From 44c9ab843b4008241e5412abaabcdee8d141db61 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 8 Dec 2022 09:18:43 -0500 Subject: [PATCH 1/3] MNT: Update changes and zenodo scripts Handle squash commits in changelog and preserve UTF-8 characters in Zenodo snippet. --- .maint/update_changes.sh | 19 ++++++++++++++++--- .maint/update_zenodo.py | 2 +- 2 files changed, 17 insertions(+), 4 deletions(-) diff --git a/.maint/update_changes.sh b/.maint/update_changes.sh index 2b258a22c..13b9b2c96 100644 --- a/.maint/update_changes.sh +++ b/.maint/update_changes.sh @@ -26,9 +26,22 @@ echo $( printf "%${#HEADER}s" | tr " " "=" ) >> newchanges echo "" >> newchanges # Search for PRs since previous release -git log --grep="Merge pull request" `git describe --tags --abbrev=0`..HEAD --pretty='format: * %b %s' | sed 's/Merge pull request \#\([^\d]*\)\ from\ .*/(\#\1)/' >> newchanges -echo "" >> newchanges -echo "" >> newchanges +MERGE_COMMITS=$( git log --grep="Merge pull request\|(#.*)$" `git describe --tags --abbrev=0`..HEAD --pretty='format:%h' ) +for COMMIT in ${MERGE_COMMITS//\n}; do + SUB=$( git log -n 1 --pretty="format:%s" $COMMIT ) + if ( echo $SUB | grep "^Merge pull request" ); then + # Merge commit + PR=$( echo $SUB | sed -e "s/Merge pull request \#\([0-9]*\).*/\1/" ) + TITLE=$( git log -n 1 --pretty="format:%b" $COMMIT ) + else + # Squashed merge + PR=$( echo $SUB | sed -e "s/.*(\#\([0-9]*\))$/\1/" ) + TITLE=$( echo $SUB | sed -e "s/\(.*\) (\#[0-9]*)$/\1/" ) + fi + echo " * $TITLE (#$PR)" >> newchanges +done +echo >> newchanges +echo >> newchanges # Add back the Upcoming header if it was present if [[ "$UPCOMING" == "0" ]]; then diff --git a/.maint/update_zenodo.py b/.maint/update_zenodo.py index 44cfea7d5..187e95b52 100755 --- a/.maint/update_zenodo.py +++ b/.maint/update_zenodo.py @@ -120,4 +120,4 @@ def get_git_lines(fname='line-contributors.txt'): if isinstance(creator['affiliation'], list): creator['affiliation'] = creator['affiliation'][0] - zenodo_file.write_text('%s\n' % json.dumps(zenodo, indent=2)) + zenodo_file.write_text('%s\n' % json.dumps(zenodo, indent=2, ensure_ascii=False)) From dcf5a98b8cb4be1702beb6aca1c6e58668935335 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 8 Dec 2022 09:25:12 -0500 Subject: [PATCH 2/3] DOC: Update zenodo ordering --- .zenodo.json | 68 ++++++++++++++++++++++++++++------------------------ 1 file changed, 37 insertions(+), 31 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index d40a1b790..74fb69501 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -4,22 +4,16 @@ "contributors": [ { "affiliation": "Department of Radiology, Lausanne University Hospital and University of Lausanne", - "name": "Provins, C\u00e9line", + "name": "Provins, Céline", "orcid": "0000-0002-1668-9629", "type": "Researcher" }, { - "affiliation": "Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toru\u0144", + "affiliation": "Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń", "name": "Finc, Karolina", "orcid": "0000-0002-0157-030X", "type": "Researcher" }, - { - "affiliation": "University of Texas at Austin", - "name": "de la Vega, Alejandro", - "orcid": "0000-0001-9062-3778", - "type": "Researcher" - }, { "affiliation": "Department of Psychology, Stanford University", "name": "Feingold, Franklin", @@ -27,21 +21,21 @@ "type": "Researcher" }, { - "affiliation": "Department of Psychology, New York University", - "name": "Benson, Noah C.", - "orcid": "0000-0002-2365-8265", + "affiliation": "Department of Neuroscience, University of Pennsylvania, PA, USA", + "name": "Tooley, Ursula A.", + "orcid": "0000-0001-6377-3885", "type": "Researcher" }, { - "affiliation": "Charite Universitatsmedizin Berlin, Germany", - "name": "Waller, Lea", - "orcid": "0000-0002-3239-6957", + "affiliation": "Department of Psychology, New York University", + "name": "Benson, Noah C.", + "orcid": "0000-0002-2365-8265", "type": "Researcher" }, { - "affiliation": "Department of Neuroscience, University of Pennsylvania, PA, USA", - "name": "Tooley, Ursula A.", - "orcid": "0000-0001-6377-3885", + "affiliation": "University of Texas at Austin", + "name": "de la Vega, Alejandro", + "orcid": "0000-0001-9062-3778", "type": "Researcher" }, { @@ -56,6 +50,12 @@ "orcid": "0000-0001-5504-8579", "type": "Researcher" }, + { + "affiliation": "Charite Universitatsmedizin Berlin, Germany", + "name": "Waller, Lea", + "orcid": "0000-0002-3239-6957", + "type": "Researcher" + }, { "affiliation": "Department of Psychology, University of California, Berkeley", "name": "Lurie, Daniel J.", @@ -80,12 +80,6 @@ "orcid": "0000-0001-7936-9991", "type": "Researcher" }, - { - "affiliation": "Department of Radiology, Weill Cornell Medicine", - "name": "Jamison, Keith W.", - "orcid": "0000-0001-7139-6661", - "type": "Researcher" - }, { "affiliation": "McLean Hospital Brain Imaging Center, MA, USA", "name": "Frederick, Blaise B.", @@ -99,9 +93,9 @@ "type": "Researcher" }, { - "affiliation": "CENIR, INSERM U1127, CNRS UMR 7225, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle \u00e9pini\u00e8re, ICM, F-75013, Paris, France", - "name": "Valabregue, Romain", - "orcid": "0000-0002-1814-9570", + "affiliation": "Department of Radiology, Weill Cornell Medicine", + "name": "Jamison, Keith W.", + "orcid": "0000-0001-7139-6661", "type": "Researcher" }, { @@ -147,11 +141,17 @@ "type": "Researcher" }, { - "affiliation": "SIMEXP Lab, CRIUGM, University of Montr\u00e9al, Montr\u00e9al, Canada", + "affiliation": "SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada", "name": "Bellec, Pierre", "orcid": "0000-0002-9111-0699", "type": "Researcher" }, + { + "affiliation": "Montreal Neurological Institute, McGill University", + "name": "Bhagwat, Nikhil", + "orcid": "0000-0001-6073-7141", + "type": "Researcher" + }, { "affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA", "name": "Cieslak, Matthew", @@ -202,7 +202,7 @@ }, { "affiliation": "Cyceron, UMS 3408 (CNRS - UCBN), France", - "name": "Naveau, Mika\u00ebl", + "name": "Naveau, Mikaël", "orcid": "0000-0001-6948-9068", "type": "Researcher" }, @@ -226,7 +226,7 @@ }, { "affiliation": "Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London", - "name": "Stoji\u0107, Hrvoje", + "name": "Stojić, Hrvoje", "orcid": "0000-0002-9699-9052", "type": "Researcher" }, @@ -236,6 +236,12 @@ "orcid": "0000-0002-0533-6035", "type": "Researcher" }, + { + "affiliation": "CENIR, INSERM U1127, CNRS UMR 7225, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France", + "name": "Valabregue, Romain", + "orcid": "0000-0002-1814-9570", + "type": "Researcher" + }, { "affiliation": "Center for Brain Imaging, New York University", "name": "Velasco, Pablo", @@ -279,7 +285,7 @@ }, { "affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland", - "name": "Provins, C\u00e9line", + "name": "Provins, Céline", "orcid": "0000-0002-1668-9629" }, { @@ -303,7 +309,7 @@ "orcid": "0000-0001-6347-7939" }, { - "affiliation": "SIMEXP Lab, CRIUGM, University of Montr\u00e9al, Montr\u00e9al, Canada", + "affiliation": "SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada", "name": "Pinsard, Basile", "orcid": "0000-0002-4391-3075" }, From 0950ee0bd865974186e1de5153143e4ced12cf77 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Sun, 11 Dec 2022 10:52:18 -0500 Subject: [PATCH 3/3] DOC: 22.1.0 changelog --- CHANGES.rst | 51 +++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 49 insertions(+), 2 deletions(-) diff --git a/CHANGES.rst b/CHANGES.rst index 57db00827..d55592f6b 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,12 +1,59 @@ +22.1.0 (December 12, 2022) +========================== +New feature release in the 22.1.x series. + +This is an incremental improvement on the 22.0.x series, including features and fixes that +are backwards incompatible with the 22.0.x work tree. + +Several significant issues with susceptibility distortion correction (SDC) have been fixed +in `SDCFlows 2.2.0`_, in addition to the changes listed below. +If you have been seeing issues with SDC in 21.0.x or 22.0.x, please test out this version +and submit issues. + +Additionally, this version includes improvements to structural preprocessing, generating +morphometric ``.shape.gii`` files from FreeSurfer derivatives. + +Finally, this release introduces a method for estimating the carbon footprint of using +fMRIPrep. Add ``--track-carbon`` to your command to try this out. Note that it does not work +in Docker containers, but should work for Singularity containers. + +With thanks to Nikhil Bhagwat for contributions. + + + * FIX: Conform --reports-only to match post-run report generation (#2900) + * FIX: Remove cortex masking during vol2surf sampling (#2879) + * FIX: Do not attempt to calculate TA if SliceTiming is degenerate (#2901) + * FIX: Pass CrownCompCor components to GatherConfounds (#2897) + * FIX: Output brain mask and boldref in BOLD space if individual echos requested (#2852) + * FIX: Check for empty ACompCor results before trying to rename (#2851) + * FIX: Filter sbrefs by BIDS filters if available (#2843) + * ENH: Provide free memory estimate to unwarp_wf for better resources allocation (#2910) + * ENH: Add migas telemetry in addition to sentry (#2817) + * ENH: Tag memory based on data shape, annotate T2SMap (#2898) + * ENH: Add of carbon tracker to estimate workflow emissions (#2834) + * ENH: Output BOLD HMC transforms and reference volume (#2860) + * RF: CIFTI generation (#2884) + * DOC: Correct description of --longitudinal behavior (#2905) + * MNT: Update fast track outputs, use latest smriprep (#2894) + * MNT: Deprecate ``--topup-max-vols`` (#2881) + * MNT: Add a ``--debug pdb`` to allow easier line-by-line debugging (#2871) + * MNT: Generate more verbose reports (here, showing fieldmaps) if running in debug mode (#2872) + * DOCKER: Build wheel and install in two-stage build (#2859) + * CI: Various updates (#2899) + * CI: Test on Python 3.10, bump actions versions (#2895) + * CI: Fix non-fasttrack outputs for maint/21.0.x (#2866) + +.. _`SDCFlows 2.2.0`: https://github.com/nipreps/sdcflows/releases/2.2.0 + 22.0.2 (September 27, 2022) =========================== A patch release in the 22.0.x series. This release increases the minimum Nipype version to include better error messages on failures. Additionally, this includes a fix to allow SyN distortion correction in combination with the -`--ignore fieldmaps` option. +``--ignore fieldmaps`` option. - * MAINT: Add `pre-commit`, dev installation for consistent styling (#2857) + * MAINT: Add ``pre-commit``, dev installation for consistent styling (#2857) * CI: Upgrade docker orb (#2858) 22.0.1 (September 13, 2022)