.com>
 William Triplett <wtriplett@gmail.com> William Triplett <wtriplett@ufl.edu>
 Wolfgang Pauli <Wolfgang.m.Pauli@gmail.com> Wolfgang Pauli <Wolfgang.m.Pauli@gmail.com>
 Xiangzhen Kong <bnucon@gmail.com> bnucon <bnucon@gmail.com>

.zenodo.json

@@ -89,23 +89,28 @@
       "name": "Clark, Daniel",
       "orcid": "0000-0002-8121-8954"
     },
-    {
-      "affiliation": "National Institute of Mental Health",
-      "name": "Nielson, Dylan M.",
-      "orcid": "0000-0003-4613-6643"
-    },
     {
       "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University",
       "name": "Dewey, Blake E",
       "orcid": "0000-0003-4554-5058"
     },
+    {
+      "affiliation": "National Institute of Mental Health",
+      "name": "Nielson, Dylan M.",
+      "orcid": "0000-0003-4613-6643"
+    },
     {
       "name": "Madison, Cindee"
     },
     {
       "affiliation": "Molecular Imaging Research Center, CEA, France",
       "name": "Bougacha, Salma"
     },
+    {
+      "affiliation": "Stanford University",
+      "name": "\u0106iri\u0107 , Rastko",
+      "orcid": "0000-0001-6347-7939"
+    },
     {
       "affiliation": "National Institutes of Health",
       "name": "Clark, Michael G. "
@@ -115,16 +120,16 @@
       "name": "Dayan, Michael",
       "orcid": "0000-0002-2666-0969"
     },
-    {
-      "affiliation": "Dartmouth College",
-      "name": "Visconti di Oleggio Castello, Matteo",
-      "orcid": "0000-0001-7931-5272"
-    },
     {
       "affiliation": "UC Berkeley",
       "name": "Clark, Dav",
       "orcid": "0000-0002-3982-4416"
     },
+    {
+      "affiliation": "Dartmouth College",
+      "name": "Visconti di Oleggio Castello, Matteo",
+      "orcid": "0000-0001-7931-5272"
+    },
     {
       "affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering",
       "name": "Keshavan, Anisha",
@@ -141,16 +146,16 @@
     {
       "name": "Berleant, Shoshana"
     },
-    {
-      "affiliation": "Dartmouth College: Hanover, NH, United States",
-      "name": "Halchenko, Yaroslav O.",
-      "orcid": "0000-0003-3456-2493"
-    },
     {
       "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
       "name": "Christian, Horea",
       "orcid": "0000-0001-7037-2449"
     },
+    {
+      "affiliation": "Dartmouth College: Hanover, NH, United States",
+      "name": "Halchenko, Yaroslav O.",
+      "orcid": "0000-0003-3456-2493"
+    },
     {
       "affiliation": "UC San Diego",
       "name": "Cipollini, Ben",
@@ -171,6 +176,10 @@
       "name": "Rokem, Ariel",
       "orcid": "0000-0003-0679-1985"
     },
+    {
+      "affiliation": "Indiana University, IN, USA",
+      "name": "Koudoro, Serge"
+    },
     {
       "affiliation": "Montreal Neurological Institute and Hospital",
       "name": "DuPre, Elizabeth",
@@ -189,6 +198,11 @@
       "name": "Varoquaux, Gael",
       "orcid": "0000-0003-1076-5122"
     },
+    {
+      "affiliation": "The Centre for Addiction and Mental Health",
+      "name": "Joseph, Michael",
+      "orcid": "0000-0002-0068-230X"
+    },
     {
       "affiliation": "Athena EPI, Inria Sophia-Antipolis",
       "name": "Wassermann, Demian",
@@ -245,14 +259,14 @@
       "name": "Iqbal, Shariq",
       "orcid": "0000-0003-2766-8425"
     },
+    {
+      "name": "Schwartz, Yannick"
+    },
     {
       "affiliation": "University of Washington",
       "name": "Richie-Halford, Adam",
       "orcid": "0000-0001-9276-9084"
     },
-    {
-      "name": "Schwartz, Yannick"
-    },
     {
       "affiliation": "University College London",
       "name": "Malone, Ian B.",
@@ -341,6 +355,11 @@
       "affiliation": "Child Mind Institute",
       "name": "Giavasis, Steven"
     },
+    {
+      "affiliation": "NIMH IRP",
+      "name": "Lee, John A.",
+      "orcid": "0000-0001-5884-4247"
+    },
     {
       "name": "Correa, Carlos"
     },
@@ -414,11 +433,6 @@
     {
       "name": "Hallquist, Michael"
     },
-    {
-      "affiliation": "Dartmouth College",
-      "name": "Ma, Feilong",
-      "orcid": "0000-0002-6838-3971"
-    },
     {
       "affiliation": "TIB \u2013 Leibniz Information Centre for Science and Technology and University Library, Hannover, Germany",
       "name": "Leinweber, Katrin",
@@ -434,6 +448,16 @@
       "name": "Grignard, Martin",
       "orcid": "0000-0001-5549-1861"
     },
+    {
+      "affiliation": "Dartmouth College",
+      "name": "Ma, Feilong",
+      "orcid": "0000-0002-6838-3971"
+    },
+    {
+      "affiliation": "Department of Neuropsychiatry, University of Pennsylvania",
+      "name": "Cieslak, Matthew",
+      "orcid": "0000-0002-1931-4734"
+    },
     {
       "affiliation": "INRIA-Saclay, Team Parietal",
       "name": "Chawla, Kshitij",
@@ -577,6 +601,10 @@
     {
       "name": "Nickson, Thomas"
     },
+    {
+      "name": "Crusoe, Michael R.",
+      "orcid": "0000-0002-2961-9670"
+    },
     {
       "name": "Brett, Matthew"
     },

doc/changelog/1.X.X-changelog

@@ -1,3 +1,22 @@
+1.2.0 (May 09, 2019)
+====================
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/31?closed=1)
+
+  * FIX: Parsing of filename in AlignEpiAnatPy when filename does not have + (https://github.com/nipy/nipype/pull/2909)
+  * FIX: Import nibabel reorientation bug fix (https://github.com/nipy/nipype/pull/2912)
+  * FIX: Update FNIRT outputs for warped_file log_file to include cwd (https://github.com/nipy/nipype/pull/2900)
+  * FIX: Sort conditions in bids_gen_info to ensure consistent order (https://github.com/nipy/nipype/pull/2867)
+  * FIX: Some traits-5.0.0 don't work with Python 2.7 (https://github.com/nipy/nipype/pull/1)
+  * ENH: CompCor enhancement (https://github.com/nipy/nipype/pull/2878)
+  * ENH: Do not override caught exceptions with FileNotFoundError from unfinished hashfile (https://github.com/nipy/nipype/pull/2919)
+  * ENH: More verbose description when a faulty results file is loaded (https://github.com/nipy/nipype/pull/2920)
+  * ENH: Add all DIPY workflows dynamically  (https://github.com/nipy/nipype/pull/2905)
+  * ENH: Add mrdegibbs and dwibiascorrect from mrtrix3 (https://github.com/nipy/nipype/pull/2904)
+  * TEST: Fix CI builds (https://github.com/nipy/nipype/pull/2927)
+  * MAINT: Reduce deprecation warnings (https://github.com/nipy/nipype/pull/2903)
+
+
 1.1.9 (February 25, 2019)
 =========================
 

doc/conf.py

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "1.1.9"
+release = "1.2.0"
 
 # 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: `1.1.9 <http://nipype.readthedocs.io/en/1.1.9/>`_ `1.1.8 <http://nipype.readthedocs.io/en/1.1.8/>`_
+Previous versions: `1.2.0 <http://nipype.readthedocs.io/en/1.2.0/>`_ `1.1.9 <http://nipype.readthedocs.io/en/1.1.9/>`_
 
 
 .. container:: doc2

docker/generate_dockerfiles.sh

@@ -90,8 +90,8 @@ function generate_main_dockerfile() {
     --user neuro \
     --miniconda create_env=neuro \
                 conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
-                               icu=58.1 libxml2 libxslt matplotlib mkl "numpy!=1.16.0" paramiko
-                               pandas psutil scikit-learn scipy traits=4.6.0' \
+                               libxml2 libxslt matplotlib mkl "numpy!=1.16.0" paramiko
+                               pandas psutil scikit-learn scipy traits' \
                 pip_install="pytest-xdist" \
                 activate=true \
     --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \