daf661c3edd949f8ac2cd70e4a725d9a055cc0c3,skbio/tree/_tree.py,TreeNode,shear,#TreeNode#Any#,411

Before Change

        while len(list(tcopy.tips())) != len(ids):
            for n in list(tcopy.tips()):
                if n.name not in ids:
                    n.parent.remove(n)

        tcopy.prune()

        return tcopy

After Change

        marked = set()
        for tip in tcopy.tips():
            if tip.name in ids:
                marked.add(tip)
                for anc in tip.ancestors():
                    if anc in marked:
                        break
                    else:
                        marked.add(anc)

        for node in list(tcopy.traverse()):
            if node not in marked:
                node.parent.remove(node)

Instances