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Merge pull request #72 from jni/fix-path-ordering

Fixes #71

The implementations of summarise() and the Skeleton class have diverged significantly. The way that paths are traversed are totally different. Rather than reconciling, I decided to move towards "soft" deprecation of summarise and preferring the Skeleton class as an API for the future.

As a result of #71, I've implemented csr.Skeleton.summarize as a method, which replicates (and improves upon) the functionality fo summarise.

This PR also fixes a number of deprecations in dependencies like NumPy, SciPy, and Matplotlib.

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