Update to 2.4.0

[gregdenay]

A range of modifications for better code, easier maintenance and some convienience utilities:

New features

• Added a Taxonomy.copy() method as a shorthand for copy.deepcopy(Taxonomy)
• Added an inplace argument to Taxonomy methods filterRanks() and prune(), allowing chose whether to return a modified deepcopy of the instance od modifiy it in place

Improvements

• Unit tests now use temporary directories to test IO methods
• The Taxonomy.filter() method will now return a ValueError when attempting to use root rank in the filtering instead of creating new root Nodes

Pending deprecation

• Taxonomy.from_json will be removed in 3.0.0, it is replaced by read_json, a module level constructor.
• load will be removed in 3.0.0, it is replaced by read_json, a module level constructor.
• Taxonomy.from_taxdump will be removed in 3.0.0, it is replaced by read_taxdump, a module level constructor.
• load_ncbi will be removed in 3.0.0, it is replaced by read_ncbi, a better-named module level constructor.

Bug Fix

• Taxonomy.listDescendant now does filter output based on the ranks parameter
• Repaired Node.node_info output to actually use newlines instead of printing '\n'