Refactor igraph.Graph output of Nerve, modify `fit` behaviour of Nerve, add `store_edge_elements` kwarg to Nerve and make_mapper_pipeline, add Nerve and ParallelClustering to docs

[ulupo]

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 This PR stemmed from the idea of integrating giotto-tda more tightly with our python-igraph backend for Mapper graphs. Specifically, I believe that storing all Mapper node attributes as a graph-level dictionary (with key "node_metadata") does not follow the recommended practice for storing vertex attributes in igraph.Graph objects, see https://igraph.org/python/doc/tutorial/tutorial.html#setting-and-retrieving-attributes. Instead, it seems to be that one should fully exploit the VertexSeq data structure which is accessible via graph.vs -- and similarly the EdgeSeq data structure which is accessible via graph.es.

In this PR:

1. Node metadata is stored as vertex attributes accessible by graph.vs[attr_name][node_id] or graph.vs[node_id][attr_name] for attr_name in ["pullback_set_label", "partial_cluster_label", "node_elements"].
2. "node_id" is removed from node attributes as it always coincided with theigraph.Graph node number anyway.
3. Sizes of intersections are automatically stored as edge weights, accessible by graph.es["weight"].
4. A "store_intersections" kwarg has been added to Nerve and make_mapper_pipeline to allow storing indices of node intersections as edge attributes, accessible via graph.es["edge_elements"].
5. The logic of the Nerve.fit_transform code has been simplified.
6. The attributes nodes_ and edges_ previously stored by Nerve.fit have been removed. Now the entire graph is stored as graph_ instead.
7. The documentation of make_mapper_pipeline has been improved
8. ParallelClustering and Nerve have been exposed in the __init__ and in the oline docs. This is because their docstrings might be useful to the user.
9. Two new tests have been added to test_nerve to check that the new store_edge_elements kwarg works as expected, and that min_intersection works as expected.
10. The test coverage for the Mapper visualisation modules has been increased.
11. Tests have been created for plot_betti_curves and plot_betti_surfaces.
12. plotly_params kwargs have been added to the plot methods of some transformers in gtda/diagrams/representations which had been forgotten in #441.
13. Existing tests, the mapper quickstart notebook, and the mapper plotting functions have been adapted.

Any other comments? The behaviour of the mapper plotting functions is completely unchanged.

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.
• [x] I have added tests to cover my changes.
• [x] All new and existing tests passed. I used pytest to check this on Python tests.

[ulupo]

@wreise it would be great if you could generate a test dump for the documentation (and notebooks) following these changes, so that we can check they look OK.

[ulupo]

@lewtun I've made changes following your suggestions.