notebooks are broken

[denisri]

I'm trying to look at deep_folding for the first time, so I naturally look at the notebooks, but cannot use most of them:

• https://github.com/neurospin/deep_folding/blob/main/notebooks/moving_average_use_case.ipynb:
  • the moving_averages import is not defined and I cannot find it as a github project. It is also used from within the module deep_folding.anatomist_tools.utils.remove_hull
  • colorado is also used but is not cited in dependencies
• https://github.com/neurospin/deep_folding/blob/main/notebooks/run_bounding_box.ipynb:
  the program and module deep_folding/anatomist_tools/bounding_box.py is not at the expected location
• https://github.com/neurospin/deep_folding/blob/main/notebooks/run_dataset_gen_piupe.ipynb:
  • needs tqdm.notebook which is in tqdm>=4.36. I can fix this in the requirements.
  • also needs moving_averages
• https://github.com/neurospin/deep_folding/blob/main/notebooks/run_mask.ipynb:
  deep_folding/anatomist_tools/mask.py is not at the expected location
• https://github.com/neurospin/deep_folding/blob/main/notebooks/run_preprocessing_brainvisa.ipynb:
  also an import error in:

    from deep_folding.anatomist_tools import transform
  

• https://github.com/neurospin/deep_folding/blob/main/notebooks/run_transform.ipynb:
  deep_folding/anatomist_tools/transform.py is not at the expected location (same as above I guess)

Well I have finally found moving_averages (because I thought I have heard about it), it is renamed
point-colud-pattern-mining but this has to be explained or described in a dependency.

[JoelChavas]

Je m'en occupe

[JoelChavas]

I have fixed:

• the install: pip3 install -e . -> it will install all dependencies including dico_toolbox, moving_averages, colorado
• the tests: python3 -m pytest
• the notebooks
  Should work now