Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit: MIAL Super-Resolution Toolkit v2.0.1

Version 2.0.1

Date: December 24, 2020

Merry Christmas from the MIASRTK team 🎁 🎄!

This corresponds to the release of MIAL Super-Resolution Toolkit 2.0.1, that includes in particular full support with Singularity and more! See below.

Major change

• Review setup.py for publication of future release of pymialsrtk to PyPI (See pull request 59).
• Review creation of entrypoint scripts of the container for compatibility with Singularity (See pull request 60).
• Use MapNode for all interfaces that apply a processing independently to a list of images (See pull request 68).
• Use the nipype sphinx extension to generate API documentation (See pull request 65).
• Review the --manual option flag which takes as input a directory with brain masks (See pull request 51).

New feature

• pymialsrtk enables to skip different steps in the super-resolution pipeline (See pull request 63).
• Support of Singularity to execute MIALSTK on high-performance computing cluster (See pull request 60).
• pymialsrtk implements for convenience a Python wrapper that generates the Singularity command line of the BIDS App for you, prints it out for reporting purposes, and then executes it without further action needed (See pull request 61).

Software development life cycle

• Add test-python-install job to CircleCI to test the creation of the distribution wheel to PyPI and test its installation via pip (See pull request 34).
• Add deploy-pypi-release job to CircleCI to publish the package of a new release to PyPI (See pull request 59).

• Add build-singularity, test-singularity, deploy-singularity-latest, and deploy-singularity-release jobs in CircleCI to build, test and deploy a Singularity image of MIALSRTK to Sylabs.io (See pull request 34). The tests includes:

  • Test 03: Run BIDS App on the sample data/ BIDS dataset with the --manual_masks option without code coverage.
  • Test 04: Run BIDS App on the sample data/ BIDS dataset with automated brain extraction (masking) without code coverage.

More...

Please check pull request 53 for more change details and development discussions.

Contributors

• @pdedumast
• @sebastientourbier