2.0.2

🐛 Bug Fix

• Fixes bug in determining whether to unzip or untar ANTs download #680 (@tclose)
• add new FSL version and update libopenblas name for ubuntu 24.04 #682 (@stebo85)
• [BOT] update pre-commit hooks #681 (@Remi-Gau @github-actions[bot])

Authors: 4

• @github-actions[bot]
• Remi Gau (@Remi-Gau)
• Steffen Bollmann (@stebo85)
• Tom Close (@tclose)

2.0.1

🐛 Bug Fix

• adds latest ANTs versions #679 (@tclose)
• Updated copyright period to be inclusive of 2025 #678 (@tclose)
• [BOT] update pre-commit hooks #674 (@Remi-Gau @github-actions[bot])
• adds the latest dcm2niix versions to neurodocker #675 (@tclose)
• Accept conda TOS #676 (@tclose)
• [BOT] update pre-commit hooks #672 (@Remi-Gau @github-actions[bot])
• removed broken cat12 build and updated with new build #671 (@stebo85)
• Update cat12.yaml - cat12 changed versioning scheme #670 (@stebo85)
• Update cat12.yaml to add new version 12.9 #669 (@stebo85)

Authors: 4

• @github-actions[bot]
• Remi Gau (@Remi-Gau)
• Steffen Bollmann (@stebo85)
• Tom Close (@tclose)

2.0.0

💥 Breaking Change

• Bump peter-evans/create-pull-request from 6 to 7 #641 (@dependabot[bot])

🚀 Enhancement

• reorder readme #668 (@satra)
• [BOT] update pre-commit hooks #667 (@Remi-Gau @github-actions[bot])
• Create release #666 (@satra)

🐛 Bug Fix

• Fix/builds #665 (@satra)
• Fix/builds #664 (@satra)
• fix: jq from source needs dependencies #663 (@satra)
• ref: use org secret and bump base images and toolkits #651 (@satra @iishiishii)
• [BOT] update pre-commit hooks #658 (@Remi-Gau @github-actions[bot])
• reverting ' ' around nii.gz because it wasn't working #661 (@stebo85)
• Update freesurfer.yaml #660 (@stebo85)
• add fsl 6.0.7.16 #659 (@stebo85)
• [BOT] update pre-commit hooks #650 (@Remi-Gau @github-actions[bot])
• [BOT] update pre-commit hooks #649 (@Remi-Gau @github-actions[bot])
• add fsl 6.0.7.14 #648 (@stebo85)
• [BOT] update pre-commit hooks #647 (@Remi-Gau @github-actions[bot])
• [MAINT] Drop python 3.8 and support 3.13 #646 (@Remi-Gau)
• [BOT] update pre-commit hooks #644 (@Remi-Gau @github-actions[bot])
• Update matlabmcr.yaml R2023b to Update 9 #643 (@stebo85)
• add new FSL version #642 (@stebo85)
• [BOT] update pre-commit hooks #639 (@Remi-Gau @github-actions[bot])
• [BOT] update pre-commit hooks #637 (@Remi-Gau @github-actions[bot])
• [MAINT] drop types all from pre-commit config #636 (@Remi-Gau)
• [BOT] update pre-commit hooks #634 (@Remi-Gau @github-actions[bot])
• Fix typo in CHANGELOG.md to pacify codespell #631 (@Remi-Gau)
• [BOT] update pre-commit hooks #633 (@Remi-Gau @github-actions[bot])
• [BOT] update pre-commit hooks #630 (@Remi-Gau @github-actions[bot])

⚠️ Pushed to master

• Update release.yml (@satra)

Authors: 6

• @dependabot[bot]
• @github-actions[bot]
• Remi Gau (@Remi-Gau)
• Satrajit Ghosh (@satra)
• Steffen Bollmann (@stebo85)
• Thuy Dao (@iishiishii)

1.0.1

🐛 Bug Fix

• FIX use --transform in freesurfer's template to generalize across freesurfer versions to strip leading freesurfer/ folder #626 (@mvdoc)
• FIX remove comment from freesurfer env line #622 (@mvdoc)
• FIX add default header and entrypoint to docker and singularity files #623 (@mvdoc)
• [BOT] update pre-commit hooks #627 (@Remi-Gau @github-actions[bot])
• Fix typo of "softwares" #624 (@yarikoptic)
• [BOT] update pre-commit hooks #621 (@Remi-Gau @github-actions[bot])

Authors: 4

• @github-actions[bot]
• Matteo Visconti di Oleggio Castello (@mvdoc)
• Remi Gau (@Remi-Gau)
• Yaroslav Halchenko (@yarikoptic)

1.0.0

💥 Breaking Change

• Bump actions/checkout from 3 to 4 #582 (@dependabot[bot])
• Bump actions/checkout from 3 to 4 #573 (@dependabot[bot])
• Bump actions/stale from 5 to 8 #560 (@dependabot[bot])
• Bump actions/checkout from 2 to 3 #557 (@dependabot[bot])
• Bump actions/setup-python from 2 to 4 #556 (@dependabot[bot])

🐛 Bug Fix

• [BOT] update pre-commit hooks #616 (@Remi-Gau @github-actions[bot])
• [BOT] update pre-commit hooks #614 (@Remi-Gau @github-actions[bot])
• make scripts executable after build #615 (@stebo85)
• [BOT] update pre-commit hooks #613 (@Remi-Gau @github-actions[bot])
• Use HTTPS for NeuroDebian APT listing urls #612 (@TheChymera)
• [BOT] update pre-commit hooks #610 (@Remi-Gau @github-actions[bot])
• [FIX] Update branch in update_precommit_hooks.yml #609 (@Remi-Gau)
• [ENH] package with hatchling and switch to pyproject.toml #607 (@Remi-Gau)
• [MAINT] update linting config and CI #604 (@Remi-Gau)
• fixed flake8 errors from #597 #598 (@Vbitz)
• Added "--add" command line option to add tar files as docker layers. #597 (@Vbitz)
• added versions to Library PATH #593 (@stebo85)
• update matlabmcr #592 (@stebo85)
• [FIX] add url bids validator #591 (@Remi-Gau)
• [DOC] add list of supported softwares #587 (@Remi-Gau)
• [ENH] add templates bids_validator #586 (@Remi-Gau)
• [MAINT] test build jq #589 (@Remi-Gau)
• [ENH] test on python 3.12 #588 (@Remi-Gau)
• Update fsl.yaml #583 (@stebo85)
• [DOC] update doc #569 (@Remi-Gau)
• [ENH] implement more recent mrtrix version #579 (@Remi-Gau)
• Update examples.rst #578 (@stebo85)
• added FSL interactivity note #576 (@stebo85)
• Include FSL license auto-yes example #575 (@stebo85)
• [MAINT] Update stale.yml #577 (@Remi-Gau)
• [FIX] install the proper dependencies for doc build #574 (@Remi-Gau)
• [DOC] auto doc main CLI #463 (@Remi-Gau)
• [FIX] use local var for software name in bootstrap workflow #572 (@Remi-Gau)
• [FIX] use env variable in bootstrap workflow #571 (@Remi-Gau)
• [INFRA] add possibility to only build a single workflow #570 (@Remi-Gau)
• [MAINT] test build of conda as part of the bootstrap workflow #566 (@Remi-Gau)
• [MAINT] minimize file changes that can trigger the bootstrap workflow #564 (@Remi-Gau)
• set python version for format job #563 (@stebo85)
• Add mamba option to miniconda #562 (@Shotgunosine)
• [MAINT] remove oldest distro in automated build testing #559 (@Remi-Gau)
• [MAINT] split format checking and testing in CI #554 (@Remi-Gau)
• [MAINT] Simplify type annotations #551 (@Remi-Gau)
• apply isort and all pre-commit hooks #549 (@Remi-Gau)
• Mcr bug #471 (@stebo85)
• Add codespell: config, pre-commit, workflow + 1 typo fixed #544 (@yarikoptic @stebo85)
• added freesurfer 7.3.2 #547 (@stebo85)
• add fsl 6.0.7.1 #543 (@stebo85)
• added freesurfer 7.4.1 #542 (@hjbockholt)
• Fixing my update for mcr2023a #540 (@dnkennedy)
• Update matlabmcr.yaml #539 (@dnkennedy)
• Update years to have full range of years of the project #534 (@yarikoptic)
• Update cat #533 (@stebo85)

⚠️ Pushed to master

• Change name of parent directory (@kaczmarj)

🏠 Internal

• Upgrade intuit auto to 11.1.6 (most recent) #617 (@yarikoptic)

🔩 Dependency Updates

• Bump actions/setup-python from 4 to 5 #594 (@dependabot[bot])
• Bump actions/stale from 8 to 9 #595 (@dependabot[bot])

Authors: 11

• @dependabot[bot]
• @github-actions[bot]
• David Kennedy (@dnkennedy)
• Dylan Nielson (@Shotgunosine)
• H. Jeremy Bockholt (@hjbockholt)
• Horea Christian (@TheChymera)
• Jakub Kaczmarzyk (@kaczmarj)
• Joshua Scarsbrook (@Vbitz)
• Remi Gau (@Remi-Gau)
• Steffen Bollmann (@stebo85)
• Yaroslav Halchenko (@yarikoptic)

0.9.5

🐛 Bug Fix

• Afni missing dependencies for suma #512 (@stebo85)
• modifying value for entry point to allow -arg or --arg #515 (@djarecka @kaczmarj)
• Mcr missing deb libxp6 #526 (@stebo85)
• NEW: Add support for FSL version 6.0.6 onwards #527 (@ghisvail)
• Enable build of docs with Sphinx 6 #525 (@ghisvail)
• Add FSL version 6.0.5.2 #523 (@ghisvail)
• Update ants.yaml #521 (@araikes @kaczmarj)
• [FIX] fix link to build dashboard #517 (@Remi-Gau)
• Update cli.rst #514 (@sooyounga @djarecka)
• updated version tags and added latest tag clarification to docs #516 (@sooyounga)
• Minc install from deb and rpm #509 (@stebo85)
• fix: repo info (@satra)
• [INFRA] test docker builds in CI #487 (@Remi-Gau @pre-commit-ci[bot] @satra)
• do not install sphinx 6.x #505 (@kaczmarj)
• add bad versions to et file #502 (@satra)
• [TESTS] check black style in github actions #501 (@kaczmarj)

⚠️ Pushed to master

• Update README.md (@djarecka)
• add workflow token (@satra)
• add commit agent (@satra)
• add all changed files (@satra)
• Update bootstrap.yml (@satra)
• simplify git commit (@satra)
• allow writing actions (@satra)
• remove on demand (@satra)
• fix docs build (@satra)
• fix: syntax (@satra)
• testing sphinx build (@satra)

📝 Documentation

• changed base image for AFNI to fedora:35 #520 (@stebo85 @kaczmarj)

Authors: 9

• @araikes
• @pre-commit-ci[bot]
• Dorota Jarecka (@djarecka)
• Ghislain Vaillant (@ghisvail)
• Jakub Kaczmarzyk (@kaczmarj)
• Remi Gau (@Remi-Gau)
• Satrajit Ghosh (@satra)
• Sooyoung Ahn (@sooyounga)
• Steffen Bollmann (@stebo85)

0.9.4

🐛 Bug Fix

• fix the types in --copy and --entrypoint #500 (@kaczmarj)
• add long_description to setup.cfg #465 (@kaczmarj)
• [FIX] add regression test for 498 #499 (@Remi-Gau)

Authors: 2

• Jakub Kaczmarzyk (@kaczmarj)
• Remi Gau (@Remi-Gau)

0.9.3

🐛 Bug Fix

• FIX: skip minification tests on M1/M2 macs and run them otherwise #497 (@kaczmarj)
• Add/ants24x #473 (@araikes @kaczmarj)

Authors: 2

• @araikes
• Jakub Kaczmarzyk (@kaczmarj)

0.9.2

🐛 Bug Fix

• fix: auto setup #496 (@satra)
• enh: add release workflow #495 (@satra)
• remove empty lines #488 (@satra)
• FIX: --version output in containers #493 (@kaczmarj)
• fix: remove py 3.7 and add apptainer 1.1.5 #490 (@satra)
• fix: adjust optionEatAll for click >= 8 #492 (@satra)
• update pre-commit #482 (@Remi-Gau)

⚠️ Pushed to master

• fix: install mypy stubs (@satra)
• fix: mypy configuration (@satra)

Authors: 3

• Jakub Kaczmarzyk (@kaczmarj)
• Remi Gau (@Remi-Gau)
• Satrajit Ghosh (@satra)

0.9.1

Minor update to fix #451

What's Changed

• fix path to include cli/minify/_trace.sh by @kaczmarj in #464

Full Changelog: 0.9.0...0.9.1