Adopt TestKraken for CPAC

[gkiar]

Posted by @djarecka

[XinhuiLi]

Action items:

• Modify TestKraken tests for C-PAC v1.8
  • PR: [wip, tmp] Sucyli test/cpac ReproNim/testkraken#107
• Test different versions of tools (e.g. AFNI)
  • PR: ✅ Test fully-specified images ReproNim/testkraken#108
• Test other C-PAC skull-stripping methods (e.g. FSL, ANTs):
  • Currently users can edit C-PAC pipeline config to test different skull-stripping methods, it would be better to add options in TestKraken via testkraken_spec.yml file to overwrite C-PAC pipeline config
• Adding user provided description in testkraken
  • PR: [enh] user defined description of the env fields ReproNim/testkraken#105
• Adding option to use output from one specific environment as a reference data

[shnizzedy]

• Test different versions of tools (e.g. AFNI)

Once we have TestKraken tests ready to run, I think this will specify the specific combinations of software versions that we (the C-PAC team) are currently most interested in comparing.

(I don't know if it's my computer or Docker Hub, but those took a looong time to push)

[shnizzedy]

@effigies you can see what I've been doing here above, and Xinhui's fork is here

[shnizzedy]

GitHub Actions Usage limits

[djarecka]

Future plans and open issues:

• adding option to test various software in different environment
• right now testkraken needs permission to build a docker container - should we allow to use it pre-build container in places where you can't run docker build command?
• how can we improve the html website with final report
• adding more tests from CPAC
• should we use a specific input and reference data from nmind?
• should we move from CircleCI?
• what would be the best way to adding testkraken to external projects.
• using bash commands to check what is installed inside container (in case the user doesn't want to build the container with testkraken)