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

0.9.0

On this sunny day, August 4, 2022, we welcome Neurodocker version 0.9.0. Thank you to all who have contributed!

What's Changed

• Escape single quotes in printf to neurodocker_specs.json by @tclose in #443
• Fix afni recipe spaces + R packages + python by @stebo85 in #456
• Add freesurfer 7.3.0 and 7.3.1 by @jennydaman in #459
• added _Renderer.labels method that enables adding labels with special chars in the label name by @tclose in #453
• Fix for issue #449 by @pwighton in #462

New Contributors

• @tclose made their first contribution in #443
• @jennydaman made their first contribution in #459

Full Changelog: 0.8.0...0.9.0

Thank you GitHub for automatically generating the release notes above! We appreciate it.

Version 0.8.0

Greetings! Version 0.8.0 of Neurodocker is a refactor of the codebase. A generic Dockerfile and Singularity recipe generator has been implemented, known as reproenv (the source is in this repository). Neurodocker defines recipes to install common neuroimaging software, and reproenv uses these recipes to generate the container specs.

As always, please ask any questions using our GitHub issues. We hope you enjoy Neurodocker!