Add `mode` kwarg to KNeighborsGraph, refactor input-output formats in gtda.graphs, turn outputs of KNeighborsGraph and TransitionGraph into asymmetric adjacency matrices

[ulupo]

Reference issues/PRs Inspired by the discussion in #108, but only insofar as with this PR it would be possible to do IsoMap up until the distance matrix calculation (no embedding step).

Types of changes

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

Description

• Adds a mode kwarg to KNeighborsGraph so that, when it is set to 'distance', KNeighborsGraph and GraphGeodesicDistance together give all the steps in the IsoMap algorithm minus the embedding one.
• Uses check_point_clouds consistently in gtda.graphs so that list input is now also accepted.
• Avoids returning ragged 1D ndarray output, preferring lists instead, for consistency with other transformers returning collections of variable-size arrays.
• The dtype of sparse matrices returned by KNeighborsGraph and TransitionGraph is now int (0-1 adjacency matrices).
• The matrices returned by KNeighborsGraph and TransitionGraph are now not necessarily symmetric, meaning that:
  • A point j can be among the k-nearest neighbors of point i without the reverse being necessarily true
  • TransitionGraph now encodes the direction of time: entry ij is 1 only if j follows i in the time series (and not vice-versa).
  • The rationale for this is that a) GraphGeodesicDistance is unaffected because it has the option directed=False; b) VietorisRipsPersistence and FlagserPersistence work just fine with sparse asymmetric matrices.

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.