Merge tag '1.1.9' into debian

1.1.9 (February 25, 2019)

Full changelog: https://github.com/nipy/nipype/milestone/30?closed=1

  * FIX: Make positional arguments to LaplacianThickness require previous argument (nipy#2848)
  * FIX: Import math and csv modules for bids_gen_info (nipy#2881)
  * FIX: Ensure outputs can be listed in camino.ProcStreamlines by defining instance variable (nipy#2739)
  * ENH: Allow afni.MaskTool to take multiple input files (nipy#2892)
  * ENH: Add flags dictionary input to spm.Level1Design (nipy#2861)
  * ENH: Threshold stddev once only in TSNR (nipy#2883)
  * ENH: Add workbench.CiftiSmooth interface (nipy#2871)
  * DOC: Replace initialism typo in comment with intended phrase (nipy#2875)
  * DOC: Fix typos in ANTs Registration input documentation (nipy#2869)

* tag '1.1.9': (34 commits)
  MNT: Update changelog
  MNT: Add Katherine Bottenhorn, Paul Mihai to Zenodo
  MNT: Add kchawla-pi to Zenodo, update mailmap and ordering
  add to zenodo
  MNT: Update zenodo ordering
  Update .zenodo.json
  afni utils.py - masktool - InputMultiPath for in_file argument
  MNT: Update .zenodo ordering
  MNT: Add Oliver Contier name to .zenodo.json
  Update nipype/interfaces/spm/model.py
  ENH: Add zenodo updating script
  MNT: Update mailmap to avoid renames in script
  MNT: Update .mailmap, .zenodo.json
  MNT: Version 1.1.9
  DOC: 1.1.9 changelog
  ENH: minor - compute non degenerate stddev map once
  BF: regenerated test_auto_LaplacianThickness using wonderfully long running tools/checkspecs.py
  TEST: Thorough test of LaplacianThickness requirement cascade
  FIX: Requires error text was backwards
  import math and csv modules for bids_gen_info
  ...

Author: yarikoptic

.mailmap

@@ -10,10 +10,13 @@ Alexander Schaefer <[email protected]> aschaefer <aschaefer@aschaefer-U36
 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]>
+Andrew Floren <[email protected]> afloren <[email protected]>
 Andrey Chetverikov <[email protected]> Andrey Chetverikov <[email protected]>
 Andrey Chetverikov <[email protected]> achetverikov <[email protected]>
+Anibal Sólon Heinsfeld <[email protected]> anibalsolon <[email protected]>
 Anisha Keshavan <[email protected]> Anisha Keshavan <[email protected]>
 Anisha Keshavan <[email protected]> akeshavan <[email protected]>
+Ariel Rokem <[email protected]> Ariel Rokem <[email protected]>
 Ariel Rokem <[email protected]> arokem <[email protected]>
 Ariel Rokem <[email protected]> arokem <[email protected]>
 Arman Eshaghi <[email protected]> armaneshaghi <[email protected]>
@@ -22,26 +25,19 @@ Ashely Gillman <[email protected]> ashgillman <[email protected]>
 Basille Pinsard <[email protected]> bpinsard <[email protected]>
 Basille Pinsard <[email protected]> bpinsard <[email protected]>
 Ben Cipollini <[email protected]> Ben Cipollini <[email protected]>
+Benjamin Acland <[email protected]> Ben Acland <[email protected]>
 Benjamin Yvernault <[email protected]> Benjamin Yvernault <[email protected]>
 Benjamin Yvernault <[email protected]> byvernault <[email protected]>
 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]>
-Chris Filo Gorgolewski <[email protected]> Chris Gorgolewski <[email protected]>
-Chris Filo Gorgolewski <[email protected]> Krzysztof Gorgolewski <[email protected]>
-Chris Filo Gorgolewski <[email protected]> filo <filo@filo-Precision-M6500>
-Chris Filo Gorgolewski <[email protected]> filo <filo@filo-dtc-laptop>
-Chris Filo Gorgolewski <[email protected]> filo <filo@filolaptop>
 Christopher J. Markiewicz <[email protected]> Chris Markiewicz <[email protected]>
+Christopher J. Markiewicz <[email protected]> Chris Markiewicz <[email protected]>
 Christopher J. Markiewicz <[email protected]> Christopher J. Johnson <[email protected]>
 Christopher J. Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
 Christopher J. Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
-Christopher J. Markiewicz <[email protected]> Chris Markiewicz <[email protected]>
 Cindee Madison <[email protected]> cindeem
 Cindee Madison <[email protected]> cindeem <>
 Colin Buchanan <[email protected]> Colin Buchanan <cbuchanan@cray4.(none)>
@@ -54,10 +50,13 @@ Daniel Ginsburg <[email protected]> danginsburg <daniel.gins
 Daniel McNamee <[email protected]> danmc <[email protected]>
 David Ellis <[email protected]> David Ellis <[email protected]>
 David Ellis <[email protected]> David Ellis <[email protected]>
+David Mordom <[email protected]> dmordom <[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]>
+Dylan M. Nielson <[email protected]> Dylan <[email protected]>
+Dylan M. Nielson <[email protected]> Dylan Nielson <[email protected]>
+Eduard Ort <[email protected]> eort <[email protected]>
 Elizabeth DuPre <[email protected]> emdupre <[email protected]>
 Erik Ziegler <[email protected]> Erik <[email protected]>
 Erik Ziegler <[email protected]> Erik Ziegler <[email protected]>
@@ -73,6 +72,8 @@ 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]>
+Gio Piantoni <[email protected]> Gio at UMCU <[email protected]>
+Guillaume Flandin <[email protected]> Guillaume <[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]>
@@ -90,12 +91,16 @@ 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]> Joerg Stadler <[email protected]>
 Joerg Stadler <[email protected]> Jörg Stadler <[email protected]>
+John Lee <[email protected]> john anthony lee <[email protected]>
+John Lee <[email protected]> leej3 <[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]>
+Kai Schlamp <[email protected]> medihack <[email protected]>
+Katherine Bottenhorn <[email protected]> 62442katieb <[email protected]>
+Katherine Bottenhorn <[email protected]> Katie Bottenhorn <[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]>
@@ -105,6 +110,18 @@ 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]>
+Kornelius Podranski <[email protected]> Kornelius <[email protected]>
+Krzysztof J. Gorgolewski <[email protected]> Chris Filo Gorgolewski <[email protected]>
+Krzysztof J. Gorgolewski <[email protected]> Chris Filo Gorgolewski <filo@filo-Precision-M6500.(none)>
+Krzysztof J. Gorgolewski <[email protected]> Chris Filo Gorgolewski <[email protected]>
+Krzysztof J. Gorgolewski <[email protected]> Chris Filo Gorgolewski <[email protected]>
+Krzysztof J. Gorgolewski <[email protected]> Chris Gorgolewski <[email protected]>
+Krzysztof J. Gorgolewski <[email protected]> Krzysztof Gorgolewski <[email protected]>
+Krzysztof J. Gorgolewski <[email protected]> filo <filo@filo-Precision-M6500>
+Krzysztof J. Gorgolewski <[email protected]> filo <filo@filo-Precision-M6500>
+Krzysztof J. Gorgolewski <[email protected]> filo <filo@filo-dtc-laptop>
+Krzysztof J. Gorgolewski <[email protected]> filo <filo@filolaptop>
+Kshitij Chawla <[email protected]> Kshitij Chawla (kchawla-pi) <[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]>
@@ -113,39 +130,45 @@ 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]>
+Matteo Visconti di Oleggio Castello <[email protected]> Matteo Visconti dOC <[email protected]>
+Matteo Visconti di Oleggio Castello <[email protected]> Matteo Visconti dOC <[email protected]>
+Matteo Visconti di Oleggio Castello <[email protected]> mvdoc <[email protected]>
 Michael Clark <[email protected]> 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 Notter <[email protected]> miykael <[email protected]>
+Michael Philipp Notter <[email protected]> Michael Notter <[email protected]>
+Michael Philipp 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]>
+Miguel Molina-Romero <[email protected]> Miguel Molina <[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]>
+Paul Sharp <[email protected]> psharp1289 <[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]>
+Sami Kristian Andberg <[email protected]> Sami Andberg <[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>
 Shoshana Berleant <[email protected]> Shoshana Berleant <[email protected]>
-Simon R <[email protected]> Simon Rothmeier <[email protected]>
+Simon Rothmei <[email protected]> Simon R <[email protected]>
+Simon Rothmei <[email protected]> Simon Rothmeier <[email protected]>
 Siqi Liu <[email protected]> siqi liu <[email protected]>
 Siqi Liu <[email protected]> sql <[email protected]>
 Steven Giavasis <[email protected]> Steven Giavasis <[email protected]>

.travis.yml

@@ -60,9 +60,6 @@ matrix:
           NIPYPE_EXTRAS="doc,tests,nipy,profiler"
           EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
           CI_SKIP_TEST=1
-  allow_failures:
-    - python: 2.7
-      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:

.zenodo.json

@@ -141,21 +141,26 @@
     {
       "name": "Berleant, Shoshana"
     },
-    {
-      "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
-      "name": "Horea, Christian",
-      "orcid": "0000-0001-7037-2449"
-    },
     {
       "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": "UC San Diego",
       "name": "Cipollini, Ben",
       "orcid": "0000-0002-7782-0790"
     },
+    {
+      "affiliation": "ARAMIS LAB, Brain and Spine Institute (ICM), Paris, France.",
+      "name": "Guillon, Je\u0301re\u0301my",
+      "orcid": "0000-0002-2672-7510"
+    },
     {
       "affiliation": "Montreal Neurological Institute and Hospital",
       "name": "Markello, Ross",
@@ -186,7 +191,7 @@
     },
     {
       "affiliation": "Athena EPI, Inria Sophia-Antipolis",
-      "name": "Wassermann , Demian",
+      "name": "Wassermann, Demian",
       "orcid": "0000-0001-5194-6056"
     },
     {
@@ -196,7 +201,7 @@
     },
     {
       "affiliation": "Vrije Universiteit, Amsterdam",
-      "name": "Gilles de Hollander",
+      "name": "de Hollander, Gilles",
       "orcid": "0000-0003-1988-5091"
     },
     {
@@ -210,6 +215,11 @@
     {
       "name": "Buchanan, Colin"
     },
+    {
+      "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.",
+      "name": "Tabas, Alejandro",
+      "orcid": "0000-0002-8643-1543"
+    },
     {
       "name": "Tungaraza, Rosalia"
     },
@@ -251,6 +261,10 @@
     {
       "name": "Dubois, Mathieu"
     },
+    {
+      "name": "Heinsfeld, Anibal S\u00f3lon",
+      "orcid": "0000-0002-2050-0614"
+    },
     {
       "affiliation": "Child Mind Institute",
       "name": "Frohlich, Caroline"
@@ -259,6 +273,11 @@
       "affiliation": "University of Iowa",
       "name": "Welch, David"
     },
+    {
+      "affiliation": "Florida International University",
+      "name": "Bottenhorn, Katherine",
+      "orcid": "0000-0002-7796-8795"
+    },
     {
       "name": "Kent, James"
     },
@@ -328,6 +347,11 @@
     {
       "name": "Ghayoor, Ali"
     },
+    {
+      "affiliation": "Otto-von-Guericke-University Magdeburg, Germany",
+      "name": "Contier, Oliver",
+      "orcid": "0000-0002-2983-4709"
+    },
     {
       "name": "K\u00fcttner, Ren\u00e9"
     },
@@ -358,6 +382,11 @@
       "affiliation": "The University of Sydney",
       "name": "Liu, Siqi"
     },
+    {
+      "affiliation": "Leibniz Institute for Neurobiology",
+      "name": "Stadler, J\u00f6rg",
+      "orcid": "0000-0003-4313-129X"
+    },
     {
       "affiliation": "University of Pennsylvania",
       "name": "Kahn, Ari E.",
@@ -377,11 +406,6 @@
       "affiliation": "MPI CBS Leipzig, Germany",
       "name": "Lampe, Leonie"
     },
-    {
-      "affiliation": "Leibniz Institute for Neurobiology",
-      "name": "Stadler, J\u00f6rg",
-      "orcid": "0000-0003-4313-129X"
-    },
     {
       "affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China; Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands",
       "name": "Kong, Xiang-Zhen",
@@ -410,6 +434,11 @@
       "name": "Grignard, Martin",
       "orcid": "0000-0001-5549-1861"
     },
+    {
+      "affiliation": "INRIA-Saclay, Team Parietal",
+      "name": "Chawla, Kshitij",
+      "orcid": "0000-0002-7517-6321"
+    },
     {
       "name": "Salvatore, John"
     },
@@ -463,11 +492,6 @@
     {
       "name": "Cheung, Brian"
     },
-    {
-      "affiliation": "The University of Texas at Austin",
-      "name": "Floren, Andrew",
-      "orcid": "0000-0003-3618-2056"
-    },
     {
       "name": "Urchs, Sebastian"
     },
@@ -476,20 +500,30 @@
       "name": "Durnez, Joke",
       "orcid": "0000-0001-9030-2202"
     },
+    {
+      "affiliation": "CNRS, UMS3552 IRMaGe",
+      "name": "Condamine, Eric",
+      "orcid": "0000-0002-9533-3769"
+    },
     {
       "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry",
       "name": "Geisler, Daniel",
       "orcid": "0000-0003-2076-5329"
     },
     {
-      "affiliation": "University of illinois urbana champaign",
-      "name": "Sharp, Paul"
+      "affiliation": "The University of Texas at Austin",
+      "name": "Floren, Andrew",
+      "orcid": "0000-0003-3618-2056"
     },
     {
       "affiliation": "Institute of Neuroinformatics, ETH/University of Zurich",
       "name": "Gerhard, Stephan",
       "orcid": "0000-0003-4454-6171"
     },
+    {
+      "affiliation": "University of Illinois Urbana Champaign",
+      "name": "Sharp, Paul"
+    },
     {
       "affiliation": "Technical University Munich",
       "name": "Molina-Romero, Miguel",
@@ -540,10 +574,6 @@
     {
       "name": "Tarbert, Claire"
     },
-    {
-      "affiliation": "Vrije Universiteit Amsterdam",
-      "name": "Ort, Eduard"
-    },
     {
       "name": "Nickson, Thomas"
     },
@@ -564,6 +594,10 @@
     {
       "name": "Flandin, Guillaume"
     },
+    {
+      "affiliation": "Vrije Universiteit Amsterdam",
+      "name": "Ort, Eduard"
+    },
     {
       "name": "Shachnev, Dmitry"
     },
@@ -600,6 +634,11 @@
     {
       "name": "McDermottroe, Conor"
     },
+    {
+      "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.",
+      "name": "Mihai, Paul Glad",
+      "orcid": "0000-0001-5715-6442"
+    },
     {
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",

doc/changelog/1.X.X-changelog

@@ -1,3 +1,19 @@
+1.1.9 (February 25, 2019)
+=========================
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/30?closed=1)
+
+  * FIX: Make positional arguments to LaplacianThickness require previous argument (https://github.com/nipy/nipype/pull/2848)
+  * FIX: Import math and csv modules for bids_gen_info (https://github.com/nipy/nipype/pull/2881)
+  * FIX: Ensure outputs can be listed in camino.ProcStreamlines by defining instance variable (https://github.com/nipy/nipype/pull/2739)
+  * ENH: Allow afni.MaskTool to take multiple input files (https://github.com/nipy/nipype/pull/2892)
+  * ENH: Add flags dictionary input to spm.Level1Design (https://github.com/nipy/nipype/pull/2861)
+  * ENH: Threshold stddev once only in TSNR (https://github.com/nipy/nipype/pull/2883)
+  * ENH: Add workbench.CiftiSmooth interface (https://github.com/nipy/nipype/pull/2871)
+  * DOC: Replace initialism typo in comment with intended phrase (https://github.com/nipy/nipype/pull/2875)
+  * DOC: Fix typos in ANTs Registration input documentation (https://github.com/nipy/nipype/pull/2869)
+
+
 1.1.8 (January 28, 2019)
 ========================