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Recent Releases of neurodocker

neurodocker - 2.0.2

🐛 Bug Fix

Authors: 4

- Python
Published by satra 7 months ago

neurodocker - 2.0.1

🐛 Bug Fix

Authors: 4

- Python
Published by satra 7 months ago

neurodocker - 2.0.0

💥 Breaking Change

🚀 Enhancement

🐛 Bug Fix

⚠️ Pushed to master

Authors: 6

- Python
Published by satra 12 months ago

neurodocker - 1.0.1

🐛 Bug Fix

Authors: 4

- Python
Published by satra over 1 year ago

neurodocker - 1.0.0

💥 Breaking Change

🐛 Bug Fix

⚠️ Pushed to master

  • Change name of parent directory (@kaczmarj)

🏠 Internal

🔩 Dependency Updates

Authors: 11

- Python
Published by satra over 1 year ago

neurodocker - 0.9.5

🐛 Bug Fix

⚠️ Pushed to master

📝 Documentation

Authors: 9

- Python
Published by satra almost 3 years ago

neurodocker - 0.9.4

🐛 Bug Fix

Authors: 2

- Python
Published by satra about 3 years ago

neurodocker - 0.9.3

🐛 Bug Fix

Authors: 2

- Python
Published by satra about 3 years ago

neurodocker - 0.9.2

🐛 Bug Fix

⚠️ Pushed to master

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

Authors: 3

- Python
Published by satra about 3 years ago

neurodocker - 0.9.1

Minor update to fix #451

What's Changed

  • fix path to include cli/minify/_trace.sh by @kaczmarj in https://github.com/ReproNim/neurodocker/pull/464

Full Changelog: https://github.com/ReproNim/neurodocker/compare/0.9.0...0.9.1

- Python
Published by kaczmarj over 3 years ago

neurodocker - 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 https://github.com/ReproNim/neurodocker/pull/443
  • Fix afni recipe spaces + R packages + python by @stebo85 in https://github.com/ReproNim/neurodocker/pull/456
  • Add freesurfer 7.3.0 and 7.3.1 by @jennydaman in https://github.com/ReproNim/neurodocker/pull/459
  • added _Renderer.labels method that enables adding labels with special chars in the label name by @tclose in https://github.com/ReproNim/neurodocker/pull/453
  • Fix for issue #449 by @pwighton in https://github.com/ReproNim/neurodocker/pull/462

New Contributors

  • @tclose made their first contribution in https://github.com/ReproNim/neurodocker/pull/443
  • @jennydaman made their first contribution in https://github.com/ReproNim/neurodocker/pull/459

Full Changelog: https://github.com/ReproNim/neurodocker/compare/0.8.0...0.9.0

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

- Python
Published by kaczmarj over 3 years ago

neurodocker - 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!

- Python
Published by kaczmarj almost 4 years ago

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)

- Python
Published by kaczmarj almost 6 years ago

neurodocker - 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

- Python
Published by kaczmarj over 6 years ago

neurodocker - 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

- Python
Published by kaczmarj almost 7 years ago

neurodocker - Version 0.4.3

Additions

  • Adds the nd_freeze utility for (Neuro)Debian base images. This allows users to pin the apt sources to a particular date and time and is very useful in creating reproducible builds. Otherwise, calls to apt-get update make builds non-deterministic (#240).

Fixes

  • Wraps pip and conda packages in single quotes. This prevents the execution of shell commands like > in numpy>=1.10 (#239).

- Python
Published by kaczmarj about 7 years ago

neurodocker - Version 0.4.2

Additions

  • Ability to output JSON representation of the neurodocker specification
  • exclude_paths option in FSL to exclude specific paths from tarball extraction
  • Python 3.7 support

Fixes

  • Install shared libraries required for matlab compiler runtime 2010a
  • Add back in nlopt dependency in afni
  • PATH variable in afni

Enhancements

  • Allows use of miniconda base environment (--miniconda use_env=base ...
  • Adds ANTs versions 2.3.1 and 2.3.1, statically compiled on CentOS 6
  • Adds matlab compiler runtime 2018b
  • Misc. improvements to the reprozip trace wrapper shell script
  • Installs desktop manager when installing VNC
  • Raises more specific error on dockerfile / singularity recipe generation

- Python
Published by kaczmarj over 7 years ago

neurodocker - Version 0.4.1

This release includes various fixes, enhancements, and additions.

Additions

  • vnc command-line option. This installs a VNC server in the container, and optionally starts it at container runtime.
  • mrtrix3 source installation

Fixes

  • $PATH variable is set properly in neurodocker generate singularity.
  • apt_opts="" and yum_opts="" now remove all options in apt-get install and yum install except for -y.
  • allow conda environments built from yaml file to be activated at container runtime.

Enhancements

  • Improvements in error-handling in neurodocker reprozip trace.
  • mrtrix3 binaries are pre-built on centos 6.
  • update nipype tutorial example

- Python
Published by kaczmarj over 7 years ago

neurodocker - Version 0.4.0

We are happy to introduce Neurodocker version 0.4.0. This release includes an entirely rewritten core and support for generating Singularity recipes.

As always, if you run into problems using Neurodocker, please submit an issue.

Breaking changes

  • CLI for generate commands follows the syntax neurodocker generate [docker|singularity].
  • FreeSurfer license file option is removed. License files should be added at container runtime.
  • --spm becomes --spm12.
  • --miniconda signature has been changed to use create_env and use_env in lieu of env_name.

Additions

  • Singularity recipe generation
  • Matlab Compiler Runtime can be installed independently of SPM12
  • Larger suite of examples

Enhancements

  • Software installation instructions are written in a templating language
  • Matlab Compiler Runtime URLs use HTTPS.

- Python
Published by kaczmarj over 7 years ago

neurodocker - Version 0.4.0 release candidate 1

This is the second release candidate for neurodocker version 0.4.0.

Fixes

  • pip installation (previously, the required yaml files were not being installed).
  • matlab compiler runtime uses https urls
  • documentation is fixed and all examples are functional
  • examples are updated to new command line interface

Adds

  • --run-bash command line option

Users of this release may notice that features may be have dropped while converting from the old class-based to the new template-based framework. This is not intentional in most cases, so please submit an issue if a feature that you use has been lost.

- Python
Published by kaczmarj almost 8 years ago

neurodocker - Version 0.4.0 release candidate 0

This is the first release candidate for neurodocker version 0.4.0, which adds support for generating Singularity recipes (and involves a near complete rewrite of neurodocker).

Dockerfiles and Singularity files are generated from templates of installation instructions.

Users of this release may notice that features may be have dropped while converting from the old class-based to the new template-based framework. This is not intentional in most cases, so please submit an issue if a feature that you use has been lost.

Additions

  • Singularity recipes can now be generated.
  • Matlab Compiler Runtime can be installed independently.

Breaking changes

  • CLI for generate commands follows the syntax neurodocker generate docker/singularity
  • FreeSurfer license file option is removed. License files should be added at container runtime.
  • --spm becomes --spm12

Fixes

  • SPM12 takes a specific version release now and does not install dev unless the user requests it.

- Python
Published by kaczmarj almost 8 years ago

neurodocker - Version 0.3.2

Changes:

  • Adds dcm2niix.
  • Replaces option add_to_path with activate in Miniconda installation. activate=True will activate the environment in the entrypoint of the container.
  • Makes R installation optional for AFNI.
  • Adds option to install Python for AFNI.
  • Adds examples.

- Python
Published by kaczmarj over 8 years ago

neurodocker - Version 0.3.1

Changes:

  • Installs shared libraries for FSL on apt and yum.
  • Allows creation of conda environment from YAML file.
  • Adds support for FSL eddy 5.0.11 pre-release.
  • Fixes bug in AFNI install: installs shared library libnlopt-dev.

- Python
Published by kaczmarj over 8 years ago

neurodocker - Version 0.3.0

Breaking changes: - Removes python_version option for Miniconda. Instead, specify python version in conda_install.

Changes: - Adds support for MINC and PETPVC (thanks to @sulantha2006). - Adds Dockerfile instructions ARG, LABEL, and VOLUME. - Adds convenience option --run-bash. - Adds bc/dc as dependency for FSL. - Renames neurodocker/dockerfile.py to neurodocker/generate.py. - Miscellaneous fixes.

At this point, the Neurodocker latest Docker image will be removed. Users will be asked to use specific versions of Neurodocker. An image with the latest master branch will also be available (tagged as master).

- Python
Published by kaczmarj over 8 years ago

neurodocker - Version 0.2.0

  • neurodocker generate respects order of arguments when generating Dockerfile.
  • Default entrypoint bash script is used (/neurodocker/startup.sh), and packages shell files are sourced there. This eliminates the need for some ENV layers.
  • Add options --user, --install, --env, --expose. Options can be used multiple times.
  • Use git describe for neurodocker version.
  • Test software packages as non-root user.
  • Update testing to only build Docker image if the Dockerfile has changed.
  • Fix whiteout file issue in Miniconda installation.
  • Add perl to FreeSurfer dependencies.
  • Add cli command neurodocker reprozip-merge to merge multiple ReproZip pack files.
  • Updated tests to cover additions.

- Python
Published by kaczmarj over 8 years ago

neurodocker - Version 0.1.0

Neurodocker version 0.1.0 allows users to generate Dockerfiles with specified versions of neuroimaging analysis software.

Features

  • Generate Dockerfiles from the command-line.
  • Generate Dockerfiles, build Docker images, run Docker containers, and collect output in a Python script.
  • Install ANTs, FreeSurfer, FSL, Miniconda, MRtrix3, SPM, and NeuroDebian packages (see below for more information).
  • Supply arbitrary Dockerfile instructions.

Supported software

| name | installation method(s) | | ----- | ---------------------- | | ANTs | binaries, compile from source | | FreeSurfer | binaries | | FSL | binaries, install script | | Miniconda | install script | | MRtrix3 | binaries, compile from source | | SPM | standalone SPM (with MCR) |

- Python
Published by kaczmarj over 8 years ago