Releases: ReproNim/neurodocker
Releases · ReproNim/neurodocker
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
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
0.9.3
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
Authors: 3
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.
Contributors
tclose, pwighton, and 2 other contributors
Assets 3
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!
Version 0.7.0
Say hello to Neurodocker version 0.7.0. This includes several additions and bug fixes, as well as a new container minification method.
Additions
neurodocker-minifyCLI command to minify containers in-place and preserving the ability to use the minified output interactively. This is an improvement of the original minification method, because using the older method, minimized images typically could not be used interactively afterwards. In other words, the original minification process was too aggressive (#258)- Matlab compiler runtime 2019 and 2015aSP1 for SPM12 (#304)
- Versioneer for version management (#308)
- SPM12 version r7487 and r7771 (#319)
- Adds FSL versions 6.0.2 and 6.0.3 (#324)