From e6dcf51483bd9a667bb57c18a37c9559bbaa91de Mon Sep 17 00:00:00 2001 From: Chris Markiewicz <effigies@gmail.com> Date: Wed, 20 Mar 2024 16:36:27 -0400 Subject: [PATCH 1/5] Update mailmap --- .mailmap | 27 ++++++++++++++++----------- 1 file changed, 16 insertions(+), 11 deletions(-) diff --git a/.mailmap b/.mailmap index 1f6bdee6fc..cadfb0ccef 100644 --- a/.mailmap +++ b/.mailmap @@ -1,10 +1,10 @@ Abel A. González Orozco <glez.orzco@gmail.com> Aimi Watanabe <watanabe.aimi@gmail.com> Aimi Watanabe <watanabe.aimi@gmail.com> stymy <rschadmin@cmi-rsch-li002.childmind.org> -Alejandro Tabas <alextabas@gmail.com> -Alejandro Tabas <alextabas@gmail.com> <qtabas@gmail.com> Alejandro de la Vega <aleph4@gmail.com> Alejandro de la Vega <aleph4@gmail.com> <delavega@utexas.edu> +Alejandro Tabas <alextabas@gmail.com> +Alejandro Tabas <alextabas@gmail.com> <qtabas@gmail.com> Alexander Schaefer <alexschaefer83@gmail.com> Alexander Schaefer <alexschaefer83@gmail.com> <aschaefer@aschaefer-U36SD.(none)> Alexander Schaefer <alexschaefer83@gmail.com> <aschaefer@melisse.cbs.mpg.de> @@ -65,9 +65,11 @@ Dylan M. Nielson <adenosine@gmail.com> Dylan M. Nielson <adenosine@gmail.com> <Dylan.Nielson@nih.gov> Eduard Ort <e.ort@vu.nl> Elizabeth DuPre <emd222@cornell.edu> +Eric Condamine <econdami@yahoo.fr> +Eric Condamine <econdami@yahoo.fr> <37933899+servoz@users.noreply.github.com> Erik Ziegler <erik.sweed@gmail.com> -Erik Ziegler <erik.sweed@gmail.com> <erik.ziegler@ulg.ac.be> Erik Ziegler <erik.sweed@gmail.com> <erik@erik-ubuntu.(none)> +Erik Ziegler <erik.sweed@gmail.com> <erik.ziegler@ulg.ac.be> Fabio Bernardoni <fabio.bernardoni@uniklinikum-dresden.de> Fabio Bernardoni <fabio.bernardoni@uniklinikum-dresden.de> <fb.brnrdn@gmail.com> Feilong Ma <mafeilong@gmail.com> @@ -76,7 +78,8 @@ Franz Liem <franz.liem@gmail.com> Franz Liem <franz.liem@gmail.com> <franz.liem> Fred Loney <loneyf@ohsu.edu> Gael Varoquaux <gael.varoquaux@normalesup.org> -Gal Ben-Zvi <hershkovitz1@mail.tau.ac.il> +Gal Kepler <galkepler@gmail.com> +Gal Kepler <galkepler@gmail.com> <hershkovitz1@mail.tau.ac.il> Gavin Cooper <Gavin.Cooper@newcastle.edu.au> <gjcooper@gmail.com> Ghislain Vaillant <ghislain.vaillant@icm-institute.org> Ghislain Vaillant <ghislain.vaillant@icm-institute.org> <ghisvail@users.noreply.github.com> @@ -96,11 +99,11 @@ Janosch Linkersdörfer <linkersdoerfer@gmail.com> Jason Wong <jf126dolphin@gmail.com> Jason Wong <jf126dolphin@gmail.com> <jasonwong73@ucla.edu> Jens Kleesiek <kleesiek@uni-heidelberg.de> -Jessica Forbes <jessica-forbes@uiowa.edu> Jérémy Guillon <jeremy.guillon@inria.fr> <jeremy.guillon@etu.upmc.fr> -Joerg Stadler <Joerg.Stadler@lin-magdeburg.de> <Stadler@lin-magdeburg.de> +Jessica Forbes <jessica-forbes@uiowa.edu> Joerg Stadler <Joerg.Stadler@lin-magdeburg.de> <joerg.stadler@lin-magdeburg.de> Joerg Stadler <Joerg.Stadler@lin-magdeburg.de> <jstadler@ilin-magdeburg.de> +Joerg Stadler <Joerg.Stadler@lin-magdeburg.de> <Stadler@lin-magdeburg.de> John A. Lee <johnleenimh@gmail.com> John A. Lee <johnleenimh@gmail.com> <leej3@users.noreply.github.com> Joke Durnez <joke.durnez@gmail.com> @@ -110,9 +113,9 @@ Junhao WEN <anbai106@hotmail.com> Kai Schlamp <schlamp@gmx.de> Katherine Bottenhorn <kbott006@fiu.edu> Kesshi Jordan <Kesshi.Jordan@ucsf.edu> -Kesshi Jordan <Kesshi.Jordan@ucsf.edu> <kesshi.jordan@gmail.com> Kesshi Jordan <Kesshi.Jordan@ucsf.edu> <kesshijordan@D-108-179-130-38.dhcp4.washington.edu> Kesshi Jordan <Kesshi.Jordan@ucsf.edu> <kesshijordan@D-69-91-152-99.dhcp4.washington.edu> +Kesshi Jordan <Kesshi.Jordan@ucsf.edu> <kesshi.jordan@gmail.com> Kesshi Jordan <Kesshi.Jordan@ucsf.edu> <kesshijordan@iPhone-010060104098.ucsf.edu> Kesshi Jordan <Kesshi.Jordan@ucsf.edu> <kjordan@codd.radiology.ucsf.edu> Kevin Sitek <ksitek@mit.edu> @@ -122,10 +125,10 @@ Kornelius Podranski <kilo13@web.de> Kristofer Montazeri <kristofer.montazeri@gmail.com> 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-Precision-M6500.(none)> -Krzysztof J. Gorgolewski <krzysztof.gorgolewski@gmail.com> <filo@filo-Precision-M6500> Krzysztof J. Gorgolewski <krzysztof.gorgolewski@gmail.com> <filo@filo-dtc-laptop> Krzysztof J. Gorgolewski <krzysztof.gorgolewski@gmail.com> <filo@filolaptop> +Krzysztof J. Gorgolewski <krzysztof.gorgolewski@gmail.com> <filo@filo-Precision-M6500> +Krzysztof J. Gorgolewski <krzysztof.gorgolewski@gmail.com> <filo@filo-Precision-M6500.(none)> Krzysztof J. Gorgolewski <krzysztof.gorgolewski@gmail.com> <krzysztof.gorgolewski+fake@gmail.com> Kshitij Chawla <kc.insight.pi@gmail.com> Leonie Lampe <leonie.lampe@gmail.com> @@ -163,8 +166,8 @@ Oliver Contier <o.contier@gmail.com> <oliver.contier@ovgu.de> Olivia Stanley <oliviawstanley@gmail.com> Oscar Esteban <code@oscaresteban.es> Oscar Esteban <code@oscaresteban.es> <code@oscaresteban> -Pablo Polosecki <pipolose@us.ibm.com> <pipolose@pipoloses-MacBook-Air.local> Pablo Polosecki <pipolose@us.ibm.com> <pipolose@pipoloses-air.watson.ibm.com> +Pablo Polosecki <pipolose@us.ibm.com> <pipolose@pipoloses-MacBook-Air.local> Paul Kuntke <paul@42degreesoffreedom.com> Paul Kuntke <paul@42degreesoffreedom.com> <paul@kuntke.de> Paul Sharp <psharp1289@gmail.com> @@ -185,8 +188,8 @@ Serge Koudoro <skab12@gmail.com> Sharad Sikka <ssikka25@gmail.com> Shariq Iqbal <shariqiqbal2810@gmail.com> Shariq Iqbal <shariqiqbal2810@gmail.com> <shariqiqbal2810@users.noreply.github.com> -Shoshana Berleant <berleant@stanford.edu> <shoshber@users.noreply.github.com> Shoshana Berleant <berleant@stanford.edu> Shoshana Berleant <nope> +Shoshana Berleant <berleant@stanford.edu> <shoshber@users.noreply.github.com> Shoshana Berleant <berleant@stanford.edu> Ubuntu <ubuntu@ip-172-31-43-202.us-west-2.compute.internal> Simon Rothmei <srothmei@mailbox.tu-berlin.de> Simon Rothmei <srothmei@mailbox.tu-berlin.de> <srothmei@users.noreply.github.com> @@ -210,5 +213,7 @@ Victor Saase <victor@saase.net> Weijie Huang <hwjbupt@gmail.com> William Triplett <wtriplett@gmail.com> <wtriplett@ufl.edu> Wolfgang Pauli <Wolfgang.m.Pauli@gmail.com> +Wu Jianxiao <jianxiao.wu.veronica@gmail.com> +Wu Jianxiao <jianxiao.wu.veronica@gmail.com> <vesaveronica@gmail.com> Xiangzhen Kong <bnucon@gmail.com> Yaroslav Halchenko <debian@onerussian.com> <yoh@dartmouth.edu> From 531aa3acbc1af72a1bfeda3e0d4f737f53f2b07d Mon Sep 17 00:00:00 2001 From: Chris Markiewicz <effigies@gmail.com> Date: Sun, 5 May 2024 21:16:09 -0400 Subject: [PATCH 2/5] DOC: Update 1.8.7 changelog --- doc/changelog/1.X.X-changelog.rst | 43 +++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/doc/changelog/1.X.X-changelog.rst b/doc/changelog/1.X.X-changelog.rst index f1d6bc92d3..7ece40841f 100644 --- a/doc/changelog/1.X.X-changelog.rst +++ b/doc/changelog/1.X.X-changelog.rst @@ -1,3 +1,46 @@ +1.8.7 (May 06, 2024) +==================== + +Bug-fix release in the 1.8.x series. + + * FIX: Add cropped files to dcm2niix output (https://github.com/nipy/nipype/pull/3609) + * FIX: Deduplicate dcm2niix output (https://github.com/nipy/nipype/pull/3610) + * FIX: Parse commas in CSV fields (https://github.com/nipy/nipype/pull/3637) + * FIX: MRTrix3 change inputs position for MRTransform (https://github.com/nipy/nipype/pull/3611) + * FIX: Use out_prefix instead of "w" in spm.Normalize12 (https://github.com/nipy/nipype/pull/3600) + * FIX: Fix typo in spm.Normalize12 process (https://github.com/nipy/nipype/pull/3599) + * FIX: DWIPreproc issue (https://github.com/nipy/nipype/pull/3596) + * FIX: DWIPreproc issue (https://github.com/nipy/nipype/pull/3596) + * FIX: Fix bugs with ``fsl_out=True`` and ``lta_out=True`` (https://github.com/nipy/nipype/pull/3583) + * FIX: Test failures (https://github.com/nipy/nipype/pull/3587) + * FIX: update merge_imgs input type of dcm2niix Node (https://github.com/nipy/nipype/pull/3548) + * FIX: update sample_random_points and random_seed type of ProbTrackXBaseInputSpec (https://github.com/nipy/nipype/pull/3556) + * FIX: update self.inputs.optimization in outputs for GTMPVC (https://github.com/nipy/nipype/pull/3571) + * ENH: Add functions to mrtrix3 interface (https://github.com/nipy/nipype/pull/3613) + * ENH: Update PETsurfer interface (https://github.com/nipy/nipype/pull/3602) + * ENH: Add 'hsvs' option to 5ttgen + mrtransform fix (https://github.com/nipy/nipype/pull/3630) + * ENH: add STC PVC to PETPVC interface (https://github.com/nipy/nipype/pull/3634) + * ENH: Add GenericLabel to ANTS ApplyTransforms. (https://github.com/nipy/nipype/pull/3617) + * ENH: Issue 3553 add mvecs to dcm2niix (https://github.com/nipy/nipype/pull/3554) + * ENH: add contrast outputs for EstimatedModel (https://github.com/nipy/nipype/pull/3577) + * ENH: Issue 3345: Adding FreeSurfer longitudinal interfaces (https://github.com/nipy/nipype/pull/3529) + * ENH: Enable SPM voxel-based FDR (https://github.com/nipy/nipype/pull/3558) + * REF: io.open() → open() (https://github.com/nipy/nipype/pull/3575) + * REF: Stop using deprecated import internally (https://github.com/nipy/nipype/pull/3561) + * DOC/FIX: Fix wrong name, should be al_ea (https://github.com/nipy/nipype/pull/3629) + * DOC: Fix typos newly found by codespell (https://github.com/nipy/nipype/pull/3606) + * STY: Apply ruff/pyupgrade rules (https://github.com/nipy/nipype/pull/3647) + * STY: Adjusted variable names for clarity and codespell false positives (https://github.com/nipy/nipype/pull/3627) + * STY: Remove duplicated trait in EddyOutputSpec (https://github.com/nipy/nipype/pull/3568) + * STY: Black edits (https://github.com/nipy/nipype/pull/1) + * MNT: Configure dependabot to update GH workflows (https://github.com/nipy/nipype/pull/3597) + * MNT: Replace deprecated locale.getdefaultlocale (https://github.com/nipy/nipype/pull/3590) + * MNT: Require Python 3.8+, auto-upgrade syntax (https://github.com/nipy/nipype/pull/3588) + * CI: Test Python 3.12 support (https://github.com/nipy/nipype/pull/3638) + * CI: Test on Python 3.11 (https://github.com/nipy/nipype/pull/3589) + * CI/FIX: configure codespell, add workflow, typos fixed (https://github.com/nipy/nipype/pull/3549) + + 1.8.6 (April 05, 2023) ====================== From 48d79806fd8abc2fd3b97674d651e661b89d11a7 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz <effigies@gmail.com> Date: Thu, 21 Mar 2024 10:11:54 -0400 Subject: [PATCH 3/5] CI: Replace set-output commands --- .github/workflows/tutorials.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tutorials.yml b/.github/workflows/tutorials.yml index 46aa42d25c..d920ed435d 100644 --- a/.github/workflows/tutorials.yml +++ b/.github/workflows/tutorials.yml @@ -18,7 +18,7 @@ jobs: steps: - name: Start time id: start - run: echo "::set-output name=start_time::$(date +'%Y-%m-%dT%H:%M:%S%z')" + run: echo start_time=$(date +'%Y-%m-%dT%H:%M:%S%z') >> $GITHUB_OUTPUT - name: Trigger Nipype tutorial Github Action run: | set -x @@ -38,7 +38,7 @@ jobs: # fail if not extracted [[ -n $RUN_ID ]] || exit 1 - echo "::set-output name=run_id::$RUN_ID" + echo run_id=$RUN_ID >> $GITHUB_OUTPUT - name: Check if action completed timeout-minutes: 120 run: | From 235fcac38229e7a971060b21bee032674ca3f3f7 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz <effigies@gmail.com> Date: Thu, 21 Mar 2024 10:12:50 -0400 Subject: [PATCH 4/5] MNT: 1.8.7 --- nipype/info.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/info.py b/nipype/info.py index a550e4b389..38ccabc06e 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -5,7 +5,7 @@ # nipype version information # Remove .dev0 for release -__version__ = "1.8.7.dev0" +__version__ = "1.8.7" def get_nipype_gitversion(): From 391c2387019f56b5fdc1dc2e1bd6b04f3aaa7c31 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz <effigies@gmail.com> Date: Sun, 5 May 2024 21:18:53 -0400 Subject: [PATCH 5/5] Update Zenodo --- .zenodo.json | 124 +++++++++++++++++++++++++-------------------------- 1 file changed, 62 insertions(+), 62 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index d01d2409e3..2e70875161 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -61,6 +61,11 @@ "name": "Manhães-Savio, Alexandre", "orcid": "0000-0002-6608-6885" }, + { + "affiliation": "Dartmouth College: Hanover, NH, United States", + "name": "Halchenko, Yaroslav O.", + "orcid": "0000-0003-3456-2493" + }, { "affiliation": "UC Berkeley", "name": "Clark, Dav", @@ -76,19 +81,14 @@ "name": "Dayan, Michael", "orcid": "0000-0002-2666-0969" }, - { - "affiliation": "Dartmouth College: Hanover, NH, United States", - "name": "Halchenko, Yaroslav O.", - "orcid": "0000-0003-3456-2493" - }, - { - "name": "Loney, Fred" - }, { "affiliation": "Department of Psychology, Stanford University", "name": "Norgaard, Martin", "orcid": "0000-0003-2131-5688" }, + { + "name": "Loney, Fred" + }, { "affiliation": "Florida International University", "name": "Salo, Taylor", @@ -275,6 +275,16 @@ { "name": "Mordom, David" }, + { + "affiliation": "Sagol School of Neuroscience, Tel Aviv University", + "name": "Kepler, Gal", + "orcid": "0000-0002-5655-9423" + }, + { + "affiliation": "CEA", + "name": "Papadopoulos Orfanos, Dimitri", + "orcid": "0000-0002-1242-8990" + }, { "affiliation": "ARAMIS LAB, Brain and Spine Institute (ICM), Paris, France.", "name": "Guillon, Jérémy", @@ -318,11 +328,6 @@ "name": "Gillman, Ashley", "orcid": "0000-0001-9130-1092" }, - { - "affiliation": "Sagol School of Neuroscience, Tel Aviv University", - "name": "Kepler, Gal", - "orcid": "0000-0002-5655-9423" - }, { "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", @@ -336,6 +341,11 @@ { "name": "Salvatore, John" }, + { + "affiliation": "Medical College of Wisconsin", + "name": "Espana, Lezlie", + "orcid": "0000-0002-6466-4653" + }, { "affiliation": "CNRS LTCI, Telecom ParisTech, Université Paris-Saclay", "name": "Gramfort, Alexandre", @@ -363,15 +373,14 @@ "name": "Schaefer, Alexander", "orcid": "0000-0001-6488-4739" }, - { - "affiliation": "CEA", - "name": "Papadopoulos Orfanos, Dimitri", - "orcid": "0000-0002-1242-8990" - }, { "affiliation": "UniversityHospital Heidelberg, Germany", "name": "Kleesiek, Jens" }, + { + "affiliation": "Department of Neurology, BG-University Hospital Bergmannsheil Bochum, Germany", + "name": "Butry, Lionel" + }, { "affiliation": "Nathan s Kline institute for psychiatric research", "name": "Sikka, Sharad" @@ -379,16 +388,16 @@ { "name": "Schwartz, Yannick" }, - { - "affiliation": "Medical College of Wisconsin", - "name": "Espana, Lezlie", - "orcid": "0000-0002-6466-4653" - }, { "affiliation": "The University of Iowa", "name": "Ghayoor, Ali", "orcid": "0000-0002-8858-1254" }, + { + "affiliation": "ARAMIS Lab, Paris Brain Institute", + "name": "Vaillant, Ghislain", + "orcid": "0000-0003-0267-3033" + }, { "affiliation": "NIMH IRP", "name": "Lee, John A.", @@ -407,11 +416,6 @@ "name": "Liem, Franz", "orcid": "0000-0003-0646-4810" }, - { - "affiliation": "ARAMIS Lab, Paris Brain Institute", - "name": "Vaillant, Ghislain", - "orcid": "0000-0003-0267-3033" - }, { "affiliation": "Neurospin/Unicog/Inserm/CEA", "name": "Perez-Guevara, Martin Felipe", @@ -471,6 +475,11 @@ "affiliation": "University of Iowa", "name": "Welch, David" }, + { + "affiliation": "CNRS, UMS3552 IRMaGe", + "name": "Condamine, Eric", + "orcid": "0000-0002-9533-3769" + }, { "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences", "name": "Contier, Oliver", @@ -546,6 +555,11 @@ "affiliation": "Boston University", "name": "Perkins, L. Nathan" }, + { + "affiliation": "Lund University", + "name": "Anijärv, Toomas Erik", + "orcid": "0000-0002-3650-4230" + }, { "name": "Zhou, Dale" }, @@ -581,6 +595,11 @@ "affiliation": "Dept of Medical Biophysics, Univeristy of Western Ontario", "name": "Stanley, Olivia" }, + { + "affiliation": "Flywheel.io, Minneapolis, MN, USA.", + "name": "Velasco, Pablo", + "orcid": "0000-0002-5749-6049" + }, { "name": "Küttner, René" }, @@ -589,6 +608,11 @@ "name": "Pauli, Wolfgang M.", "orcid": "0000-0002-0966-0254" }, + { + "affiliation": "Research Centre Juelich", + "name": "Wu, Jianxiao", + "orcid": "0000-0002-4866-272X" + }, { "affiliation": "Weill Cornell Medicine", "name": "Xie, Xihe", @@ -623,11 +647,6 @@ "name": "Margulies, Daniel S.", "orcid": "0000-0002-8880-9204" }, - { - "affiliation": "CNRS, UMS3552 IRMaGe", - "name": "Condamine, Eric", - "orcid": "0000-0002-9533-3769" - }, { "affiliation": "Dartmouth College", "name": "Ma, Feilong", @@ -751,6 +770,11 @@ { "name": "Modat, Marc" }, + { + "affiliation": "University of Tübingen and MPI for Biological Cybernertics", + "name": "Bannert, Michael M.", + "orcid": "0000-0003-1010-7517" + }, { "affiliation": "University of Waterloo", "name": "Mukhometzianov, Rinat", @@ -849,11 +873,6 @@ "name": "Pannetier, Nicolas", "orcid": "0000-0002-0744-5155" }, - { - "affiliation": "Flywheel.io, Minneapolis, MN, USA.", - "name": "Velasco, Pablo", - "orcid": "0000-0002-5749-6049" - }, { "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences", "name": "Numssen, Ole", @@ -886,35 +905,16 @@ { "name": "Tambini, Arielle" }, - { - "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.", - "name": "Mihai, Paul Glad", - "orcid": "0000-0001-5715-6442" - }, - { - "affiliation": "University of Tübingen and MPI for Biological Cybernertics", - "name": "Bannert, Michael M.", - "orcid": "0000-0003-1010-7517" - }, - { - "affiliation": "Research Centre Juelich", - "name": "Wu, Jianxiao", - "orcid": "0000-0002-4866-272X" - }, - { - "affiliation": "Department of Neurology, BG-University Hospital Bergmannsheil Bochum, Germany", - "name": "Butry, Lionel" - }, - { - "affiliation": "Lund University", - "name": "Anijärv, Toomas Erik", - "orcid": "0000-0002-3650-4230" - }, { "affiliation": "Azienda Ospedaliero-Universitaria di Modena", "name": "Genovese, Maurilio", "orcid": "0000-0002-8154-8224" }, + { + "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.", + "name": "Mihai, Paul Glad", + "orcid": "0000-0001-5715-6442" + }, { "affiliation": "Department of Psychology, Stanford University", "name": "Gorgolewski, Krzysztof J.",