Update (neuro)docker image

[yarikoptic]

not even know if bidsonym is still worth (re)trying on my dataset but can't reliably do it without getting a container ;-) hence decided to possibly duplicate efforts with @Remi-Gau of

• 70

and see the container built.

If finished, closes #79

Ideally

• [x] see it finish building cleanly
• [x] see it work on some sample
  • there are warnings (#84) and may be that is why deface_wf report in index.html has nothing really.. so it kinda works but still might be buggy
• [x] add bids-validator-deno . I already added deno into recipe to be installed in conda, so then we could install new schema-based validator there

current gotchas

• [x] https://github.com/ReproNim/neurodocker/issues/620 - worked around, seems to be working just fine

  (dev3) yoh@typhon:/mnt/DATA/data/yoh/BIDSonym$ docker run -it --rm bidsonym:local
  docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "/neurodocker/startup.sh": stat /neurodocker/startup.sh: no such file or directory: unknown.

• [x] some conflicting specs, filed https://github.com/miykael/gif_your_nifti/issues/17 . I kinda fixed up right there and used here... not sure if my fix up is totally kosher (might relate to those warnings in #84 too)

  ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
  gif-your-nifti 0.2.1 requires imageio<2.28, but you have imageio 2.34.1 which is incompatible.
  Successfully installed argparse-1.4.0 bidsonym-0.0.6+17.g8417c18.dirty citeproc-py-0.6.0 duecredit-0.10.2 imageio-2.34.1 nilearn-0.10.4 scikit-learn-1.5.0 threadpoolctl-3.5.0
  WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
  Removing intermediate container 6706dd6d886d

[yarikoptic]

note that apparently there is no credentials added for docker pushes so no attempt to build even made.

Run docker/login-action@v2
  with:
    ecr: auto
    logout: true
Error: Username and password required

I will reorder commands so we could see if it at least builds ok etc.

[yarikoptic]

I am done with this as far I consider it done. Includes fixes from

• 83 as well

[yarikoptic]

@PeerHerholz please review&merge!