[Biopython] KDTree and trie

Michiel de Hoon mjldehoon at yahoo.com
Sat Mar 24 07:37:44 UTC 2018


Dear all,
KDTree and trie are two modules in Biopython implementing tree-based data structures. These modules are quite old and have some issues that cannot be easily resolved in their current location as top-level modules (Bio.trie and Bio.KDTree, respectively). Additionally these modules could use some cleanup.
Would there be any objections to move these modules to a new module (maybe Bio.datastructures)? ("move" meaning create a new module and deprecate and later remove the existing two modules).
If so, are we OK with the name Bio.datastructures or does anybody have other suggestions?
The functionality of trie and KDTree under Bio.datastructures would be the same, though some of the implementation may be updated to current practice in modern Python (e.g. using attributes instead of accessor functions).
-Michiel
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