From a5a6c3979a46721b9a956742d3214e334fcf0bba Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 18 Sep 2019 10:04:21 -0400 Subject: [PATCH 01/10] MNT: Update changelog, Zenodo ordering --- doc/changelog/1.X.X-changelog | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog index 71363170df..82747d9903 100644 --- a/doc/changelog/1.X.X-changelog +++ b/doc/changelog/1.X.X-changelog @@ -1,3 +1,24 @@ +1.2.3 (September 23, 2019) +========================== + +Python 1.2.3 will be the last version to support Python 3.4. + +##### [Full changelog](https://github.com/nipy/nipype/milestone/35?closed=1) + + * FIX: Patch Path.mkdir for Python 2 (https://github.com/nipy/nipype/pull/3037) + * FIX: Drop deprecated message argument to ``FileNotFoundError`` (https://github.com/nipy/nipype/pull/3035) + * FIX: Handle NIFTI extensions in ``afni.Qwarp`` (https://github.com/nipy/nipype/pull/3028) + * FIX: Disallow returning ``None`` in ``pipeline.utils.load_resultfile`` (https://github.com/nipy/nipype/pull/3023) + * ENH: Allow afni.CatMatvec to accept empty string opkeys (https://github.com/nipy/nipype/pull/2943) + * ENH: Add ``mrrtrix3.MRResize`` interface (https://github.com/nipy/nipype/pull/3031) + * ENH: Add version check / telemetry to Nipype (https://github.com/nipy/nipype/pull/3027) + * ENH: Update MCFLIRT outputs for FSL 6+ (https://github.com/nipy/nipype/pull/3029) + * ENH: Lightweight node cache checking (https://github.com/nipy/nipype/pull/3026) + * ENH: Avoid loading result from file when writing reports (https://github.com/nipy/nipype/pull/3024) + * ENH: replace portalocker with filelock (https://github.com/nipy/nipype/pull/3025) + * MAINT: Set minimum yapf for `checkspecs` to 0.27 (https://github.com/nipy/nipype/pull/3033) + + 1.2.2 (September 07, 2019) ========================== From 9d1fec77f043636ce5316bd8bd24c92ba28cc962 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 18 Sep 2019 16:25:44 -0400 Subject: [PATCH 02/10] DOC: Update mailmap, zenodo --- .mailmap | 2 ++ .zenodo.json | 77 ++++++++++++++++++++++-------------------- tools/update_zenodo.py | 1 - 3 files changed, 42 insertions(+), 38 deletions(-) diff --git a/.mailmap b/.mailmap index 946919557c..9f2b618d78 100644 --- a/.mailmap +++ b/.mailmap @@ -126,6 +126,7 @@ Kshitij Chawla Kshitij Chawla (kchawla-pi) Leonie Lmape Lukas Snoek Lukas Snoek Marcel Falkiewicz Marcel Falkiewicz +Martin Perez-Guevara Mathias Goncalves Mathias Goncalves Mathias Goncalves mathiasg Mathieu Dubois Mathieu Dubois @@ -153,6 +154,7 @@ Michael Waskom mwaskom Miguel Molina-Romero Miguel Molina Murat Bilgel Murat Bilgel Oliver Contier oliver-contier +Olivia Stanley Oscar Esteban Oscar Esteban Oscar Esteban oesteban Pablo Polosecki pipolose diff --git a/.zenodo.json b/.zenodo.json index 06bd8a4ebc..668974fd2d 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -78,6 +78,10 @@ "affiliation": "Shattuck Lab, UCLA Brain Mapping Center", "name": "Wong, Jason" }, + { + "affiliation": "Concordia University", + "name": "Benderoff, Erin" + }, { "name": "Modat, Marc" }, @@ -147,8 +151,9 @@ "name": "Berleant, Shoshana" }, { - "affiliation": "Concordia University", - "name": "Benderoff, Erin" + "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", @@ -156,9 +161,9 @@ "orcid": "0000-0001-7037-2449" }, { - "affiliation": "Dartmouth College: Hanover, NH, United States", - "name": "Halchenko, Yaroslav O.", - "orcid": "0000-0003-3456-2493" + "affiliation": "The Centre for Addiction and Mental Health", + "name": "Joseph, Michael", + "orcid": "0000-0002-0068-230X" }, { "affiliation": "UC San Diego", @@ -202,11 +207,6 @@ "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", @@ -250,14 +250,14 @@ "affiliation": "Nathan s Kline institute for psychiatric research", "name": "Sikka, Sharad" }, + { + "name": "Forbes, Jessica" + }, { "affiliation": "University College London", "name": "Mancini, Matteo", "orcid": "0000-0001-7194-4568" }, - { - "name": "Forbes, Jessica" - }, { "affiliation": "Duke University", "name": "Iqbal, Shariq", @@ -295,10 +295,6 @@ { "name": "Kent, James" }, - { - "name": "Heinsfeld, Anibal S\u00f3lon", - "orcid": "0000-0002-2050-0614" - }, { "name": "Watanabe, Aimi" }, @@ -325,6 +321,10 @@ "name": "Eshaghi, Arman", "orcid": "0000-0002-6652-3512" }, + { + "name": "Heinsfeld, Anibal S\u00f3lon", + "orcid": "0000-0002-2050-0614" + }, { "name": "Ginsburg, Daniel" }, @@ -378,9 +378,15 @@ { "name": "K\u00fcttner, Ren\u00e9" }, + { + "name": "Perez-Guevara, Martin" + }, { "name": "Millman, Jarrod" }, + { + "name": "Lai, Jeff" + }, { "name": "Zhou, Dale" }, @@ -402,16 +408,16 @@ "affiliation": "The University of Sydney", "name": "Liu, Siqi" }, - { - "affiliation": "University of Pennsylvania", - "name": "Kahn, Ari E.", - "orcid": "0000-0002-2127-0507" - }, { "affiliation": "Leibniz Institute for Neurobiology", "name": "Stadler, J\u00f6rg", "orcid": "0000-0003-4313-129X" }, + { + "affiliation": "University of Pennsylvania", + "name": "Kahn, Ari E.", + "orcid": "0000-0002-2127-0507" + }, { "affiliation": "University College London", "name": "P\u00e9rez-Garc\u00eda, Fernando", @@ -503,15 +509,6 @@ "affiliation": "Boston University", "name": "Perkins, L. Nathan" }, - { - "name": "Marina, Ana" - }, - { - "name": "Mattfeld, Aaron" - }, - { - "name": "Noel, Maxime" - }, { "affiliation": "University of Amsterdam", "name": "Lukas Snoek", @@ -521,9 +518,18 @@ "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany", "name": "Weninger, Leon" }, + { + "name": "Marina, Ana" + }, + { + "name": "Mattfeld, Aaron" + }, { "name": "Matsubara, K" }, + { + "name": "Noel, Maxime" + }, { "name": "Cheung, Brian" }, @@ -570,6 +576,9 @@ { "name": "Weinstein, Alejandro" }, + { + "name": "Tambini, Arielle" + }, { "affiliation": "Duke University", "name": "Broderick, William", @@ -611,9 +620,6 @@ { "name": "Tarbert, Claire" }, - { - "name": "Tambini, Arielle" - }, { "name": "Nickson, Thomas" }, @@ -679,9 +685,6 @@ "name": "Pellman, John", "orcid": "0000-0001-6810-4461" }, - { - "name": "Perez-Guevara, Martin" - }, { "name": "Khanuja, Ranjeet" }, diff --git a/tools/update_zenodo.py b/tools/update_zenodo.py index 163f88084d..5617772d75 100755 --- a/tools/update_zenodo.py +++ b/tools/update_zenodo.py @@ -46,7 +46,6 @@ {"affiliation": "Child Mind Institute / Nathan Kline Institute", "name": "Pellman, John", "orcid": "0000-0001-6810-4461"}, - {"name": "Perez-Guevara, Martin"}, {"name": "Khanuja, Ranjeet"}, {"affiliation": "Medical Imaging & Biomarkers, Bioclinica, Newark, CA, USA.", From 64455007be98bf6b544899bf78c769b8c7889227 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 18 Sep 2019 16:26:01 -0400 Subject: [PATCH 03/10] MNT: Simplify mailmap --- .mailmap | 357 +++++++++++++++++++++++++------------------------------ 1 file changed, 163 insertions(+), 194 deletions(-) diff --git a/.mailmap b/.mailmap index 9f2b618d78..2a1480a874 100644 --- a/.mailmap +++ b/.mailmap @@ -1,199 +1,168 @@ +Aimi Watanabe Aimi Watanabe stymy -Aimi Watanabe stymy -Alejandro Tabas qTabs -Alejandro Tabas qtabs -Alejandro de la Vega adelavega -Alejandro de la Vega delavega4 -Alexander Schaefer Alexander Schaefer -Alexander Schaefer alexschaefer83 -Alexander Schaefer aschaefer -Alexandre M. Savio Alexandre M. S -Alexandre M. Savio Alexandre M. S -Alexandre M. Savio Alexandre Manhaes Savio -Andrew Floren afloren -Andrey Chetverikov Andrey Chetverikov -Andrey Chetverikov achetverikov -Anibal Sólon Heinsfeld anibalsolon -Anisha Keshavan Anisha Keshavan -Anisha Keshavan akeshavan -Ariel Rokem Ariel Rokem -Ariel Rokem arokem -Ariel Rokem arokem -Arman Eshaghi armaneshaghi -Ashely Gillman Ashley Gillman -Ashely Gillman ashgillman -Basille Pinsard bpinsard -Basille Pinsard bpinsard -Ben Cipollini Ben Cipollini -Benjamin Acland Ben Acland -Benjamin Meyers <34044274+BenjaminMey@users.noreply.github.com> BenjaminMey <34044274+BenjaminMey@users.noreply.github.com> -Benjamin Yvernault Benjamin Yvernault -Benjamin Yvernault byvernault -Blake Dewey Blake Dewey -Blake Dewey blakedewey -Blake Dewey blakedewey -Brendan Moloney moloney -Caroline Froehlich carolFrohlich -Christopher J. Markiewicz Chris Markiewicz -Christopher J. Markiewicz Chris Markiewicz -Christopher J. Markiewicz Christopher J. Johnson -Christopher J. Markiewicz Christopher J. Markiewicz -Christopher J. Markiewicz Christopher J. Markiewicz -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 Mordom dmordom -David Welch David Welch -Dimitri Papadopoulos Orfanos Dimitri Papadopoulos -Dmytro belevtsoff -Dylan M. Nielson Dylan -Dylan M. Nielson Dylan Nielson -Eduard Ort eort -Elizabeth DuPre emdupre -Erik Ziegler Erik -Erik Ziegler Erik Ziegler -Erik Ziegler erik -Erik Ziegler erikz -Erik Ziegler swederik -Feilong Ma Ma Feilong -Fernando Pérez-García Fernando -Franz Liem fliem -Franz Liem fliem -Fred Loney FredLoney -Gael Varoquaux GaelVaroquaux -Gael Varoquaux GaelVaroquaux -Gavin Cooper gjcooper -Gilles de Hollander Gilles86 -Gio Piantoni Gio at UMCU -Guillaume Flandin Guillaume -Hans Johnson Hans Johnson -Hans Johnson hjmjohnson -Horea Christian Horea Christian -Isaac Schwabacher ischwabacher -Jakub Kaczmarzyk jakubk -Jakub Kaczmarzyk kaczmarj -James Kent jdkent -Janosch Linkersdörfer Januzz -Jason Wong Jason -Jason Wong Jason W -Jason Wong Jason W -Jason Wong jason -Jason Wong jason-wg -Jens Kleesiek JensNRAD -Jessica Forbes jessicaforbes -Jérémy Guillon GUILLON Jeremy -Joerg Stadler Joerg Stadler -Joerg Stadler Joerg Stadler -Joerg Stadler Jörg Stadler -John A. Lee john anthony lee -John A. Lee leej3 -Joke Durnez jokedurnez -Josh Warner JDWarner -Josh Warner Josh Warner (Mac) -Kai Schlamp medihack -Katherine Bottenhorn 62442katieb -Katherine Bottenhorn Katie Bottenhorn -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 -Kornelius Podranski Kornelius -Krzysztof J. Gorgolewski Chris Filo Gorgolewski -Krzysztof J. Gorgolewski Chris Filo Gorgolewski -Krzysztof J. Gorgolewski Chris Filo Gorgolewski -Krzysztof J. Gorgolewski Chris Filo Gorgolewski -Krzysztof J. Gorgolewski Chris Gorgolewski -Krzysztof J. Gorgolewski Krzysztof Gorgolewski -Krzysztof J. Gorgolewski filo -Krzysztof J. Gorgolewski filo -Krzysztof J. Gorgolewski filo -Krzysztof J. Gorgolewski filo -Kshitij Chawla Kshitij Chawla (kchawla-pi) -Leonie Lampe Leonie Lmape -Lukas Snoek Lukas Snoek -Marcel Falkiewicz Marcel Falkiewicz +Alejandro Tabas +Alejandro Tabas +Alejandro de la Vega +Alejandro de la Vega +Alexander Schaefer +Alexander Schaefer +Alexander Schaefer +Alexandre M. Savio +Alexandre M. Savio +Andrew Floren +Andrey Chetverikov +Andrey Chetverikov +Anibal Sólon Heinsfeld +Anisha Keshavan +Anisha Keshavan +Ariel Rokem +Ariel Rokem +Arman Eshaghi +Ashely Gillman +Basille Pinsard +Basille Pinsard +Ben Cipollini +Benjamin Acland +Benjamin Meyers <34044274+BenjaminMey@users.noreply.github.com> +Benjamin Yvernault +Benjamin Yvernault +Blake Dewey +Blake Dewey +Blake Dewey +Brendan Moloney +Caroline Froehlich +Christopher J. Markiewicz +Christopher J. Markiewicz +Christopher J. Markiewicz +Cindee Madison +Colin Buchanan +Colin Buchanan +Daniel Brenner +Daniel Clark +Daniel Geisler +Daniel Ginsburg +Daniel McNamee +David Ellis +David Ellis +David Mordom +David Welch +Dimitri Papadopoulos Orfanos +Dmytro Belevtsoff +Dylan M. Nielson +Dylan M. Nielson +Eduard Ort +Elizabeth DuPre +Erik Ziegler +Erik Ziegler +Erik Ziegler +Feilong Ma +Fernando Pérez-García +Franz Liem +Franz Liem +Fred Loney +Gael Varoquaux +Gavin Cooper +Gilles de Hollander +Gio Piantoni +Guillaume Flandin +Hans Johnson +Horea Christian +Isaac Schwabacher +Jakub Kaczmarzyk +James Kent +Janosch Linkersdörfer +Jason Wong +Jason Wong +Jens Kleesiek +Jessica Forbes +Jérémy Guillon +Joerg Stadler +Joerg Stadler +Joerg Stadler +John A. Lee +Joke Durnez +Josh Warner +Kai Schlamp +Katherine Bottenhorn +Kesshi Jordan +Kesshi Jordan +Kesshi Jordan +Kesshi Jordan +Kesshi Jordan +Kesshi Jordan +Kevin Sitek +Kevin Sitek +Kornelius Podranski +Krzysztof J. Gorgolewski +Krzysztof J. Gorgolewski +Krzysztof J. Gorgolewski +Krzysztof J. Gorgolewski +Krzysztof J. Gorgolewski +Krzysztof J. Gorgolewski +Krzysztof J. Gorgolewski +Kshitij Chawla +Leonie Lampe +Lukas Snoek +Marcel Falkiewicz Martin Perez-Guevara -Mathias Goncalves Mathias Goncalves -Mathias Goncalves mathiasg -Mathieu Dubois Mathieu Dubois -Mathieu Dubois duboism -Matteo Mancini matteomancini -Matteo Visconti di Oleggio Castello Matteo Visconti dOC -Matteo Visconti di Oleggio Castello Matteo Visconti dOC -Matteo Visconti di Oleggio Castello mvdoc -Matthew Cieslak Matt Cieslak -Michael Clark Clark -Michael Dayan Michael -Michael Dayan Michael +Mathias Goncalves +Mathieu Dubois +Mathieu Dubois +Matteo Mancini +Matteo Visconti di Oleggio Castello +Matteo Visconti di Oleggio Castello +Matthew Cieslak +Michael Clark +Michael Dayan +Michael Dayan Michael Dayan mick-d -Michael Dayan Michael -Michael Joseph mjoseph -Michael Joseph Michael Joseph -Michael Philipp Notter Michael Notter -Michael Philipp Notter miykael -Michael Waskom Michael Waskom -Michael Waskom Michael Waskom -Michael Waskom Michael Waskom -Michael Waskom mwaskom -Michael Waskom mwaskom -Michael Waskom mwaskom -Miguel Molina-Romero Miguel Molina -Murat Bilgel Murat Bilgel -Oliver Contier oliver-contier +Michael Dayan +Michael Joseph +Michael Philipp Notter +Michael Philipp Notter +Michael Waskom +Michael Waskom +Michael Waskom +Miguel Molina-Romero +Murat Bilgel +Oliver Contier Olivia Stanley -Oscar Esteban Oscar Esteban -Oscar Esteban oesteban -Pablo Polosecki pipolose -Pablo Polosecki pipolose -Paul Sharp psharp1289 -Ranjit Khanuja RanjitK -Rastko Ćirić rciric -Rastko Ćirić Rastko Ćirić -Rastko Ćirić rciric -Ross Markello Ross Markello -Russell Poldrack Russ Poldrack -Russell Poldrack poldrack -Salma Bougacha Salma BOUGACHA -Salma Bougacha salma -Salma Bougacha salma1601 -Sami Kristian Andberg Sami Andberg -Satrajit Ghosh Satrajit Ghosh -Sebastian Urchs sebastian -Serge Koudoro skoudoro -Sharad Sikka ssikka -Shariq Iqbal shariqiqbal2810 -Shariq Iqbal shariqiqbal2810 +Oscar Esteban +Oscar Esteban +Pablo Polosecki +Pablo Polosecki +Paul Sharp +Ranjit Khanuja +Rastko Ćirić +Rastko Ćirić +Rastko Ćirić +Ross Markello +Russell Poldrack +Russell Poldrack +Salma Bougacha +Sami Kristian Andberg +Satrajit Ghosh +Sebastian Urchs +Serge Koudoro +Sharad Sikka +Shariq Iqbal +Shariq Iqbal Shoshana Berleant Shoshana Berleant -Shoshana Berleant Shoshana Berleant -Simon Rothmei Simon R -Simon Rothmei Simon Rothmeier -Siqi Liu siqi liu -Siqi Liu sql -Steven Giavasis Steven Giavasis -Steven Giavasis sgiavasis -Steven Giavasis sgiavasis -Steven Tilley Steven Tilley -Tristan Glatard Tristan Glatard -Victor Férat Victor -Victor Férat Victor Ferat -Victor Férat Victor Férat -Victor Saase vsaase -Weijie Huang forwho -William Triplett William Triplett -Wolfgang Pauli Wolfgang Pauli -Xiangzhen Kong bnucon -Yaroslav Halchenko Yaroslav Halchenko +Shoshana Berleant +Simon Rothmei +Simon Rothmei +Siqi Liu +Steven Giavasis +Steven Giavasis +Steven Giavasis +Steven Tilley +Tristan Glatard +Victor Férat +Victor Férat +Victor Férat +Victor Saase +Weijie Huang +William Triplett +Wolfgang Pauli +Xiangzhen Kong +Yaroslav Halchenko From dca1a0381fe67aef0433e1a75d5fdff6ffa55154 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 18 Sep 2019 21:28:03 -0400 Subject: [PATCH 04/10] MNT: Version 1.2.3 --- doc/conf.py | 2 +- nipype/info.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index bdf938a70c..10ac3c36db 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 = "1.2.2" +release = "1.2.3" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/nipype/info.py b/nipype/info.py index deec53aee5..dcdbfa593e 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -9,7 +9,7 @@ # nipype version information # Remove -dev for release -__version__ = '1.2.3-dev' +__version__ = '1.2.3' def get_nipype_gitversion(): From bf0a965368e66fec387643a3a245c0ce3cf62e21 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 18 Sep 2019 21:34:28 -0400 Subject: [PATCH 05/10] MNT: Request rerender on initial feedstock update --- tools/feedstock.sh | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tools/feedstock.sh b/tools/feedstock.sh index b34aae2c8b..b37dba8671 100755 --- a/tools/feedstock.sh +++ b/tools/feedstock.sh @@ -108,6 +108,10 @@ Updating feedstock to release branch * URL = https://github.com/$SRCREPO/archive/$REF.tar.gz * SHA256 = \`$SHA256\` + +--- + +@conda-forge-admin, please rerender. END fi From c15bd757c2c37090f5f3e4343d7a0891952799e0 Mon Sep 17 00:00:00 2001 From: Sin Kim Date: Thu, 19 Sep 2019 12:25:21 +0900 Subject: [PATCH 06/10] MNT: Add Kim, Sin to .zenodo.json --- .mailmap | 1 + .zenodo.json | 5 +++++ 2 files changed, 6 insertions(+) diff --git a/.mailmap b/.mailmap index 2a1480a874..380d937cb2 100644 --- a/.mailmap +++ b/.mailmap @@ -92,6 +92,7 @@ Kesshi Jordan Kevin Sitek Kevin Sitek +Kim, Sin Kornelius Podranski Krzysztof J. Gorgolewski Krzysztof J. Gorgolewski diff --git a/.zenodo.json b/.zenodo.json index 668974fd2d..259b53e926 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -408,6 +408,11 @@ "affiliation": "The University of Sydney", "name": "Liu, Siqi" }, + { + "affiliation": "Korea Advanced Institute of Science and Technology", + "name": "Kim, Sin", + "orcid": "0000-0003-4652-3758" + }, { "affiliation": "Leibniz Institute for Neurobiology", "name": "Stadler, J\u00f6rg", From f930a40762b8e907e3dd5244e254e77c1798bb86 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Thu, 19 Sep 2019 10:59:16 -0400 Subject: [PATCH 07/10] MNT: Add Junhao WEN to .zenodo.json --- .mailmap | 1 + .zenodo.json | 5 +++++ 2 files changed, 6 insertions(+) diff --git a/.mailmap b/.mailmap index 380d937cb2..ced66b4099 100644 --- a/.mailmap +++ b/.mailmap @@ -82,6 +82,7 @@ Joerg Stadler John A. Lee Joke Durnez Josh Warner +Junhao WEN Kai Schlamp Katherine Bottenhorn Kesshi Jordan diff --git a/.zenodo.json b/.zenodo.json index 259b53e926..fba3546a77 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -535,6 +535,11 @@ { "name": "Noel, Maxime" }, + { + "affiliation": "University of Pennsylvania", + "name": "Junhao WEN", + "orcid": "0000-0003-2077-3070" + }, { "name": "Cheung, Brian" }, From eb12503fea3f38a06e14c108522c80e61109436e Mon Sep 17 00:00:00 2001 From: oesteban Date: Fri, 20 Sep 2019 12:12:47 -0700 Subject: [PATCH 08/10] MAINT: Revision of Zenodo update script Unlocks first position as per private conversation with @chrisgorgo --- tools/update_zenodo.py | 109 +++++++++++++++++++++-------------------- 1 file changed, 56 insertions(+), 53 deletions(-) diff --git a/tools/update_zenodo.py b/tools/update_zenodo.py index 163f88084d..7600c0b94d 100755 --- a/tools/update_zenodo.py +++ b/tools/update_zenodo.py @@ -1,46 +1,15 @@ #!/usr/bin/env python3 +"""Update and sort the creators list of the zenodo record.""" +import sys +import shutil +from pathlib import Path import json from fuzzywuzzy import fuzz, process -import shutil -import os import subprocess as sp -if os.path.exists('line-contributions.txt'): - with open('line-contributions.txt', 'rt') as fp: - lines = fp.readlines() -else: - if shutil.which('git-line-summary'): - print("Running git-line-summary on nipype repo") - lines = sp.check_output(['git-line-summary']).decode().split('\n') - else: - raise RuntimeError("Install Git Extras to view git contributors") - -data = [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line] - -# load zenodo from master -with open('.zenodo.json', 'rt') as fp: - zenodo = json.load(fp) -zen_names = [' '.join(val['name'].split(',')[::-1]).strip() - for val in zenodo['creators']] - -name_matches = [] - -for ele in data: - matches = process.extract(ele, zen_names, scorer=fuzz.token_sort_ratio, - limit=2) - # matches is a list [('First match', % Match), ('Second match', % Match)] - if matches[0][1] > 80: - val = zenodo['creators'][zen_names.index(matches[0][0])] - else: - # skip unmatched names - print("No entry to sort:", ele) - continue - - if val not in name_matches: - name_matches.append(val) - +CREATORS_LAST_ORCID = '0000-0002-5312-6729' # This ORCID should go last # for entries not found in line-contributions -missing_entries = [ +MISSING_ENTRIES = [ {"name": "Varada, Jan"}, {"name": "Schwabacher, Isaac"}, {"affiliation": "Child Mind Institute / Nathan Kline Institute", @@ -61,31 +30,65 @@ {"name": "Lai, Jeff"} ] -for entry in missing_entries: - name_matches.append(entry) - def fix_position(creators): + """Place Satra last.""" # position first / last authors - f_authr = None l_authr = None - for i, info in enumerate(creators): - if info['name'] == 'Gorgolewski, Krzysztof J.': - f_authr = i - if info['name'] == 'Ghosh, Satrajit': - l_authr = i + for info in creators: + if 'orcid' in info and info['orcid'] == CREATORS_LAST_ORCID: + l_authr = info - if f_authr is None or l_authr is None: + if l_authr is None: raise AttributeError('Missing important people') - creators.insert(0, creators.pop(f_authr)) - creators.insert(len(creators), creators.pop(l_authr + 1)) + creators.remove(l_authr) + creators.append(l_authr) return creators -zenodo['creators'] = fix_position(name_matches) +if __name__ == '__main__': + contrib_file = Path('line-contributors.txt') + lines = [] + if contrib_file.exists(): + print('WARNING: Reusing existing line-contributors.txt file.', file=sys.stderr) + lines = contrib_file.read_text().splitlines() -with open('.zenodo.json', 'wt') as fp: - json.dump(zenodo, fp, indent=2, sort_keys=True) - fp.write('\n') + if not lines and shutil.which('git-line-summary'): + print("Running git-line-summary on nipype repo") + lines = sp.check_output(['git-line-summary']).decode().splitlines() + contrib_file.write_text('\n'.join(lines)) + + if not lines: + raise RuntimeError('Could not find line-contributors from git repository ' + '(hint: please install git-extras).') + + data = [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line] + + # load zenodo from master + zenodo_file = Path('.zenodo.json') + zenodo = json.loads(zenodo_file.read_text()) + zen_names = [' '.join(val['name'].split(',')[::-1]).strip() + for val in zenodo['creators']] + + name_matches = [] + for ele in data: + matches = process.extract(ele, zen_names, scorer=fuzz.token_sort_ratio, + limit=2) + # matches is a list [('First match', % Match), ('Second match', % Match)] + if matches[0][1] > 80: + val = zenodo['creators'][zen_names.index(matches[0][0])] + else: + # skip unmatched names + print("No entry to sort:", ele) + continue + + if val not in name_matches: + name_matches.append(val) + + for entry in MISSING_ENTRIES: + name_matches.append(entry) + + zenodo['creators'] = fix_position(name_matches) + zenodo_file.write_text(json.dumps(zenodo, indent=2, sort_keys=True)) From eeeb6509b768bdabaafdb6b61d77b0284dc8c09a Mon Sep 17 00:00:00 2001 From: oesteban Date: Fri, 20 Sep 2019 12:55:31 -0700 Subject: [PATCH 09/10] fix: pin Chris G. to second-last author of the creators list [skip ci] --- tools/update_zenodo.py | 52 ++++++++++++++++++++---------------------- 1 file changed, 25 insertions(+), 27 deletions(-) diff --git a/tools/update_zenodo.py b/tools/update_zenodo.py index 7600c0b94d..2784044b4e 100755 --- a/tools/update_zenodo.py +++ b/tools/update_zenodo.py @@ -7,7 +7,8 @@ from fuzzywuzzy import fuzz, process import subprocess as sp -CREATORS_LAST_ORCID = '0000-0002-5312-6729' # This ORCID should go last +# These ORCIDs should go last +CREATORS_LAST = ['Gorgolewski, Krzysztof J.', 'Ghosh, Satrajit'] # for entries not found in line-contributions MISSING_ENTRIES = [ {"name": "Varada, Jan"}, @@ -30,24 +31,6 @@ {"name": "Lai, Jeff"} ] - -def fix_position(creators): - """Place Satra last.""" - # position first / last authors - l_authr = None - - for info in creators: - if 'orcid' in info and info['orcid'] == CREATORS_LAST_ORCID: - l_authr = info - - if l_authr is None: - raise AttributeError('Missing important people') - - creators.remove(l_authr) - creators.append(l_authr) - return creators - - if __name__ == '__main__': contrib_file = Path('line-contributors.txt') lines = [] @@ -55,14 +38,16 @@ def fix_position(creators): print('WARNING: Reusing existing line-contributors.txt file.', file=sys.stderr) lines = contrib_file.read_text().splitlines() - if not lines and shutil.which('git-line-summary'): + git_line_summary_path = shutil.which('git-line-summary') + if not lines and git_line_summary_path: print("Running git-line-summary on nipype repo") - lines = sp.check_output(['git-line-summary']).decode().splitlines() + lines = sp.check_output([git_line_summary_path]).decode().splitlines() contrib_file.write_text('\n'.join(lines)) if not lines: - raise RuntimeError('Could not find line-contributors from git repository ' - '(hint: please install git-extras).') + raise RuntimeError("""\ +Could not find line-contributors from git repository.%s""" % """ \ +git-line-summary not found, please install git-extras. """ * (git_line_summary_path is None)) data = [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line] @@ -71,8 +56,10 @@ def fix_position(creators): zenodo = json.loads(zenodo_file.read_text()) zen_names = [' '.join(val['name'].split(',')[::-1]).strip() for val in zenodo['creators']] + total_names = len(zen_names) + len(MISSING_ENTRIES) name_matches = [] + position = 1 for ele in data: matches = process.extract(ele, zen_names, scorer=fuzz.token_sort_ratio, limit=2) @@ -85,10 +72,21 @@ def fix_position(creators): continue if val not in name_matches: + if val['name'] not in CREATORS_LAST: + val['position'] = position + position += 1 + else: + val['position'] = total_names + CREATORS_LAST.index(val['name']) name_matches.append(val) - for entry in MISSING_ENTRIES: - name_matches.append(entry) + for missing in MISSING_ENTRIES: + missing['position'] = position + position += 1 + name_matches.append(missing) + + zenodo['creators'] = sorted(name_matches, key=lambda k: k['position']) + # Remove position + for creator in zenodo['creators']: + del creator['position'] - zenodo['creators'] = fix_position(name_matches) - zenodo_file.write_text(json.dumps(zenodo, indent=2, sort_keys=True)) + zenodo_file.write_text('%s\n' % json.dumps(zenodo, indent=2, sort_keys=True)) From dd38a83f2b6542161d1f250e0ced975fa382f326 Mon Sep 17 00:00:00 2001 From: oesteban Date: Fri, 20 Sep 2019 15:25:00 -0700 Subject: [PATCH 10/10] rel(1.2.3): update ``.zenodo.json`` testing the new update script closes #3043 --- .zenodo.json | 63 +++++++++++++++++++++++++--------------------------- 1 file changed, 30 insertions(+), 33 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index fba3546a77..ac9972984b 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -1,10 +1,5 @@ { "creators": [ - { - "affiliation": "Department of Psychology, Stanford University", - "name": "Gorgolewski, Krzysztof J.", - "orcid": "0000-0003-3321-7583" - }, { "affiliation": "Department of Psychology, Stanford University", "name": "Esteban, Oscar", @@ -78,10 +73,6 @@ "affiliation": "Shattuck Lab, UCLA Brain Mapping Center", "name": "Wong, Jason" }, - { - "affiliation": "Concordia University", - "name": "Benderoff, Erin" - }, { "name": "Modat, Marc" }, @@ -150,6 +141,10 @@ { "name": "Berleant, Shoshana" }, + { + "affiliation": "Concordia University", + "name": "Benderoff, Erin" + }, { "affiliation": "Dartmouth College: Hanover, NH, United States", "name": "Halchenko, Yaroslav O.", @@ -352,14 +347,14 @@ "affiliation": "UniversityHospital Heidelberg, Germany", "name": "Kleesiek, Jens" }, - { - "name": "Erickson, Drew" - }, { "affiliation": "NIMH IRP", "name": "Lee, John A.", "orcid": "0000-0001-5884-4247" }, + { + "name": "Erickson, Drew" + }, { "affiliation": "Child Mind Institute", "name": "Giavasis, Steven" @@ -384,9 +379,6 @@ { "name": "Millman, Jarrod" }, - { - "name": "Lai, Jeff" - }, { "name": "Zhou, Dale" }, @@ -409,9 +401,9 @@ "name": "Liu, Siqi" }, { - "affiliation": "Korea Advanced Institute of Science and Technology", - "name": "Kim, Sin", - "orcid": "0000-0003-4652-3758" + "affiliation": "University of Pennsylvania", + "name": "Kahn, Ari E.", + "orcid": "0000-0002-2127-0507" }, { "affiliation": "Leibniz Institute for Neurobiology", @@ -419,9 +411,9 @@ "orcid": "0000-0003-4313-129X" }, { - "affiliation": "University of Pennsylvania", - "name": "Kahn, Ari E.", - "orcid": "0000-0002-2127-0507" + "affiliation": "Korea Advanced Institute of Science and Technology", + "name": "Kim, Sin", + "orcid": "0000-0003-4652-3758" }, { "affiliation": "University College London", @@ -515,25 +507,25 @@ "name": "Perkins, L. Nathan" }, { - "affiliation": "University of Amsterdam", - "name": "Lukas Snoek", - "orcid": "0000-0001-8972-204X" + "name": "Marina, Ana" }, { - "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany", - "name": "Weninger, Leon" + "name": "Mattfeld, Aaron" }, { - "name": "Marina, Ana" + "name": "Noel, Maxime" }, { - "name": "Mattfeld, Aaron" + "affiliation": "University of Amsterdam", + "name": "Lukas Snoek", + "orcid": "0000-0001-8972-204X" }, { - "name": "Matsubara, K" + "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany", + "name": "Weninger, Leon" }, { - "name": "Noel, Maxime" + "name": "Matsubara, K" }, { "affiliation": "University of Pennsylvania", @@ -586,9 +578,6 @@ { "name": "Weinstein, Alejandro" }, - { - "name": "Tambini, Arielle" - }, { "affiliation": "Duke University", "name": "Broderick, William", @@ -630,6 +619,9 @@ { "name": "Tarbert, Claire" }, + { + "name": "Tambini, Arielle" + }, { "name": "Nickson, Thomas" }, @@ -714,6 +706,11 @@ { "name": "Lai, Jeff" }, + { + "affiliation": "Department of Psychology, Stanford University", + "name": "Gorgolewski, Krzysztof J.", + "orcid": "0000-0003-3321-7583" + }, { "affiliation": "MIT, HMS", "name": "Ghosh, Satrajit",