TreeSwift v1.1.44

• Updated MRCA algorithm to be faster when the MRCA is relatively lower in the tree
  • Before, when looking for the MRCA of n nodes, I would do a complete upward traversal for the first n-1 nodes, and on the n-th upward traversal, I would stop the moment I found a node that's been visited n times (which is the MRCA)
  • Now, I use a queue to explore the tree upwards from the given nodes until finding a node that has been visited n times

TreeSwift v1.1.43

• Simplified handling gzip files
• Fixed issue when reading Nexus files with tab-delimited (rather than space-delimited) TRANSLATE lines

TreeSwift v1.1.42

• Updated Tree.extract_tree* function behavior
  • Before, if the user passed in any non-set iterable for labels, it would automatically run labels = set(labels) to convert it to a set
  • If the user passed in a string, this would result in a set containing the unique individual letters of the string
    • E.g. if labels == 'HELLO', this would result in labels == {'H', 'E', 'L', 'O'}
  • However, the most likely user behavior for passing in a single string as labels would be to do something like tree.extract_tree_without(single_label) to try to remove just that single label
    • This would have resulted in converting single_label (a string) into a set containing the unique letters of single_label
  • I've updated these functions to first check if labels is a string, and if so, run labels = {labels} instead (to convert it into a set containing just that single string)
  • Thanks for catching this, @pekarj!
• The suppress_unifurcations warning I added in v1.1.40 would warn the user when deleting a Node that had a non-None label, node attributes, or edge attributes
  • I've updated this warning to also not warn the user when deleting a Node that only has the empty string as its label (and no node/edge attributes)

TreeSwift v1.1.41

• Added Tree.find_node() and Node.num_nodes()

TreeSwift v1.1.40

• Added warning if suppress_unifurcations will delete a Node that has a label and/or node_params/edge_params
  • To suppress all warnings in a Python script, you can add warnings.filterwarnings('ignore') to the top of the script
    • See the relevant Python documentation for more details regarding handling warnings
  • Thanks, @pekarj!

TreeSwift v1.1.39

• Fixed a bug in Tree.distance_between when one node is the other's parent
  • Thanks, @yueyujiang!

TreeSwift v1.1.38

• Fixed a typo that caused infinite recursion when attempting to copy a treeswift.Node object (thanks, @JSdoubleL!)

TreeSwift v1.1.37

• Added write_tree_nexus function to Tree objects

TreeSwift v1.1.36

• Fixed bug where node_params and edge_params weren't getting copied when extracting a subtree or copying a tree (thanks, @pekarj!)

TreeSwift v1.1.35

• Added ability to parse Newick files where a single tree is written across multiple lines