diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 253c1c6919..826a62fe9f 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -1,3 +1,11 @@ +# Thu Oct 31 10:01:38 2024 -0400 - effigies@gmail.com - STY: black [ignore-rev] +bd0d5856d183ba3918eda31f80db3b1d4387c55c +# Thu Mar 21 13:34:09 2024 -0400 - effigies@gmail.com - STY: black [ignore-rev] +c52fece0cf154c1a93a55b202d088f08924a023e +# Sun Mar 17 10:58:12 2024 -0400 - effigies@gmail.com - STY: black [ignore-rev] +e447b92bcb3b9ed9e35394d6edef1d91b7c424e6 +# Sun Mar 17 10:44:57 2024 -0400 - effigies@gmail.com - STY: black +f1a8909d233ed2a707b6ee8937504eea9ee7f154 # Tue Feb 27 14:28:18 2024 -0500 - effigies@gmail.com - STY: black 2024.2 [ignore-rev] f1cbc1c941f8d02659f8ef245aac0862efb80ccf # Mon Sep 11 13:36:40 2023 +0200 - 37933899+servoz@users.noreply.github.com - run black for nipype/interfaces/spm/preprocess.py 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: | diff --git a/.mailmap b/.mailmap index 1f6bdee6fc..4c5bd5de4d 100644 --- a/.mailmap +++ b/.mailmap @@ -1,10 +1,10 @@ Abel A. González Orozco Aimi Watanabe Aimi Watanabe stymy -Alejandro Tabas -Alejandro Tabas Alejandro de la Vega Alejandro de la Vega +Alejandro Tabas +Alejandro Tabas Alexander Schaefer Alexander Schaefer Alexander Schaefer @@ -65,9 +65,12 @@ Dylan M. Nielson Dylan M. Nielson Eduard Ort Elizabeth DuPre +Emmanuelle Gourieux <47973414+manuegrx@users.noreply.github.com> +Eric Condamine +Eric Condamine <37933899+servoz@users.noreply.github.com> Erik Ziegler -Erik Ziegler Erik Ziegler +Erik Ziegler Fabio Bernardoni Fabio Bernardoni Feilong Ma @@ -76,7 +79,8 @@ Franz Liem Franz Liem Fred Loney Gael Varoquaux -Gal Ben-Zvi +Gal Kepler +Gal Kepler Gavin Cooper Ghislain Vaillant Ghislain Vaillant @@ -96,11 +100,11 @@ Janosch Linkersdörfer Jason Wong Jason Wong Jens Kleesiek -Jessica Forbes Jérémy Guillon -Joerg Stadler +Jessica Forbes Joerg Stadler Joerg Stadler +Joerg Stadler John A. Lee John A. Lee Joke Durnez @@ -110,9 +114,9 @@ Junhao WEN Kai Schlamp Katherine Bottenhorn Kesshi Jordan -Kesshi Jordan Kesshi Jordan Kesshi Jordan +Kesshi Jordan Kesshi Jordan Kesshi Jordan Kevin Sitek @@ -122,10 +126,10 @@ Kornelius Podranski Kristofer Montazeri Krzysztof J. Gorgolewski Krzysztof J. Gorgolewski -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 @@ -143,6 +147,8 @@ Matteo Mancini Matteo Visconti di Oleggio Castello Matteo Visconti di Oleggio Castello Matthew Cieslak +Maurilio Genovese +Maurilio Genovese <125388969+mauriliogenovese@users.noreply.github.com> Michael Clark Michael Dayan Michael Dayan @@ -163,8 +169,8 @@ Oliver Contier Olivia Stanley Oscar Esteban Oscar Esteban -Pablo Polosecki Pablo Polosecki +Pablo Polosecki Paul Kuntke Paul Kuntke Paul Sharp @@ -185,8 +191,8 @@ Serge Koudoro Sharad Sikka Shariq Iqbal Shariq Iqbal -Shoshana Berleant Shoshana Berleant Shoshana Berleant +Shoshana Berleant Shoshana Berleant Ubuntu Simon Rothmei Simon Rothmei @@ -210,5 +216,7 @@ Victor Saase Weijie Huang William Triplett Wolfgang Pauli +Wu Jianxiao +Wu Jianxiao Xiangzhen Kong Yaroslav Halchenko diff --git a/.zenodo.json b/.zenodo.json index a0823fef52..5ddb9a71dd 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", @@ -77,17 +82,17 @@ "orcid": "0000-0002-2666-0969" }, { - "affiliation": "Dartmouth College: Hanover, NH, United States", - "name": "Halchenko, Yaroslav O.", - "orcid": "0000-0003-3456-2493" + "affiliation": "Department of Psychology, Stanford University", + "name": "Norgaard, Martin", + "orcid": "0000-0003-2131-5688" }, { "name": "Loney, Fred" }, { - "affiliation": "Department of Psychology, Stanford University", - "name": "Norgaard, Martin", - "orcid": "0000-0003-2131-5688" + "affiliation": "CEA", + "name": "Papadopoulos Orfanos, Dimitri", + "orcid": "0000-0002-1242-8990" }, { "affiliation": "Florida International University", @@ -232,6 +237,11 @@ "name": "de Hollander, Gilles", "orcid": "0000-0003-1988-5091" }, + { + "affiliation": "Sagol School of Neuroscience, Tel Aviv University", + "name": "Kepler, Gal", + "orcid": "0000-0002-5655-9423" + }, { "affiliation": "Indiana University, IN, USA", "name": "Koudoro, Serge" @@ -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", @@ -459,6 +463,11 @@ "name": "Pérez-García, Fernando", "orcid": "0000-0001-9090-3024" }, + { + "affiliation": "Azienda Ospedaliero-Universitaria di Modena", + "name": "Genovese, Maurilio", + "orcid": "0000-0002-8154-8224" + }, { "name": "Blair, Ross" }, @@ -471,6 +480,11 @@ "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 +560,11 @@ "affiliation": "Boston University", "name": "Perkins, L. Nathan" }, + { + "affiliation": "Lund University", + "name": "Anijärv, Toomas Erik", + "orcid": "0000-0002-3650-4230" + }, { "name": "Zhou, Dale" }, @@ -581,6 +600,11 @@ "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 +613,11 @@ "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 +652,6 @@ "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", @@ -696,6 +720,11 @@ "name": "Van, Andrew", "orcid": "0000-0002-8787-0943" }, + { + "affiliation": "Department of Psychological and Brain Sciences, Dartmouth College", + "name": "Petre, Bogdan", + "orcid": "0000-0002-8437-168X" + }, { "affiliation": "MPI-CBS; McGill University", "name": "Steele, Christopher John", @@ -751,6 +780,11 @@ { "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 +883,6 @@ "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", @@ -891,30 +920,6 @@ "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": "Department of Psychology, Stanford University", "name": "Gorgolewski, Krzysztof J.", @@ -924,11 +929,6 @@ "affiliation": "MIT, HMS", "name": "Ghosh, Satrajit", "orcid": "0000-0002-5312-6729" - }, - { - "affiliation": "Department of Psychological and Brain Sciences, Dartmouth College", - "name": "Petre, Bogdan", - "orcid": "0000-0002-8437-168X" } ], "keywords": [ diff --git a/doc/changelog/1.X.X-changelog.rst b/doc/changelog/1.X.X-changelog.rst index f1d6bc92d3..b150eece35 100644 --- a/doc/changelog/1.X.X-changelog.rst +++ b/doc/changelog/1.X.X-changelog.rst @@ -1,3 +1,75 @@ + +1.9.0 (October 31, 2024) +======================== + +New feature release in the 1.9.0 series. + + * FIX: Remove exists=True from fsl.MotionOutliers output that might not exist (https://github.com/nipy/nipype/pull/1428) + * FIX: Improve evaluate_connect_function errors across Python versions (https://github.com/nipy/nipype/pull/3655) + * FIX: Changed inheritance of TensorMetricsInputSpec (https://github.com/nipy/nipype/pull/3663) + * 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: Support HDF5 (mat 7.3) SPM.mat files (https://github.com/nipy/nipype/pull/3650) + * ENH: FILMGLS gifti output support in surface mode (https://github.com/nipy/nipype/pull/3652) + * ENH: Added available inputs for MRTrix3's 5ttgen (https://github.com/nipy/nipype/pull/3658) + * 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: Replace deprecated pkgutil.find_loader with importlib.util.find_spec (https://github.com/nipy/nipype/pull/3692) + * 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: Patch doc/conf.py to work with latest ReadTheDocs (https://github.com/nipy/nipype/pull/3691) + * 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/pycodestyle rules (E) (https://github.com/nipy/nipype/pull/3689) + * STY: Apply ruff rules (RUF) again (https://github.com/nipy/nipype/pull/3688) + * STY: Apply ruff/Pyflakes rules (F) (https://github.com/nipy/nipype/pull/3681) + * STY: Apply ruff/Perflint rules (PERF) again (https://github.com/nipy/nipype/pull/3687) + * STY: Apply ruff/flake8-comprehensions preview rules (C4) (https://github.com/nipy/nipype/pull/3686) + * STY: Apply ruff/flake8-simplify rules (SIM) (https://github.com/nipy/nipype/pull/3676) + * STY: Apply ruff/flake8-bugbear rules (B) (https://github.com/nipy/nipype/pull/3671) + * STY: Apply ruff/flake8-comprehensions rules (C4) (https://github.com/nipy/nipype/pull/3680) + * STY: Apply ruff/Perflint rules (PERF) (https://github.com/nipy/nipype/pull/3674) + * STY: Apply ruff/flake8-implicit-str-concat rules (ISC) (https://github.com/nipy/nipype/pull/3679) + * STY: Apply ruff/flake8-pie rules (PIE) (https://github.com/nipy/nipype/pull/3678) + * STY: Apply ruff/flake8-raise rules (RSE) (https://github.com/nipy/nipype/pull/3677) + * STY: Apply ruff/flynt rules (FLY) (https://github.com/nipy/nipype/pull/3675) + * STY: Apply ruff rules (RUF) (https://github.com/nipy/nipype/pull/3673) + * STY: Codespell (https://github.com/nipy/nipype/pull/3672) + * STY: Apply ruff/refurb rules (https://github.com/nipy/nipype/pull/3648) + * 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: Replace deprecated imghdr (https://github.com/nipy/nipype/pull/3659) + * MNT: Use regular ".now" instead of ".utcnow" with UTC zone (https://github.com/nipy/nipype/pull/3670) + * MNT: Apply assorted repo-review rules (https://github.com/nipy/nipype/pull/3682) + * MNT: Drop traits upper bound (https://github.com/nipy/nipype/pull/3685) + * 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) ====================== diff --git a/nipype/info.py b/nipype/info.py index 7b68ec909c..3b006ae161 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__ = "1.9.0" def get_nipype_gitversion(): diff --git a/tools/update_zenodo.py b/tools/update_zenodo.py index 4560b4fc79..359740363b 100755 --- a/tools/update_zenodo.py +++ b/tools/update_zenodo.py @@ -1,4 +1,12 @@ #!/usr/bin/env python3 +# /// script +# requires-python = ">=3.11" +# dependencies = [ +# "fuzzywuzzy", +# "gitpython", +# "python-levenshtein", +# ] +# /// """Update and sort the creators list of the zenodo record.""" import git import json