Update gudhi bindings to latest changes on August 2020

[reds-heig]

Reference issues/PRs Supersedes #466. Partially addresses #307.

Types of changes

• [ ] Bug fix (non-breaking change which fixes an issue)
• [ ] New feature (non-breaking change which adds functionality)
• [x] Breaking change (fix or feature that would cause existing functionality to change)

Description

This PR integrates latest changes on gudhi modules, it also add the c++ code for the new Collapser feature.

Latest version of Gudhi requires Eigen as a dependency, fortunately, Eigen is a header only library, and we where able to add it as a git submodule directly.

Also integrating changes from @ulupo of setup.py, azure-pipelines.yml and docker_scripts.sh

Screenshots (if appropriate)

Any other comments?

@ulupo I think that this PR should only update the Gudhi bindings, and in a different PR, we should integrate the Collapser bindings for python, what do you think ?

Checklist

• [x] I have read the guidelines for contributing.
• [x] My code follows the code style of this project. I used flake8 to check my Python changes.
• [x] My change requires a change to the documentation.
• [x] I have updated the documentation accordingly.
• [ ] I have added tests to cover my changes.
• [x] All new and existing tests passed. I used pytest to check this on Python tests.

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:x: julian

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[ulupo]

@ulupo I think that this PR should only update the Gudhi bindings, and in a different PR, we should integrate the Collapser bindings for python, what do you think ?

Totally agree!

[gtauzin]

Is the plan to include the collapser as an invisible step in each of the persistence transformer? This seems to be such an amazing achievement from the GUDHI team, I am really looking forward to trying it out!

[ulupo]

@gtauzin as far as I understand it, the collapser only works on flag complexes, so we would presumably only offer it for VietorisRipsPersistence (and maybe FlagserPersistence when directed is False; WeakAlphaPersistence should be fast enough without it). I don't know about SparseRipsPersistence, but we could look into it.