From 07d41fb49dd4e7628ec79e5db1bd0ac63874964c Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Mon, 17 Sep 2018 22:40:31 -0400 Subject: [PATCH 1/7] MAINT: Bump version string to 1.1.3 --- nipype/info.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/info.py b/nipype/info.py index 219fa90a05..0da3b2bafe 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -11,7 +11,7 @@ # full release. '.dev' as a version_extra string means this is a development # version # Remove -dev for release -__version__ = '1.1.3-dev' +__version__ = '1.1.3' def get_nipype_gitversion(): From 5d3fcade17feb7e5f534230adbd63fef3787ee35 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 18 Sep 2018 08:23:16 -0400 Subject: [PATCH 2/7] DOC: Changelog 1.1.3 --- doc/changelog/1.X.X-changelog | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index ba1489f89b..d7dfae7f23 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -1,3 +1,19 @@ +1.1.3 (September 24, 2018) +========================== + +##### [Full changelog](https://github.com/nipy/nipype/milestone/24?closed=1) + + * FIX: Add informative error for interfaces that fail to return valid runtime object (https://github.com/nipy/nipype/pull/2692) + * FIX: Construct MCFLIRT output paths relative to out_file (https://github.com/nipy/nipype/pull/2703) + * FIX: SLURM plugin polling (https://github.com/nipy/nipype/pull/2693) + * FIX: Handle missing substring in SPM docs (https://github.com/nipy/nipype/pull/2691) + * ENH: Add colorFA output to DIPY DTI interface (https://github.com/nipy/nipype/pull/2695) + * RF: Use runtime.cwd in Rename (https://github.com/nipy/nipype/pull/2688) + * DOC: Fix naming of motion parameters (roll/yaw swapped) (https://github.com/nipy/nipype/pull/2696) + * DOC: Update links to user and developer help forums (https://github.com/nipy/nipype/pull/2686) + * CI: Test 3.7, resume testing nipy extras (https://github.com/nipy/nipype/pull/2682) + + 1.1.2 (August 11, 2018) ======================= From 51867ccd3c06b39e5e83087f361d14b8ca6126cd Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 19 Sep 2018 10:38:38 -0400 Subject: [PATCH 3/7] DOC: Update version strings --- doc/conf.py | 2 +- doc/documentation.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 2278981f47..94f3a97b5c 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -82,7 +82,7 @@ # The short X.Y version. version = nipype.__version__ # The full version, including alpha/beta/rc tags. -release = "1.1.1" +release = "1.1.3" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/doc/documentation.rst b/doc/documentation.rst index 06690ccc90..e185750448 100644 --- a/doc/documentation.rst +++ b/doc/documentation.rst @@ -9,7 +9,7 @@ Documentation :Release: |version| :Date: |today| -Previous versions: `1.1.0 `_ `1.0.4 `_ +Previous versions: `1.1.2 `_ `1.1.1 `_ .. container:: doc2 From 7310cf6400392c343b43e35d925471af21d27187 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 19 Sep 2018 10:39:02 -0400 Subject: [PATCH 4/7] DOC: .mailmap (low-hanging fruit) --- .mailmap | 52 +++++++++++++++++++++++++++++++++++++++++++--------- 1 file changed, 43 insertions(+), 9 deletions(-) diff --git a/.mailmap b/.mailmap index 59d6d745a2..ce76aa989f 100644 --- a/.mailmap +++ b/.mailmap @@ -7,6 +7,7 @@ Alexander Schaefer aschaefer Alexandre M. S Alexandre M. Savio Alexandre M. S Alexandre M. Savio Alexandre Manhaes Savio +Andrey Chetverikov achetverikov Anisha Keshavan Anisha Keshavan Anisha Keshavan akeshavan Ariel Rokem arokem @@ -14,7 +15,6 @@ Ariel Rokem arokem Arman Eshaghi armaneshaghi Ashely Gillman Ashley Gillman Ashely Gillman ashgillman -Andrey Chetverikov achetverikov Basille Pinsard bpinsard Basille Pinsard bpinsard Ben Cipollini Ben Cipollini @@ -24,6 +24,7 @@ Blake Dewey Blake Dewey Blake Dewey blakedewey Blake Dewey blakedewey Brendan Moloney moloney +Caroline Froehlich carolFrohlich Chris Filo Gorgolewski Chris Filo Gorgolewski Chris Filo Gorgolewski Chris Filo Gorgolewski Chris Filo Gorgolewski Chris Filo Gorgolewski @@ -40,21 +41,28 @@ Cindee Madison cindeem Cindee Madison cindeem <> Colin Buchanan Colin Buchanan Colin Buchanan colinbuchanan +Daniel Brenner brennerd +Daniel Brenner brennerd11 Daniel Clark dclark87 +Daniel Geisler daniel-ge Daniel Ginsburg danginsburg Daniel McNamee danmc David Ellis David Ellis David Ellis David Ellis David Welch David Welch +Dimitri Papadopoulos Orfanos Dimitri Papadopoulos Dmytro belevtsoff +Dylan Nielson Dylan +Elizabeth DuPre emdupre Erik Ziegler Erik Erik Ziegler Erik Ziegler Erik Ziegler erik Erik Ziegler erikz Erik Ziegler swederik Fernando Pérez-García Fernando -Franz Liem fliem Franz Liem fliem +Franz Liem fliem +Fred Loney FredLoney Gael Varoquaux GaelVaroquaux Gael Varoquaux GaelVaroquaux Gavin Cooper gjcooper @@ -63,40 +71,66 @@ Hans Johnson Hans Johnson Hans Johnson hjmjohnson Horea Christian Horea Christian Isaac Schwabacher ischwabacher -James Kent jdkent Jakub Kaczmarzyk kaczmarj +Jakub Kaczmarzyk jakubk +James Kent jdkent +Janosch Linkersdörfer Januzz Jason Wong Jason -Jason Wong jason -Jason Wong Jason W Jason Wong Jason W +Jason Wong Jason W +Jason Wong jason Jason Wong jason-wg Jens Kleesiek JensNRAD +Jérémy Guillon GUILLON Jeremy +Jessica Forbes jessicaforbes Joerg Stadler Joerg Stadler Joerg Stadler Jörg Stadler Joke Durnez jokedurnez Josh Warner Josh Warner (Mac) Kai Schlamp medihack Jessica Forbes jessicaforbes +Katie Bottenhorn 62442katieb +Kesshi Jordan Kesshi Jordan +Kesshi Jordan Kesshi Jordan +Kesshi Jordan Kesshi Jordan +Kesshi Jordan Kesshi Jordan +Kesshi Jordan Kesshi Jordan +Kesshi Jordan Kesshi jordan +Kesshi Jordan kesshijordan Kevin Sitek sitek +Kevin Sitek sitek Leonie Lampe Leonie Lmape Lukas Snoek Lukas Snoek Mathias Goncalves mathiasg +Mathieu Dubois Mathieu Dubois +Mathieu Dubois duboism Matteo Mancini matteomancini Matteo Visconti dOC mvdoc -Michael Dayan Michael +Matteo Visconti dOC Matteo Visconti dOC +Michael Clark Clark Michael Dayan Michael +Michael Dayan Michael Michael Dayan mick-d -Michael Clark Clark Michael Notter miykael Michael Waskom Michael Waskom Michael Waskom Michael Waskom Michael Waskom mwaskom -Michael Waskom mwaskom Michael Waskom mwaskom +Michael Waskom mwaskom +Oliver Contier oliver-contier Oscar Esteban Oscar Esteban Oscar Esteban oesteban +Pablo Polosecki pipolose +Pablo Polosecki pipolose +Ranjit Khanuja RanjitK +Ross Markello Ross Markello Russell Poldrack Russ Poldrack Russell Poldrack poldrack +Salma Bougacha Salma BOUGACHA +Salma Bougacha salma +Salma Bougacha salma1601 Satrajit Ghosh Satrajit Ghosh +Sebastian Urchs sebastian +Sharad Sikka ssikka Shariq Iqbal shariqiqbal2810 Shariq Iqbal shariqiqbal2810 Shoshana Berleant Shoshana Berleant @@ -111,5 +145,5 @@ Tristan Glatard Tristan Glatard vsaase William Triplett William Triplett Wolfgang Pauli Wolfgang Pauli +Xiangzhen Kong bnucon Yaroslav Halchenko Yaroslav Halchenko -pipolose pipolose From 30ed5cf74343f6f011c474765fbc8465e5a987ee Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 19 Sep 2018 19:06:10 -0400 Subject: [PATCH 5/7] MAINT: A few more .mailmap entries --- .mailmap | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/.mailmap b/.mailmap index ce76aa989f..6a13f46ee1 100644 --- a/.mailmap +++ b/.mailmap @@ -1,5 +1,7 @@ Aimi Watanabe stymy Aimi Watanabe stymy +Alejandro Tabas qTabs +Alejandro Tabas qtabs Alejandro de la Vega adelavega Alexander Schaefer Alexander Schaefer Alexander Schaefer alexschaefer83 @@ -7,6 +9,7 @@ Alexander Schaefer aschaefer Alexandre M. S Alexandre M. Savio Alexandre M. S Alexandre M. Savio Alexandre Manhaes Savio +Andrey Chetverikov Andrey Chetverikov Andrey Chetverikov achetverikov Anisha Keshavan Anisha Keshavan Anisha Keshavan akeshavan @@ -71,8 +74,8 @@ Hans Johnson Hans Johnson Hans Johnson hjmjohnson Horea Christian Horea Christian Isaac Schwabacher ischwabacher -Jakub Kaczmarzyk kaczmarj Jakub Kaczmarzyk jakubk +Jakub Kaczmarzyk kaczmarj James Kent jdkent Janosch Linkersdörfer Januzz Jason Wong Jason @@ -81,11 +84,12 @@ Jason Wong Jason W Jason Wong jason Jason Wong jason-wg Jens Kleesiek JensNRAD -Jérémy Guillon GUILLON Jeremy Jessica Forbes jessicaforbes +Jérémy Guillon GUILLON Jeremy Joerg Stadler Joerg Stadler Joerg Stadler Jörg Stadler Joke Durnez jokedurnez +Josh Warner JDWarner Josh Warner Josh Warner (Mac) Kai Schlamp medihack Jessica Forbes jessicaforbes Katie Bottenhorn 62442katieb @@ -100,18 +104,21 @@ Kevin Sitek sitek Kevin Sitek sitek Leonie Lampe Leonie Lmape Lukas Snoek Lukas Snoek +Marcel Falkiewicz Marcel Falkiewicz +Mathias Goncalves Mathias Goncalves Mathias Goncalves mathiasg Mathieu Dubois Mathieu Dubois Mathieu Dubois duboism Matteo Mancini matteomancini -Matteo Visconti dOC mvdoc Matteo Visconti dOC Matteo Visconti dOC +Matteo Visconti dOC mvdoc Michael Clark Clark Michael Dayan Michael Michael Dayan Michael Michael Dayan mick-d Michael Notter miykael Michael Waskom Michael Waskom +Michael Waskom Michael Waskom Michael Waskom Michael Waskom Michael Waskom mwaskom Michael Waskom mwaskom From 09092762e89cd2aa06a108cdaad6b43c54ba2d3d Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 19 Sep 2018 19:08:58 -0400 Subject: [PATCH 6/7] DOC: Update changelog --- doc/changelog/1.X.X-changelog | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index d7dfae7f23..f1d63af29b 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -3,6 +3,7 @@ ##### [Full changelog](https://github.com/nipy/nipype/milestone/24?closed=1) + * FIX: Return afni.Qwarp outputs as absolute paths (https://github.com/nipy/nipype/pull/2705) * FIX: Add informative error for interfaces that fail to return valid runtime object (https://github.com/nipy/nipype/pull/2692) * FIX: Construct MCFLIRT output paths relative to out_file (https://github.com/nipy/nipype/pull/2703) * FIX: SLURM plugin polling (https://github.com/nipy/nipype/pull/2693) From 65530abd5d07fb3f16538c6af92af1a448eff716 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 19 Sep 2018 19:19:57 -0400 Subject: [PATCH 7/7] MAINT: Update Zenodo with latest line counts --- .zenodo.json | 107 ++++++++++++++++++++++++++------------------------- 1 file changed, 55 insertions(+), 52 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index e4883ed9e5..3efcfa9c87 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -25,6 +25,11 @@ "name": "Ellis, David Gage", "orcid": "0000-0002-3718-6836" }, + { + "affiliation": "MIT", + "name": "Jarecka, Dorota", + "orcid": "0000-0003-1857-8129" + }, { "affiliation": "The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland", "name": "Notter, Michael Philipp", @@ -35,11 +40,6 @@ "name": "Johnson, Hans", "orcid": "0000-0001-9513-2660" }, - { - "affiliation": "MIT", - "name": "Jarecka, Dorota", - "orcid": "0000-0003-1857-8129" - }, { "name": "Burns, Christopher" }, @@ -94,9 +94,18 @@ "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": "Dartmouth College", "name": "Visconti di Oleggio Castello, Matteo", @@ -133,13 +142,9 @@ "name": "Berleant, Shoshana" }, { - "affiliation": "National Institute of Mental Health", - "name": "Nielson, Dylan M.", - "orcid": "0000-0003-4613-6643" - }, - { - "affiliation": "Molecular Imaging Research Center, CEA, France", - "name": "Bougacha, Salma" + "affiliation": "MIT", + "name": "Kaczmarzyk, Jakub", + "orcid": "0000-0002-5544-7577" }, { "affiliation": "INRIA", @@ -166,6 +171,11 @@ "name": "Rokem, Ariel", "orcid": "0000-0003-0679-1985" }, + { + "affiliation": "Montreal Neurological Institute and Hospital", + "name": "DuPre, Elizabeth", + "orcid": "0000-0003-1358-196X" + }, { "name": "Moloney, Brendan" }, @@ -184,21 +194,11 @@ "name": "Horea, Christian", "orcid": "0000-0001-7037-2449" }, - { - "affiliation": "MIT", - "name": "Kaczmarzyk, Jakub", - "orcid": "0000-0002-5544-7577" - }, { "affiliation": "Vrije Universiteit, Amsterdam", "name": "Gilles de Hollander", "orcid": "0000-0003-1988-5091" }, - { - "affiliation": "Montreal Neurological Institute and Hospital", - "name": "DuPre, Elizabeth", - "orcid": "0000-0003-1358-196X" - }, { "affiliation": "Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation; University of Queensland", "name": "Gillman, Ashley", @@ -232,6 +232,9 @@ "name": "Mancini, Matteo", "orcid": "0000-0001-7194-4568" }, + { + "name": "Forbes, Jessica" + }, { "name": "Schwartz, Yannick" }, @@ -251,23 +254,20 @@ "affiliation": "University of Iowa", "name": "Welch, David" }, - { - "name": "Forbes, Jessica" - }, { "name": "Kent, James" }, { "name": "Watanabe, Aimi" }, - { - "name": "Cumba, Chad" - }, { "affiliation": "Research Group Neuroanatomy and Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany", "name": "Huntenburg, Julia M.", "orcid": "0000-0003-0579-9811" }, + { + "name": "Cumba, Chad" + }, { "affiliation": "Harvard University - Psychology", "name": "Kastman, Erik", @@ -383,6 +383,10 @@ "name": "Chetverikov, Andrey", "orcid": "0000-0003-2767-6310" }, + { + "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany", + "name": "Weninger, Leon" + }, { "name": "Salvatore, John" }, @@ -412,6 +416,11 @@ "affiliation": "Boston University", "name": "Perkins, L. Nathan" }, + { + "affiliation": "University of Amsterdam", + "name": "Lukas Snoek", + "orcid": "0000-0001-8972-204X" + }, { "name": "Marina, Ana" }, @@ -419,18 +428,18 @@ "name": "Mattfeld, Aaron" }, { - "name": "Noel, Maxime" + "name": "Matsubara, K" }, { - "affiliation": "University of Amsterdam", - "name": "Lukas Snoek", - "orcid": "0000-0001-8972-204X" + "name": "Noel, Maxime" }, { - "name": "Matsubara, K" + "name": "Cheung, Brian" }, { - "name": "Cheung, Brian" + "affiliation": "The University of Texas at Austin", + "name": "Floren, Andrew", + "orcid": "0000-0003-3618-2056" }, { "name": "Rothmei, Simon" @@ -455,19 +464,14 @@ "orcid": "0000-0003-2076-5329" }, { - "affiliation": "The University of Texas at Austin", - "name": "Floren, Andrew", - "orcid": "0000-0003-3618-2056" + "affiliation": "University of illinois urbana champaign", + "name": "Sharp, Paul" }, { "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", @@ -476,6 +480,9 @@ { "name": "Weinstein, Alejandro" }, + { + "name": "Tambini, Arielle" + }, { "affiliation": "Duke University", "name": "Broderick, William", @@ -492,6 +499,9 @@ { "name": "Harms, Robbert" }, + { + "name": "Khanuja, Ranjeet" + }, { "name": "Schlamp, Kai" }, @@ -506,14 +516,15 @@ { "name": "Tarbert, Claire" }, - { - "name": "Tambini, Arielle" - }, { "affiliation": "University of Texas at Austin", "name": "De La Vega, Alejandro", "orcid": "0000-0001-9062-3778" }, + { + "affiliation": "Vrije Universiteit Amsterdam", + "name": "Ort, Eduard" + }, { "name": "Nickson, Thomas" }, @@ -534,10 +545,6 @@ { "name": "Flandin, Guillaume" }, - { - "affiliation": "Vrije Universiteit Amsterdam", - "name": "Ort, Eduard" - }, { "name": "Shachnev, Dmitry" }, @@ -574,10 +581,6 @@ { "name": "McDermottroe, Conor" }, - { - "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany", - "name": "Weninger, Leon" - }, { "affiliation": "MIT, HMS", "name": "Ghosh, Satrajit",