REL: Connectome Mapper Release v3.0.0

[sebastientourbier]

Dedicated to the development of release v3.0.0, that includes in particular:

New features

• Ability to use custom segmentation and parcellation ENH: Add capability for custom segmentation and parcellation formatted following BIDS #88

• Generate generic label-index mapping tsv files along with the parcellation files, in accordance to BIDS derivatives.

• Add commandline interfaces that generate the docker and singularity images ENH: add singularity CLI to wrap calls to the Singularity BIDS APP image #109 ENH: add docker CLI to wrap calls to the Docker BIDS APP image #115 ENH: Python wrapper for docker run command #112 ENH: Python wrapper for singularity run command. #113 FIX: Adjust the implementation of the python wrappers  #130

• Build the docker image with multiple stage builds and BUILDKIT to speedup the process ENH: Add capability for custom segmentation and parcellation formatted following BIDS #88

Major change

• Lausanne2008 parcellation scheme has been removed and completely replaced by Lausanne2018
  (commit b25e0fa)

Improvements

• Improve error message in the GUI Enh/release/v3.0.0/enhanced bidsappman messages #114

• Rename directories for the derivatives produced by cmp (cmp, freesurfer, nipype) to cmp-<version>, freesurfer-<version>, and nipype-<version> to comply with BIDS 1.4.0+.

Continuous integration

• Refactor massively the tests in the config file of CircleCI after they have changed their pricing plans (Dec 1, 2021). Code was also improved by defining commands. ENH: Add capability for custom segmentation and parcellation formatted following BIDS #88

and a few more...

Please check the documentation changelog for a full list of changes.

[codecov]

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