Skip to content

Commit a1997f3

Browse files
committed
Merge remote-tracking branch 'upstream/master' into tran
2 parents fa40394 + dcc013b commit a1997f3

File tree

113 files changed

+1891
-3479
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

113 files changed

+1891
-3479
lines changed

.circleci/config.yml

+11-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
_machine_kwds: &machine_kwds
2-
image: circleci/classic:201710-02
2+
image: circleci/classic:201808-01
33

44
_store_artifacts_kwds: &store_artifacts_kwds
55
path: /home/circleci/work/tests
@@ -356,6 +356,16 @@ jobs:
356356
pip install dist/nipype-*-py2.py3-none-any.whl
357357
# Futures should not install in Python 3
358358
test $(pip show futures 2>/dev/null | wc -l) = "0"
359+
- run:
360+
name: Validate Python 3.7 installation
361+
command: |
362+
pyenv local 3.7.0
363+
pip install --upgrade pip
364+
# Pre-install a version of numpy that will not pass
365+
pip install numpy==1.15.0
366+
pip install dist/nipype-*-py2.py3-none-any.whl
367+
# Numpy should be upgraded to >= 1.15.3
368+
test "$(pip show numpy | grep Version)" \> "Version: 1.15.2"
359369
- store_artifacts:
360370
path: /home/circleci/nipype/dist
361371

.zenodo.json

+72-70
Original file line numberDiff line numberDiff line change
@@ -74,47 +74,47 @@
7474
"affiliation": "Department of Psychology, Stanford University",
7575
"name": "Waskom, Michael"
7676
},
77-
{
78-
"affiliation": "Developer",
79-
"name": "Clark, Daniel",
80-
"orcid": "0000-0002-8121-8954"
81-
},
8277
{
8378
"affiliation": "Shattuck Lab, UCLA Brain Mapping Center",
8479
"name": "Wong, Jason"
8580
},
8681
{
87-
"name": "Loney, Fred"
82+
"name": "Modat, Marc"
8883
},
8984
{
90-
"name": "Modat, Marc"
85+
"name": "Loney, Fred"
9186
},
9287
{
93-
"affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University",
94-
"name": "Dewey, Blake E",
95-
"orcid": "0000-0003-4554-5058"
88+
"affiliation": "Developer",
89+
"name": "Clark, Daniel",
90+
"orcid": "0000-0002-8121-8954"
9691
},
9792
{
9893
"affiliation": "National Institute of Mental Health",
9994
"name": "Nielson, Dylan M.",
10095
"orcid": "0000-0003-4613-6643"
10196
},
97+
{
98+
"affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University",
99+
"name": "Dewey, Blake E",
100+
"orcid": "0000-0003-4554-5058"
101+
},
102102
{
103103
"name": "Madison, Cindee"
104104
},
105105
{
106106
"affiliation": "Molecular Imaging Research Center, CEA, France",
107107
"name": "Bougacha, Salma"
108108
},
109+
{
110+
"affiliation": "National Institutes of Health",
111+
"name": "Clark, Michael G. "
112+
},
109113
{
110114
"affiliation": "Dartmouth College",
111115
"name": "Visconti di Oleggio Castello, Matteo",
112116
"orcid": "0000-0001-7931-5272"
113117
},
114-
{
115-
"affiliation": "National Institutes of Health",
116-
"name": "Clark, Michael G. "
117-
},
118118
{
119119
"affiliation": "Mayo Clinic, Neurology, Rochester, MN, USA",
120120
"name": "Dayan, Michael",
@@ -141,16 +141,6 @@
141141
{
142142
"name": "Berleant, Shoshana"
143143
},
144-
{
145-
"affiliation": "MIT",
146-
"name": "Kaczmarzyk, Jakub",
147-
"orcid": "0000-0002-5544-7577"
148-
},
149-
{
150-
"affiliation": "INRIA",
151-
"name": "Varoquaux, Gael",
152-
"orcid": "0000-0003-1076-5122"
153-
},
154144
{
155145
"affiliation": "UC San Diego",
156146
"name": "Cipollini, Ben",
@@ -176,9 +166,24 @@
176166
"name": "DuPre, Elizabeth",
177167
"orcid": "0000-0003-1358-196X"
178168
},
169+
{
170+
"affiliation": "MIT",
171+
"name": "Kaczmarzyk, Jakub",
172+
"orcid": "0000-0002-5544-7577"
173+
},
179174
{
180175
"name": "Moloney, Brendan"
181176
},
177+
{
178+
"affiliation": "INRIA",
179+
"name": "Varoquaux, Gael",
180+
"orcid": "0000-0003-1076-5122"
181+
},
182+
{
183+
"affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
184+
"name": "Horea, Christian",
185+
"orcid": "0000-0001-7037-2449"
186+
},
182187
{
183188
"affiliation": "Athena EPI, Inria Sophia-Antipolis",
184189
"name": "Wassermann , Demian",
@@ -189,24 +194,19 @@
189194
"name": "Hanke, Michael",
190195
"orcid": "0000-0001-6398-6370"
191196
},
192-
{
193-
"affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
194-
"name": "Horea, Christian",
195-
"orcid": "0000-0001-7037-2449"
196-
},
197197
{
198198
"affiliation": "Vrije Universiteit, Amsterdam",
199199
"name": "Gilles de Hollander",
200200
"orcid": "0000-0003-1988-5091"
201201
},
202+
{
203+
"name": "Mordom, David"
204+
},
202205
{
203206
"affiliation": "Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation; University of Queensland",
204207
"name": "Gillman, Ashley",
205208
"orcid": "0000-0001-9130-1092"
206209
},
207-
{
208-
"name": "Mordom, David"
209-
},
210210
{
211211
"name": "Buchanan, Colin"
212212
},
@@ -218,11 +218,6 @@
218218
"name": "Pauli, Wolfgang M.",
219219
"orcid": "0000-0002-0966-0254"
220220
},
221-
{
222-
"affiliation": "Duke University",
223-
"name": "Iqbal, Shariq",
224-
"orcid": "0000-0003-2766-8425"
225-
},
226221
{
227222
"affiliation": "Nathan s Kline institute for psychiatric research",
228223
"name": "Sikka, Sharad"
@@ -235,6 +230,11 @@
235230
{
236231
"name": "Forbes, Jessica"
237232
},
233+
{
234+
"affiliation": "Duke University",
235+
"name": "Iqbal, Shariq",
236+
"orcid": "0000-0003-2766-8425"
237+
},
238238
{
239239
"name": "Schwartz, Yannick"
240240
},
@@ -268,11 +268,6 @@
268268
{
269269
"name": "Cumba, Chad"
270270
},
271-
{
272-
"affiliation": "Harvard University - Psychology",
273-
"name": "Kastman, Erik",
274-
"orcid": "0000-0001-7221-9042"
275-
},
276271
{
277272
"affiliation": "SRI International",
278273
"name": "Nichols, B. Nolan",
@@ -291,14 +286,20 @@
291286
"name": "Schaefer, Alexander",
292287
"orcid": "0000-0001-6488-4739"
293288
},
289+
{
290+
"affiliation": "Harvard University - Psychology",
291+
"name": "Kastman, Erik",
292+
"orcid": "0000-0001-7221-9042"
293+
},
294294
{
295295
"affiliation": "Washington University in St Louis",
296296
"name": "Acland, Benjamin",
297297
"orcid": "0000-0001-6392-6634"
298298
},
299299
{
300-
"affiliation": "Child Mind Institute",
301-
"name": "Giavasis, Steven"
300+
"affiliation": "University of Zurich",
301+
"name": "Liem, Franz",
302+
"orcid": "0000-0003-0646-4810"
302303
},
303304
{
304305
"affiliation": "UniversityHospital Heidelberg, Germany",
@@ -308,10 +309,8 @@
308309
"name": "Erickson, Drew"
309310
},
310311
{
311-
"name": "K\u00fcttner, Ren\u00e9"
312-
},
313-
{
314-
"name": "Haselgrove, Christian"
312+
"affiliation": "Child Mind Institute",
313+
"name": "Giavasis, Steven"
315314
},
316315
{
317316
"name": "Correa, Carlos"
@@ -320,9 +319,7 @@
320319
"name": "Ghayoor, Ali"
321320
},
322321
{
323-
"affiliation": "University of Zurich",
324-
"name": "Liem, Franz",
325-
"orcid": "0000-0003-0646-4810"
322+
"name": "K\u00fcttner, Ren\u00e9"
326323
},
327324
{
328325
"name": "Millman, Jarrod"
@@ -336,6 +333,9 @@
336333
{
337334
"name": "Blair, Ross"
338335
},
336+
{
337+
"name": "Haselgrove, Christian"
338+
},
339339
{
340340
"affiliation": "1 McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montr\u00e9al, 3801 University Street, WB-208, H3A 2B4, Qu\u00e9bec, Canada. 2 University of Lyon, CNRS, INSERM, CREATIS., Villeurbanne, 7, avenue Jean Capelle, 69621, France.",
341341
"name": "Glatard, Tristan",
@@ -386,8 +386,9 @@
386386
"orcid": "0000-0003-2767-6310"
387387
},
388388
{
389-
"affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
390-
"name": "Weninger, Leon"
389+
"affiliation": "GIGA Institute",
390+
"name": "Grignard, Martin",
391+
"orcid": "0000-0001-5549-1861"
391392
},
392393
{
393394
"name": "Salvatore, John"
@@ -403,9 +404,6 @@
403404
"name": "Craddock, R. Cameron",
404405
"orcid": "0000-0002-4950-1303"
405406
},
406-
{
407-
"name": "Inati, Souheil"
408-
},
409407
{
410408
"name": "Hinds, Oliver"
411409
},
@@ -414,6 +412,13 @@
414412
"name": "Cooper, Gavin",
415413
"orcid": "0000-0002-7186-5293"
416414
},
415+
{
416+
"affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
417+
"name": "Weninger, Leon"
418+
},
419+
{
420+
"name": "Inati, Souheil"
421+
},
417422
{
418423
"affiliation": "Boston University",
419424
"name": "Perkins, L. Nathan"
@@ -443,9 +448,6 @@
443448
"name": "Floren, Andrew",
444449
"orcid": "0000-0003-3618-2056"
445450
},
446-
{
447-
"name": "Rothmei, Simon"
448-
},
449451
{
450452
"name": "Urchs, Sebastian"
451453
},
@@ -454,17 +456,16 @@
454456
"name": "Durnez, Joke",
455457
"orcid": "0000-0001-9030-2202"
456458
},
457-
{
458-
"name": "Mertz, Fred"
459-
},
460-
{
461-
"name": "Haehn, Daniel"
462-
},
463459
{
464460
"affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry",
465461
"name": "Geisler, Daniel",
466462
"orcid": "0000-0003-2076-5329"
467463
},
464+
{
465+
"affiliation": "University of Texas at Austin",
466+
"name": "De La Vega, Alejandro",
467+
"orcid": "0000-0001-9062-3778"
468+
},
468469
{
469470
"affiliation": "University of illinois urbana champaign",
470471
"name": "Sharp, Paul"
@@ -479,6 +480,9 @@
479480
"name": "Molina-Romero, Miguel",
480481
"orcid": "0000-0001-8054-0426"
481482
},
483+
{
484+
"name": "Haehn, Daniel"
485+
},
482486
{
483487
"name": "Weinstein, Alejandro"
484488
},
@@ -493,6 +497,9 @@
493497
{
494498
"name": "Saase, Victor"
495499
},
500+
{
501+
"name": "Rothmei, Simon"
502+
},
496503
{
497504
"affiliation": "University of Helsinki",
498505
"name": "Andberg, Sami Kristian",
@@ -518,11 +525,6 @@
518525
{
519526
"name": "Tarbert, Claire"
520527
},
521-
{
522-
"affiliation": "University of Texas at Austin",
523-
"name": "De La Vega, Alejandro",
524-
"orcid": "0000-0001-9062-3778"
525-
},
526528
{
527529
"affiliation": "Vrije Universiteit Amsterdam",
528530
"name": "Ort, Eduard"

README.rst

+5-4
Original file line numberDiff line numberDiff line change
@@ -11,8 +11,8 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
1111
.. image:: https://codecov.io/gh/nipy/nipype/branch/master/graph/badge.svg
1212
:target: https://codecov.io/gh/nipy/nipype
1313

14-
.. image:: https://www.codacy.com/project/badge/182f27944c51474490b369d0a23e2f32
15-
:target: https://www.codacy.com/app/krzysztof-gorgolewski/nipy_nipype
14+
.. image:: https://api.codacy.com/project/badge/Grade/452bfc0d4de342c99b177d2c29abda7b
15+
:target: https://www.codacy.com/app/nipype/nipype?utm_source=github.com&utm_medium=referral&utm_content=nipy/nipype&utm_campaign=Badge_Grade
1616

1717
.. image:: https://img.shields.io/pypi/v/nipype.svg
1818
:target: https://pypi.python.org/pypi/nipype/
@@ -34,8 +34,9 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
3434
:target: http://gitter.im/nipy/nipype
3535
:alt: Chat
3636

37-
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.581704.svg
38-
:target: https://doi.org/10.5281/zenodo.581704
37+
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.596855.svg
38+
:target: https://doi.org/10.5281/zenodo.596855
39+
:alt: Citable DOI
3940

4041
Current neuroimaging software offer users an incredible opportunity to
4142
analyze data using a variety of different algorithms. However, this has

doc/_static/nipy-logo-bg-138x120.png

-29.2 KB
Binary file not shown.

doc/_static/reggie2.png

-9.31 KB
Binary file not shown.

doc/_templates/navbar.html

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<link rel="stylesheet" href="http://www.google.com/cse/style/look/default.css" type="text/css" />
1+
<link rel="stylesheet" href="https://www.google.com/cse/style/look/default.css" type="text/css" />
22
<style type="text/css">
33
a.navbar {
44
color: {{ theme_linkcolor }};

doc/about.rst

+1-1
Original file line numberDiff line numberDiff line change
@@ -215,7 +215,7 @@ this way you can use the initial paper published in 2011 (see below).
215215
month = "08",
216216
doi = "10.3389/fninf.2011.00013",
217217
pubmed = "21897815",
218-
url = "http://dx.doi.org/10.3389/fninf.2011.00013",
218+
url = "https://doi.org/10.3389/fninf.2011.00013",
219219
issn = "1662-5196"}
220220

221221

0 commit comments

Comments
 (0)