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!

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-minify CLI 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)

Fixes

• Switches to root user at beginning of every dockerfile (#306)
• Adds -y switch to conda clean --all (#323)

Version 0.6.0

We are pleased to welcome neurodocker version 0.6.0 to the world. This release adds a few things and fixes a few bugs.

Additions

• mricron
• telemetry

Fixes

• remove files specific to spm in /tmp instead of /tmp/*, which caused problems with singularity
• fsleyes installation works now

Version 0.5.0

Hello Neurodocker users! I am pleased to announce version 0.5.0, which adds FSL 6 and 6.0.1 and fixes several bugs. The jump to 0.5 from 0.4 is meant to indicate Neurodocker's approach towards stability. If you encounter issues using this version, please submit an issue or a pull request.

Run the versioned Docker image with docker run --rm kaczmarj/neurodocker:0.5.0

Additions

• FSL 6.0.0 and 6.0.1

Fixes

• check if a user exists before creating them
• remove fsl dependency that cannot be found in some repositories
• afni system package names
• run nd_freeze before removing the apt list
• use conda clean --all instead of conda clean -tipsy
• set USER=$(whoami) if USER is not set
• do not remove /tmp/* or /var/tmp/* (this caused issues when building singularity images)
• add save method to singularity generator
• use new URL for libpng12-0 in afni template