Skip to content

Commit

Permalink
Merge tag '21.0.0rc2'
Browse files Browse the repository at this point in the history 
21.0.0rc2

First official release after migrating the repository into the *NiPreps*' organization.
This release updates the Docker image with up-to-date dependencies, updates
*MRIQC*'s codebase to the latest *NiTransforms* and includes some minor bugfixes.
Finally, this release also contains a major code style overhaul by Zvi Baratz.
With thanks to @ZviBaratz, @nbeliy, @octomike, @benkay86, @verdurin, and @utooley for their contributions.

  * FIX: ``template_resolution`` deprecation warning (#941)
  * FIX: Set entity ``datatype`` in ``BIDSLayout`` queries (#942)
  * FIX: T2w image of MNI template unavailable in Singularity (#940)
  * FIX: Release process -- Docker deployment not working + Python package lacks WebAPI token (#938)
  * FIX: Revise building documentation at RTD after migration (#935)
  * FIX: Final touch-ups in the maintenance of Docker image + CI (#928)
  * FIX: Update unit tests (#927)
  * FIX: Update dependencies and repair BOLD workflow accordingly (#926)
  * FIX: Update dependencies and repair T1w workflow accordingly (#925)
  * FIX: Set ``matplotlib`` on ``Agg`` output mode (#892)
  * ENH: Optimize *PyBIDS*' layout initialization (#939)
  * ENH: Refactored long strings to a :mod:`mriqc.messages` module (#901)
  * ENH: Refactored :mod:`mriqc.interfaces.common` module (#901)
  * DOC: Various fixes to "Running mriqc" section (#897)
  * MAINT: Updates to ``CONTRIBUTORS.md`` file
  * MAINT: Revise Docker image settings & CircleCI (#937)
  * MAINT: Finalize transfer to ``nipreps`` organization (#936)
  * MAINT: Relicensing to Apache-2.0, for compliance with *NiPreps* and prior transfer to the org (#930)
  * MAINT: New Docker layer caching system of other *NiPreps* (#929)
  * MAINT: Code style overhaul (#901)
  * MAINT: Update ``Dockerfile`` and catch-up with *fMRIPrep*'s (#924)
  * STY: Run ``black`` at the top of the repo (#932)
  • Loading branch information
@oesteban
oesteban committed Oct 4, 2021
2 parents 13f4922 + 112e4e9 commit 43cb90b
Show file tree
Hide file tree
Showing 8 changed files with 145 additions and 95 deletions.
27 changes: 26 additions & 1 deletion .mailmap
View file
Original file line number Diff line number Diff line change
@@ -1,10 +1,26 @@
Adam Huffman <bloch@verdurin.com>
Adam Huffman <bloch@verdurin.com> verdurin
Asier Erramuzpe <asier.erramuzpe@gmail.com>
Asier Erramuzpe <asier.erramuzpe@gmail.com> erramuzpe
Bennet Fauber <justbennet@users.noreply.github.com>
Bennet Fauber <justbennet@users.noreply.github.com> justbennet
Christopher J. Markiewicz <effigies@gmail.com>
Christopher J. Markiewicz <effigies@gmail.com> <effigies@bu.edu>
Christopher J. Markiewicz <effigies@gmail.com> <markiewicz@stanford.edu>
Conrad Ma <Conrad@Conrads-MacBook-Pro.local>
Conrad Ma <Conrad@Conrads-MacBook-Pro.local> Conrad
Conrad Ma <Conrad@Conrads-MacBook-Pro.local> 394822740
Conrad Ma <Conrad@Conrads-MacBook-Pro.local> <394822740@qq.com>
Conrad Ma <Conrad@Conrads-MacBook-Pro.local> <maconrad49@gmail.com>
Dylan Nielson <adenosine@gmail.com>
Dylan Nielson <adenosine@gmail.com> Dylan <Dylan.Nielson@nih.gov>
James D. Kent <james-kent@uiowa.edu>
James D. Kent <james-kent@uiowa.edu> <jamesdkent21@gmail.com>
James D. Kent <james-kent@uiowa.edu> jdkent
James D. Kent <james-kent@uiowa.edu> Fred Mertz <mertzf@bargle.argle>
John A. Lee <johnleenimh@gmail.com>
John A. Lee <johnleenimh@gmail.com> john anthony lee
John A. Lee <johnleenimh@gmail.com> leej3
Krzysztof J. Gorgolewski <krzysztof.gorgolewski@gmail.com>
Krzysztof J. Gorgolewski <krzysztof.gorgolewski@gmail.com> <chris.gorgolewski@gmail.com>
Krzysztof J. Gorgolewski <krzysztof.gorgolewski@gmail.com> <filo@filo-dtc-laptop>
Expand All @@ -16,8 +32,17 @@ Mathias Goncalves <goncalves.mathias@gmail.com>
Mathias Goncalves <goncalves.mathias@gmail.com> mathiasg
Mathias Goncalves <goncalves.mathias@gmail.com> <mathiasg@mit.edu>
Mathias Goncalves <goncalves.mathias@gmail.com> <mathiasg@stanford.edu>
Michael G. Clark <michael.clark3@nih.gov>
Michael G. Clark <michael.clark3@nih.gov> mgclark
Michael G. Clark <michael.clark3@nih.gov> Michael Clark
Michael Krause <krause@mpib-berlin.mpg.de>
Michael Krause <krause@mpib-berlin.mpg.de> octomike
NiPreps Bot <nipreps@gmail.com>
NiPreps Bot <nipreps@gmail.com> nipreps-bot
Pablo Velasco <pablo.velasco@nyu.edu>
Pablo Velasco <pablo.velasco@nyu.edu> pvelasco
Oscar Esteban <code@oscaresteban.es>
Oscar Esteban <code@oscaresteban.es> <oesteban@stanford.edu>
Ross Blair <rblair2@stanford.edu>
Ross Blair <rblair2@stanford.edu> <rosswilsonblair@gmail.com>

William Triplett <wtriplet@stanford.edu>
9 changes: 5 additions & 4 deletions .maint/CONTRIBUTORS.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,22 +12,23 @@ Before every release, unlisted contributors will be invited again to add their n
| Beliy | Nikita | @nbeliy | | CRC ULiege, Liege, Belgium |
| Birman | Daniel | @dbirman | 0000-0003-3748-6289 | Department of Psychology, Stanford University, CA, USA |
| Blair | Ross W. | @rwblair | 0000-0003-3007-1056 | Department of Psychology, Stanford University, CA, USA |
| Clark | Michael | @mgclark | | |
| Clark | Michael G. | @mgclark | | National Institutes of Health, USA |
| Durnez | Joke | @jokedurnez | 0000-0001-9030-2202 | Department of Psychology, Stanford University, CA, USA |
| Erramuzpe | Asier | @erramuzpe | 0000-0002-9402-2184 | Computational Neuroimaging Lab, BioCruces Health Research Institute |
| Fauber | Bennet | @justbennet | | University of Michigan, Ann Arbor, USA |
| Garcia-Dias | Rafael | @garciadias | 0000-0001-9332-1580 | Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK |
| Ghosh | Satrajit S. | @satra | 0000-0002-5312-6729 | McGovern Institute for Brain Research, MIT, MA, USA; and Department of Otolaryngology, Harvard Medical School, MA, USA |
| Goncalves | Mathias | @mgxd | 0000-0002-7252-7771 | Department of Psychology, Stanford University, CA, USA |
| Gorgolewski | Krzysztof J. | @chrisgorgo | 0000-0003-3321-7583 | Google LLC |
| Huffman | Adam | @verdurin | | |
| Huffman | Adam | @verdurin | | Department of Physics, Imperial College London, London, UK |
| Kay | Benjamin | @benkay86 | | Washington University School of Medicine, St.Louis, MO, USA |
| Kent | James D. | @jdkent | 0000-0002-4892-2659 | Neuroscience Program, University of Iowa |
| Lee | John | @leej3 | | Quansight, Dublin, Ireland |
| Krause | Michael | @octomike | | Max Planck Institute for Human Development, Berlin, Germany |
| Lee | John A. | @leej3 | | Quansight, Dublin, Ireland |
| Nichols | Thomas | @nicholst | 0000-0002-4516-5103 | Oxford Big Data Institute, University of Oxford, Oxford, GB |
| Nielson | Dylan | @Shotgunosine | 0000-0003-4613-6643 | Section on Clinical and Computational Psychiatry, National Institute of Mental Health, Bethesda, MD, USA |
| Salo | Taylor | @tsalo | 0000-0001-9813-3167 | Department of Psychology, Florida International University, FL, USA |
| Tooley | Ursula A. | @utooley | 0000-0001-6377-3885 | Department of Neuroscience, University of Pennsylvania, PA, USA |
| Triplett | William | @wtriplett | 0000-0002-9546-1306 | University of Florida: Gainesville, Florida, US |
| Varada | Jan | @jvarada | | Functional MRI Facility, National Institute of Mental Health, Bethesda, MD, USA |
| Velasco | Pablo | @pvelasco | 0000-0002-5749-6049 | Center for Brain Imaging, New York University, NY, USA |
| | Michael | @octomike | | Max Planck Institute for Human Development, Berlin, Germany |
4 changes: 3 additions & 1 deletion .maint/FORMER.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,6 @@ By adding your name to this list you are giving up on all your responsibilities
Should you desire to be considered back as a contributor or maintainer, please remove your name from this list and proceed as prescribed in the governance documents.

| **Lastname** | **Name** | **Handle** |
| --- | --- | --- |
| --- | --- | --- |
| Bot | NiPreps | @nipreps-bot |
| Ma | Conrad | @394822740 |
11 changes: 6 additions & 5 deletions .maint/PIs.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,11 @@ When a PI ceases serving as such, by default, their name will be placed in the `
By having your name in this list you are agreeing to abide by the governance documents and to abide by all of the Organization's polices, including the code of conduct, trademark policy, and antitrust policy.
If you are participating because of your affiliation with another organization (designated below), you represent that you have the authority to bind that organization to these policies.

| **Lastname** | **Name** | **Handle** | **ORCID** | **Affiliation** | **Position** |
| **Lastname** | **Name** | **Handle** | **ORCID** | **Affiliation** |
| --- | --- | --- | --- | --- | --- |
| Esteban | Oscar | @oesteban | 0000-0001-8435-6191 | Department of Radiology, Lausanne University Hospital and University of Lausanne | -1 |
| Poldrack | Russell A. | @poldrack | 0000-0001-6755-0259 | Department of Psychology, Stanford University, CA, USA | -2 |
| Thomas | Adam G. | | 0000-0002-2850-1419 | Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA | |
| Marret | Sean | | 0000-0001-8179-6511 | Functional MRI Facility, National Institute of Mental Health, Bethesda, MD, USA | |
| Esteban | Oscar | @oesteban | 0000-0001-8435-6191 | Department of Radiology, Lausanne University Hospital and University of Lausanne |
| Gorgolewski | Krzysztof J. | @chrisgorgo | 0000-0003-3321-7583 | Google LLC |
| Poldrack | Russell A. | @poldrack | 0000-0001-6755-0259 | Department of Psychology, Stanford University, CA, USA |
| Thomas | Adam G. | | 0000-0002-2850-1419 | Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA |
| Marret | Sean | | 0000-0001-8179-6511 | Functional MRI Facility, National Institute of Mental Health, Bethesda, MD, USA |

7 changes: 5 additions & 2 deletions .maint/update_authors.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -186,7 +186,9 @@ def zenodo(
zen_pi = _namelast(reversed(read_md_table(Path(pi).read_text())))

zenodo["creators"] = zen_creators
zenodo["contributors"] = zen_contributors + zen_pi
zenodo["contributors"] = zen_contributors + [
pi for pi in zen_pi if pi not in zen_contributors
]
creator_names = {
c["name"] for c in zenodo["creators"]
if c["name"] != "<Unknown Name>"
Expand Down Expand Up @@ -246,11 +248,12 @@ def publication(
_namelast(read_md_table(Path(maintainers).read_text()))
+ _namelast(read_md_table(Path(contributors).read_text()))
)
former_names = _namelast(read_md_table(Path(former_file).read_text()))

hits, misses = sort_contributors(
members,
get_git_lines(),
exclude=_namelast(read_md_table(Path(former_file).read_text())),
exclude=former_names,
)

pi_hits = _namelast(reversed(read_md_table(Path(pi).read_text())))
Expand Down
105 changes: 55 additions & 50 deletions .zenodo.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,43 +14,65 @@
}
],
"contributors": [
{
"orcid": "0000-0003-3321-7583",
"affiliation": "Google LLC",
"name": "Krzysztof J. Gorgolewski",
"type": "Researcher"
},
{
"affiliation": "Neuroscience Program, Tel-Aviv University",
"name": "Zvi Baratz",
"type": "Researcher"
},
{
"orcid": "0000-0003-3321-7583",
"affiliation": "Google LLC",
"name": "Krzysztof J. Gorgolewski",
"orcid": "0000-0003-4613-6643",
"affiliation": "Section on Clinical and Computational Psychiatry, National Institute of Mental Health, Bethesda, MD, USA",
"name": "Dylan Nielson",
"type": "Researcher"
},
{
"orcid": "0000-0003-3748-6289",
"affiliation": "Functional MRI Facility, National Institute of Mental Health, Bethesda, MD, USA",
"name": "Jan Varada",
"type": "Researcher"
},
{
"orcid": "0000-0003-3007-1056",
"affiliation": "Department of Psychology, Stanford University, CA, USA",
"name": "Daniel Birman",
"name": "Ross W. Blair",
"type": "Researcher"
},
{
"orcid": "0000-0002-9546-1306",
"affiliation": "University of Florida: Gainesville, Florida, US",
"name": "William Triplett",
"type": "Researcher"
},
{
"affiliation": "CRC ULiege, Liege, Belgium",
"name": "Nikita Beliy",
"type": "Researcher"
},
{
"affiliation": "Quansight, Dublin, Ireland",
"name": "John A. Lee",
"type": "Researcher"
},
{
"orcid": "0000-0001-6377-3885",
"affiliation": "Department of Neuroscience, University of Pennsylvania, PA, USA",
"name": "Ursula A. Tooley",
"type": "Researcher"
},
{
"orcid": "0000-0003-3007-1056",
"affiliation": "Department of Psychology, Stanford University, CA, USA",
"name": "Ross W. Blair",
"affiliation": "University of Michigan, Ann Arbor, USA",
"name": "Bennet Fauber",
"type": "Researcher"
},
{
"affiliation": "Functional MRI Facility, National Institute of Mental Health, Bethesda, MD, USA",
"name": "Jan Varada",
"orcid": "0000-0002-4892-2659",
"affiliation": "Neuroscience Program, University of Iowa",
"name": "James D. Kent",
"type": "Researcher"
},
{
Expand All @@ -72,9 +94,8 @@
"type": "Researcher"
},
{
"orcid": "0000-0002-9402-2184",
"affiliation": "Computational Neuroimaging Lab, BioCruces Health Research Institute",
"name": "Asier Erramuzpe",
"affiliation": "Department of Physics, Imperial College London, London, UK",
"name": "Adam Huffman",
"type": "Researcher"
},
{
Expand All @@ -84,68 +105,52 @@
"type": "Researcher"
},
{
"orcid": "0000-0001-9332-1580",
"affiliation": "Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK",
"name": "Rafael Garcia-Dias",
"affiliation": "Center for Brain Imaging, New York University, NY, USA",
"name": "Pablo Velasco",
"type": "Researcher"
},
{
"orcid": "0000-0003-4613-6643",
"affiliation": "Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA",
"name": "Dylan Nielson",
"orcid": "0000-0002-5312-6729",
"affiliation": "McGovern Institute for Brain Research, MIT, MA, USA; and Department of Otolaryngology, Harvard Medical School, MA, USA",
"name": "Satrajit S. Ghosh",
"type": "Researcher"
},
{
"orcid": "Washington University School of Medicine, St.Louis, MO, USA",
"name": "Benjamin Kay",
"type": "Researcher",
"affiliation": "Unknown affiliation"
},
{
"affiliation": "Center for Interdisciplinary Brain Sciences Research, Stanford University, CA, USA",
"name": "Aaron Piccirilli",
"type": "Researcher"
},
{
"name": "@justbennet",
"type": "Researcher",
"affiliation": "Unknown affiliation"
},
{
"name": "Adam Huffman",
"type": "Researcher",
"affiliation": "Unknown affiliation"
},
{
"orcid": "0000-0002-4892-2659",
"affiliation": "Neuroscience Program, University of Iowa",
"name": "James D. Kent",
"orcid": "0000-0002-9402-2184",
"affiliation": "Computational Neuroimaging Lab, BioCruces Health Research Institute",
"name": "Asier Erramuzpe",
"type": "Researcher"
},
{
"affiliation": "Quansight, Dublin, Ireland",
"name": "John Lee",
"affiliation": "Washington University School of Medicine, St.Louis, MO, USA",
"name": "Benjamin Kay",
"type": "Researcher"
},
{
"affiliation": "Max Planck Institute for Human Development, Berlin, Germany",
"name": "Michael",
"orcid": "0000-0003-3748-6289",
"affiliation": "Department of Psychology, Stanford University, CA, USA",
"name": "Daniel Birman",
"type": "Researcher"
},
{
"name": "Michael Clark",
"type": "Researcher",
"affiliation": "Unknown affiliation"
"affiliation": "National Institutes of Health, USA",
"name": "Michael G. Clark",
"type": "Researcher"
},
{
"affiliation": "Center for Brain Imaging, New York University, NY, USA",
"name": "Pablo Velasco",
"affiliation": "Max Planck Institute for Human Development, Berlin, Germany",
"name": "Michael Krause",
"type": "Researcher"
},
{
"orcid": "0000-0002-5312-6729",
"affiliation": "McGovern Institute for Brain Research, MIT, MA, USA; and Department of Otolaryngology, Harvard Medical School, MA, USA",
"name": "Satrajit S. Ghosh",
"orcid": "0000-0001-9332-1580",
"affiliation": "Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK",
"name": "Rafael Garcia-Dias",
"type": "Researcher"
},
{
Expand Down
Loading

0 comments on commit 43cb90b

Please sign in to comment.