Clean up experimental, deprecated and redundant code

[ntfrgl]

Needs to be done before first public release. Some of this code that may be useful at some point should be moved to some kind of plug-in container classes.

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Originally reported by: Jonathan Donges Originally created on: 2014-06-17

[ntfrgl]

To be removed:

• core.network.Network
  • _get_eigenvector_centrality_slow()
  • _get_arenas_betweenness_slow()
  • _get_newman_betweenness_badly()

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Original comment by: ntfrgl Original comment on: 2014-06-25

[ntfrgl]

Some of these functions could be used as consistency checks in the test suite.

[fkuehlein]

The above mentioned methods have been remove from Network and many more such cleanups have been made as of v0.7.0. Still, the issue continues to apply.

[fkuehlein]

Here's a list of methods that are currently not covered by tests and contain especially many lines and/or appear to be unused or redundant. Most of this code is marked as experimental. For the sake of test coverage and to streamline the package it should either be tested or removed, especially those methods that contain most lines of code.

Of course, adding tests would be the preferable option, but might reveal unnoticed bugs (e.g. as with #229) and for the listed methods especially I am often lacking the theoretical background to understand what they should do. Therefore we should first review whether this code is even still wanted/needed.

• core.Network:
  • GrowPreferentially{_old}()(281 lines): what is the difference between the two? see issue 229 for bug
  • do_nsi_pca_clustering(), do_nsi_clustering(), do_nsi_hamming_clustering()(630 lines): experimental methods
• core.GeoNetwork:
  • shuffled_by_distance_copy()(59 lines): has a couple of FIXMEs
  • nsi_connected_hamming_cluster_tree()(42 lines): experimental
  • boundary()(155 lines): experimental
• utils.Navigator:
  • full class: currently omitted in coverage statistics but still, do we want it?

Note that there are still many more uncovered methods in the package, including some very low hanging fruits.